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CHARACTERIZATION OF T H E HUMAN FACTOR XII (HAGEMAN FACTOR)
CDNA AND THE GENE
DEBORAH E. COOL
A THESIS SUBMITTED IN PARTIAL FULFILMENT OF
THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
in
- T H E FACULTY OF GRADUATE STUDIES
Department of Biochemistry
We accept this thesis as conforming
to the required standard
THE UNIVERSITY OF BRITISH COLUMBIA
October, 1987
© Deborah E. Cool, 1987
In presenting this thesis in partial fulfilment of the requirements for an advanced
degree at the University of British Columbia, I agree that the Library shall make it
freely available for reference and study. I further agree that permission for extensive
copying of this thesis for scholarly purposes may be granted by the head of my
department or by his or her representatives. It is understood that copying or
publication of this thesis for financial gain shall not be allowed without my written
permission.
Department
The University of British Columbia 1956 Main Mall Vancouver, Canada V6T 1Y3
DE-6(3/81)
ABSTRACT
A human liver cDNA library was screened by colony hybridization with two mixtures of
synthetic oligodeoxyribonucleotides as probes. These oligonucleotides encoded regions of
0-factor X l l a as predicted from the amino acid sequence. Four positive clones were isolated
that contained D N A coding for most of factor XI I mRNA. A second human liver cDNA
library was screened by colony hybridization with 3 zP-labeled cDNA clones obtained from
the first screen and two identical clones were isolated.
D N A sequence analysis of these overlapping clones showed that they contained D N A coding
for the signal peptide sequence, the complete amino acid sequence of plasma factor XII , a
T G A stop codon, a 3' untranslated region of 150 nucleotides, and a poly A + tail. The cDNA
sequence predicts that plasma factor XII consists of 596 amino acid residues. Within the
predicted amino acid sequence of factor XII , were identified three peptide bonds that are
cleaved by kallikrein during the formation of j3-factor X l l a .
Comparison of the structure of factor XII with other proteins revealed extensive sequence
identity with regions of tissue-type plasminogen activator (the epidermal growth factor-like
region and the kringle region) and fibronectin (type I and type II homologies). As the type
II region of fibronectin contains a collagen-binding site, the homologous region in factor XII
may be responsible for the binding of factor XII to collagen. The carboxyl-terminal region of
factor XII shares considerable amino acid sequence homology with other serine proteases
including trypsin and many clotting factors.
A human genomic phage library was screened by using a human factor XII cDNA as a
ii
hybridization probe. Two overlapping phage clones were isolated which contain the entire
human factor XII gene. D N A sequence and restriction enzyme analysis of the clones
indicate that the gene is approximately 12 kbp in size and is comprised of 13 introns and 14
exons. Exons 3 through 14 are contained in a genomic region of only 4.2 kbp with introns
ranging in size from 80 to 554 bp.
The multiple regions found in the coding sequence of FXII that are homologous to putative
domains in fibronectin and tissue-type plasminogen activator are contained on separate
exons in the factor XII gene. The intron/exon gene organization is similar to the serine
protease gene family of plasminogen activators and not to the clotting factor family.
Analysis of the 5' flanking region of the gene shows that it does not contain the typical
T A T A and C A A T sequences found in other genes. This is consistent with the finding that
transcription of the gene is initiated at multiple start sites.
iii
LIST OF ABBREVIATIONS
A Adenosine
ATP Adenosinetriphosphate
bp Base Pair(s)
BSA Bovine Serum Albumin
C Cytosine
2 +
Ca Calcium ions
dNTP Deoxynucleotidetriphosphate
DNA Deoxyribonucleic Acid
DNase Deoxyribonuclease
ddNTP Dideoxynucleotidetriphosphate
DTT Dithiothreitol
EDTA Ethylenediaminetetraacetic Acid
EtBr Ethidium Bromide
G Guanosine
Gla 7-Carboxyglutamic Acid
GuHCl Guanidine Hydrochloride
hnRNA Heterogenous Nuclear RNA
IPTG Isopropyl-beta-D-Thiogalactopyranoside
Kbp Kilobase Pair(s)
Krpm Thousand Revolutions Per Minute
LB Luria Broth
mA Milliamps
min Minute (s) mRNA Messenger RNA
iv
N Any Nucleotide (G, A, T or C)
OD Optical Density
pfu Plaque Forming Unit
PA Plasminogen Activator(s)
R Purine (A or G)
RNA Ribonucleic Acid
RNase Ribonuclease
rRNA Ribosomal RNA
TEMED N,N,N',N'-Tetramethylethylenediamine
tPA Tissue-Type Plasminogen Activator
Tris ' Tris(hydroxymethyl)aminomethane
tRNA Transer RNA
TJ Uridine
UV Ultra Violet
V Volts
T Thimidine
W Watts
X-Gal 5-Bromo-4-Chloro-3-Indoyl-|3-D
-Galactopyroside
Y Pyrimidine (T or C)
v
T A B L E O F C O N T E N T S
Abstract ii
List of Abbreviations iv
Table of Contents vi
List of Tables ix
List of Figures x
Acknowledgements xii
I. Introduction 1 A . T H E C O N T A C T S Y S T E M OF P L A S M A 1
1. The Biochemistry of the Surface Activation Components 2 a. The Catalytic Mechanism of Serine Proteases 5 b. Factor XII 6 c. Prekallikrein and Factor X I 12 d. High Molecular Weight Kininogen 14
2. A Model of the Surface Activation Mechanism 15 B. P H Y S I O L O G I C A L F U N C T I O N S OF T H E C O N T A C T S Y S T E M 18
1. Blood Coagulation 18 2. Fibrinolysis 21
a. Plasminogen and Its Activators 22 3. The Inflammatory Response 24 4. Conversion of Prorenin to Renin 26
C. T H E S T R U C T U R E OF E U K A R Y O T I C S T R U C T U R A L G E N E S 26 1. Promoters 26 2. Introns and Exons 28 3. Transcription and Processing 28
D. M E C H A N I S M S OF G E N E E V O L U T I O N 29 1. Gene Duplication 29 2. Gene Fusions 30 3. Exon Shuffling 30
E . E V O L U T I O N OF A M I N O ACID A N D D N A S E Q U E N C E 30 1. Molecular Clock 30 2. Intron Sliding 31
F . P R O T E I N DOMAINS OF T H E C O A G U L A T I O N A N D P L A S M I N O G E N A C T I V A T O R G E N E S 32
1. Trypsin-Like Family of Serine Proteases 32 G. E V O L U T I O N OF T H E SERINE P R O T E A S E S 36 H . O B J E C T I V E S 37
II. Materials and Methods 39 A . M A T E R I A L S 39 B. STRAINS, VECTORS A N D M E D I A 40
1. Bacterial Strains 40 2. Vectors 41
vi
3. Media . 41 C. G E L ELECTROPHORESIS 42
1. Neutral Agarose Gels 42 2. Formaldehyde Agarose Gels 43 3. Neutral Polyacrylamide Gels 43 4. Denaturing Polyacrylamide Gels 44
D. ISOLATION OF D N A 45 1. Small-scale Isolation of Plasmid D N A 45 2. Large-scale Isolation of Plasmid D N A 46 3. Small-scale Isolation of X D N A 47 4. Large-scale Isolation of X D N A 48 5. Isolation of Single-stranded Plasmid D N A 49
E . ISOLATION O F P O L Y A+ RNA 50 F . O L I G O N U C L E O T I D E SYNTHESIS A N D PURIFICATION 51 G. L A B E L I N G O F D N A 53
1. Labeling With 3 2P by Nick Translation 53 2. Labeling with T4 Polynucleotide Kinase 53
H . SCREENING A PLASMID LIBRARY 54 I. SCREENING XPHAGE LIBRARIES 56 J . D N A SUBCLONING 57
1. Production of D N A Fragments for Ligation 57 2. Ligation of D N A into p U C l 3 or M13 Vectors 58 3. Transformation of D N A into Bacteria 59
K. B L O T HYBRIDIZATIONS 60 1. Southern Blot Analysis of Genomic and Cloned D N A 60 2. Northern Blot Analysis 61
L . D N A S E Q U E N C E A N A L Y S I S 62 1. Screening M13 Clones 62 2. D N A Sequence Analysis 63 3. Computer Analysis of D N A Sequence Data 65
M . MAPPING T H E E N D OF A mRNA TRANSCRIPT 65 1. Primer Extension Analysis 65 2. Nuclease S1 Mapping 67
III. Results 69 A. C H A R A C T E R I Z A T I O N O F T H E H U M A N FXII cDNA 69
1. Isolation of Factor XII cDNA Clones 69 2. Sequence Analysis of Human Factor XII cDNA Clones 76 3. Predicted Amino Acid Sequence of Human Factor XII 79 4. 5'End of the Factor X n c D N A 80 5. A 2.40 kb mRNA From Liver Codes For Human Factor XII 83
B. T H E H U M A N F A C T O R XII G E N E 86 1. Isolation and Characterization of Factor XII Genomic Clones 86 2. Southern Blot Analysis of the Human FXII Gene 91 3. Localization of Intron/Exon Junctions 94 4. Nucleotide Sequence of the Human Factor XII Gene 97 5. Transciption Initiation Site of the Factor XII Gene 101
IV. Discussion 109 A. CHARACTERIZATION O F T H E H U M A N F A C T O R XII cDNA 109
vii
1. Characterization of Factor XII cDNA Clones 109 2. Factor XII Is Synthesized as a Prescursor 110
B. HOMOLOGIES WITH O T H E R PROTEINS I l l 1. Amino-Terminal End of the Zymogen Form of Factor XII 113 2. Fibronectin Homology 114 3. Epidermal Growth Factor Homology. 118 4. Kringle Homology 118 5. Proline-Rich Domain 119 6. Serine Protease Domain 119 7. Plasminogen Activator Homology 124 8. Physiological Significance of the Homologous Protein Domains 125
C. A PERSPECTIVE O N T H E R O L E O F T H E C O N T A C T S Y S T E M IN HOMEOSTASIS 126
D. D N A S E Q U E N C E A N A L Y S I S OF T H E H U M A N F A C T O R XII G E N E .... 128 E . A N A LY SIS OF T H E PROMOTER REGION IN T H E H U M A N FXII G E N E ....
129 1. The C A A T Element 130 2. The T A T A Box 131
F. P U T A T I V E PROTEIN DOMAINS A R E F O U N D O N S E P A R A T E E X O N S 133
G. E V O L U T I O N O F T H E F A C T O R XII G E N E 136 1. Evolution of the Amino Terminal Half of Factor XII 137 2. Evolution of the Serine Protease Domain of Factor XII 142 3. Intron/Exon Sliding 146
H . A M O D E L FOR T H E E V O L U T I O N O F T H E H U M A N F A C T O R XII G E N E ... 147
Concluding Remarks 150
V. Literature Cited 151
viii
LIST OF TABLES
I. D N A Sequencing Mixes 64
II. Nucleotide Sequence of Intron/Exon Junctions in the FXII Gene 95
III. Frequencies of Nucleotides at Intron/Exon Junctions 96
IV. Size and Position of Exons and Introns in the FXII Gene 97
V. Per-cent Homologies Between the Amino Acid Sequence in the/3-factor X l l a and Pancreatic Serine Proteases Catalytic Domains 123
VI. Summary of TATA-Like Elements Found in Liver Specific and Coagulation Genes . 130
ix
LIST OF FIGURES
1. The Blood Coagulation Cascade 3
2. Schematic Diagram of 0-factor X l l a 8
3. Schematic Diagram of the Surface-Dependent Contact Activation Mechanism 16
4. Amino Acid Sequence Homologies in Coagulation Factor Zymogens 33
5. Predicted Oligonucleotide Sequences for 0-factor X l l a 70
6. Double Oligonucleotide Screen For Factor XII cDNA 72
7. Restriction Enzyme Map and Sequencing Strategy for Factor XII cDNA 74
8. Nucleotide Sequence of Factor XII cDNA 77
9. Nucleotide Sequence of a cDNA for the FXII Signal Peptide 82
10. Size Determination of the Factor XII mRNA Using rRNA Markers 84
11. Southern Blot Analysis of FXII Genomic Clones 87
12. Intron/Exon Organization of the FXII Gene 90
13. Genomic D N A Southern Blot Analysis of the FXII Gene 92
14. Partial D N A Sequence of the FXII Gene 98
15. Nuclease S i Mapping of the FXII Gene 102
16. Primer Extension Analysis of the FXII Gene 104
17. Northern Blot Analysis of the 5' End of the FXII Gene 107
18. Proposed Model for Factor XII 112
19. Amino Acid Sequence Homologies of FXII With Other Proteins 115
20. Amino Acid Sequence Alignment of the Catalytic Domain of FXII With Other Serine Proteases 121
21. Schematic Diagram of FXII and Positions of Introns 134
22. N-Terminal Exon Organization in the Plasminogen Activators and FXII 138
23. Comparison of Exon Organization of the Serine Protease Domain in Some Serine Proteases 143
x
ACKNOWLEDGEMENTS
I would like to thank the members of my supervisory committee, Drs. Jim Richards and
Peter Candido for their kind support and advice throughout this project. I would also like to
thank the members of the MacGillivray lab, those past and present, for their good natured
humour, for tolerating Molly and for the much appreciated technical advice and for their
tremendous support during my work in the lab. I would especially like to acknowledge my
great supervisor, Dr. Ross MacGillivray (or "Ross") who has taught me always to try to
achieve a high standard of excellence in science and to take pride and pleasure in the work.
Thank you Ross, I am grateful for all the assistance you have given me. I would like to
thank Dr. M . J . Smith who was my Masters of Science Degree supervisor and who became
a good friend and encouraged me throughout my Ph.D. degree. Finally, I would especially
like to thank my husband, for his unending encouragement during my graduate degrees and
for all his help in preparation of my manuscripts and this thesis.
xii
I. INTRODUCTION
A. THE CONTACT SYSTEM OF PLASMA
Organisms can respond to invasion by foreign substances, to trauma and to internal
disorders by the activation of four plasma systems: they are the complement systems, the
contact (Hageman) activated clotting system, the extrinsic clotting system and the
fibrinolytic system (Ratnoff and Saito, 1979; Cochrane and Griffin, 1982; Pesce and
Dosekun, 1983; Sundsmo and Fair, 1983; Colman, 1984). Maintenance of a homeostatic
environment in vivo may be a result of the synergism that exists between these plasma
systems (Cochrane, 1980; Bennett and Ogston, 1981). At least the coagulation and
fibrinolytic systems can be activated both in vivo and in vitro by a mechanism described as
"surface-mediated" or "contact phase" activation which requires a negatively charged
surface as well as the appropriate plasma proteins (reviewed in Ratnoff and Saito, 1979).
In vitro studies have also demonstrated that the contact activation mechanism plays a role
in the inflammatory response, in the production of kinins and in the conversion of prorenin
to renin (Bennett and Ogston, 1981; Cochrane and Griffin, 1982). The proteins which are
primarily responsible for the surface activation reactions are factor XII (Hageman factor),
prekallikrein (Fletcher factor), high molecular weight (HMW) kininogen (Fitzerald factor)
and factor XI (PTA, plasma thromboplastin antecedent) (Davie et al., 1979). Factor XII
and H M W kininogen have surface binding properties and therefore are essential in the
surface activation mechanism. The following review will describe the physical and
biochemical properties of the components involved in contact activation; this will include
mainly the role of factor XII in surface activation of the plasma systems listed above and
the subsequent relevance of factor XII to the maintenance of homeostasis in living
1
Introduction / 2
organisms.
1. The Biochemistry of the Surface Activation Components
The characteristic enzymatic reaction in the plasma systems described above is the action of
serine proteases. Similar to the pancreatic serine proteases, trypsin (Marquart et al.,
1983), chymotrypsin (Cohen et al., 1981) and elastase (Sawyer et al., 1978), the proteases
involved are synthesized in precursor forms and are activated by limited proteolysis (Davie
et al., 1979; Jackson and Nemerson, 1980). The active enzymes have a trypsin-like
specificity with a preference for argininyl peptide bonds and contain the conserved
activation and catalytic site residues described for the pancreatic enzymes (Jackson and
Nemerson, 1980). Unlike the digestive enzymes, the proteases required in the complex
plasma systems have long amino terminal polypeptide domains that appear to be important
in functions such as metal-binding, surface binding or fibrin binding and in their regulation
(Jackson and Nemerson,11980). The zymogens in the contact system are activated by
limited proteolysis (discussed below) resulting in a cascade of enzymatic reactions in which
inactive zymogens are converted to active serine proteases that act upon each other in a
controlled and step-wise manner (Jackson and Nemerson, 1980). The physiological
significance of the cascade mechanism is the amplification of reactions by a few initiator
molecules resulting in a massive amount of end-product such as fibrin from the blood
coagulation cascade (Fig. 1) (Davie et al., 1979; Jackson and Nemerson, 1980) or plasmin
from the fibrinolytic cascade (Collen, 1979).
/ 3
Figure 1: The Blood Coagulation Cascade
Outline of the mammalian blood coagulation cascade with the intrinsic pathway (left) and
extrinsic pathway (right) converging at the activation of factor X to factor Xa, and ending
with the formation of the insoluble fibrin clot. Bars represent the polypeptide chains
(proportional to polypeptide chain length) with molecular weights indicated below. Intra
molecular disulfide bridges are indicated by lines between the two chains (from Neurath,
1984).
S u r f a c e H M W K i n i n o g e n K a l l i k r c i r i
XII
XI
: 60K 27K' • S O K 27K<
• 2 5 K J 2 5 K
K a l l i k r e l n X I L . X L
va C o 2 * , P - l i p i d
5K 32K 70 K P r o t h r o m b i n T h r o m b i n
F i b r i n o g e n F i b r i n
XCI„
F i b r i n ( X - l l n k e d )
Introduction / 5
a. The Catalytic Mechanism of Serine Proteases
The catalytic mechanism of peptide bond cleavage is the same for all serine proteases and
has been intensively studied. The classical model of serine protease catalysis is the
"charge-transfer relay" mechanism (see Creighton, 1984) involving the catalytic triad of
amino acid residues which consists of His 5 7 , Asp l t 2 and the active site Ser l i S in
chymotrypsin. These amino acids are conserved in all serine proteases and are essential
residues in the hydrolysis of amide and ester bonds. In the charge-transfer relay
mechanism the polypeptide binds to the S i binding site pocket, and the oxygen of the
carbonyl group in the amide linkage undergoes nucleophilic attack by the hydroxyl group of
S e r 1 9 5 , which has been polarized by H i s 5 7 ; a tetrahedral intermediate is formed and is
further stabilized by the transfer of a hydrogen ion to A s p x 0 2 . The hydrogen ion from
S e r x , 5 is then transferred to the leaving group, and an acyl-enzyme intermediate is formed.
This intermediate undergoes nucleophilic attack by an incoming water molecule, and the
tetrahedral intermediate is formed again resulting in the transfer of the polypeptide chain to
water and restoration of the serine hydroxyl group in the protease active site.
Aspects of the charge-transfer relay theory have been disputed, however, based on high
resolution X-ray diffraction studies on trypsin-substrate complexes and on neutron
diffraction studies which can readily position hydrogen atoms (Creighton, 1984). One
fundamental change is that interactions between the enzyme and substrate take place
which make the active site more energetically suited to the tetrahedral intermediate
conformation than to the substrate, products or the acyl-enzyme intermediate
conformations. The carbonyl group in the scissile bond becomes distorted when entering the
active site and begins assuming the tetrahedral conformation. This is stabilized by three
Introduction / 6
hydrogen bonds. The first hydrogen bond is between the backbone carbonyl group at
residue 214 and the backbone -NH- group of the P x residue (the amino terminal residue to
the scissile bond). The other two hydrogen bonds are between the carbonyl oxygen of P i
and the two backbone -NH- groups of residues 213 and 215 of the enzyme, which form the
oxyanion binding site. Polarization between the negative charge on the oxygen atom and
the positive charge on the carbon atom of the carbonyl group is large enough that the carbon
atom will be susceptible to nucleophilic attack by the oxygen in the hydroxyl group of
Ser x , s . When this occurs the hydrogen atom of the serine residue is transferred to His 5 7 ,
and the acyl-enzyme intermediate is formed. An important feature of this reaction is that
the Asp x 0 2 residue is not needed for the extra positive charge assumed transiently by
His 5 7 but the residue appears to be essential in orienting the substrate in the active site
through hydrogen bonding and in maintaining the His 5 7 conformation during catalysis so
that the hydrogen atom of the imadazole ring is not on the N e (which accepts the Serx , s
hydrogen atom) but on the N ° atom of the ring (see Creighton, 1984).
b. Factor XII
Factor XII, or Hageman factor, was so named after the individual in which the deficiency
was first discovered (Ratnoff and Colopy, 1955). Although factor XII circulates in plasma
at very low concentrations (approximately 30 Mg/ml), it has been highly purified from
human, bovine, rabbit and guinea pig plasmas (Cochrane and Wuepper, 1971; Movat and
Ozge-Anway, 1974; Revak et al., 1974; Griffin and Cochrane, 1976; Fujikawa et al.,
1977a,b; Claeys and Collen, 1977; Fujikawa and Davie, 1981; Yamamoto and Cochrane,
1981). The complete amino acid sequence of 596 amino acid residues and the identification
of glycosylation sites of human factor XII have only recently been determined for the human
Introduction / 7
protein (Fujikawa and McMullen, 1983; McMullen and Fujikawa, 1985) because of the
difficulty in isolating large quantities of the protein from plasma for amino acid sequence
analysis. Prior to the commencement of the work described in this thesis, the only known
amino acid sequence for bovine factor XII was at the amino-terminus of the zymogen and
around the active site serine residue in the serine protease domain. Soon after this project
was initiated, however, the entire amino acid sequence of the serine protease domain of the
human protein, 0-factor X l l a (Fig. 2) was reported (Fujikawa and McMullen, 1983) which
aided in the identification of cloned cDNAs of human factor XII.
Human factor XII is a glycoprotein containing 16.8% carbohydrate including 4.2% hexose,
4.7% hexosamine and 7.9% N-acetylneuraminic acid. The protein is synthesized in the liver
and secreted into blood as a single polypeptide chain with N-glycosylation on Asn and
O-glycosylation on Thr and Ser residues (Fujikawa and McMullen, 1983;McMullen and
Fujikawa, 1985). Glycosylation is intimately involved in protein secretion (Blobel et al.,
1979). Carbohydrate attachment occurs during protein synthesis (N-glycosylation) and in
the Golgi apparatus (O-glycosylation). Proteins which are to be glycosylated are
synthesized on the rough endoplasmic reticulum and contain an amino-terminal extension
called a "signal sequence" which is 16 to 30 residues in length and has a hydrophobic core
(Blobel et al., 1979). During protein synthesis, the signal peptide sequence is bound by a
"signal recognition protein", and the complex is subsequently directed to the endoplasmic
reticulum membrane. The nascent strand is transported through the membrane and is
cleaved on the lumen side by a resident signal peptidase. The specificity of the enzyme
recognition site has been described (Watson, 1984). The protein is then shuttled to the
Golgi apparatus by an unknown mechanism where it is glycosylated. Secreted proteins are
transported from the Golgi apparatus to the plasma membrane in secretory vesicles and
/ 8
Figure 2: Schematic Diagram of 0-factor Xlla
The open bars represent the human factor XII molecule with "Site 1" and "Site 2" arrows
indicating the kallikrein cleavage sites of the zymogen generating the three polypeptide
chains of M r 40,000 (amino terminal fragment), 12,000 and 30,000 (carboxy terminal
fragment with serine protease activity) (from Fujikawa and McMullen, 1983). The amino
acid sequence shows the amino terminal nanopeptide (L-chain of (3-factor Xlla) generated by
kallikrein cleavage at unknown sites in either the M r 40,000 or the 12,000 fragments;
partial amino acid sequence of the serine protease domain is given in the H-chain of 0-factor
Xl la .
Site2 Site I
1 1 lleProProTrp 40,000 H 12,000 |—fvdiValGlyGly 30,000
AsnGlyProLeuSerCysGlyGlnArg Vol ValGlyQy Cys GlyAsp(g)GlyGly-
L-Chain of£ -Factor Xlla H-Chain of£-Factor Xlla
Introduction / 10
enter plasma upon membrane fusion. The form of factor XII found in plasma is a
single-chain polypeptide ( M r 80,000) with an isoleucine residue at the amino terminus. In
the prefactor XII, this He residue is presumedly preceded by the bond cleaved by signal
peptidase.
The zymogen form of factor XII is activated in plasma by partial proteolysis by kallikrein
generating an active serine protease (Davie et al., 1979; Jackson and Nemerson, 1980).
There are multiple sites in factor XII that are susceptible to cleavage by a number of
proteases including kallikrein, plasmin and trypsin (Margolis, 1958; Kaplan and Austen,
1971; Meier et al., 1977; Dunn and Kaplan, 1982). Limited proteolysis by kallikrein
activates surface-bound factor XII and produces two active enzyme forms, a-factor X l l a and
/3-factor X l l a . A single cleavage of the zymogen generates a-factor X l l a while two more
subsequent cleavages by kallikrein yield 0-factor X l l a (Revak et al., 1974; Dunn et al.,
1982; Fujikawa and McMullen, 1983). Both active enzymes consist of two polypeptide
chains held together by a disulfide bond (Revak et al., 1974, 1977). A/p/io-factor X l l a is
comprised of two polypeptide chains of M r 52,000 and 28,000 while j3-factor X l l a consists of
two polypeptide chains of M r 2,000 and 28,000. Amino-terminal sequence analysis has
shown that the M r 52,000 fragment in a-factor X l l a is derived from the amino-terminal
region of factor XII (Fujikawa et al., 1980b) and contains the surface-binding site (Revak
and Cochrane, 1976; Revak et al., 1977). However, the M r 2,000 fragment of /3-factor X l l a
does not bind to surfaces. The M r 28,000 fragments of both a- and j3-factor X l l a are
identical and contain the catalytic domain derived from the carboxy-terminal region of factor
XII (Revak et al, 1974, 1977). The catalytic domain of a- and B-factor X l l a shares
extensive amino acid sequence homology with other serine proteases, including many blood
clotting factors (see Jackson and Nemerson, 1980; Fujikawa and McMullen, 1983). The
Introduction / 11
sequence homology is highest at the activation regions and near the active sites of these
proteases.
Factor XII and a-factor X l l a readily bind to anionic surfaces such as silicates, dextran
sulfate and sulfatides in vitro (Ratnoff and Rosenblum, 1958; Fujikawa et al., 1977, 1980a).
In vivo, these binding properties may be responsible for the activation of factor XII when it
comes in contact with collagen or platelet membranes (Wilner et al, 1968; Harpel, 1972).
Surface-bound factor XII has enzyme activity towards its protein substrates, prekallikrein
and factor XI (McMillin et al., 1974; Saito, 1977; Heimark et al., 1980) (see below).
Surface-bound a-factor X l l a is further cleaved by kallikrein resulting in 0-factor X l l a which
is free to enter plasma since it no longer has the fragment of M r 52,000 which contains the
surface binding property of the molecule.
Various in vivo and in vitro substrates for activated factor XII have been described in the
literature and include prekallikrein, factor XI and factor VII (reviewed in Cochrane and
Griffin, 1982). The serine protease recognizes the sequence Thr-Arg-Ile (in prekallikrein)
and Pro-Arg-Ue (in FXI) and cleaves the polypeptide bond carboxy-terminal to the Arg
residues.
The serine proteases including the digestion enzymes show little amino acid sequence
identity (less than 40%) except in a few regions which are important in the catalytic
reaction. However this amount of homology may transfer to an 85% tertiary structural
homology (James et al., 1978). This observation has allowed the construction of computer
generated models of the serine protease domains of a number of clotting factors including
thrombin, FIXa, F X a (Furie et al., 1982) and FXII (Cool et al., 1985). The means of
Introduction / 12
substrate specificity of the enzymes remains unclear (Furie et al., 1982) but probably
results from the surface topology which would be unique for each protein. This kind of
specificity is essential in the ordered amplification of the coagulation and fibrinolytic
cascades (see Davie et al., 1979; Jackson and Nemerson, 1980).
Activated factor XII is regulated in plasma by inhibitors. The major plasma inhibitor for
0-factor X l l a is the Cl-inhibitor (de Agostini et al., 1984) which is the major proteolytic
inhibitor of the proteolytic enzymes derived from the first component of complement
(Ziccardi, 1981). The Cl-inhibitor is also the primary inactivator of plasma kallikrein
(Schapira et al., 1982; Van der Graaf et al., 1983). Kinetic studies (de Agostini et al., 1984)
with human plasma and purified Cl-inhibitor, a2-antiplasmin and antithrombin III showed
that 74% of ^-factor X l l a was inhibited by Cl-inhibitor and the remaining activated protein
inhibited equally by a2-antiplasmin antithrombin III. A complex of 145,000 daltons was
detected by SDS-polyacrylamide gel electrophoresis which represents a 1:1 stoichiometric
relationship between 0-factor X l l a and Cl-inhibitor (de Agostini et al., 1984).
c. Prekallikrein and Factor XI
Prekallikrein and factor XI circulate in plasma as zymogen forms of serine proteases and
are involved in the surface-dependent initiation of the coagulation cascade (Davie et al.,
1979; Jackson and Nemerson, 1980). Prekallikrein is also involved in the contact activation
of fibrinolysis (Bouma et al., 1980; Mandle and Kaplan, 1977; Colman, 1969), kinin
generation (Kerbiriou and Griffin, 1979; Nakayasu and Nagasawa, 1979; Mori and
Nagasawa, 1981) and the inflammatory response (Kaplan, 1978; Collen, 1979; Cochrane,
1980; Bouma and Griffin, 1981; Colman, 1984).
Introduction / 13
Prekallikrein and factor XI circulate in plasma as inactive zymogens in complexes with
H M W kininogen (Mandel et al, 1976; Thompson et al, 1977). The proteinases, purified
from rabbit, bovine and human plasmas (reviewed in Cochrane and Griffin, 1982), are also
glycoproteins synthesized by the liver and secreted (Davie et al., 1979; Jackson and
Nemerson, 1980). Prekallikrein enters plasma as a single chain polypeptide with a
molecular weight of 88,000 (Mandle and Kaplan, 1977; Bouma et al., 1980; Heimark and
Davie, 1981) whereas factor XI (Bouma and Griffin, 1977; Kurachi and Davie, 1977, 1981)
is the only serine protease secreted as a dimer with a molecular weight of 55,000 to 63,000
for the monomer. The proteins are activated by a single proteolytic cleavage by factor X l l a
(Revak et al, 1974; Fujikawa et al, 1980c; Bock et al, 1981; Tans and Griffin, 1982;
Griffin and Cochrane, 1976; Bouman and Griffin, 1977; Kurachi et al, 1980; Ohkubo et al,
1982) producing two chain molecules with amino-terminal heavy chains containing the
substrate-HMW kininogen-binding sites and carboxy-terminal light chains which bear the
serine protease domains (Mandle and Kaplan, 1977; van der Graaf et al, 1983b).
Recently the complete amino acid sequence of both human prekallikrein (Chung et al, 1986)
and factor XI (Fujikawa et al, 1986) have been determined by partial amino acid sequence
of the purified proteins and by prediction of amino acid sequences from isolated cDNA
clones. The two proteins were found to share 86% amino acid sequence identity.
Alignment of half-cysteine residues shows that these two proteins share a structural domain
of 91 amino acid residues which is repeated four times in both proteins. This repeat is
present in the heavy chains of the prekallikrein and factor XI molecules and does not exhibit
sequence homology with any other known protein. It is possible that this repeat is
important in the H M W kininogen interaction in the molecule.
Introduction / 14
d. High Molecular Weight Kininogen
High molecular weight kininogen is a nonenzymatic cofactor which greatly enhances the
surface activation of the various plasma systems described below (Griffin and Cochrane,
1976; Meier et al., 1977; Revak et al, 1977; Griffin, 1978; van der Graaf et al, 1982). The
protein is synthesized in the liver and is secreted into plasma as a glycoprotein ( M r
110,000) containing 13% carbohydrate (Jackson and Nemerson, 1980; Burgess and
Esmouf, 1985). Human H M W kininogen is cleaved twice by kallikrein giving a two chain
molecule held together by a disulfide bond and releasing a small peptide (approximately
1200 daltons) called bradykinin (Saito, 1977; Jackson and Nemerson, 1980). This cleavage
reaction occurs only when the H M W kininogen/ prekallikrein complex has bound to a
negatively charged surface and prekallikrein is activated by factor Xl la . The sites of
interaction between prekallikrein (or factor XI) and H M W kininogen are on the light chain in
H M W kininogen (the carboxy-terminal region) and on the heavy chain of prekallikrein (the
amino-terminal half of the molecule) (or FXI) (Bock et al., 1985). The interaction is
noncovalent, and a 1:1 complex is formed between these proteins. The light chain of H M W
kininogen has a histidine rich region that is adjacent and carboxy-terminal to the bradykinin
domain in the molecule and is probably responsible for binding to surfaces since deletion of
this region removes coagulation enhancement ability of the molecule (Cochrane and Griffin,
1979; Kerbiriou etal., 1980; Silverberg et al., 1980).
An important product of the kallikrein-HMW kininogen reaction is the nonapeptide,
bradykinin. The physiological functions of kinins have been studied intensely; their roles in
the organism are varied and include participation in the inflammatory response, in renal
function and in the regulation of the cardiovascular system (Bennett and Ogston, 1981; Diz,
Introduction / 15
1985).
2. A Model of the Surface Activation Mechanism
The enzymatic mechanism for surface activation (Cochrane and Griffin, 1982) is still
speculative but a schematic diagram (Fig. 3) from Griffin and Cochrane (1976) illustrating
coagulation initiation can be used to describe the essential steps (Bouma and Griffin, 1981).
The complexes, prekallikrein/HMW kininogen and factor XI /HMW kininogen, and factor XII
bind to negatively charged surfaces, presumably surfaces that are produced during injury
and involve the vascular basement membrane. However, highly purified forms of collagen
added to plasma did not activate factor XII as might be expected as collagen is an important
interstitial molecule (Griffin et aZ.,1975; Fujikawa et al., 1980a). Surfaces play an essential
role in the contact system during the coagulation and fibrinolytic cascade reactions as they
allow the molecules involved to assemble and to act upon one another. For example, the
result of the factors binding to the surface during contact activation is a burst of enzymatic
activity to produce fibrin or plasmin in a matter of seconds.
Factor XII is the first zymogen to be activated in the contact activation mechanism (Griffin,
1981) although it is still unknown how the first molecule is activated. The protein becomes
more susceptible to cleavage when bound to a surface (Griffin, 1978), and it is possible that
small amounts of a-factor X l l a in plasma could be responsible for the initial reaction
(Heimark et al., 1980; Rosing et al., 1985). Therefore, according to the model, an active
form of factor XII cleaves surface-bound factor XII molecules in a slow enzymatic reaction
which is followed by the activation of surface-bound prekallikrein generating kallikrein
(Griffin, 1981). The initiation reactions are now greatly enhanced since prekallikrein and
/ 16
Figure 3: Schematic Diagram of the Surface-Dependent Contact Activation
Mechanism
Schematic diagram of the surface-dependent reactions involved in contact phase activation
of various plasma systems including the coagulation and fibrinolysis cascades (from Griffin
and Cochrane, 1979). PK: Prekallikrein; Kal: Kallikrein; HMWKgn: H M W kininogen; H F :
Hageman Factor (factor XII).
Introduction / 18
factor XII can undergo reciprocal proteolysis (Figure 3). Kallikrein, binding weakly to
H M W kininogen, (Thompson et al., 1983) dissociates from the cofactor and activates many
other factor XII molecules (Tans et al., 1986) as well as generating bradykinin from H M W
kininogen. AZp/ia-factor X l l a displays greater activity towards surface-bound factor XI
than to prekallikrein (Griffin, 1981) and so FXI is preferentially hydrolyzed, resulting in a
cascade of enzymatic reactions. Factor XIa does not dissociate readily from H M W
kininogen (Bouma et al., 1983) and is probably inhibited by its plasma inhibitor (a x -protease
inhibitor) (Scott et al., 1982) in its complex form. Kallikrein cleaves factor X l l a a second
time and generates 0-factor X l l a which is no longer surface bound and enters plasma. The
lifetime of both activated factor XII and prekallikrein in plasma is very short since they are
inhibited rapidly by the Cl-inhibitor (Schreiber et al., 1973).
B. PHYSIOLOGICAL FUNCTIONS OF THE CONTACT SYSTEM
1. Blood Coagulation
Haemostasis is the spontaneous arrest of blood flow during injury to a blood vessel (Guyton,
1977). Survival of the organism with a closed circulatory system such as in the
vertebrates, depends on rapid initiation at the site of injury resulting in blood coagulation
(Davie et al., 1979; Jackson and Nemerson, 1980). Platelets circulate in plasma and adhere
to the subendothelial walls of torn vessels forming a platelet plug. Circulating molecules,
the coagulation proteases, respond to platelet aggregation with the subsequent deposition of
fibrin at the site of injury (Guyton, 1977). Many of the proteins involved are inactive
zymogen forms of serine proteases and were discovered in patients with abnormal
thromboplastin times resulting in a tendency to bleed (Bloom, 1981). At least 14 proteins
Introduction / 19
found in plasma and tissue are required in blood coagulation as well as phospholipid and
C a 2 + (Jackson and Nemerson, 1980; Burgess and Esnouf, 1985). The participating
molecules interact with one another in a cascade effect (Fig. 1) whereby one molecule
activates many others resulting in the conversion of a large number of fibrinogen molecules
to fibrin (Davie and Ratnoff, 1964; MacFarlane, 1964). Fibrin is cross-linked and forms an
insoluble fibrin clot which reinforces the platelet plug and prevents loss of fluid.
The order in which the coagulation factors are activated depends on which factors are
involved when the coagulation cascade is initiated (Davie et al., 1979; Jackson and
Nemerson, 1980). There are two enzymatic pathways, the intrinsic and the extrinsic
pathway, which converge at a common step involving the activation of factor X. Figure 1
depicts the reactions in the coagulation cascade described in mammals. The intrinsic
pathway is initiated by factor XII activation of prekallikrein and factor XI in the presence of
a negatively charged surface and high molecular weight (HMW) kininogen (Griffin, 1981),
as described previously. Initiation of the extrinsic pathway requires tissue factor released
from tissue during injury. Tissue factor is a lipoprotein and acts as a cofactor which
accelerates the activation of factor X by factor V i l a (Davie et al., 1979; Zur and Nemerson,
1981). The intrinsic pathway (Davie and Ratnoff, 1964) derives its activation molecules
strictly from plasma whereas the extrinsic pathway (Zur and Nemerson, 1981) utilizes
proteins from tissue extract; however, both pathways are usually activated upon injury to a
blood vessel. Figure 1 also shows that the extrinsic pathway can be initiated by the
kallikrein/factor X l l a systems by activating factor VII (Kisiel et al., 1977; Radcliffe et al.,
1977; Seligsohn et al., 1979). Coagulation initiation via the extrinsic pathway has also been
demonstrated in vitro by cold dependent activation of factor VII (Seligsohn et al. 1978).
Introduction / 20
The blood coagulation cascade is an elegant illustration of regulation of a complicated
biological process through the action of a single type of enzymatic reaction- polypeptide
chain cleavage by a serine protease (Davie et al., 1979; Jackson and Nemerson, 1980). The
proteins involved are inactive zymogen forms of serine proteases and upon activation will
recognize their specific zymogen substrate in the cascade and activate it by limited
proteolysis at a specific site(s) and always after an arginine residue (Davie et al., 1979;
Jackson and Nemerson, 1980). For example, coagulation factors XII, XI, X, IX, VII and
prothrombin are partially cleaved to produce active serine proteases (Xlla, XIa, Xa, IXa
and thrombin) shown in Figure 1. Cofactors such as V, VIII, H M W kininogen or tissue
factor are required in some of these proteolytic reactions in addition to phospholipid and
C a 2 + for the vitamin K-dependent coagulation proteins (factors VII, IX, X and prothrombin)
(Suttie, 1985). Specific glutamic acid residues found at the amino-terminal regions of these
coagulation proteins are converted to 7-carboxyglutamic acid (Gla) by a vitamin
K-dependent carboxylase. The Gla residues are required in the C a 2 + bridging of the
Gla-containing proteins to phospholipid membranes prior to their activation (Suttie, 1985).
The culmination of all these reactions in the cascade is the polymerization of fibrin molecules
(Doolittle, 1984) to reinforce the platelet plug. The fibrin network is strengthened by the
formation of covalent cross links between monomers by the transglutaminase factor XIHa
which effectively stops the loss of blood (Curtis, 1981). The activated serine proteases are
rapidly inhibited by plasma inhibitors and by feedback inhibition loops (Davie et al., 1979;
Jackson and Nemerson, 1980) which will prevent the proteases from acting at any other
site.
Although factor XII and kallikrein are central components of the surface activation
mechanism in blood coagulation, individuals with either plasma deficiency are
Introduction / 21
assymptomatic. However, plasma coagulation times are greatly reduced and during
extreme trauma or surgical procedures, the bleeding disorder may become life-threatening
(Ratnoff and Saito, 1979; Griffin, 1981). It is reasonable that the coagulation system has
evolved in such a way that it is activated by more than one mechanism since it is crucial
that upon injury, the flow of blood must be arrested.
2. Fibrinolysis
In mammals the dissolution of fibrin clots requires the activation of the fibrinolytic
enzymatic system (Collen, 1979). Plasminogen is the major precursor which is activated
upon cleavage by a serine protease called plasminogen activator (Wiman, 1978). The
product, plasmin, is a trypsin-like serine protease that cleaves 50-60 bonds in fibrin
(Doolittle, 1981). Plasmin exhibits broad substrate specificity and therefore is inhibited
rapidly in plasma by a 2-antiplasmin in a 1:1 stoichiometric complex (Wiman and Collen,
1977). Within the complex the active site serine residue of plasmin interacts with the
carbonyl group of a leucine residue of the inhibitor to form a covalent bond (Wiman and
Collen, 1977). The rate of the inhibition reaction is one of the fastest described for
protein-protein interactions and is one order of magnitude greater than the inhibition rate of
reaction for trypsin by its inhibitors (Wiman and Collen, 1978). The action of the
fibrinolytic enzymes is not limited to the dissolution of blood clots but also function in other
biological phenomena such as tissue repair (Astrup, 1978), malignant transformation
(Reich, 1975), macrophage function (Reich, 1975), ovulation (Strickland, 1978) and embryo
implantation (Strickland, 1978).
Introduction / 22
a. Plasminogen and Its Activators
Human plasminogen is a single chain glycoprotein (M 90,000) of which the entire amino
acid sequence has been determined (Sottrup-Jensen et al., 1978a,b). Two forms of the
molecule are found in plasma, Glu-plasminogen and Lys-plasminogen. Lys-plasminogen is
a proteolytic degradation form of Glu-plasminogen. Lys-plasminogen is the most common
form isolated from plasma and is activated by plasminogen activators by limited proteolysis
between A r g 5 6 0 - V a l 5 t l . The resulting plasmin molecule consists of a heavy chain and a
light chain held together by a disulfide bond. The heavy chain has five characteristic
kringle domains which are responsible for the binding of plasmin to fibrin. The light chain
has the active site which has the His, Asp and Ser of the catalytic triad found in all serine
proteases. Activation of Glu-plasminogen is much slower than Lys-plasminogen but the
final product is the same, Lys-plasmin. Activation of plasminogen by the plasminogen
activators is greatly enhanced in the presence of fibrin.
Plasminogen activation is a complicated process which is not yet clearly understood. The
protein may be activated along three different pathways: an intrinsic pathway in which all
the components are found in plasma; an extrinsic pathway in which the enzymes required
originate from tissues and, an exogenous pathway in which therapeutic substances such as
urokinase and streptokinase are involved (Collen, 1979; Gaffney, 1981;Mullertz, 1984).
Intrinsic fibrinolysis is activated in the presence of factor XII, prekallikrein and H M W
kininogen and a negatively charged surface (Collen, 1979). The mechanism of activation is
not known, and its physiological relevance is unclear. However, plasma deficient in factor
XII shows a greatly reduced plasmin generation time (Ratnoff, 1969; Meier et al., 1977).
Introduction / 23
Physiologicially, a few factor XII deficient individuals have shown a tendency towards deep
venous thrombosis and pulmonary embolism (see Ratnoff and Saito, 1979; Cochrane and
Griffin, 1982).
Plasminogen activators are serine proteases which are present in many different tissues,
organs and secretions and have various functions (Collen, 1980; Bachmann and Kruithof,
1984). Tissue-type plasminogen activator (tPA) (M 70,000) (Pennica et al, 1983) is a
single-chain glycoprotein of 530 amino acids. It is not clear whether tissue-type
plasminogen activator is synthesized as a zymogen form of the serine protease since both
single-chain and double-chain forms are active and are found in plasma (Bachmann and
Kruithof, 1984). The double-chain molecule is produced by limited proteolysis of the bond
between A r g 2 7 „-I le 2 7 b y plasmin, plasma kallikrein or by factor Xa (Wallen et al., 1983;
Ichinose et al., 1984). In the activation of plasminogen, the enzyme is active only when
bound to fibrin and not when bound to fibrinogen. Because of its high affinity for fibrin
(dissociation constant, 150 nM) and considering the high concentration of plasma fibrinogen
(5 to 10 MM), tPA is almost quantitatively bound to the clot during blood coagulation. In the
presence of fibrin, the catalytic activity of t-PA towards Glu-plasminogen increases more
than 500-fold, making the activator a very specific and potent fibrinolytic effector molecule.
Urokinase plasminogen activator ( M r 53,000) has been isolated from urine and kidney
tissue and is a single-chain glycoprotein consisting of 411 amino acid residues (Salerno et al.,
1984; Riccio et al., 1985). The physiological importance of this plasminogen activator has
been associated with the role of plasminogen activators in tissue degradation and
remodeling although it is not known how urokinase functions (see Nagamine et al., 1985;
Riccio et al., 1985). The protein is synthesized as a zymogen form of a serine protease and
Introduction / 24
is activated by partial proteolysis generating a two-chain molecule (Wun et al., 1982).
3. The Inflammatory Response
The inflammatory response to vascular injury is the process whereby the blood flow is
increased by vasodilatation, vascular permeability is increased, leucocytes are summoned
by chemical attractants (chemotaxis) and fibrin is deposited and removed (Bennett and
Ogston, 1981; Wright, 1982). Closer examination of these reactions reveals that the
mulitiple plasma systems, coagulation, fibrinolysis, complement and kinin generation,
become intimately linked (Pesce and Dosekun, 1983; Sundsmo and Fair, 1983; Colman,
1984). Vasodilatation is caused by a number of agents including bradykinin which is a
plasma product from the contact activation mechanism and results from cleavage of H M W
kininogen by kallikrein. Other vasodilators are found in plasma and platelets and interact
with collagen, thrombin or components of the complement system. Permeability of vascular
tissue has been associated with activation of factor XII, with kinins generated from H M W
kininogen and with small peptides derived from the complement systems (C3a and C5a)
that stimulate the release of vasoactive amines from mast cells. Neutrophils
(polymorphonuclear leukocytes) are elicited from plasma to the site of injury through the
action of chemotaxis (Wright, 1982). Kallikrein and tissue plasminogen activator are
chemotactic for neutrophils as well as the complement components, C3, C5 and C5b67
(Bennett and Ogston, 1981). As part of the host defense mechanism, neutrophils penetrate
the vascular site, undergo degranulation and remove foreign material by phagocytosis
(opsonized microorganisms, cellular debris or immunoglubulin and complement fixed to a
substrate which is not susceptible to phagocytosis) (Wright, 1982). Extracellular release of
chemical substances such as proteases and lysosomal constituents by neutrophils causes
tissue damage and inflammation (Wright, 1982).
Introduction / 25
The role of kallikrein and factor X l l a in the neutrophil aggregation and degranulation
reactions has been described (Schapira et al., 1982; Wachtfogel et al., 1983; Wachtfogel et
al., 1986). The involvement of factor X l l a was measured by elastase and lactoferrin
released from neutrophil granules in vitro (Wachtfogel et al., 1986). This release was
stimulated by increasing amounts of FXIIa. Furthermore, Plow (1982) showed that
neutrophil release of elastase was associated with blood coagulation. Pertinent to these
events is that elastase is a major fibrinolytic protease that dissolves clots during the
inflammatory process (Plow, 1980). The possible role of contact activation in the
inflammatory response mechanism is clearly demonstrated in the neutrophil reactions and
the release of elastase. Components of the complement system may also be acted upon by
the contact activation proteases since it has been demonstrated that rabbit kallikrein
generated chemotactic activity for neutrophils from rabbit C5 (Wiggins et al., 1981).
Dissolution of the fibrin deposited at sites of inflamed tissue is required in the resolution
phase of the inflammatory process (Bennett and Ogston, 1981). As described above,
elastase released from neutrophils is one mechanism which is independent of the fibrinolytic
system that results in the removal of fibrin. However, plasmin is also often available at
these sites of injuries (Bennett and Ogston, 1981). Plasminogen is probably activated by
plasminogen activators released from endothelial cells. The plasminogen activators can be
activated via the contact activation system. Factor X l l a and kallikrein would be available
since coagulation would have been initiated earlier on at the damaged tissue site to produce
the fibrin clot.
Introduction / 26
4. Conversion of Prorenin to Renin
Angiotensin II is a hypertensive agent required in the regulation of blood pressure.
Angiotensinogen is synthesized as an inactive precursor which is partially hydrolyzed by
renin to produce Angiotensin I, a less active form of Angiotensin II (Derkx et al., 1976). A
dipeptidase-converting enzyme, found in pulmonary endothelial cells, removes a dipeptide
from Angiotensin I producing Angiotensin II (Erdos, 1979). The enzyme also destroys
bradykinin in a similar reaction by cleaving the carboxy-terminal dipeptide, Phe-Arg (Erdos,
1979). Renin also circulates in plasma as an inactive zymogen. Prorenin can be activated
in vitro by partial proteolysis by plasmin, trypsin, urinary kallikrein or plasma kallikrein
(Cochrane and Griffin, 1982). It has been suggested that factor Xlla does not cleave
prorenin directly but becomes necessary in its activation of plasma prekallikrein (Bennett
and Ogston, 1981; Cochrane and Griffin, 1982). The importance of the contact system
activation mechanism in vivo in the prorenin conversion reaction is questionable although
plasma deficient in factor Xlla or kallikrein exhibit abnormal surface dependent activation
of prorenin (Derkx et al., 1979; Sealy et al, 1979).
C. THE STRUCTURE OF EUKARYOTIC STRUCTURAL GENES
1. Promoters
Expression of genes transcribed by RNA polymerase II is regulated by regions in the
genome which are usually 5' to the coding sequence and are not transcribed (reviewed in
Hansen and Sharp, 1984; Dynan and Tjian, 1985). These regions are important in
regulating transcription levels, in determining specific sites of transcript initiation and in
Introduction / 27
determining rates of gene transcription. These various functions of the 5' region are
accomplished by recognition of sequence motifs by RNA polymerase II and by important
regulatory proteins, most of which are unknown (Hansen and Sharp, 1984). The composite
promoter consists of three regions. The first is the initiation region, spanning from
nucleotide -50 to +10 where nucleotide +1 is the point of transcription initiation, and
including the " T A T A " and cap sites. The second region is the immediate upstream
sequence extending from nucleotides -50 to -110. The third region consists of the enhancer
(activator or potentiator) sequences whose positions vary widely (Hansen and Sharp, 1984).
The best described and most commonly found features of 5' regions in genes are the
" T A T A " and "CAAT" sequences that are located approximately 30 bp and 80 bp
respectively, from the start of the coding sequence in the gene (Breathnach and Chambon,
1981; Hansen and Sharp, 1984). The role of the " T A T A " sequence is to allow transcription
to proceed at approximately 25 bp downstream at a single site and in some cases to enhance
transcription rates (Hansen and Sharp, 1984). The "CAAT" sequences are upstream
regulatory elements initially found in globin genes where they act by increasing
transcription rates (Benoist et al., 1980; Hansen and Sharp, 1984). However, sequence
elements that enhance transcription can vary depending on the gene and not all genes have
C A A T elements (Hansen and Sharp, 1984). For example, the presence of inducible
enhancer sequences have been described for a number of genes (Kessel and Khoury, 1983)
including the heat shock genes (Lindquist, 1986), mouse metallothioniein I gene (Brinster et
al., 1982), the human interferon-^ gene (Kessel and Khoury, 1983) and the human
interferon-a1 gene (Ragg and Weissmann, 1983). Inducible genes are responsive to heat,
high metal concentrations, hormones and other agents (Kessel and Khoury, 1983).
Introduction / 28
2. Introns and Exons
R N A Polymerase II transcribed genes and some t R N A genes are found i n the genome as
mosaics of coding (exon) and noncoding (intron) regions. The discovery of heterogeneous
nuclear R N A lead to the realization that transcripts entering the cytoplasm that were
polyadenylated were in reduced forms of this nuclear R N A (Breathnach and Chambon,
1981). Introns were described (Breathnach et al., 1977) and the splicing apparatus
revealed (Abelson, 1979) which elucidated the heterogeneous nuclear R N A processing
mechanism in the nucleus (see L e w i n , 1983) . This splicing mechanism for R N A Polymerase
II depends on recognition of conserved sequences at the donor and recipient sites of the
introns by smal l nuclear R N A s and the subsequent cleavage by splicing proteins (Lerner
and Steitz, 1979). The sizes of introns are not conserved between members of gene families
and va ry greatly. The m i n i m u m size of a eukaryotic intron is about 80 bp which m a y be
due to the constraints caused by the splicing mechanism (Wieringa et al., 1984).
3. Transcription and Processing
N e w l y transcribed h n R N A s are processed in the nucleus in order to direct their export from
the nucleus to the cytoplasm and to allow correct protein translat ion to occur at the
appropriate start site in the m R N A . Sites of init iation (Baker and Ziff, 1981; Man ley ,
1983) and termination (Birnstiel et al., 1985) of transcription in genes are poorly defined
and are subject to variat ion amongst eukaryotic genes. Transcr ipt ion of most genes begins
wi th a purine but cytosine or uridine have also been found (Baker and Ziff, 1981; Man ley ,
1983). Nontransla ted 5' ends of m R N A s are usual ly 20 to 80 bp in length in 70% of m R N A
5' sequences compiled by Kozak (1984). The processing reactions include (i) 5' capping, (ii)
Introduction / 29
removal of part of the 3' untranslated region and subsequent addition of a poly A + tract
(approximately 200 bases in length) and (iii) removal of the the introns. Capping at the 5'
end is important for efficient splicing of introns (Grabowski et al., 1985) and in translation
(Shatkin, 1985). Polyadenylation occurs after part of the 3' untranslated region has been
removed by a nuclease (Breathnach and Chambon, 1981) approximately 20 bp downstream
of a conserved AAUAAA site (Proudfoot and Brownlee, 1976). This sequence is required
for nuclease activity but is not required in the polyadenylation reaction (Montell et al.,
1983). After the introns have been excised the mature transcript can pass through the
nuclear matrix and enter the cytoplasm where it is translated on the ribosome to produce
the polypeptide chain (Nevins, 1983).
D. MECHANISMS OF GENE EVOLUTION
1. Gene Duplication
Gene families have arisen by the mechanism of gene duplication (Li, 1983) resulting in
proteins with common structure and function (Edgell et al., 1983). If the time of divergence
between two related genes is large, then the genes begin to evolve differently and may
assume new functions such in the lysozyme-a lactalbumin family (Hall et al., 1982) and in
the immunoglobulin superfamily (Hood et al., 1985). The serine protease family of proteins
provides a good example of gene duplication events with subsequent mutations during
divergence. The resulting proteins maintain some amino acid sequence identity such that
they retain the basic structure for their enzymatic reactions as serine proteases
(Hewett-Emmett et al.', 1981; Patthy, 1985).
Introduction / 30
2. Gene Fusions
Variety in the genes can result from the fusion of one gene, or parts thereof, with another
unrelated gene to give a new kind of protein (Doolittle, 1985). Polymorphism in the clotting
genes has been attributed partially to this mechanism (Doolittle, 1985; Neurath, 1985)
during gene duplication events (Calos and Miller, 1980).
3. Exon Shuffling
Complex proteins are usually encoded by genes made up of introns and exons (see above).
It has been suggested (Gilbert, 1978; Blake, 1978; 1983; Rogers, 1985) that the proteins
consist of functional and structural domains that can be identified in related proteins. In
addition, introns demarcate these coding regions as separate exons in eukaryotic genes.
The importance of this concept in evolution is that these exons can be inserted by an exon
shuffling mechanism into other genes within the genome (Gilbert, 1978; Blake, 1978; 1983;
Rogers, 1985). In this model, protein domains on separate exons can be exchanged between
genes and may confer new structure and possibly new function to the recipient molecule.
E. EVOLUTION OF AMINO ACID AND DNA SEQUENCE
1. Molecular Clock
A phylogeny of species can be established by determining the rate of evolution of a
conserved protein family within different species (Zuckerkandl and Pauling, 1965; Wilson et
al., 1977; L i et al., 1985). The validity of this argument is dependent on random mutation
Introduction / 31
of D N A occuring at a constant rate which manifests itself as a constant rate of amino acid
substitution (Zuckerkandl and Pauling, 1965). This constant rate of change of protein
sequence is called the "molecular clock" and when established for a particular protein,
divergence times between species can be assessed. Sometimes, protein evolution is not
constant due to selective pressures on organisms (Wilson et al., 1977). Also, it has been
shown (Wilson et al., 1977; Li et al., 1985) that regions within a protein diverge at different
rates. This allows the detection of protein domains that may be more functionally
important to the organism than other regions of the molecule.
2. Intron Sliding
Members of protein families exhibit regions of variation in the protein that would have
arisen not from amino acid point mutations nor from insertion of domains from other
proteins but from intron sequence within the gene (Craik et al., 1983). The mechanism by
which small amino acid regions have been inserted into proteins is called intron/exon sliding,
and if the junction has shifted in such a way as to maintain the correct translational reading
frame, then it is possible that the new protein sequence could be retained through natural
selection. These small inserts are often found on the surface of molecules where tertiary
structural modifications are most easily tolerated, and they are usually not greater than 13
amino acids in length (Craik et al., 1983). Examples of intron sliding have been found in the
dihydrofolate reductase and serine protease gene families (Craik et al., 1983).
Introduction / 32
F. PROTEIN DOMAINS OF THE COAGULATION AND PLASMINOGEN
ACTIVATOR GENES
1. Trypsin-Like Family of Serine Proteases
The trypsin-like family of serine proteases has been conserved since the time of divergence
of prokaryotes and eukaryotes (Neurath, 1984). These enzymes exhibit diverse functions
such as digestion, coagulation, fibrinolysis, complement activation, neuropeptide processing
and fertilization of germ cells (Neurath and Walsh, 1976). The serine protease domains of
the trypsin-like enzymes share approximately 40% amino acid sequence identity and have
been assumed to share a common mechanism of proteolysis (Young et al, 1978;
Hewett-Emmett et aZ.,1981).
The trypsinogen, chymotrypsinogen and proelastase proteins differ from the coagulation
and fibrinolysis enzymes in their amino-terminal domains. The digestive enzymes all have
short amino-terminal extensions which are released upon activation by proteolysis.
However, the coagulation and fibrinolysis proteins have very large amino-terminal
fragments that consist of multiple putative domains within these proteases (Figure 4)
(Jackson and Nemerson, 1980; Zur and Nemerson, 1981; Doolittle, 1985). Protein
homologies were detected by alignment of common amino acid residues, especially the
cysteine residues which suggest conserved tertiary structure in disulfide bridging patterns.
These regions may have important roles in regulation and selective activation on and by
other serine proteases of the cascade (Jackson and Nemerson, 1980).
The vitamin K-dependent proteins (see above) have a common "Gla-rich" domain which is
/ 33
Figure 4: Amino Acid Sequence Homologies in Coagulation Factor Zymogens
Comparison of the structures of coagulation and fibrinolytic zyymogens to trypsinogen. The
solid bar represents the catalytic region in the proteases, the cross hatched region
represents the Gla region, K represents the kringles, E represents regions homologous to
epidermal growth factor precursor, 1 represent regions homologous to the type I homology
of fibronectin, and A represents the homologous regions found in factor XI and prekallikrein.
the lengths of the bars are approximately proportional to the lengths ofthe polypeptide
chains. Arrows represent the locations of peptide bonds that are cleaved during the
activation of the zymogens. Solid lines below the proteins represent disulfide bridges and do
not necessarily represent their true locations.
PROTHROMBIN V/A K I K
FACTOR VII
FACTOR IX
FACTOR X
PROTEIN C
FACTOR XI
PREKALLIKREIN
FACTOR XII
A 1 A I A 1 A
PLASMINOGEN K I K I K 1 K I K T
TISSUE T Y P E PLASMINOGEN ACTIVATOR
1 I E I K .1 K. I
UROKINASE E K
TRYPSINOGEN
Introduction / 35
contiguous with a prepro leader sequence (see Fung et al., 1985). These proteins include
prothrombin (MacGillivray and Davie, 1984; Degen et al., 1983), factor VII (Hagen et al.,
1986), factor IX (Kurachi and Davie, 1982; Jaye et al., 1983), factor X (Fung et al., 1984,
1985; Leytus et al., 1986) and protein C (Long et al., 1984; Foster and Davie, 1984;
Beckmann et al., 1985) and protein S (Dahlback etal., 1986; Lundwall et al., 1987; Hoskins
et al., 1987). The amino acid sequence of a seventh vitamin K-dependent protein called
protein Z has recently been determined (Hojrup et al., 1985) though the role of this protein is
not known.
A "kringle" structure that consists of 80 amino acid residues with six characteristic cysteine
residues (Magnusson et al., 1975) is found in plasminogen (Sottrup-Jensen et ah, 1978),
tissue-type plasminogen activator (Pennica et al., 1983), urokinase plasminogen activator
(Verde et al., 1984) as well as in prothrombin (Magnusson et al., 1975). The function of the
kringle is not known but plasminogen kringle 4 may be associated with binding to fibrin
molecules.
Another region found in both blood coagulation and fibrinolysis cascade zymogens is the
epidermal growth factor like domain (Blomquist et al, 1984; Doolittle et al., 1984). This
region has been identified in factor VII (Hagen et al., 1986), factor IX (Kurachi and Davie,
1982; Jaye et al, 1983) factor X (Fung et al, 1984, 1985; Leytus et al, 1984) protein C
(Long et al, 1984; Foster and Davie, 1984; Beckmann et al, 1985), protein Z (Hojrup et al,
1985) and the plasminogen activators (Pennica et al, 1983; Verde et al, 1984). The
epidermal growth factor domain is present in the 19 kdal fragment of vaccinia virus and
several other proteins (Blomquist et al, 1984; Doolittle et al, 1984). In many of the
EGF-like regions, a specific aspartic acid or asparagine residue is converted to
Introduction / 36
j3-hydroxyaspartic acid or 0-hydroxyasparagine, respectively.
Tissue-type plasminogen activator has a region that is homologous to the type I homology
found in fibronectin (Ny et al., 1983; Freizner-Degen et al., 1985). This region has fibrin
binding activity in fibronectin (Petersen et al., 1983; Yamada, 1983) and bears
approximately 40% amino acid sequence identity with tissue-type plasminogen activator
(Ny et al., 1984; Friezner-Degen et al, 1985).
G. EVOLUTION OF THE SERINE PROTEASES
Analysis of the blood coagulation and fibrinotysis families of serine proteases aids in
determining the evolutionary process of the genes and how they diversified. Furthermore,
by comparing these genes between species it is possible to determine a time scale within
which these evolutionary events had occured. Patthy (1985) provides a model utilizing the
exon shuffling mechanism to describe how these families of proteins arrived at their present
day form and from this type of speculation we may be able to determine the relationships of
newly characterized blood coagulation and fibrinolysis proteins. With the help of
biotechnology it has become possible to predict the amino acid sequence of many of these low
abundance plasma and tissue proteins. For example cDNA sequences of blood coagulation
proteins prothrombin (MacGillivray et al, 1980; Degen et al, 1983; MacGillivray and
Davie, 1984; MacGillivray et al, 1986; Jorgensen et al, 1987), factor VII (Hagen et al,
1986), factor IX (Kurachi and Davie, 1982; Jaye et al, 1983; McGraw et al, 1986) factor X
(Fung et al, 1984, 1985; Leytus et al, 1984; 1986) protein C (Long et al, 1984; Foster and
Davie, 1984; Beckmann et al, 1985) and protein S (Dahlback et al, 1986; Lundwall et al,
1987; Hoskins et al, 1987) have been determined. Furthermore, the cDNA sequences of
Introduction / 37
the fibrinolytic proteins plasminogen (Malinowski et al., 1984), tissue-type plasminogen
activator (Pennica et al., 1983) and urokinase (Verde et al, 1984) have been determined.
From the cDNA sequences it is possible to predict the amino acid sequences of the zymogens
as well as to predict any regions which are cleaved by the cell prior to secretion such as the
prepro peptides and the signal peptides. Therefore, this kind of technology has been
extremely beneficial in the complete characterization of proteins. However, these
techniques do not provide secondary structure data such as disulfide bridging patterns nor
the identification of glycosylated residues.
fl. OBJECTIVES
The contact system of activation of the various plasma systems described above may be an
important physiological phenomenon required for maintaining homeostasis in the organism.
Central to this mechanism is the glycoprotein, factor XII, which possesses the
surface-binding property that is critical in the initiation reaction. The physical and
biochemical means by which factor XII plays a role in the contact activation may be inferred
from the protein sequence. Recombinant D N A technology will be used to obtain cDNA
sequences from which the amino acid sequence can be predicted to circumvent the expensive
and time consuming processes of protein purification and sequencing using the standard
Edman degradation protein sequencing method. The cDNA can also be used as a probe for
obtaining the factor XII gene.
The evolutionary history of factor XII will be determined from the gene structure since the
family of serine proteases is well characterized and it may be possible to gain a better
Introduction / 38
understanding of the evolution of this old and complex family of genes. Many proteins with
common function belong to the same family and it is possible that FXII is more closely
related to the surface activating proteases, prekallikrein or factor XI, or it may even have
regions of protein homology related to the binding domain of HMW kininogen that had been
acquired through an exon shuffling mechanism in the genome. Clearly, from the
determination of both the amino acid sequence and the gene structure for human factor XII,
greater insight will be gained into the function and evolution of this protein.
II. MATERIALS AND METHODS
A. MATERIALS
Agarose, acrylamide, bisacrylamide, urea, ammonium persulphate, Sephadex G-25 and
T E M E D were from Bio-Rad Laboratories. Oligo (dT) cellulose (type 7) was from P .L .
Biochemicals. Yeast extract, casamino acids, bacto-tryptone and bacto-agar were Difco
grade from the Grand Island Biological Company. NZamine type A was from Sheffield
Products. Nitrocellulose sheets and circles (82 and 132 mm) (BA-85) of 0.45 ym pore size
were from Millipore or Schleicher and Schuell. 3 2 P-labeled deoxyribonucleotide
triphosphates (3000 Ci/mmole; 1 Ci = 3.7 x I O 1 0 Bq) were from Amersham. Phenol
(British Drug Houses Ltd.) was redistilled before use (boiling point 180°C) and frozen in
portions at -20°C. Deoxy- and dideoxy-ribonucleotide triphosphates and the M13
sequencing primer (heptadecanucleotide) were from PL-Pharmacia.
Isopropyl-0D-thiogalactopyranoside (IPTG),
5-bromo-4-chloro-3-indolyl/3-D-galactopyranoside (X-Gal), ethidium bromide, yeast transfer
R N A (tRNA), ampicillin, tetracycline, chloramphenicol, ribonuclease A and
deoxyribonuclease I were from Sigma. Cesium chloride was from Cabot Berylco Ltd.
Ultragel AcA54 was from L K B . Most of the oligodeoxyribonucleotides including some of the
M13 sequencing primer used, were synthesized on an Applied Biosystems 890A D N A
Synthesizer (by Tom Atkinson, Dept. of Biochemistry) and purified by denaturing
polyacrylamide gel electrophoresis prior to use (Atkinson and Smith, 1984). One
oligonucleotide pool was synthesized and purified by Dr. M . Zoller at Cold Spring Harbor
Laboratories, New York. A l l other chemicals were of reagent grade or better and were
purchased from either Sigma Chemical Co., Fisher Scientific, or British Drug Houses Ltd.
39
Materials and Methods / 40
Restriction endonucleases, T4 D N A ligase, T4 D N A Polymerase, T4 polynucleotide kinase
and bovine serum albumin (nuclease free) were from New England Biolabs, Bethesda
Research Laboratories or PL-Pharmacia. Nuclease S i was from Boehringer-Mannheim
and avian myoblastosis virus reverse transcriptase was from Promega Biotec. D N A
polymerase I and D N A polymerase I Klenow fragment were from Boehringer-Mannheim or
PL-Pharmacia. Adult human liver was obtained from kidney donor patients. Liver
samples were cut into 0.5 cm slices, rinsed in sterile PBS (10 mM sodium phosphate pH7.5 ,
150 m M NaCl), frozen in liquid nitrogen and stored at - 7 0 ° C . Human genomic D N A was
isolated by Dr. Colin Hay (Dept. of Biochemistry) and Escherichia coli rRNA was provided
by Dr. P. Dennis (Dept. of Biochemistry).
B. STRAINS, VECTORS AND MEDIA
1. Bacterial Strains
E. coli MC1061 (araD 139, A(ara, leu) 7697, AlacX74, galU-, gal K - , hsr - , hsm +, str A)
(Casadaban and Cohen, 1980) was host for the liver cDNA library cloned into the plasmid
pKT218 containing cloned liver cDNA (Prochownik et al, 1983). E. coli C600 (F-, thi-1,
thr-1, leuB6, l acYl , tonA21, supE44,\-) (Maniatis et al., 1982) was host for human
genomic D N A cloned into the XCharon28 vector (Blattner, et al., 1977). E. coli JM83 (ara,
Alacpro, strA, thi-, 080, lacZAMl5) (Vieira and Messing, 1982) was host for the
transformation of pUC13 vector (Vieira and Messing ,1982) and was obtained from Dr.
Jim Stone, Dept. of Microbiology, U B C . E. coli JM103 (Alacpro, supE, thi-, straA, sbcB15,
endA, hsdR-, F \ traD36, proAB, lacIQ, lacZAM15 (Messing, 1983) was host for
transformation of M13 mp 8, 9, 18 and 19 vectors (Messing, 1983). E. coli RY1088
Materials and Methods / 41
[AlacU169, supE, supF, hsdR-, hsdM + , metB, trpR, tonA21, proC::Tn5(pMC9), pMC9 is
pBR322-lacIQ] (Young and Davis, 1983a,b) was host for screening and isolation of D N A
cloned into the Xgt l l vector (Young and Davis, 1983a,b).
2. Vectors
The M13 mp 8, 9, 18 and 19 vectors (Messing, 1983) were used for D N A sequence analysis.
Small fragments of cloned D N A were subcloned into the vector p U C l 3 (Vieira and Messing,
1982), obtained from Dr. Mark Zoller, (Dept. of Biochemistry, University of British
Columbia) for restriction endonuclease mapping and hybridization probes.
3. Media
The medium for growth of E. coli hosts for X clones was N Z C Y M (Maniatis et al, 1982),
which is lOg NZamine type A, 2g M g C l 2 , 5g NaCl, 5g yeast extract, lg casamino acids per
litre and the pH was adjusted to 7.5 with NaOH. Phage X libraries were plated on
NZCYM-agar plates (1.5% w/v) plates with an overlay of NZCYM-agarose (0.7% w/v) when
screening or NZCYM-agar (0.7% w/v) when titering phage libraries or stocks. Phage were
diluted or stored in S M buffer (5.8g NaCl, 2g M g S 0 4 - 7 H 2 0 , 50 ml IM Tris-HCl pH7.5, 5
ml 2% gelatin per liter). Luria broth (5g yeast extract, lOg bacto-tryptone and lOg NaCl
per liter) (Maniatis et al., 1982) was used as medium for growth of E. coli JM83 containing
the p U C l 3 plasmid derivative. For selection of E. coli JM83 colonies transformed with pUC
derivatives containing cloned DNA, cultures were plated on LB-agar (1.5% w/v) plates
supplemented with 50 ug/ml ampicillin. A liver cDNA library in E. coli MCl061/pKT218
vector screened on LB-agar (1.5% w/v) plates supplemented with tetracycline (12.5 ug/ml).
Materials and Methods / 42
All D N A cloned into M13 vectors and transformed into JM103 was amplified in Y T medium
(Maniatis et al., 1982), which is 5g yeast extract, 8g bacto-tryptone and 5g NaCl per liter.
Phage M13 transformants were plated on YT-agar (1.5% w/v) plates overlayed with
YT-agar (0.7% w/v). E. coli JM103 was maintained on minimal medium plates (Messing,
1983), which were made up as follows: 3g of agar in 160 ml H 2 0 (sterilized and cooled to
5 5 ° C ) was mixed with 40 ml 5X salts (2.1g K 2 H P 0 4 , 0.9g K H 2 P 0 4 , 0.2g ( N H 4 ) 2 S 0 4 ,
0. 1g NaCitrate.7H 2 0 per 40 ml), 2 ml 20% glucose, 0.2 ml 20% M g S 0 4 - 7 H 2 0 and 0.1 ml
10 mg/ml thiamine. Each of these solutions was sterilized separately by autoclaving except
for thiamine which was filter sterilized. Large-scale cultures (more than 500 ml) of E. coli
JM83 or MC1061 containing pUC or pKT218 plasmid vectors, respectively, were grown in
Luria broth in the presence of the appropriate antibiotic. These cultures were further
treated with chloramphenicol (250 ug/ml) in the mid-log phase of growth.
C. GEL ELECTROPHORESIS
1. Neutral Agarose Gels
Electrophoresis grade agarose was boiled in d H 2 0 (added according to the percentage w/v
agarose gel required) for 10 minutes, cooled to 5 0 ° C and the appropriate volume of 5OX
T A E buffer (2M Tris-OH, I M glacial acetic acid, 0.1M E D T A , pH7.2) was added to a final
dilution of IX T A E (Maniatis et al., 1982). To stain nucleic acids in the gel, a volume of
ethidium bromide solution (10 mg/ml) was added to the cooled gel before pouring so that the
final concentration of ethidium bromide was 0.5 ug/ml. The gel was poured into a mold and
was allowed to set for 1 hour. D N A samples were adjusted to IX loading buffer with a 10
times concentrated stock (in 30% ficoll, 0.2% xylene cyanol, 0.2% bromophenol blue) before
Materials and Methods / 43
loading. Electrophoresis was carried out in IX TAE buffer at 1-3 volts/cm after which the
DNA was visualized by irradiation of UV light (260 nm or 360 nm).
2. Formaldehyde Agarose Gels
RNA fragments were separated in agarose gels prepared with a denaturing agent such as
formaldehyde (Maniatis et al., 1982) as follows. An agarose solution (usually 0.6% w/v
final concentration) was boiled and cooled to 60°C. The gel solution was adjusted to 2.2M
formaldehyde (pH less than 4.0) and IX running buffer from a 5X running buffer stock
(0.2M MOPS pH7.0, 50mM sodium acetate, 5mM EDTA) and poured into a mini-gel mold.
RNA samples were prepared in a 20M1 loading volume consisting of 4.5yg RNA (up to 20/ig),
2.0/ul 5X running buffer, 3.5M1 formaldehyde (pH4.0) and lO.Oyl formamide and heated for
20 minutes at 50°C. The samples were electrophoresed for 1.5 hours at 15V/cm, and lanes
containing ribosomal markers were excised and prepared for staining while the region of the
gel containing mRNA was treated for a Northern blot transfer (below). The gel with the
marker lanes was washed with sterile d H 20 for 2 hours with 5 changes of water. The gel
was soaked in 0.1M ammonium acetate for 1 hour with one change of buffer followed by a
final solution of 0.1M ammonium acetate, 0.1M 0-mercaptoethanol and 0.5yg/ml ethidium
bromide for 1 to 3 hours. Prior to visualization with UV light, the gel was destained for 2
hours in the same buffer but without ethidium bromide.
3. Neutral Polyacrylamide Gels
A 30% (w/v) stock solution of acrylamide (29:1 acrylamide:bisacrylamide) in H 2 0 was
prepared and diluted according to the percent gel required. A 10X TBE buffer stock
Materials and Methods / 44
solution (0.89M Tris-OH, 0.89M boric acid, 25 m M E D T A , pH 8.3) was added so that the
gel solution was IX T B E buffer and the solution was degassed using a water aspirator.
Ammonium persulphate (0.066% w/v) and T E M E D (0.04% w/v) were added to initiate
polymerization, the gel was poured and was allowed to polymerize for 1 hour. A 10X stock
of loading buffer was added to the D N A samples which were then adjusted to 0.3% ficol,
0.002% bromophenol blue, 0.002% xylene cyanol. The gel was subject to electrophoresis
6V/cm in IX T B E buffer. DNA was visualized by staining the gel with a solution of
ethidium bromide (lug/ml) in IX T B E buffer followed by irradiation under U V light
(260nm).
4. Denaturing Polyacrylamide Gels
A 40% (w/v) stock solution of acrylamide (38:2 acrylamide:bisacrylamide) was prepared,
and an appropriate volume was added to d H 2 0 , 10XTBE buffer (for a final concentration of
1XTBE buffer) and urea (for a final concentration of 8.3M) to attain the correct percentage
of gel required. The urea was dissolved in the solution in a 3 7 ° C water bath, and then the
solution was degassed. Polymerization was initiated with the addition of ammonium
persulphate and T E M E D to final concentrations of 0.066% (w/v) and 0.024% (w/v),
respectively. The gel was poured and allowed to polymerize for 2 hours. The D N A samples
were applied after heating at 9 0 ° C in loading buffer (98% deionized formamide, lOmM
E D T A , 0.02% xylene cyanol, 0.02% bromophenol blue) for 3 minutes. D N A fragments
separated in denaturing gels were visualized by autoradiography after drying under
vacuum with a Bio-Rad gel drier at 8 0 ° C for 20-30 minutes, and exposing to Kodak XK-1
film, with or without intensifying screens (Dupont Lightning Plus).
Materials and Methods / 45
D. ISOLATION OF DNA
1. Small-scale Isolation of Plasmid DNA
Overnight cultures of E. coli containing recombinant plasmids were grown in Luria broth or
Y T medium in the presence of the appropriate antibiotic at 3 7 ° C . Plasmid DNA was
isolated from 1.5 ml of the culture according to the method of Birnboim and Doly (1979) and
described in Maniatis et al. (1982). The bacterial culture was centrifuged for 30 seconds in
an Eppendorf microfuge and the supernatant was discarded. The pellet was resuspended in
I O O M I of a solution (at 4°C) containing 50 mM glucose, lOmM E D T A , 25 m M Tris-HCl, pH
8.0, and 4 mg/ml lysozyme and incubated at room temperature for 5 minutes. A lysis
solution (200/il of 0.2% NaOH, 1% SDS) was added and incubated on ice for 5 minutes. The
SDS was precipitated by the addition of 150M1 of a potassium acetate solution (60 ml 5M
potassium acetate, 11.5 ml glacial acetic acid, 28.5 ml d H 2 0 , pH 4.8) followed by incubation
at 4 ° C for 5 minutes. Cellular debris and potassium dodecylsulfate were removed by
centrifugation in an Eppendorf centrifuge for 10 minutes at 4 ° C . The supernatant (350^1)
was removed carefully and extracted with an equal volume of phenohchloroform (1:1, v:v).
The phases were separated by centrifugation for 2 minutes in an Eppendorf centrifuge, and
two volumes of 95% ethanol were added to the supernatant. The mixture was incubated at
room temperature for 5 minutes. The D N A was recovered by centrifugation in an
Eppendorf centrifuge for 5 minutes. The pellet was washed with 1 ml of 70% ethanol,
recentrifuged and air dried. The plasmid D N A pellet was resuspended in 2bu\ T E buffer
(lOmM Tris-HCl, pH 8.0, 1 m M EDTA) .
2. Large-scale Isolation of Plasmid DNA
Materials and Methods / 46
Large volumes (500 ml) of Luria broth were innoculated with 3 ml of a fresh overnight
culture of E. coli containing plasmid DNA (antibiotics were added depending on the host
resistance) and grown at 37°C with vigorous shaking until the OD600nm of the culture was
0.5. At this time 250 mg chloramphenicol was added, and the culture was shaken for 12-16
hours at 37°C. Cells were collected by centrifugation at 5 krpm for 10 minutes in a GS-3
rotor (Sorvall) at 4°C. The supernatant was discarded, and the cells were frozen at -20°C.
The cells were resuspended on ice in a solution of 25% (w/v) sucrose, 50 mM Tris-HCl, pH
8.0 and 1.5 mg/ml lysozyme so that the final volume of the cell suspension was 5.0 ml. The
suspension was transferred to a 25 ml Oakridge tube (Beckman) and kept on ice. The cells
were lysed by the addition of 10ml of a 0.2N NaOH, 1%SDS solution and incubated on ice
for 10 minutes. The SDS and cell debris were precipitated with 7.5ml of a 3M potassium
acetate solution pH4.8 and incubated on ice for 10 minutes. (The potassium acetate
solution was prepared from 60ml of 5M potassium acetate to which were added 11.5 ml
glacial acetic acid and 28.5 ml dH20.) The lysis mixture was centrifuged at 35 krpm, 4°C
for 30 minutes in a Ti60 rotor (Beckman). The supernatant was decanted into a 50 ml
centrifuge tube, 0.6 volumes of isopropanol was added, and the DNA was precipitated at
room temperature for 15 minutes. The plasmid DNA was collected by centrifugation at 9
krpm for 30 minutes at room temperature in an HB-4 rotor (Sorvall). The pellet was
resuspended in T E buffer, and solid CsCl was added for a final concentration of l g CsCl/ml
plasmid DNA solution. The solution was adjusted to a final volume of 13.5ml to which was
added 300 M1 of a solution of ethidium bromide (10 mg/ml). The solution was placed into a
Beckman heat sealable tube and was centrifuged in a Ti70.1 rotor (Beckman) for 20 hours
at 20°C at 60 krpm. Plasmid DNA was observed with UV light irradiation (360 nm) as a
Materials and Methods / 47
band midway in the tube. The band was isolated by puncturing the tube with an 18 gauge
syringe, and the ethidium bromide was removed from the DNA solution by multiple
extractions with water saturated isopropanol. When the DNA solution was no longer pink
in color, the extraction was repeated two more times, and the solution was diluted 4 times
with dH 20. The DNA was precipitated by the addition of 3M sodium acetate (to a final
concentration of 0.2M) and two volumes of 95% ethanol. The suspension was left at -20°C
overnight. The precipitated DNA was recovered by centrifugation at 9 krpm and 4°C for
30 minutes in an HB-4 rotor.
3. Small-scale Isolation of X DNA
A fresh culture of host cells was grown overnight in NZCYM medium containing 0.02%
maltose at 37°C with shaking. A plug of agar containing a single phage plaque was added
to I O O M I of the culture, and the phage were preabsorbed to the host cells for 15 minutes at
37°C. The culture was transferred to 20 ml of prewarmed NZCYM and shaken vigorously
at 37°C until total cell lysis was observed. Chloroform (lOOyl) was added, and the culture
was shaken for a further 5 minutes. Cell debris was removed by centrifugation at 5 krpm
and 4°C for 5 minutes in an HB-4 rotor. The supernatant was transferred to a 50ml
centrifuge tube which contained 6ml of 50% PEG (polyethylene glycol 6000, Carbowax
8000) and 3ml of 5M NaCl, and the phage were precipitated at 4°C overnight. The phage
particles were collected by centrifugation at 5 krpm and 4°C for 15 minutes in an HB-4
rotor, and the supernatant was completely removed. The phage pellet was resuspended in
500M1 of DNAsel buffer (50mM Tris-HCl pH7.5, 5mM MgCl 2, 0.5mM CaCl 2) which
contained 5*ig DNAsel and 50/ig RNAseA. The reaction mixture was incubated at 37°C for
30 minutes, and then the cellular debris removed by centrifugation in an Eppendorf
Materials and Methods / 48
centrifuge at 4°C for 5 minutes. The supernatant was adjusted to 1% SDS, 5mM EDTA,
and then 100/Lig of proteinase K (predigested for 1 hour at 65°C) was added and incubated
at 65°C for 1 hour. The DNA solution was extracted twice with phenohchloroform (1:1),
and the DNA was precipitated by the addition of sodium acetate to 0.3M and 2 volumes of
95% ethanol followed by incubation at -20°C overnight. The precipitated DNA was
collected by centrifugation at 9 krpm and 4°C for 15 minutes in an HB-4 rotor. The pellet
was washed with 1 ml 70% ethanol, air dried and resuspended in 50/ul TE buffer.
4. Large-scale Isolation of X DNA
The large-scale isolation of XDNA has been described in Maniatis et al. (1982). A fresh
overnight culture of host bacteria was grown in NZCYM containing 0.02% maltose, and the
OD600nm was taken. A volume of culture was centrifuged (at 3 krpm for 5 minutes in an
HB-4 rotor at 4°C) which corresponded to 2 x l O 1 0 bacteria (1 OD600nm = 8 x 10 s
cells/ml). The bacteria were resuspended in 1 ml SM medium, and 2 x 10' phage were
added. The phage were preabsorbed to the bacteria at 37°C for 15 minutes after which
they were transferred to 450 ml of pre warmed NZCYM medium and shaken vigorously
until total cell lysis was observed. The culture was adjusted to a final concentration of 1%
chloroform and 1M NaCl and shaken for a further 10 minutes. The debris was removed by
centrifugation in a GS-3 rotor at 5 krpm and 4°C for 10 minutes. DNAsel and RNaseA
(50Mg each) were added to the phage supernatant and incubated at 4°C for 1 hour. The
phage particles were precipitated overnight at 4°C by the addition of 33g PEG. Phage were
collected by centrifugation in a GS-3 rotor at 5 krpm and 4°C for 10 minutes. The pellet
was resuspended in SM for a final volume of 5 ml after which the suspension was extracted
with chloroform. The aqueous supernatant was adjusted to a final volume of 13.5 ml with
Materials and Methods / 49
S M buffer containing 0.75 g CsCl/ml S M buffer and transferred to a Beckman heat sealable
tube. The phage were subjected to isopycnic centrifugation in a Ti70.1 rotor for 16-18
hours at room temperature and 60 krpm. A blue band midway in the gradient was
observed by shining a light on the gradient. The band was extracted with an 18 gauge
needle, and the CsCl solution containing Xphage was adjusted to 0.02% gelatin and then
transferred to a dialysis bag. The CsCl solution was exchanged with a solution of lOmM
Tris-HCl pH8.0, 25mM NaCl, lOmM M g C l 2 by dialyzing two times against a 1000-fold
volume excess of buffer. Extraction of D N A from the CsCl purified phage particles was
performed as described for the small-scale preparation of Xphage DNA.
5. Isolation of Single-stranded Plasmid DNA
D N A sequence was obtained from purified (Messing, 1983) single-stranded M13 DNA.
Agar plugs containing M13 phage plaques representing D N A cloned into the M13mp8,9,18
or 19 vectors were removed from the agar plate, transferred to 2ml Y T and grown
overnight with shaking at 3 7 ° C . Bacterial cells from 1.5 ml of the overnight culture were
removed by centrifugation in an Eppendorf centrifuge, and 650M1 of the supernatant was
transferred to a tube containing 300yl 40% P E G and 300M1 5M NaCl. The phage were
allowed to precipitate for 15 minutes at room temperature and were collected by
centrifugation in an Eppendorf centrifuge for 5 minutes. The pellet was resuspended in
200M1 of low salt buffer (20mM Tris-HCl pH7.5, 20mM NaCl, ImM EDTA). The phage
were extracted with 200^1 of phenol (redistilled and saturated in T E buffer) followed by two
extractions with an equal volume of phenol/chloroform (1:1, v:v). The D N A in the aqueous
phase was precipitated overnight at - 2 0 ° C in a final concentration of 0.3M sodium acetate
with 2 volumes of 95% ethanol. The D N A was collected by centrifugation, and the pellet
Materials and Methods / 50
was resuspended in 50u\ 0.3M sodium acetate and reprecipitated with 2 volumes of 95%
ethanol overnight at - 2 0 ° C . The final D N A pellet was resuspended in 40yl low salt buffer.
E. ISOLATION OF POLY A* RNA
All glassware was baked at 1 8 0 ° C overnight, and pipet tips, centrifuge and Eppendorf
tubes and solutions were autoclaved. Human liver R N A was isolated by the method of
Chirgwin et al. (1979). Frozen liver (-70°C) was homogenized using a Polytron
homogenizer in an appropriate volume of buffer [7.5M guanidine hydrochloride (GuHCl),
25mM sodium citrate pH7.0 and 0.1M DTT] so that lOml/g tissue was obtained. A
10%(w/v) N-lauryl sarcosine solution was added to a final concentration 0.5% (w/v), and the
insoluble matter was removed by centrifugation at 5 krpm for 30 minutes in an HB-4 rotor
at 4 ° C . The R N A solution was adjusted to 33% ethanol, and R N A was precipitated
overnight at - 2 0 ° C . RNA was collected by centrifugation at 5 krpm in an SS-34 rotor at
0 ° C for 30 minutes, and the pellet resuspended in half of the starting volume of GuHCl
buffer. The removal of insoluble material by low speed centrifugation, precipitation of RNA
and resuspension in a half volume of GuHCl buffer was repeated two more times. The final
RNA pellet was resuspended in a small volume of d H z O , and the concentration of RNA was
determined from absorption at 260nm [lOD260nm = 40 mg/ml (Davis et al., 1980)]. RNA
was stored in d H 2 0 at - 7 0 ° C .
PolyA + mRNA was isolated by chromatography on a column of oligo-dT cellulose (Edmonds
et al., 1971; Aviv and Leder, 1972). The solution of total R N A was adjusted to a final
concentration of 0.4M sodium acetate pH7.5, 0.1% SDS and applied to the column
equilibrated in column buffer (0.4M sodium acetate pH7.5, 0.1% SDS and 1 m M EDTA).
Materials and Methods / 51
The unbound R N A fraction was reapplied three times. The column was washed until the
OD260nm of the eluate was below 0.05. PolyA + RNA was eluted from the column with 1
m M E D T A , 0.1% SDS. The OD260nm of each fraction was determined and those
containing R N A were pooled. The solution of RNA was adjusted to 0.3M sodium acetate
pH4.8 to which two volumes of 95% ethanol were added, and the RNA was precipitated
overnight at - 2 0 ° C . RNA was resuspended in d H 2 0 at a high concentration and stored at
- 7 0 ° C .
F. OLIGONUCLEOTIDE SYNTHESIS AND PURIFICATION
Oligonucleotides were synthesized (by Tom Atkinson, Dept. of Biochemistry) with an
Applied Biosystems 380A D N A Synthesizer (Atkinson and Smith, 1984). Two pools of
mixed heptadecadeoxyribonucleotides were used as hybridization probes in the screening of
the human cDNA liver library. Pool I (5 ' -dTCRAAYTGRTGNCCCCA-3' , where R
represents both dG and dA, Y represents dT and dC, and N represents dG, dA, dT and dC)
was complementary to the mRNA sequence coding for amino acid residues 133-138 of
(3-factor X l l a (Fujikawa and McMullen, 1983) (Fig. 5). Pool II
(5'-dCCYTGRCANGCYTCNGT-3') was complementary to the mRNA coding for residues
182-188 of ^-factor Xl la . Two oligonucleotides were synthesized which correspond to parts
of the cDNA sequence (5 ' -CGAAAGTGTTGACTCCA-3 ' and
5 ' -GGCCAAAGGTCTTGGAAA-3 ' ) and used to probe for specific regions in the gene and for
nuclease S i mapping and Northern blot analysis.
The synthetic products required purification by polyacrylamide gel electrophoresis and
passage through Sep-Pac columns (Atkinson and Smith, 1984). Dried pellets of the newly
Materials and Methods / 52
synthesized oligonucleotides were resuspended in 90u\ d H 2 0 . A I O M I volume was
transferred to 20yl deionized formamide and heated at 90 °C for 3 minutes. The
oligonucleotide sample and a sample of dye-formamide [xylene cyanol (mobility equivalent
to 45 bases) and bromophenol blue (mobility equivalent to 12 bases) (Maniatis et al., 1982)]
were applied to a 20% polyacrylamide-8M urea gel (42 cm) and electrophoresed at 1500V
until the bromophenol blue had migrated two-thirds of the gel length. The gel was
transferred to Saran Wrap and placed over a thin layer chromatography (TLC) plate, and
the single-stranded D N A was visualized with U V irradiation (260nm). The band
corresponding to the correct length of oligonucleotide was excised and eluted in 1.5 ml of
buffer containing 0.5M ammonium acetate, lOmM magnesium acetate by incubation at
3 7 ° C overnight. The solution was vortexed vigorously and centrifuged for 5 minutes in an
Eppendorf centrifuge and the supernatant removed. The debris was resuspended in 0.5ml
of the elution buffer, vortexed, centrifuged and the supernatant pooled with the 1.5ml
obtained previously. A Sep-Pac was attached to a 5ml syringe and was washed with 10ml
H P L C grade acetonitrile followed by 10ml d H 2 0 . A new syringe was used for each
solution. The sample was loaded onto the small column and pushed through while collecting
the eluate in Eppendorf tubes. The column, loaded with DNA, was washed with 5ml d H 2 0
and 1ml fractions of the wash solution were collected. To elute the oligonucleotide from the
SepPac column, 6ml of 60% methanol (or 20% acetonitrile) were pushed through the
column, and 1 ml fractions collected. The D N A eluted in the first three fractions was
detected by absorbance at 260nm. The concentration was determined from the OD260nm
(lOD = 33yg). Fractions containing significant amounts of D N A were dried in a Speed vac
at 80 °C for 3 hours. The pellet was resuspended in the appropriate volume of d H 2 0 and
was stored at - 2 0 ° C .
Materials and Methods / 53
G. LABELING OF DNA
1. Labe l ing With 3 2 P by Nick Translation
D N A for use as hybridization probes was labeled with 3 2 P by nick translation (Maniatis et
al, 1975). D N A (100-500 ng) was labeled in 50^1 of 50 m M Tris-HCl pH7.5, 5 m M M g C l 2 ,
0.05 mg/ml BSA, 10 m M (3-mercaptoethanol, 20 tfM dGTP, 20 «M TTP, 1.4 iM dATP, 1.4
uM dCTP, 70 yCi a - 3 2 P dATP, 70 M C i 3 2 P dCTP, 0.2mM C a C l 2 , 50 pg DNasel and 20
units E. coli D N A polymerase I (Romberg). The reaction mixture was incubated at room
temperature for 30 minutes and then terminated by the addition of three volumes of 1%
SDS-lOmM E D T A , 25 Mg tRNA and by heating at 68°C for 10 minutes. The unicorporated
isotope was separated from the labeled D N A by chromatography on a column of Ultrogel
AcA54 (5 ml) equilibrated in lOmM Tris-HCl pH7.5, 200mM NaCl and 0.25mM E D T A .
Labeled D N A was eluted in the same buffer and collected in 200M1 fractions from the
column. Single-stranded labeled D N A used as hybridization probes was obtained by
treating the labeled duplex D N A with a tenth of a volume I M N a O H at 68°C for 10
minutes followed by the addition of a tenth of a volume 1.5M N a H 2 P 0 4 (untitrated) just
prior to use.
2. Labe l ing wi th T4 Polynucleotide Kinase
Oligonucleotides were 5'-end labeled with T4 polynucleotide kinase (Chaconas and van de
Sande, 1980) in a 20u\ reaction volume containing 33 pmoles oligonucleotide, 2.5MCi/ul
7 . 3 2 p A T P , 0.1M Tris-OH pH8.0, 0.005M dithieothrieotol, 0.01M M g C l 2 and 4 units T4
polynucleotide kinase. The reaction was incubated at 37°C for 45 minutes and stopped
Materials and Methods / 54
with 0.005M E D T A (pH8.0) and heated at 6 8 ° C for 10 minutes. Unincorporated y-32P
A T P was removed by chromatography on a column of Sephadex G-25 (superfine)
•equilibrated and eluted with 5 m M E D T A (pH 8.0). The excluded fraction was added
directly to the hybridization mixture. The specific activities obtained were usually
approximately 10 6 cpm/pmole.
H. SCREENING A PLASMID LIBRARY
A n adult human liver cDNA library (Prochownik et al., 1983) was generously provided by
Dr. S. H . Orkin (Children's Hospital Medical Center, Boston). This library consists of
double-stranded cDNA (>500 bp in length) cloned into the PstI site of pKT218 by
homopolymeric dG:dC tailing. Initially, 2 x 10 s colonies of the cDNA library were plated
directly onto ten cellulose nitrate filters (132mm diameter) placed on Luria broth plates
containing tetracycline (12.5 mg/ml). The colonies were grown at 3 7 ° C until they reached a
diameter of l-2mm from which two sets of replica filters were prepared (Hanahan and
Meselson, 1980; Fung et al., 1984). The lawn of bacteria was oriented by stabbing with an
18 gauge needle through the filter and the agar. The filters containing colonies were
removed and another filter disc was placed on top of the first filter, and the orientation
marks were placed on the new filter. The plaque lift procedure was repeated with a new
filter disc. The replica filters were transferred to fresh LB-tetracycline plates, and the
colonies were grown at 3 7 ° C until they were 3-4mm in diameter after which the filters were
transferred to LB-chloramphenicol (250Mg/ml) plates and incubated overnight at 3 7 ° C . The
master filters were stored on LB-tetracyline plates at 4 ° C . Colonies were lysed on the
filters by soaking the filters twice for 20 minutes on Whatman 3 M M paper wetted in a
solution of 0.5M NaoH, 1.5M NaCl. The replica discs were neutralized in a similar manner
Materials and Methods / 55
in a solution of IM Tris-HCl pH7.5 for 20 minutes followed by treatment with 0.5M
Tris-HCl pH7.5, 1.5M NaCl for 20 minutes. The nitrocellulose filters discs were air dried
and baked at 6 8 ° C for 16-18 hours.
The filters were hybridized and washed according to conditions described in Fung et al.
(1984). Prior to hybridization, the filter discs were washed three times in 6XSSC (1XSSC
is 0.15M NaCl, 0.015M sodium citrate pH7.0) to remove cell debris and prehybridized in
6XSSC, 2X Denhardt's solution (IX Denhardt's is 0.02% BSA, 0.02% ficol, 0.02%
polyvinylpyrrolidone) at 6 8 ° C for at least 6 hours. One set of replica filters was hybridized
with the 3 2P-labeled Pool I oligonucleotides, and the other set of filters was hybridized to the
3 2P-labeled Pool II oligonucleotides. Each hybridization solution contained 6XSSC, 2X
Dendhardt's solution, 0.2% SDS and 50-100 x 10« cpm 3 2P-labeled oligonucleotide. The
filters were hybridized for 18 hours at 3 7 ° C and then washed in 6XSSC at room
temperature for 5 minutes, 3 7 ° C for 5 minutes and then two times at 4 2 ° C for 5 minutes.
Positive clones were detected by autoradiograhy at - 7 0 ° C with an intensifier screen.
Colonies that hybridized to both pools of oligonucleotides were rescreened at lower colony
density until all the colonies plated were positive.
The cDNA library was also screened using a 3 2 P-nick translated hybridization probe
specific for FXII. Preparation of replica nitrocellulose filters and their prehybridization
conditions were the same as that for oligonucleotides but the hybridization conditions were
changed. Replica filters were hybridized in a solution of 6XSSC, 2X Dehardt's solution,
0.5% SDS and 50 x 10« cpm at 6 8 ° C for 16-18 hours. The washing conditions for the
specific probe were 4XSSC, 0.2%SDS at room temperature for 10 minutes followed by a
wash in the same buffer at 6 8 ° C . More stringent conditions for washing can be used with
Materials and Methods / 56
specific hybridization probes and so the filters were further washed at 1XSSC, 0.2%SDS for
1 hour at 6 8 ° C with three changes of buffer.
/. SCREENING XPHAGE LIBRARIES
Two Xphage libraries were screened for FXII containing sequences according to the methods
described in Benton and Davis (1977). The first was a human genomic phage library kindly
provided by Dr. P. Leder (Harvard University). This library consists of a partial Sau3A
digest of human placental D N A ligated into the BamHl site of Charon 28. One million
recombinant phage were screened by in situ hybridization. Phage were plated on E. coli
strain C600 at a density of 20,000 pfu per 15 cm diameter petri dish and grown at 3 7 ° C .
Duplicate plaque lifts were obtained using nitrocellulose filters. The filters were placed on
the plates when the phage were pin-point size and were not touching one another. The
nitrocellulose disc was oriented by stabbing the filter and the agar using a syringe needle.
The master plates were placed at 4 ° C . The Filters were transferred to a fresh plate of
medium (NZYCM) and grown overnight at 3 7 ° C . The phage were lysed on the filters in
0.5M NaOH, 1.5M NaCl for 5 minutes and neutralized in 1M Tris-HCl, pH 7.5 for 5
minutes followed by 0.5M Tris-HCl, pH7.5, 1.5M NaCl for 5 minutes. The filters were then
washed with gentle rubbing to remove debris in 3XSSC and allowed to air dry. The filters
were baked at 6 8 ° C overnight and were prepared for hybridization with specific cDNA
probes for FXII. The nitrocellulose discs were prehybridized in 6XSSC, 2X Denhardt's
solution and 0.2%SDS at 68 °C for 6 hours. A hybridization solution, consisting of the same
buffer and 50-100 x 10' cpm of a FXII hybridization probe of FXII cDNA that was labeled
by 3 2 P by nick translation, was prepared and the filters incubated at 6 8 ° C overnight. The
filters were washed at room temperature in 4XSSC, 0.5%SDS followed by two washes for
Materials and Methods / 57
30 minutes at 6 8 ° C in 2XSSC, 0.5%SDS. Positive phage were identified by
autoradiography at - 7 0 ° C with intensifier screens. Positive phage found on both replica
filters were replated and rescreened until all the phage hybrized with the probe.
A second library (Koschinsky et al., 1986) was screened and consisted of human liver cDNA
fragments (less than 500 bp in size) cloned into the EcoRl site of Xgt l l (Huynh et al, 1984).
A total of 0.5 x 10 6 phage were plated on E. coli strain RY1088 at 20,000 phage per plate
and incubated at 3 7 ° C . The screening procedure was the same as that described above for
the Xphage human genomic D N A library. The hybridization probe used was a 3 2 P-nick
translated 280 bp fragment of cDNA representing sequence encoding the N-terminal region
of FXII.
J. DNA SUBCLONING
1. Production of DNA Fragments for Ligation
D N A fragments to be subcloned were generated either by restriction endonuclease digestion
or by randomly shearing large pieces of D N A by sonication (Deininger, 1983). Restriction
endonuclease digestions were performed by using the conditions recommended by the
suppliers. Restriction fragments were electrophoresed through agarose or acrylamide gels,
and those fragments that were to be cloned were excised and recovered from the gel by
electroelution (Maniatis era/., 1982).
Random fragments of plasmid D N A were produced by sonication using a Heat Systems
Sonifier at output level 2. The D N A (10-lOOug) was sheared in 500/zl of 0.5M NaCl, 0.1M
Materials and Methods / 58
Tris-HCl, pH7.4, lOmM EDTA with 5 pulses of 5 seconds. The solution was cooled on ice
and vortexed between pulses. The resulting DNA fragments were fractionated on a 5%
polyacrylamide gel, and fragments (300-500 bp in size) were recovered by electroelution.
The DNA solution (450MD was removed from the dialysis bag and adjusted to 0.3M sodium
acetate. Two volumes of 95% ethanol were added, and the DNA was precipitated by
incubation at -20°C overnight. The fragments were collected by centrifugation in an
Eppendorf centrifuge, and the pellet was resuspended in 25yl dH 20. The ends were made
blunt-ended in a 50yl reaction of 33mM Tris-acetate, pH7.8, 66mM potassium acetate,
lOmM magnesium acetate, lOOmg/ml BSA, 0.2mM each deoxynucleotide triphosphate and
6 units T4 DNA polymerase. The reaction conditions varied depending on the conditions
recommended by the supplier. The repaired fragments were extracted with phenol and
precipitated in 0.3M sodium acetate by the addition of two volumes of 95% ethanol and
incubation at -20°C overnight. The DNA was recovered by centrifugation in an Eppendorf
centrifuge for 5 minutes, and the pellet was resuspended in lO/il TE buffer.
2. Ligation of DNA into pUCl3 or M13 Vectors
Fragments of DNA were ligated into the vectors, pUC13 or M13, in a reaction volume of
15wl consisting of DNA, 66mM Tris-HCl, pH7.5, 5mM MgCl 2, 5mM dithiothreiotol, 0.4mM
ATP and T4 DNA ligase [1 unit for blunt-ended ligations and 0.1 unit for sticky-ended
ligations (Maniatis et al., 1982)]. The amounts of insert and vector DNA used in the
ligation reactions depended on the vector: for pUCl3, 200ng insert DNA and lOOng vector
DNA were used while for M13, lOng sticky-ended insert DNA and 10 ng vector DNA were
used, and 50ng blunt-ended insert DNA and lOng vector DNA were used. Ligation of
sticky-ended DNA was for 4 hours at 16°C whereas ligation reactions of blunt-ended DNA
Materials and Methods / 59
were incubated at 1 6 ° C overnight. The ligation reactions were stored at - 2 0 ° C .
3. Transformation of DNA into Bacteria
Host bacterial cells were made competent for D N A transformation using calcium chloride
(Messing, 1983). E. coli JM83 or JM103 were grown in 50 ml L B or Y T , respectively, at
3 7 ° C with vigorous shaking until the culture reached an OD600hm of 0.2-0.4. The cells
were collected by centrifugation for 5 minutes in an HB-4 rotor at 2.5 krpm at 4 ° C , and the
pellet was resuspended in ice-cold 50mM C a C l 2 at half the original volume of culture. The
cells were incubated on ice for 40 minutes and then recovered by centrifugation as before.
The calcium chloride treated cells were resuspended in one-tenth the original volume of ice
cold C a C l 2 solution and incubated at 4 ° C for 2-18 hours. Aliquots (0.3ml) of competent
cells were transferred to glass tubes (13x100mm) placed on ice. Volumes of 2-3 u\ of the
ligation mixture containing either M13 or pUC13 vectors were used to transform JM103
and JM83 competent cells, respectively. Transformation proceeded for 40 minutes on ice
and then for 2 minutes at 4 2 ° C . JM103 transformations were plated immediately with the
addition of 10/d 100 m M IPTG, 35-50yl X-Gal (2% w/v in dimethylformamide), 0.2ml host
cells and 3ml soft Y T agar and spread on Y T plates. JM83 transformed cells were rescued
with the addition of 0.7ml L B followed by shaking at 3 7 ° C for one hour. The cells were
spread in 100/ul aliquots with 50<d X-Gal (2% w/v) onto LB-ampicillin (50yg/ml) plates. The
JM103 and JM83 plated transformants were incubated overnight at 3 7 ° C . Phage plaques
or colonies which were clear or white, respectively, contained cloned D N A whereas plaques
or colonies transformed with religated vector without insert D N A appeared blue on the
plates.
Materials and Methods / 60
K. BLOT HYBRIDIZATIONS
1. Southern Blot Analysis of Genomic and Cloned DNA
D N A was transferred to nitrocellulose filter sheets from agarose gels essentially as
described by Southern (1975). D N A samples (1 to 10 Mg) were digested by restriction
endonucleases and were separated by electrophoresis through agarose gels.
Single-stranded nicks were introduced into the D N A by irradiation using 260nm ultraviolet
light for 30 seconds. The gel was soaked in 0.5N NaOH, 0.6M NaCl for 45 minutes to
denature the D N A and then the gel was neutralized by soaking twice in a solution of 1M
Tris-HCl pH7.5, 0.6M NaCl for 30 minutes. The gel was placed on Whatman 3 M M paper
wicks which extended into the transfer buffer (10XSSC). A piece of nitrocellulose filter was
cut to the size of the gel and soaked for 10 minutes in d H 2 0 and then 10XSSC. The filter
was placed on the gel followed by two sheets of Whatman 3 M M paper and stacks of paper
towels which were cut smaller than the nitrocellulose sheet. The D N A was transferred to
the filter paper for 16 hours for plasmid or lambda D N A but 36-48 hours for genomic DNA.
After transfer, the paper towels and 3 M M paper were removed and the lane origins were
marked on the nitrocellulose filter. The filter was removed and washed in 3XSSC, air dried
and baked at 68 °C for 6 hours.
Hybridization of 3 2 P-labeled D N A to genomic DNA Southern blots was performed according
to Kan and Dozy (1978) whereas Southern blots of plasmid or lambda D N A were hybridized
as described in Maniatis et al. (1982). The nitrocellose filter sheet containing genomic
D N A was wetted in 3XSSC and prehybridized for 16 hours at 3 7 ° C in 10 ml of a solution
containing 50% formamide, 6XSSC, ImM E D T A , 0.1% SDS, lOmM Tris-HCl pH7.5, 10X
Materials and Methods / 61
Denhardt's solution, 0.05% sodium pyrophosphate, 100Mg/ml denatured herring sperm
D N A , 25/ng polyA + and 50 Mg/ml tRNA. The hybridization solution was identical to that for
prehybridization except for the addition of 20-50 x 10 6 cpm of denatured 3 2P-labeled DNA.
Hybridization was allowed to proceed for 48 hours at 3 7 ° C , and then the blot was washed
for 1 hour at room temperature in 2XSSC, IX Denhardt's solution followed by two washes
at 5 0 ° C for 45 minutes in 0.1XSSC, 0.1% SDS. The blot was rinsed twice at room
temperature in 0.1XSSC, 0.1% SDS followed by four rinses at room temperature in
0.1XSSC. After air drying the hybridized blot was exposed to Kodak XK-1 film with an
intensifier screen for 1 to 7 days at - 7 0 ° C .
The hybridization conditions used for plasmid and lambda D N A containing inserted
fragments of D N A were similar to those described in the screening of the Xphage libraries.
The baked filter was wetted in 3XSSC and prehybridized for 4 hours in 6XSSC, 2X
Denhardt's solution, 0.2% SDS at 6 8 ° C . A n identical solution was prepared which also
contained 1 to 10 x 10 6 cpm of denatured 3 2P-labeled D N A was exchanged for the
prehybridization solution. The blot was hybridized for 16 hours at 6 8 ° C followed by
washing in 4XSSC, 0.5% SDS for 10 minutes at room temperature. Subsequent washes
were in 1XSSC, 0.5% SDS at 6 8 ° C . The hybridized blots were air dried and exposed to
Kodak film 2-16 hours at room temperature.
2. Northern Blot Analysis
RNA was separated by electrophoresis in formaldehyde agarose gels and then transferred
to nitrocellulose filter sheets (Maniatis et al., 1982). The RNA was denatured in the
presence of formaldehyde (Lehrach et al., 1977) which was present in the gel and in the
Materials and Methods / 62
loading solution. After electrophoresis, the gel was treated with a solution of 50mM N a O H
for 45 minutes and then neutralized in 0.1M Tris-HCl pH7.5 for 45 minutes. The gel was
soaked in a final solution of 20XSSC for 45 minutes and then placed on Whatman 3 M M
filter paper wicks extending into a solution of transfer buffer (10XSSC). The nitrocellulose
filter paper was wetted in d H 2 0 and 10XSSC, and the RNA was transferred to the paper
for 16 hours as described above for Southern blotting. Specific mRNA species were detected
by hybridization and washing as described for Southern blots of genomic D N A (see above).
L. DNA SEQUENCE ANALYSIS
1. Screening M13 Clones
D N A fragments to be sequenced by the chain termination method (Sanger et al., 1977) were
ligated into the M13 sequencing vectors (Messing et al., 1981; Messing, 1983) as described
above. To identify the M13 phage which contain the desired insert, the M13 plaques were
screened by in situ hybridization (Benton and Davis, 1977). The M13 phage were plated on
1.5%(w/v) Y T agar plates at a density of approximately 500 plaques/plate. Nitrocellulose
filter discs (85mm) were placed over the plaques, the filter oriented with an 18 gauge needle
and then the filter was transferred to a solution of 0.5N NaOH, 1.5M NaCl for 5 minutes to
lyse the phage particles and denature the D N A on the filter. The filters were neutralized in
I M Tris-HCl pH7.5 for 5 minutes followed by a solution of 0.5M Tris-HCl pH7.5, 1.5M
NaCl for 5 minutes. The filters were air dried and baked for 6 hours at 6 8 ° C . The
nitrocellulose filter discs were washed with 3XSSC for 10 minutes at room temperature and
then prehybridized in 6XSSC, 2X Denhardt's solution and 0.2% SDS for 4 hours at 6 8 ° C .
The hybridization solution was the same as the prehybridization solution but also contained
Materials and Methods / 63
1 to 50 x 10 6 cpm of denatured 3 2P-labeled D N A to identify phage containing the D N A to
be sequenced. The filters were incubated at 6 8 ° C for 16 hours and then washed in 4XSSC,
0.5% SDS at room temperature for 10 minutes. The excess probe was removed by further
washes at 6 8 ° C in 1XSSC, 0.5% SDS with multiple exchanges of the washing buffer. The
filters were dried and exposed to Kodak-XKl film at - 7 0 ° C for 16 hours with an intensifier
screen. Selected phage plaques were transferred to Y T media, diluted approximately 10*
times and replated. M13 phage containing insert D N A from these plates were grown and
their single-stranded D N A isolated.
2. DNA Sequence Analysis
The nucleotide sequence of single stranded D N A isolated from M13 clones was determined
by the chain termination method (Sanger et al., 1977) as modified for phage M13 templates
(Messing et al., 1981). Table I shows the concentrations of the deoxy- and
dideoxy-nucleotides used in the sequencing reactions. An M13 primer ( I M I o f a solution with
0.03 OD260nm/ml) having the nucleotide sequence of 5 ' - G T A A A A C G A C G G C C A G - 3 ' was
hybridized to single stranded template D N A (in 4 ul) in a total reaction volume of 8jul that
also contained I M I d H z O and 2M1 10X Hin buffer (600 m M NaCl, lOOmM Tris-HCl pH7.5,
70mM MgCl 2 ) . The hybridization mixture was incubated at 6 8 ° C for 10 minutes and then
was allowed to cool slowly to room temperature followed by the addition of I M I of 15juM
dATP and 1.5M1 3 2 P-a-dATP (10 uCi/ul). Aliquots consisting of 2.0/xl of the hybridization
mixture were dispensed to four tubes containing 1.5/d of the appropriate
deoxy/dideoxy-nucleotide mixture (Table I). The reactions were started with the addition of
0.4 units D N A polymerase I Klenow fragment and incubated at room temperature for 15
minutes. A chase solution was added (lul of 0.5mM dATP) and the reaction mixtures were
SEQUENCING MIXES
N u c 1 e o t 1 d e d/ddG d /ddA d / d d T d /ddC
dG 7.9 1 0 9 . 4 1 5 8 . 7 1 5 7 . 9
dT 157 .6 1 0 9 . 4 7.9 1 5 7 . 9
dC 157 .4 109 .4 1 5 8 . 7 10 .5
ddG 157 .4 - - -ddA - 1 1 6 . 7 - -
ddT - - 550 .3 -
ddC _ 191 .6
T a b l e I : DNA S e q u e n c i n g M i x e s .
The numbers In the t a b l e r e f e r to the yuM c o n c e n t r a t i o n s of the
d i d e o x y and d e o x y - r I b o n u c I e o t I de t r i p h o s p h a t e s used in the s e q u e n c i n
m i x e s f o r M13 DNA s e q u e n c i n g . The v a l u e s used were t h o s e d e t e r m i n e d
D r . Joan M c P h e r s o n , D e p t . of B o t a n y , UBC.
)
Materials and Methods / 65
incubated for 20 minutes at room temperature followed by the addition of 5yl of a stop-dye
mixture (98% formamide, 10 m M E D T A pH8.0, 0.02% xylene cyanol, 0.02% bromophenol
blue). The extended products were denatured by heating to 9 2 ° C for three minutes, and
l-2yl of each reaction mixture was analyzed on 6% and 8% polyacrylamide-8M urea gels in
1XTBE buffer at lW/cm. After electrophoresis, the gels were dried and exposed to Kodak
XK-1 film overnight at room temperature.
3. Computer Analysis of DNA Sequence Data
Analysis of the D N A sequence data obtained from the sequencing gels was assisted by the
computer programs of Staden (1982) and Delaney (1982).
M. MAPPING THE END OF A MRNA TRANSCRIPT
1. Primer Extension Analysis
A hybridization primer was prepared as follows. Single stranded D N A of a fragment
representing the 5' end of the FXII mRNA was subcloned M13mpl9 and was made double
stranded and radioactive with D N A polymerase I-Klenow fragment in the following
reaction. The M13 primer was hybridized to the single stranded D N A template at 6 8 ° C for
10 minutes in a mixture consisting of 2.5yl M13 primer, 2.5yl D N A , 2.5yl 10X Hindi
buffer (1M NaCl, 0.1M Tris-HCl pH7.4, 0.07M M g C l 2 , 0.01M dithiothreiotol) and 7.5yl
d H 2 0 . The reaction was cooled slowly to room temperature and then adjusted with 2yl
15yM dATP, 3M1 ^P-a-dATP ( I O M C I / M D , 2yl 0.5mM dGTP, dCTP and T T P and 1.25 units
of Klenow fragment (2.5yl). The extension reaction was incubated for 5 minutes at room
temperature and transferred to 6 8 ° C for 10 minutes. The reaction was cooled to 3 7 ° C , and
Materials and Methods / 66
20 units of the restriction endonuclease Hinc II was added and the D N A digested for 20
minutes. A n equal volume of stop-dye mixture (98% deionized formamide, 10 m M E D T A ,
pH 7.5, 0.02% bromophenol blue, 0.02% xylene cyanol) was added and the D N A was
denatured at 9 0 ° C for 5 minutes. The D N A fragments were subjected to denaturing gel
electrophoresis through a 6% polyacrylamide-8 M urea gel. After autoradiography for 5
minutes, the gel slice containing the primer D N A (180 bp) was excised and the D N A
recovered by electroelution. The D N A was precipitated with ethanol and resuspended in
6.5M1 of a buffer containing 40 m M Pipes pH 6.7, 1 m M E D T A and 0.4 M NaCl (Kingston et
al., 1984). The mixture was added to 3yl polyA + mRNA from human liver (18yg) and 30M1
deionized formamide. Another reaction was prepared in the same manner but without
mRNA. The reaction mixtures were heated at 8 0 ° C for 15 minutes and then transferred to
a 3 0 ° C water bath for 16 hours (Kingston et al., 1984). The nucleic acids were precipitated
with 140/il of 0.3M sodium acetate (pH 5.0) and 400/il of 95% ethanol. The pellets,
containing approximately 60,000 cpm, were resuspended in 50M1 of A M V reverse
transcriptase buffer (50 m M Tris-OH pH 8.3, 20 m M KC1, 10 m M M g C l 2 , 5mM
dithiothreiotol)(Kingston et al., 1984) to which was added 30 units of A M V reverse
transcriptase. The reactions proceeded at 3 7 ° C for 1 hour and then the nucleic acids were
precipitated with 5yl of 3M sodium acetate and 125 ul of 95% ethanol. The pellets were
resuspended in 5M1 of load-dye mix and denatured at 9 0 ° C for 5 minutes. The
primer-extended product was analyzed on a 6% polyacrylamide-8 M urea gel. D N A
sequencing reactions of the template from which the original primer was obtained were used
as size markers. Following electrophoresis, the gel was dried and exposed to Kodak XK-1
film overnight at room temperature and then 3 to 14 days at - 7 0 ° C with an intensifier
screen.
2. Nuclease S i Mapping
Materials and Methods / 67
A hybridization probe was prepared in the same manner as that described above. The
single stranded primer, however, was obtained from an M13 subclone of the 450 bp Hpall
fragment that represents the 5' end of the mRNA transcript and 5' most flanking
sequences. An oligonucleotide primer (5 ' -CGAAAGTGTTGACTCCA-3' ) was synthesized on
an Applied Biosystems 380A D N A Synthesizer (Atkinson and Smith, 1984) and is
complementary to a region within the 450 bp Hpall fragment. The preparation of the long
3 2P-labeled primer was the same as that described for the primer extension reaction above.
To generate the correct hybridization probe for nuclease SI mapping, the Klenow
3 2 P-labeled D N A was digested with EcoRl and the single stranded primer was isolated from
a 6% polyacrylamide-8M urea gel as described above. Hybridization of this primer (210 bp
in length) to poly A + mRNA was as described for the primer extension reaction. Another
identical reaction was prepared except that d H 2 0 was added instead of poly A + mRNA.
After hybridization, the nucleic acids were precipitated by the addition of 140jul of 0.3M
sodium acetate and 400/ul of 95% ethanol followed by incubation at - 7 0 ° C for 20 minutes.
The nucleic acids were collected by centrifugation at 4 ° C for 10 minutes in an Eppendorf
centrifuge. To the pellets were added 270M1 nuclease S i buffer (270ul of 0.28 M NaCl,
50mM sodium acetate, 4.5mM ZnS0 4 ) , lOug denatured herring D N A and 10 to 30 units of
nuclease S i . The reaction mixture was incubated at 3 7 ° C for 15 minutes to 1 hour. The
digested D N A was precipitated with 10/ug tRNA and 600^1 95% ethanol and incubated at
- 7 0 ° C for 15 minutes. The D N A was recovered by centrifugation and the pellet
resuspended in 2.5M1 of ImM Tris-HCl pH 7.5, 0.6mM NaCl, O. lmM M g C l 2 and 2.5yl of
stop-dye mix. The sample was heated for 3 minutes at 90 °C and analyzed on a 6%
polyacrylamide-8M urea gel together with the D N A sequencing reactions of the template
Materials and Methods / 68
from which the original probe was prepared. The nuclease S1 reaction on the same
hybridization mixture was repeated with the addition of 10 ug tRNA instead of 10ug of
denatured herring DNA and 200 units of enzyme. The gel was dried and exposed to film as
described for the primer extension reaction above.
III. RESULTS
A. CHARACTERIZATION OF THE HUMAN FXII CDNA
1. Isolation of Factor XII cDNA Clones
A human liver cDNA library (provided by Dr. Stuart Orkin at Children's Hospital,
Harvard University) was screened to isolate the human FXII cDNA. Two hundred
thousand bacterial colonies of the cDNA library were screened by in situ hybridization with
two mixtures of synthetic oligonucleotides that encoded two regions of 0-factor X l l a as
predicted from the known amino acid sequence (Fig. 5). Although each of the oligonucleotide
mixtures hybridized to about 60 different colonies, only two colonies hybridized to both
(Fig. 6). After rescreening at lower colony density, plasmid D N A was isolated from the two
positives that were designated pcHXII-11 and pcHXII-14 (Fig. 7). Subsequent sequence
analysis revealed that these plasmids contained D N A coding for the known amino acid
sequence of /3-factor Xl la . Because pcHXII-11 and pcHXII-14 contained only short cDNA
inserts, 2 x 10 5 colonies of the cDNA library were rescreened with the [3 2P]-labeled Psil
insert of pcHXn-11 as a hybridization probe. Thirty-six positive clones of various lengths
were obtained; plasmids pcHXII-17 and pcHXII-501 contained the longest cDNA inserts
and were studied further. Restriction endonuclease mapping of the four positive plasmids
showed that they contained overlapping D N A (Fig. 7) except that pcHXII-17 appeared to
contain a deletion (Fig. 7, open dashed bar). This was confirmed by subsequent D N A
sequence analysis (see next section).
69
/ 70
Figure 5. Predicted Oligonucleotide Sequences for 0-factor Xlla
Flow Chart indicating the regions of the 0-factor X l l a amino acid sequence (Fujikawa and
McMullen, 1983) from which the oligonucleotide sequences were predicted; mixtures of
synthetic heptodecadeoxyribonucleotides were used as hybridization probes in screening the
liver cDNA library. The underlined numbers represent the two pools of oligonucleotides
used in the double screening technique (Figure 6). Oligo 1 and Oligo 2 sequences represent
amino acids 537 to 542 (Thr to Gly) and 486 to 491 (Trp to Glu), respectively, in the
0-factor X l l a amino acid sequence (Fig. 6).
g-factor Xlla
H,N - AsnGlyProLeuSerCys — GlyGlnArg I S I S 2
ValValGly - Cys -TrpGlyHisGlnPheGlu.
mRNA Sequence
Complementary Oligo Sequence
5 lTC^AASG\GTCCCCA 3' G T G C
32 Possible Sequences
ThrAspAlaCysGlnGly—(Ser)—ThrSerVal - COOH
J mRNA Sequence
Complementary Oligo Sequence
5'-CC^TG^CATCC^TCTGT- 31
C G C G C
128 Possible Sequences
/ 72
Figure 6: Double Oligonucleotide Screen For Factor XII cDNA
A liver cDNA library was plated at a high density (100,000 colonies/filter) and duplicate
filters were hybridized with either 3 2P-labeled oligo-1 or oligo-2 pools of synthetic
heptodecadeoxyribonucleotides (upper discs). The overlapping positive colony (arrows) was
rescreened at a lower density (200 colonies/filter) in duplicate and hybridized with the same
oligonucleotide mixtures (lower discs). Positive colonies which overlapped (arrows) were
selected and their D N A sequence determined.
/ 74
Figure 7: Restriction Enzyme Map and Sequencing Strategy for Factor XII cDNA
The bars below the restriction map represent cDNA clones; pcHXII-11, pcHXII-14,
pcHXII-17 and pcHXII-501 and include regions coding for the signal peptide (dotted bar),
the heavy chain of a-factor X l l a (solid bars) and the 3' untranslated region (slashed bar).
The open dashed line in pcHXII-17 represents a deletion (see text for details). Arrows
below the cDNA clones represent the sequencing strategy used, where each arrow
represents the M13 clone. The extent of sequencing is indicated by the length of arrows.
D N A sequence determined on the coding strand is shown by an arrow pointing left;
sequence determined on the non-coding strand is shown by an arrow pointing right. Thick
arrows represent D N A sequences obtained from randomly sheared cDNA fragments and
thin arrows represent sequence obtained from restriction enzyme fragments. The scale at
the bottom represents nucleotides in kilobase pairs.
2. Sequence Analysis of Human Factor XII cDNA Clones
Results / 76
The strategy used to determine the nucleotide sequence of the four clones, pcHXII-11, 14,
17 and 501 is shown in Figure 7. The thick arrows represent the sequence determined from
M13 phage containing randomly sheared DNA. Although more than 90% of the nucleotide
sequence was determined using this strategy, few random clones were isolated that
overlapped the Aval site or the 5' end of factor XII cDNA (Fig. 7). To complete the
nucleotide sequence analysis, plasmid pcHXII-501 (Fig. C) was digested with PstI and the
1200 bp and 280 bp fragments were isolated by polyacrylamide gel electrophoresis. The
280 bp fragment was cloned directly into the PstI site of M13mp8. The 1200 bp fragment
was digested with both Aval and Smal, and the ends were made blunt-ended using the
Klenow fragment of E. coli D N A polymerase I (Smith et al., 1979). The resulting Pstl/Aval
and AvallSmal fragments were isolated by polyacrylamide gel electrophoresis and
subsequently ligated into the Smal site of M13mpl8. The D N A sequence analysis of these
clones is shown in Fig. 7 (thin arrows).
The nucleotide sequences of the four factor XII cDNA clones were compiled into a consensus
sequence (Fig. 8) using the computer program designed by Staden (1982). Each nucleotide
in the sequence was determined an average of 6.6 times and 84% of the sequence was
determined on both strands. In the regions of overlap, the four factor XII cDNA clones
contained identical nucleotide sequences with one exception. In agreement with the
restriction map of pcHXII-17 (Fig. 7), the D N A sequence analysis showed that this plasmid
contains a deletion of 53 bp between nucleotides 1330 and 1383 (Fig. 8). The deleted region
is flanked by an inverted repeat having the sequence: CTCGC(G/C)CGTC (nucleotides
1320-1329 and nucleotides 1383-1392, Fig. 8). This deletion alters the reading frame of
/ 77
Figure 8: Nucleotide Sequence of Factor XII cDNA
The sequence was determined by analysis of the overlapping clones shown in Figure 7. The
predicted amino acid sequence of human factor XII is shown above the D N A sequence, the
oligonucleotide sequences used for screening the cDNA library are represented by boxes at
nucleotides 1,474-1,490 and 1,627-1,643. The signal peptide is numbered backwards from
the putative signal peptidase cleavage site (open arrow). The proteolytic cleavage sites that
give rise to (3-factor X l l a are shown by the heavy arrows (at amino acid residues 334, 343
and 353). The residues that make up the catalytic triad (His 393, Asp 442 and Ser 544)
are underlined. The T G A stop codon is located at nucleotides 1,807-1,809 and followed by
the 3' untranslated region (nucleotides 1,810-1,959) and a poly A + tail. The poly A +
recognition site A A T A A A is encoded by nucleotides 1,937-1,942. A carbohydrate
attachment site (Fujikawa and McMullen, 1983) is indicated by the solid diamond.
78
10 20 Leu Glu Ser Thr Leu Ser He Fro Pro Trp Clu Ala Pro Lys Clu His Lys Tyr Lys Ala Glu Glu His Thr Val Val Leu Thr Val Thr Gly Glu Pro Cys His TTG GAG TCA ACA CTT TOG ATT CCA CCT TGG GAA GCC CCC AAG GAG CAT AAG TAC AAA GCT GAA GAG CAC ACA GTC GTT CTC ACT CTC ACC GGG GAG CCC TGC CAC
15 30 45 60 75 90 105
30 40 . 5 0 60 Phe Pro Phe Gin Tyr His Arg Gin Leu Tyr His Lys Cys Thr His Lys Gly Arg Pro Gly Pro Gin Pro Trp Cys Ala Thr Thr Pro Asn Phe Asp Gin Asp Gin TTC CCC TTC CAG TAC CAC CCG CAG CTG TAC CAC AAA TGT ACC CAC AAG GGC CGG CCA GGC CCT CAG CCC TGG TGT GCT ACC ACC CCC AAC TTT GAT CAG CAC CAC
120 135 150 165 180 195 210
70 80 90 Arg Trp Gly Tyr Cys Leu Glu Pro Lys Lys Val Lys Asp His Cys Ser Lys His Ser Pro Cys Gin Lys Gly Gly Thr Cys Val Asn Het Pro Ser Gly Pro His CCA TGG GGA TAC TGT TTG GAG CCC AAG AAA GTG AAA GAC CAC TGC AGC AAA CAC AGC CCC TGC CAG AAA GGA GGG ACC TGT GTG AAC ATG CCA AGC GGC CCC CAC
225 240 255 270 285 300 315
100 110 120 130 Cys Leu Cys Pro Gin His Leu Thr Gly Asn His Cys Gin Lys Glu Lys Cys Phe Glu Pro Gin Leu Leu Arg Phe Phe His Lys Asn Glu l i e Trp Tyr Arg Thr TGT CTC TGT CCA CAA CAC CTC ACT GGA AAC CAC TGC CAG AAA GAG AAG TGC TTT GAG CCT CAG CTT CTC CGG TTT TTC CAC AAG AAT GAG ATA TGG TAT AGA ACT
330 345 360 375 390 405 420
140 150 160 Glu Gin Ala Ala Val Ala Arg Cya Gin Cys Lys Gly Pro Asp Ala His Cys Gin Arg Leu Ala Ser Gin Ala Cys Arg Thr Asn Pro Cys Leu His Gly Gly Arg GAG CAA GCA GCT GTG GCC AGA TGC CAG TGC AAG GGT CCT GAT GCC CAC TGC CAG CGG CTG GCC AGC CAG GCC TGC CCC ACC AAC CCG TGC CTC CAT GGC GCT CGC
435 450 465 480 495 510 525
170 180 190 200 Cys Leu Glu Val Glu Gly His Arg Leu Cys His Cys Pro Val Gly Tyr Thr Gly Pro Phe Cys Asp Val Asp Thr Lys Ala Ser Cys Tyr Asp Gly Arg Gly Leu TGC CTA GAG GTG GAG GGC CAC CGC CTC TGC CAC TGC CCG GTG GGC TAC ACC GGA CCC TTC TGC GAC GTG CAC ACC AAG GCA AGC TGC TAT GAT GGC CGC GGG CTC
540 555 570 585 600 615 630
210 220 230 Ser Tyr Arg Gly Leu Ala Arg Thr Thr Leu Ser Gly Ala Pro Cya Gin Pro Trp Ala Ser Glu Ala Thr Tyr Arg Asn Val Thr Ala Glu Gin Ala Arg Asn Trp AGC TAC CGC GGC CTG GCC AGG ACC ACG CTC TCC GGT GCG CCC TGT CAG CCG TGG GCC TCC GAG GCC ACC TAC CGG AAC GTG ACT GCC GAG CAA GCC CGG AAC TGG
645 660 675 690 70S 720 735
240 250 260 270 Gly Leu Gly Gly His Ala Phe Cys Arg Asn Pro Asp Asn Asp He Arg Pro Trp Cys Phe Val Leu Asn Arg Asp Arg Leu Ser Trp Glu Tyr Cys Asp Leu Ala GGA CTG GGC GGC CAC GCC TTC TGC CGG AAC CCG GAC AAC GAC ATC CGC CCG TGG TGC TTC GTG CTG AAC CGC GAC CGG CTG AGC TGG GAG TAC TGC GAC CTC GCA
750 765 780 795 810 825 840
280 290 300 Gin Cys Gin Thr Pro Thr Gin Ala Ala Pro Pro Thr Pro Val Ser Pro Arg Leu His Val Pro Leu Met Pro Ala Gin Pro Ala Pro Pro Lys Pro Gin Pro Thr CAG TGC CAG ACC CCA ACC CAG GCG GCG CCT CCG ACC CCG GTG TCC CCT AGG CTT CAT GTC CCA CTC ATG CCC GCG CAG CCG GCA COG COG AAG CCT CAG CCC ACG
855 870 885 900 915 . 930 945
310 320 330 Thr Arg Thr Pro Ser Gin Ser Gin Thr Pro Gly Ala Leu Pro Ala Asn Gly Glu Gin Pro Pro Ser Leu Thr Arg rAsn Gly Pro Leu Ser Cys Gly Gin Arg'Leu ACC CGG ACC CCC TCT CAG TCC CAG ACC CCG GGA GCC TTG CCG GCG AAC GGG GAG CAG CCG CCT TCC CTG ACC AGG AAC GGC CCA CTG AGC TGC GGG CAG CGC CTC
960 975 990 1,005 1,020 1,035 1,050
f 340 f GGA GCC TTG CCG GCG AAC GGG GAG CAG CCG CCT TCC CTG ACC AO
990 1.005 1.02
350 \f 360 370 Arg Lys Ser Leu Ser Ser Het Thr Arg'val Val Gly Gly Leu Val Ala Leu Arg Gly Ala'His Pro Tyr He Ala Ala Leu Tyr Trp Gly His Ser Phe Cys Ala CCC AAG ACT CTG TCT TCG ATG ACC CGC GTC GTT GGC GGG CTG GTG GCG CTA CGC GGG GCG CAC CCC TAC ATC GCC GCG CTG TAC TGG GGC CAC ACT TTC TGC GCC
1,065 1,080 1,095 1,110 1,125 1,140 1,155
380 390 400 410 ^ Gly Ser Leu He Ala Pro Cys Trp Val Leu Thr Ala Ala His Cys Leu Gin Asp Arg Pro Ala Pro Glu Asp Leu Thr Val Val Leu Gly Gin Glu Arg Arg Asn GGC AGC CTC ATC GCC CCC TGC TGG GTG CTG ACG GCC GCT CAC TGC CTG CAG GAC CGG CCC GCA CCC GAG CAT CTG ACC GTG GTG CTC GGC CAC CAA CGC CCT AAC
1,170 1,185 1,200 1,215 1,230, 1,245 1,260
420 430 440 His Ser Cys Glu Pro Cys Gin Thr Leu Ala Val Arg Ser Tyr Arg Leu His Glu A La Phe Ser Pro Val Ser Tyr Gin His Asp Leu Ala Leu Leu Arg Leu Gin CAC AGC TGT GAG CCG TGC CAG ACG TTG GCC GTG CGC TCC TAC CGC TTG CAC GAG GCC TTC TCC CCC GTC AGC TAC CAG CAC GAC CTG GCT CTG TTG CGC CTT CAG
1,275 1,290 1,305 1,320 1,335 1,350 1,365
450 460 470 480 Glu Asp Ala Asp Gly Ser Cys Ala Leu Leu Ser Pro Tyr Val Gin Pro Val Cys Leu Pro Ser Gly Ala Ala Arg Pro Ser Glu Thr Thr Leu Cys Gin Val Ala GAG GAT GCG GAC GGC AGC TGC GCG CTC CTG TCG CCT TAC GTT CAG CCG GTG TGC CTG CCA AGC GGC GCC GOG CGA CCC TCC GAG ACC ACG CTC TGC CAG GTG GCC
1,380 1,395 1,410 1,425 1,440 1,455 1,470
490 500 510 Gly Trp Gly His Gin Phe Glu Gly Ala Glu Glu Tyr Ala Ser Phe Leu Gin Glu Ala Gin Val Pro Phe Leu Ser Leu Glu Arg Cys Ser Ala Pro Asp Val His GGC trGG GGC CAC CAG TTC GJfS. GGG GCG GAG GAA TAT GCC AGC TTC CTG CAG GAG GCG CAG GTA CCG TTC CTC TCC CTG GAG CGC TGC TCA GCC CCG GAC GTG CAC
1,485 1,500 1,515 1,530 1,545 1,560 1,575
520 530 540 550 Gly Ser. Ser He Leu Pro Gly Met Leu Cys Ala Gly Phe Leu Glu Gly Gly Thr Asp Ala Cys Gin Gly Aap Ser Gly Gly Pro Leu Val Cys Glii Asp Gin Ala GGA TCC TCC ATC CTC CCC GGC ATG CTC TGC GCA GGG TTC CTC GAG GGC GGC |ACC GAT GCG TGC CAG OSh1 GAT TCC GGA GGC CCG CTG GTG TGT GAG GAC CAA GCT
l',S90 1,605 1,620 1,635 1,650 1,665 1,680
560 570 580 Ala Glu Arg Arg Leu Thr Leu Gin Gly He Ha Ser Trp Gly Ser Gly Cys Gly A Bp Arg Asn LyB Pro Gly Val Tyr Thr Asp Val Ala Tyr Tyr Leu Ala Trp GCA GAG CCC CGG CTC ACC CTG CAA GGC ATC ATC AGC TGG GGA TCG GGC TGT GGT GAC CGC AAC AAG CCA GGC GTC TAC ACC GAT GTG GCC TAC TAC CTG GCC TGG
1,695 1,710 1,725 1,740 1,755 1,770 1,785
590 596 He Arg Glu His Thr Val Ser STOP ATC CGG GAG CAC ACC GTT TCC TGA TTG CTC AGG GAC TCA TCT TTC CCT CCT TGG TGA TTC CGC AGT GAG AGA GTG GCT GGG GCA TGG AAG GCA AGA TTG TCT CCC
1,800 1,815 1,830 1,845 1,860 1,875 1,890
ATT CCC CCA GTG CGG CCA GCT CCG CGC CAG GAT GGC GCA GGA ACT CAA TAA AGT GCT TTG AAA ATG CTC Poly A 1,905 1,920 1,935 1,950 1,959
Results / 79
factor XII mRNA and probably represents a cloning artifact.
3. Predicted Amino Acid Sequence of Human Factor XII
Translation of the consensus cDNA sequence using the standard genetic code results in a
single open reading frame coding for human factor XII (Fig. 8). The derived amino acid
sequence agrees well with those regions of human factor XII that have been determined by
protein chemistry techniques. Nucleotides 19-78 encode the amino-terminal region of factor
XII (Fujikawa et al., 1980b; Fujikawa and Davie, 1981). Since the amino-terminal residue
of plasma factor XII is encoded by nucleotides 19-21 (Fig. 8), the factor XII cDNA sequence
also encodes part of an amino-terminal extension (nucleotides 1-18, Fig. 8). Nucleotides
1021-1047 and 1078-1806 encode the light and heavy chains of 0-factor X l l a as determined
by Fujikawa and McMullen (1983). In the presence of an anionic surface, kallikrein cleaves
factor XII at a position carboxy-terminal to A r g 3 5 3 , resulting in the formation of a-factor
X l l a (Fujikawa and McMullen, 1983). Further proteolytic cleavages occur
carboxy-terminal to A r g 3 3 4 and A r g 3 4 3 , and give rise to 0-factor Xl la . During the
formation of ^-factor X l l a , residues 1-334 and 345-353 of factor XII are removed. The
codon for the carboxy-terminal residue of the heavy chain of /3-factor X l l a (Ser-596) is
followed by a T G A stop codon (nucleotides 1807-1809, Fig. 8), a 3' untranslated region of
150 nucleotides and a polyA + tail. Nucleotides 1937-1942 contain the sequence A A T A A A
that is involved in the polyadenylation of mRNA (Proudfoot and Brownlee, 1976; Wickens
and Stephenson, 1984). This sequence occurs 17 nucleotides upstream of the polyA + tail.
The predicted amino acid sequence of factor XII corresponds to a mature protein of 596
amino acids. The amino acid composition of plasma factor XII was determined to be as
Results / 80
follows: A l a 5 1 , A r g 3 9 , A s n 1 3 , A s p 2 2 , l / 2 - C y s 4 0 , G l n 3 7 , G l u 3 1 , G l y 4 8 , H i s 2 7 , He,,
L e u 5 3 , L y s l 9 , Met 4 , P h e 1 5 , P r o 5 6 , S e r 3 6 , T h r 3 4 , T r p 1 3 , T y r 1 9 , V a l 3 0 . From the
predicted amino acid sequence, the molecular weight of plasma factor XII is 66,915 in the
absence of carbohydrate and 80,427 with the addition of 16.8% carbohydrate (Fujikawa and
Davie, 1981). Within experimental error, both the predicted amino acid composition and
molecular weight of factor XII are in excellent agreement with those determined for the
purified protein (Griffin and Cochrane, 1976; Fujikawa and Davie, 1981).
The complete amino acid sequence for human a-factor X l l a was also determined by
McMullen and Fujikawa (1985). The amino acid sequence was determined by automated
Edman degradation using peptides produced by chemical and enzymatic cleavages of factor
XII. These results appeared in the literature after the completion of the cDNA sequence for
factor XII described above. The two amino acid sequences were compared, and a serine
residue at position 314 is found in place of a proline residue reported by McMullen.and
Fujikawa (1985).
4. 5' End of the Factor XII cDNA
The factor XII cDNA clone, pcHXII-501, did not extend to the initiator methionine residue
and so another human liver cDNA library (prepared by W. Funk in Dr. MacGillivray's
laboratory) was screened with a [3 2P]-labeled 280 bp PstI probe representing nucleotides 1
to 280 of pcHXII-501. The library was prepared by using oligonucleotides as random
primers for reverse transcription of mRNA. Fragments were separated on a column of
Agarose A 0.5M, and were cloned into the expression vector Xgt l l . A library containing
small inserts (less than 500 bp) was screened for a clone that would extend further 5' to
Results / 81
pcHXII-501. A total of 1 x 10 6 Xgt l l recombinant phage were screened and two positive
clones were isolated. The nucleotide sequences of the cDNA clones (pcHXII-WF7 and
-WF9) were determined (Fig. 9). The two clones were identical and contained 220 bp
inserts and extended a further 40 bp 5' to pcHXII-501. Translation of the sequence
revealed an identical amino acid sequence to pcHXII-501 but extended the signal sequence
by a further 13 amino acid residues. At this point, there is an A T G sequence in the same
reading frame as the putative signal peptide. Therefore, the signal peptide sequence for
factor XII probably consists of 19 amino acid residues with the characteristic hydrophobic
core (Watson, 1984). Two other cDNA libraries were screened in order to obtain a longer
cDNA clone which would contain the 5' untranslated end of the mRNA but no longer clones
were isolated.
5. A 2.40 kb mRNA From Liver Codes For Human Factor XII
To determine the size of factor XII mRNA, human liver polyA + RNA was electrophoresed
on an agarose gel under denaturing conditions and transferred to nitrocellulose. The blot
was hybridized to [ 3 2P]labeled pcHXII-501, which contains 1959 bp of coding sequence.
Autoradiography revealed a single band that was 2,400 ± 100 nucleotides in size (Fig. 10).
The total length of mRNA sequenced from the cDNA clones, pcHXII-501 and pcHXII-WF7,
is 2000 nucleotides. Since eukaryotic mRNAs usually contain polyA + tails of 180-200
nucleotides (Perry, 1976) it seems that there is approximately 200 bases of mRNA
sequence still to be determined.
/ 82
Figure 9: Nucleotide Sequence of a cDNA for the, FXII Signal Peptide
A human liver cDNA library was screened with a 3 2P-labeled 5' fragment from pcHXII-501
(Figure 7) and a positive clone (pcHXII-WF7) was isolated. The nucleotide sequence of this
clone was determined and is shown. The predicted amino acid sequence is given below the
nucleotide sequence. The numbers correspond to the cDNA sequence given in Figure 8.
The open arrow indicates the signal peptidase cleavage site and the diamond shows the
initiator Methionine residue. Only 3 nucleotides of the 5' untranslated end were contained
in the pcHXII-WF7 clone.
• GCC ATG AGG GCT CTG
Met Arg Ala Leu -19
60 GAG TCA ACA CTT TCG Glu Ser Thr Leu Ser
-1
105 AAG TAC AAA GCT GAA Lys Tyr Lys Ala Glu
150 GAG CCC TGC CAC TTC Glu Pro Cys His Phe
30
195 AAA TGT ACC CAC AAG Lys Cys Thr His Lys
30 CTG CTC CTG GGG TTC Leu Leu Leu Gly Phe
• * ATT CCA CCT TGG GAA l i e Pro Pro Trp Glu
120 GAG CAC ACA GTC GTT Glu His Thr Val Val
20
165 CCC TTC CAG TAC CAC Pro Phe Gin Tyr His
210 GGC CGG CCA GGC CCT Gly Arg Pro Gly Pro
50
45 CTG CTG GTG AGC TTG Leu Leu Val Ser Leu -10
90 GCC CCC AAG GAG CAT Ala Pro Lys Glu His
10
135 CTC ACT GTC ACC GGG Leu Thr Val Thr Gly
180 CGG CAG CTG TAC CAC Arg Gin Leu Tyr His
40
225 CAG CCC TGG TGT GCT Gin Pro Trp Cys Ala
228 ACC Thr
/ 84
Figure 10: Size Determination of the Factor XII mRNA Using rRNA Markers
Human liver poly A + RNA (10 Mg) was electrophoresed in a denaturing
agarose-formaldehyde gel and was transferred to nitrocellulose. The filter was hybridized
with 3 2P-labeled pcHXII-501. The filter was exposed for 18 hours at - 7 0 ° C with Lightning
Plus intensifying screens (Dupont). The positions of RNA size standards are indicated,
including mammalian 28 S (4.72kb) and 18 S (1.87 kb) rRNA and E. coli 23 S (2.90 kb) and
16 S (1.54 kb) rRNA (Noller, 1984).
B. THE HUMAN FACTOR XII GENE
Results / 86
1. Isolation and Characterization of Factor XII Genomic Clones
The factor XII gene was isolated from a human genomic D N A library (provided by Dr. P.
Leder) which contains partial Sau3A fragments (10-20 kbp in length) inserted into the
BarriHI site of XCharon 28. One million phage from this library were screened with a
human factor XII cDNA (pcHXII-501) as a hybridization probe. This cDNA contains D N A
representing coding sequence for the complete zymogen of factor XII, 6 amino acids of the
signal peptide and the 3' untranslated region (150 bp). Two recombinant phage designated
XHFXII-27 and XHFXII-76 were purified to homogeneity by rescreening four times with the
same hybridization probe.
D N A was isolated from large scale lysates of each of the two phage and analyzed by
restriction enzyme digestion. Southern blot analysis indicated that the 5' and 3' ends of the
cDNA were represented in the two phage. SamHI and PstI digests of the clones were
hybridized with 3 2P-labeled 280bp or 360 bp PstI fragments, representing the 5' and 3' end
of the cDNA, respectively. Figure 11 shows that the 280bp PstI fragment which encodes
exons 2,3 and part of 4 (see Fig. 12) hybridized to the 2.5 and 0.6 kbp PstI fragments in
XHFXII-76 and only to the 0.6 kbp PstI fragment in XHFXII-27. The 360 bp PstI fragment
representing exon 14 (see Fig. 12) hybridized to XHFXII-27 and not to XHFXII-76. The 2.0
kbp and the 0.3 kbp PstI fragments and a very large BamHl fragment in XHFXII-27
hybridized to the 3' probe. Therefore, XHFXII-76 contains the 5' but not the 3' end of the
cDNA whereas XHFXII-27 contains the 3' end and not the 5' end of the cDNA.
/ 87
Figure 11: 5' and 3' Southern Blot Analysis of FXII Genomic Clones
Two clones (XHFXII-27, -76) were isolated from a genomic X phage library encoding the
human factor XII gene. The D N A was cleaved by restriction endonucleases, the fragments
were electrophoresed through neutral agarose gels and Southern (1975) blotted to
nitrocellulose filter paper. Two sets of filters were prepared and one set was hybridized
with a 3 2P-labeled 280 bp PstI (nucleotides 1-280, 5' end of the cDNA, Figure 9) or with a
3 2P-labeled 360 bp PstI fragment (nucleotide 1,680-3' end of the pcHXII-501 insert, Figure
9). The blots were autoradiographed for 18 hours. Left side blot is hybridized with the 280
bp fragment: A, XHFXII-76 digested with PstI (Lane P) or Bam HI (Lane B); B, XHFXII-27
digested with PstI (Lane P) or Bam HI (Lane B). Right side blot is hybridized with the 360
bp fragment: C, XHFXII-76 digested with PstI (Lane P) or BamHl (Lane B)\ D, XHFXII-27
digested with PstI (Lane P) or Bam HI (Lane B).
Results / 89
A partial restriction enzyme map of the cloned genomic D N A for FXII was constructed from
multiple restriction endonuclease digestions and Southern blot analysis of the fragments
hybridized to various 3 2P-labeled cDNA probes. The map (Fig. 12) shows that XHFXII-27
and -76 contained D N A sequence which overlapped but were not identical. Together, the
two phage span approximately 30 kb of genomic D N A , with the factor XII gene mapping to
a 12 kbp region in the middle of this D N A (Fig. 12). A second, unamplified human genomic
phage library (prepared by V. Geddes in Dr. MacGillivray's lab) was screened with
[3 2P]-labeled 280 bp PstI fragment of pcHXII-501. However, of 0.5 x 10* phage screened,
no positive clones for factor XII were isolated.
2. Southern Blot Analysis of the Human FXII Gene
The BamHl, HindTH and PstI fragments in the restriction enzyme map correspond to those
in the Southern blot (Fig. 13) of genomic D N A that was hybridized to [3 2P]-labeled factor
XII cDNA (pcHXII-501). Autoradiography revealed several hybridizing bands in each of
the restriction enzyme digests (Fig. 13). For example, the lengths of the BamHl (greater
than 9.5 and 7.6 kbp), the flmdIII (9.5 and 5.8 kbp) and the PstI (2.5, 1,5, 1.0 and 0.6 kbp)
fragments agree closely with the fragment lengths which contain exon sequence in the
restriction enzyme map (Fig. 12). The 7.6 kbp BamHl bands observed in the genomic
Southern blot compares to the 3' end of the gene including most of exon 14. The 3' BamHl
site is not shown in the restriction enzyme map. Since no other bands were observed in the
genomic Southern blot, it appears that the human genome contains a single factor XII gene.
/ 90
Figure 12: Partial Restriction Map and Intron/Exon Organization of the FXII Gene.
A partial restriction enzyme map of the gene is given. Abbreviations used are: B-BamHI;
Hp-ffpall; Bg-BglL; P-Pstl; H-HindIU; Hc-Hincll. Exons are shown in the bar above the
restriction map as black boxes and are numbered 1 through 14. The two genomic phage
clones. XHFXII-76 and XHFXII-27 are shown below the restriction enzyme map as open
bars. Breaks in the bars indicate that the phage D N A extends approximately 5.0 and 13.0
kb 5' and 3' from the gene, respectively. The scale represents kilobase pairs.
0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0- 11.0 12.0 13.0 14.0 15.0 Scale (kb) I I I l I I I I I I I I I I I I
Exons 1 2 3 4 5 6 7 8 9 10 11 12 13 14
Gene 5' I I I I 3'
Restriction BP P Bg Hp P P H H P H P P B P B P B H
Enzyme Map II j l ( l I ; L _ l I I M I I II 11 _ | Hp He p
X Clones ] / / . I XHFXII-76
XHFXII-27 I Ij —
/ 92
Figure 13: Genomic DNA Southern Blot Analysis of the FXII Gene
Human liver D N A (lOjug) was digested by various restriction enzymes and electrophoresed
in a 1.0% agarose gel. After denaturation, the D N A was trasferred to nitrocellulose and
hybridized with 3 2P-labeled pcHXII-501. The filter was autoradiographed for 4 days at
- 7 0 ° C with intensifying screens. Lane M shows the positions of the 3 2P-labeled \-Hindlll
D N A used as molecular weight markers. The human D N A was digested with EcoRl (Lane
1), Hindlll (Lane 2), Pstl (Lane 3), and BamHl (Lane 4).
Results / 94
3. Localization of Intron/Exon Junctions
To identify exon-containing D N A sequences, sonicated fragments of the genomic clone,
XHXII-27, were subcloned into M13 vectors and transformed into E. coli JM103. The
phage were plated and screened with 3 2P-labeled pcHXII-501. The D N A sequences were
determined from purified single stranded D N A of the positive phage. The intron/exon
junction sequences for exons 3 to 14 were obtained on both strands and are given in Table
II. The positions of exons 1 and 2 in XHXII-76 were determined by restriction enzyme
analysis. Small fragments containing the exons were subcloned and their D N A sequences
determined on both strands (Table II). All introns follow the G T - A G rule (Breathnach and
Chambon, 1981) except for the donor sequence of intron J which has a GC dinucleotide
instead of GT. The consensus sequences surrounding splice junctions in R N A polymerase II
transcribed genes (Mount, 1982) were also found to be in agreement with the intron/exon
junctions of the FXII gene (Table III). The localization of exons by D N A sequence analysis
and restriction enzyme mapping has shown that the FXII gene consists of 13 introns (A
through M , Table IV) and 14 exons (1-14, Table IV) of which 12 are located within 4.2 kb of
genomic D N A (Fig. 12).
4. Nucleotide Sequence of the Human Factor XII Gene
The partial D N A sequence for the human factor XII gene is shown in Fig. 14. A total of
4,735 bp of D N A sequence was determined of which 92% was obtained on both strands.
Sequence data that was obtained on one strand only was determined at least twice and
includes nucleotides -120 to -357 of the 5' end of the gene. There are 357 and 195 bp of 5'
and 3' flanking regions, respectively, given in Fig. 14. As determined by D N A sequence
95
EXON 5 ' SPL ICE 1NTRON 3' SPL ICE CODON NUMBER DONOR ACCEPTOR PHASE
1 T T C G g t g a g t A c c t t c c c t c c t c c c t t g t a gATTC 0
2 G T C T g t a a t g B a gag t g t g t t g t c c c t g c a gTTCT
3 C C T G g t a a g a C a g c c t t g t c t c t t t c t a c a gGTGT 1 1
4 AAAGg t g c t a D c c a c c a t g t c c a t c t c t c a gACCA >
5 AAAGgtgagg E c t a t c c c t c t t t g t c c c c a gAGAA
6 CAGG g t g a g c F c a c t g c g t t c c c t c c c c a a gCCTG
7 G T G G g t g a g t G g g a g c c c c c t t t c t c c t c a gACAC
8 G C C G g t g c g c H g c c c c g t c g t g t g g c t a c a gGAAC 1 1
9 GGAGgt t a gg 1 c a g c c c c t g c t c c t c c a c a gCCTT
1 0 ACCGgcgag t J c t c c c c t a c c c t c c c c g c a gGCCC 1 1
1 1 C T G G g t g c g t K c t c c t c t c c g c c c g g g t t a gCTCT
12 GAGCg taggc L a a g g c g c t c t g t g t t c gcagGGGC
1 3 CCAGg tgagc M g c t g c g t g t t t c c g a c c c a gGGTG 0
14 3 1 END
T a b l e 1 1 . N u c 1 e o t 1 d e S e q u e n c e o f I n t r o n / E x o n J u n c t i o n s In the Fa
XI I G e n e .
Exon s e q u e n c e i s shown in upper c a s e ; i n t r o n s e q u e n c e in lower c a s e .
The codon phase r e f e r s to the p o s i t i o n o f the I n t r o n In the codon
t r i p l e t . 0 - i n t r o n o c c u r s be tween c o d o n s , l - i n t r o n o c c u r s a f t e r the
f i r s t n u c l e o t i d e and I l - i n t r o n o c c u r s a f t e r the s e c o n d n u c l e o t i d e In
t h e c o d o n .
.96
Donor F r e q u e n c i e s
+ 4 + 3 + 2 + 1 -1 -2 - 3 - 4 -5 - 6
G 5 1 4 10 1 3 0 9 1 1 1 3 A 3 4 4 0 0 0 3 9 0 2 T 1 4 1 1 0 1 2 1 0 2 4 C 4 4 4 2 0 1 0 3 0 4 CON N A A G G T R A G T
C A c c e p t o r F r e q u e n c i e s
- 2 0 - 1 9 -1 8 - 1 7 -1 6 -1 5-1 4 - 1 3 -1 2-1 1 -1 0 - 9 -8 - 7 - 6 -5 - 4 -3 -2 -1 + 1 + 2 + 3 + 4
G 3 3 2 4 1 4 2 3 2 1 3 0 3 3 1 1 4 0 0 1 3 5 3 2 2 A 3 3 4 0 0 1 0 1 0 0 0 1 0 0 1 0 3 1 1 3 0 4 1 3 2 T 0 3 2 3 3 1 6 6 4 7 5 7 3 5 3 4 3 2 0 0 1 4 4 4 C 7 4 5 6 9 7 5 3 7 5 5 5 7 5 8 8 3 1 0 0 0 3 5 4 5 CON Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y N Y A G G N N N
T a b l e I I I . F r e q u e n c i e s of N u c l e o t i d e s at I n t r o n / E x o n J u n c t i o n s .
The f r e q u e n c i e s of the d i f f e r e n t n u c l e o t i d e s at the i n t r o n / e x o n
j u n c t i o n s of the human FXI I gene a re compared to the c o n s e n s u s
(CON) of Mount ( 1 9 8 2 ) . S p l i c e j u n c t i o n s a re be tween -1 and +1.
9,7
EXON
1
2
3
4
5
6
7
8
9
10
1 1
1 2
1 3
1 4
NUCLEOTIDE POSIT ION
1-105
4 7 4 1 - 4 7 9 8
7 7 9 0 - 7 8 8 9
8 0 4 6 - 8 1 1 6
8 4 1 7 - 8 5 2 7
8 6 6 6 - 8 7 9 7
8 9 3 9 - 9 0 4 3
9 1 9 1 - 9 3 5 6
9444-9661
9 7 6 7 - 9 9 9 8
1 0 2 4 2 - 1 0 3 7 8
1 0 4 6 0 - 1 0 6 0 3
1 1 1 5 9 - 1 1 3 0 7
1 1 3 9 8 - 1 1 7 1 5
LENGTH
105
57
9 9
70
1 1 0
131
104
165
21 7
231
136
1 43
1 48
320
INTRON
A
B
C
D
E
F
G
H
I
J
K
L
M
NUCLEOTIDE POSIT ION
1 0 6 - 4 7 4 0
4 7 9 9 - 7 7 8 9
7 8 9 0 - 8 0 4 5
8 1 1 6 - 8 4 1 6
8 5 2 8 - 8 6 6 5
8 7 9 8 - 8 9 3 8
9 0 4 4 - 9 1 9 0
9 3 5 7 - 9 4 4 3
9 6 6 2 - 9 7 6 6
9999 -10241
1 0 3 7 9 - 1 0 4 5 9
1 0 6 0 4 - 1 1 1 5 8
1 1 3 0 8 - 1 1 3 9 6
LENGTH
4 5 0 0 »
3 0 0 0 *
1 55
300
137
1 40
146
86
1 04
242
80
554
88
T a b l e IV. S i z e and P o s i t i o n s o f Exons and I n t r o n s in the F a c t o r XI I Gene .
• S i z e s of t h e s e i n t r o n s were e s t i m a t e d f r o m r e s t r i c t i o n enzyme a n a l y s i s
( F i g . 1 2 ) . A l l o t h e r s i z e s were d e t e r m i n e d f rom the n u c l e o t i d e s e q u e n c e
of the gene ( F i g . 1 4 ) .
/ 98
Figure 14: Partial DNA Sequence of the FXII Gene
The sequence was determined by the D N A sequence analysis of M13 clones. The predicted
amino acid sequence of FXII is given above the nucleotide sequence. Five transcriptional
start sites are indicated by triangles and circles between +1 and +33. Solid and open
triangles indicate strong and weak primer extension products, respectively; solid and open
circles represent strong and weak nuclease S i products, respectively. A solid line indicating
a possible T A T A sequence is shown at position -26. The CAAT-like sequence at position
-103 is shown as a double line. Inverted repeats are marked by arrows under the nucleotide
sequence. An open diamond represents Hpall sites that demarcate the nuclease S i primer.
A closed diamond indicates the complemented 5' end of the 180 bp primer used in the
extension reaction. The probable initiator methionine at amino acid -19 is indicated by a
box. The sizes of the larger introns are approximated from restriction enzyme mapping
(Fig. 13). The polyadenylylation signal A A T A A A (nucleotides 11693-11698) is boxed. In
the protein coding region, the cleavage site which gives rise to plasma FXII is denoted by a
closed arrow, and the two sites of cleavage which produces (3-FXIIa by kallikrein are
denoted by an open arrow.
99 CT GGG TAT TGT TCT AAG ATG CTC AGT TTA TCG TAG TTT GTT ACA TCA CAA TAG AAA ATC AAC ACA CTT CAC AGT GGA CTC CAA GAT CCC CAT GAT CTT TCA TCT
-356 -330 -300 -270
CCT TAA CCT CCT GAT CTC CAC AGG ACC CAG AGC ATA AGA ATG TCC CTT CTT CTG CTT CCA GTC CCA CTA TCT AGA AAA GAG AGG AGG AGC CCA UCT CTT CAT TTC -240 -210 -180 -150
0 ACC CCC ACC CAC AAA CTC CCA ACT TTC CGG CCC TCA AGG GGT GAC CAA GGA AGT TGC TCC ACT TCG CTT TCC ACA AAC AGC CTC TCC CCC ACC AGG CTC AGG AGG
-120 -90 -60 • -19
Q # • O O M e t A r 9 A l a L e u t e u
GCA GCT TGA CCA ATC TCT ATT TCC AAG ACC TTT GGC CAG TCC TAT TGA TCT GGA CTC CTG GAT AGG CAG CTG GAC CAA CGG ACG GAC GCC ATC AGG GCT CTG CTC -30 • 1 A • A 30 A 6 0
1 1 - A i • -io 0 • "l
Leu Leu Gly Phe Leu Leu Val Ser Leu Glu Ser Thr Leu Ser CTC CTG GGG TTC CTG CTG GTG AGC TTG GAG TCA ACA CTT TCG GTG AGT GCT GTG GGA ACC AGG ATT GTC CCA GGA TTG TTC TGG GGG GTC GCT ATC ACA GCC ATG
90 120 150 * AGC CAT GGC CTC TGC TCA TGA CCT GTG GGT CCA GGT GAC TAG GAG GCC TAT GTG GAA AGG TGA GGC CAJ CCC 4300 bp AG GCC AGC CCG GAA GGC CCA
180 210 240 GGC AGA GGA GAC AGA CAA CCA GAC TGG GTG GAT ACA AGG GCA CAG CCT GCA TTT CTG GGG GAG ATG GGC CTT AAG AAG ACA ACG GGG GGA GGT AGA AAG CGA AAG
4530 4560 4590 4620
GGT CTT GGG AAG AAA TCT CTG CAT TTC TGG GCV GTG AGA GGA AGC TGC AGA CTA GCA ACA GAT CGG TGG CAG GCT ATG ACT TAT AGT CAG TTC CCT GCC TTC TTC 4650 4680 4710
\ i 10 l i e Pro Pro Trp Glu Ala Pro Lys Glu His Lys Tyr Lys Ala Glu Glu His Thr Val V
TCT CCC TTG TAG ATT CCA CCT TCG GAA GCC CCC AAG GAG CAT AAG TAC AAA GCT GAA GAG CAC ACA GTC GGT AAG TGG CCT GGC TCC TCC TCC CGG GAA CCC TTC 4740 4770 4800 4B30
GGT GGG GAT GTG TAT GGT GCA GTC TCT GCA GTC TCA GGG CAG TCT AGT CTA GTC CCT ACC TCG TCC TAG GTC TTA TGC CCA TCG GCA CTA GAG TCA TCG TCA GCT 4860 4890 4920
GTC TCA TCC TTG AGG GCA GGG TAT GGG CTG TGT CTA AGT GCC CAC GAG CCT GGC TCG GAG CAG GTC CTT GAG ATA TGT GCT GCT GGC GCC ATC ACA CCT GGG CTC 4950 4980 5010 5040
CTC CCA GCC TTC CTC AGT TTC CCC AGC TTC TCC CCT TCT TTT CCT TTC CCC AGT ACG TCT CAT GGG CAT CAT TCA TGC CAC ACA GAG GCC AGG GCC TTC AAT GGG 5070 5100 5130
CAA GGA AGG ATC AAG AGC TTC TCT CTG GCA TCT GAA TGC CTC TGA AGC CCA'GCT TTA TGA GTT ATG AGC TGG GTC ACT CTC GGC GAG GGA TTT GAG TTC TCC AAG 5160 5190 5220 5250
20 30 al Leu Thr Val Thr Gly Glu Pro Cys His Phe Pro Phe Gin Tyr His Arg Gin Leu Tyr
CTT CAA TTT C 2500 bp — T C AGA GAG TGT GTT GTC CCT GCA GTT CTC ACT GTC ACC GGG GAG CCC TGC CAC TTC CCC TTC CAG TAC CAC CGG CAG CTG TAC 7800 7830
40 50 His Lys Cys Thr His Lys Gly Arg Pro Gly Pro Gin Pro Tr CAC AAA TGT ACC CAC AAG GGC CGG CCA GGC CCT CAG CCC TGG TAA GAC TAC GCA GAG GAG TTG GAG CAG GGG CCT GGG AGA CAT GTA CCC TCC CTC TCC TTC TCT
7860 7890 7920 7950
p Cys Ala Thr Thr CCA AGG AAC TCT GCT TGG AGA GAG GGG ACT GTG ATA GGG CAG GGT GGG CCA GGC CCC TCG GTA GAG CAG GGA AGC CTT GTC TCT TTC TAC AGG TGT GCT ACC ACC
7980 8010 8040
60 70 Pro Asn Phe Asp Gin Asp Gin Arg Trp Gly Tyr Cys Leu Glu Pro Lys Lys Val Lys A CCC AAC TTT GAT CAG GAC CAG CGA TGG GGA TAC TGT TTG GAG CCC AAG AAA GTC AAA GGT GCT ACA CAC AGC CTC TGG GGT GGC CTC GGG CTC TCT CCT CCC GCC
8070 8100 8130 8160
TCA TTA CTC TCC TGG TAT CAC CAG ACC CCA CAC ACC TGG GAT TCT GGA CCC AGC CCC TTC TCT CCC TCC ACA ATA CCC TTT GGA AGT CCA GAG GGA GAG TTC TCG 8190 8220 8250
GAA GGA GTG GTC CCA TTT TCC AGG TCG GTA AAC CAA GCT TGG AAA CTT GGA GTA GCA AGG TCA CAA GGC AAG TAG GTT CAA GAA GGG CCT TCG CCC CAG CTG TCT 8280 8310 8340 8370
BO 90 sp His Cys Ser Lys His Ser Pro Cys Gin Lys Gly Gly Thr Cys Val Asn Het Pro Ser Gly
GAC TCA GCT CCC TGC TCT TCC TTC CAC CAT GTC CAT CTC TCA GAC CAC TCC AGC AAA CAC AGC CCC TCC CAG AAA GGA GGG ACC TGT GTG AAC ATC CCA AGC GGC 8400 8430 8460
100 110 Pro His Cys Leu Cys Pro Gin His Leu Thr Gly Asn His Cys Gin Lys G CCC CAC TCT CTC TCT CCA CAA CAC CTC ACT GGA AAC CAC TGC CAG AAA GGT GAG GAG ATC TGG AGG ACC TGG GCG GGG TGC TCG GGG ACA GGG GCA ACC CTG GGC
8490 8520 8550 8580
120 lu Lys Cys Phe Glu Pro Gin Leu
CTA CAG AAT AGG TTC CTC GAT ACT CGG AGA CTT GGC ATC GTC CTA GAC TCT CCT GAG ACC ACT ATC CCT CTT TCT CCC CAG AG AAG TCC TTT GAG CCT 'CAG CTT 8610 8640 8670
130 140 150 Leu Arg Phe Phe His Lys Asn Glu l i e Trp Tyr Arg Thr Glu Gin Ala Ala Val Ala Arg Cys Gin Cys Lys Gly Pro Asp Ala His Cys Gin Arg Leu Ala Ser CTC CGG TTT TTC CAC AAG AAT GAG ATA TCG TAT AGA ACT GAG CAA GCA GCT GTC GCC AGA TCC CAG TCC AAG GGT CCT GAT GCC CAC TCC CAG CGG CTC GCC AGC
8700 8730 8760 8790
CAG GGT GAG CAG ATG GTT GGG AAC GGG CCA GGG AGG AGC GTC AGG AAG ACA GGC TGG CAG GAG GCC GGG TCG TCT GCC GGG AAG GAG AGC TCT CTC GGG GGG TCT 8820 8850 8880
160 170 la Cys Arg Thr Asn Pro Cys Leu His Gly Gly Arg Cys Leu Glu Val Glu Gly His Arg Leu Cys
TTA GGC CCA GGG GTC GCT CAC TCC GTT CCC TCC CCA AG CC TCC CGC ACC AAC CCG TCC CTC CAT GGG GGT CGC TCC CTA GAG GTC GAG GGC CAC CGC CTC TGC 8910 8940 8970 9000
180 190 His Cys Pro Val Gly Tyr Thr Gly Pro Phe Cys Asp Val A CAC TCC CCG GTC GGC TAC ACC GGA CCC TTC TGC GAC GTC GGT GAG TCA GGG TCT GGG GCA AGC AGA AGG CCA GCC CCC AGG TGG GAC GGG CTT GCC AGG AAG GAG
9030 9060 9090
200 GAG GGA GAG TCC GGA AAG CAG ATG AGA GGG AGG CAG GAG AGC CCA GCC TTC GCT GCC CAG GGA GCC CCC TTT CTC CTC AG AC ACC AAG GCA AGC TCC TAT GAT
9120 9150 9180 , 2 1 0
210 220. 230 Gly Arg Gly Leu Ser Tyr Arg Gly Leu Ala Arg Thr Thr Leu Ser Gly Ala Pro Cys Gin.Pro Trp Ala Ser Glu Ala Thr Tyr Arg Asn Val Thr Ala Glu Gin GGC CGC GGG CTC AGC TAC CGC GGC CTC GCC AGG ACC ACG CTC TCG GGT GCG CCC TCT CAG CCG TCG GCC TCG GAG GCC ACC TAC CGG AAC GTG ACT GCC GAG CAA
9240 9270 9300
99a"
Ala Arg Asn Trp Gly Leu Gly Gly His Ala Phe Cys Ar GCG CGG AAC TGG GGA CTG GGC GGC CAC GCC TTC TGC CGG TGC GCC GCG TGG GGC TGG GTG ACC CCT CCG CCC CAG GGC TCC GGG CTC CCG GCG CTC TAA CGG CGC
9330 9360 9390 9420
250 260 270 g Asn Pro Asp Asn Asp l i e Arg Pro Trp Cys Phe Val Leu Asn Arg Asp Arg Leu Ser Trp Glu Tyr Cys Asp Leu Ala Gin Cys
CCC GTC GTG TGG CTA CAG G AAC CCG GAC AAC GAC ATC CGC CCG TGG TGC TTC GTG CTG AAC CGC GAC CGG CTG AGC TGG GAG TAC TGC GAC CTG GCA CAG TGC 9450 9480 951°
280 290 300 . 310 Gin Thr Pro Thr Gin Ala Ala Pro Pro Thr Pro Val Ser Pro Arg Leu His Val Pro Leu Met Pro Ala Gin Pro Ala Pro Pro Lys Pro Gin Pro Thr Thr Arg CAG ACC CCA ACC CAG GCG GCG CCT CCG ACC CCG GTG TCC CCT AGG CTT CAT GTC CCA CTC ATG CCC GCG CAG CCG GCA CCG CCG AAG CCT CAG CCC ACG ACC CGG
9540 9570 9600 9 6 3 0
320 Thr Pro Pro Gin Ser Gin Thr Pro Gly A * ACC CCG CCT CAG TCC CAG ACC CCG GGA GGT TAG GAA GTG GGG GGG GAA GGA GGA GCC GAG AGG GCG CCG GGC GAG CTA GAT TCC GGC CAG CCG GCC GCG GGC TCC
9690 9720
CCG TCC TCA GCC CCT GCT CCT CCA CAG 9750
350
330 VT 340 la Leu Pro Ala Lys Arg Glu Gin Pro Pro Ser Leu Thr Arg Asn Gly Pro Leu Ser Cys Gly Gin Arg Leu Arg Lys CC TTG CCG GCG AAG CGG GAG CAG CCG CCT TCC CTG ACC AGG AAC GGC CCA CTG AGC TGC GGG CAG CGG CTC CGC AAG
. 9780 9810 9840
360 370 380 Ser Leu Ser Ser Met Thr Arg'val Val Gly Gly Leu Val Ala Leu Arg Gly Ala His Pro Tyr He Ala Ala Leu Tyr Trp Gly His Ser Phe Cys Ala Gly Ser ACT CTG TCT TCG ATG ACC CGC GTC GTT GGC GGG CTG GTG GCG CTA CGC GGG GCG CAC CCC TAC ATC GCC GCG CTG TAC TGG GGC CAC ACT TTC TGC GCC GGC AGC
9870 9900 9930
390 Leu He Ala Pro Cys Trp Val Leu Thr Ala Ala His Cys Leu Gin Asp Ar CTC ATC GCC CCC TGC TGG GTG CTG ACG GCC GCT CAC TGC CTG CAG GAC CGG CGA GTA CCC GCC CGC CCA GAG CCG CCC CAG GGG CCG CGG CTC CTC CGT CTC CCA
9960 9990 10020 10050
GCG CAG CTT CCA CGC TGC ACC CGA ACC CGT GCC CTA CCT TCT CCC GCC CCA CCC TTC TTT CCA CGC CCC TCC GGA GCT CCC GGG GAG GAA.GCT GGA ACA CGG GAT 10080 10110 10140
TGG GGT TCG GGA GCA GGG GGC TTC CCC AGA ACG CTT GTG GCC AGG TCT GAG AGC GCT GCC TCT CCC CTA CCC TCC CCG CAG 10170 10200 10230
g Pro Ala Pro Glu Asp Leu Thr G CCC GCA CCC GAG GAT CTG AOG
10260
410 420 430 440 Val Val Leu Gly Gin Glu Arg Arg Asn His Ser Cys Glu Pro Cys Gin Thr Leu Ala Val Arg Ser Tyr Arg Leu His Glu Ala Phe Ser Pro Val Ser Tyr Gin GTG GTG CTC GGC CAG GAA CGC CGT AAC CAC AGC TGT GAG CCG TGC CAG ACG TTG GCC GTG CGC TCC TAC CGC TTG CAC GAG GCC TTC TCG CCC GTC AGC TAC CAG
10290 10320 10350
His Asp Leu A l a Leu Leu Arg Leu CAC GAC CTG GGT GCG TGG GGG CGC CCC GCG GGG ACG GGA AGA GAG CTT GGG CAC GGC GTC CCC GCC TCA CCC TCC TCT CCG CCC GGG TTA GCT CTG TTG CGC CTT
10380 10410 10440 10470
450 460 470 480 Gin Glu Asp Ala Asp Gly Ser Cys Ala Leu Leu Ser Pro Tyr Val Gin Pro val Cys Leu Pro Ser Gly Ala Ala Arg Pro Ser Glu Thr Thr Leu Cys Gin Val CAG GAG GAT GCG GAC GGC AGC TGC GCG CTC CTG TCG CCT TAC GTT CAG CCG GTG TGC CTG CCA AGC GGC GCC CCG CGA CCC TCC GAG ACC ACG CTC TGC CAG GTG
10500 10530 10560
490 Ala Gly Trp Gly His Gin Phe Glu G GCC GGC TGG GGC CAC CAG TTC GAG GGT AGG CAC AAC TGC TAC GGG CAG GCC TAG GGG ACC AGA CCT TTG ATC ACT GGC TTA CGC GGA AGA AGC CCG CGA CTT TGG
10590 10620 10650 10680
TAT CGT TCC GGG TGC CTA CAG AAT GGG TGG CGC TGA CCT GAT GGG TTG TCA CAA TGT GTA CGT GAA TCC CAC GTA GAA TCC CAG GGC CTG CCA TTC ACT GCT GGG 10710 10740 10770
ATC CCC AAA TCT CCT GGG GAT ACA GGG AGA ATC GAA CTT GCT CTT GGT TCC CTC TGG GCC CCC CCC TCC AAA CGC CAA CTA GGA CGC TGG CCC CGC GCT CCG GGC 10800 10830 10860 10890
TAG TGT GGG AGC CAG GTT CTG CGA CTC TGC ATG GGT GGT GGG GGA GGG GTT TCT GTT TCC GCT CCC CCC ATT CAA ATC CTC GCT TTT CTC TCC ACC TCA CCC TCC 10920 10950 10980
TTG CCT ATG AAA TTG AAT TAA TGG CAC CTC CTC CCC TTC GGG CTT CCT GCG AGA CAC GAA GCG CAT CAG TGG GTT TAC AAG CGC CTG GAG CAC CTT TGT CCA TCG 11010 11040 11070 11100
500 ly Ala Glu Clu Tyr Ala Ser Phe Leu Gin Glu Ala Gin Val Pro Phe Leu
TCC GGG CGG CAA GCG TTG TCA GAT GGG GTC TGA AGA AGC CGC TCT GTG TTC GCA GGG GCG GAG CAA TAT GCC AGC TTC CTG CAG GAG GCG CAG GTA CCG TTC CTC 11130 11160 11190
510 520 530 540 Ser Leu Glu Arg Cys Ser Ala Pro Asp Val His Gly Ser Ser He Leu Pro Gly Met Leu Cys Ala Gly Phe Leu Glu Gly Gly Thr Asp Ala Cys Gin TCC CTG GAG CGC TGC TCA GCC CCG GAC GTG CAC GGA TCC TCC ATC CTC CCC GGC ATC CTC TCC CCA GGG TTC CTC GAG GGC GGC ACC GAT GCG TGC CAG GTG AGC
11220 11250 11280 11310
Gly Asp Ser Gly Gly Pro Leu TCT TAG CCC GGT TGG CGC CCT TCC CCG AGG CCG TCA GCC ACA AAT CTC AGG TCC ACA GCG CTC ACC TGC CTG TTT CCG ACC CAG GGT GAT TCC GGA GGC CCG CTG
11340 11370 U400
550 560 570 5 8 0
Val Cys Glu Asp Gin Ala Ala Glu Arg Arg Leu Thr Leu Gin Gly He l i e Ser Trp Gly Ser Gly Cys Gly Asp Arg Asn Lys Pro Gly Val Tyr Thr Asp Val GTG TGT GAG GAC CAA GCT GCA GAG CGC CGG CTC ACC CTG CAA GGC ATC ATC AGC TOO GGA TOO GGC TGT CGT GAC CGC AAC AAG CCA GGC GTC TAC ACC CAT GTG
11430 11460 11490 11520
590 596 Ala Tyr Tyr Leu Ala Trp H e Arg Glu His Thr Val Ser STOP GCC TAC TAC CTG GCC TGG ATC CGG GAG CAC ACC GTT TCC TGA TTG CTC AGG GAC TCA TCT TTC CCT CCT TGC TGA TTC CCC AGT GAG ACA GTG GCT CGG GCA TGG
11550 11580 1 1 6 1 0
AAG GCA AGA TTG TGT CCC ATT CCC CCA GTG CGG CCA GCT CCG CGC CAG GAT GGC GCA GGA ACT 0>A TAA ifcT GCT TTG AAA ATG CTG ACA AGG AAA CCT CTT TTC 11640 11670 TTTOO 11730
TTC ATG GGT CCG CCG GGA AAT GCC AAG ACA GAA AAG CGA TTC ACA GCT TCT CCA CAG CTC TCA GAG AAC AAG GTC TAT GAG ATC TTA ACG TCC AAA ATC TAG ATG 11760 11790 11820
CCA GCC CAG CTA ATG TTT ACT GAG CCT AGG ATA CTG TAT ACC AAG CCC TGT GCA AGG AGA AGC TGC ATG TTA TT 11850 11880 11910
Results / 100
analysis of the 4.2 kb region described above and by sizing of introns A and B by restriction
enzyme analysis the total length of the FXII gene is approximately 12 kb. Transcription
initiation was determined by nuclease S1 mapping and primer extension analysis (described
below) and is designated as nucleotide +1 in Figure 14. The nucleotide sequence G A C GCC
precedes the A T G codon. This sequence agrees with the consensus sequence found prior to
initiator methionine residues (Kozak, 1984). The conserved A A T A A A (Proudfoot and
Brownlee, 1976) in the 3' flanking sequence was identified at position 11693-11698. D N A
sequence analysis showed that there is an AZuI-like repetitive element (Schmid and Jelinek,
1982) at nucleotide -370 (data not shown) preceeding the 5' end of the gene for factor XII.
Furthermore, two other Alul elements were identified in intron B by D N A sequence
analysis although their positions in the gene were not determined.
The sizes of the exons and introns and their positions in the gene are given in Table IV.
Exons range in size from 57 to 320 bp, and introns range in size from 80 to 4,500 bp. Exon
14 is the largest exon (320 bp) and includes the 3' untranslated region of the mRNA. The
average length of the remaining exons is 132 bp which is similar to the average length of
eukaryotic exons of 150 bp (Naora and Deacon, 1982). The predicted size of the mRNA is
2,036 bp which is in close agreement with the size of the mRNA determined by Northern
blot analysis (2,400 +/- 100 bp, including a poly A + tail). The predicted amino acid
sequence of the gene coding sequence and the cDNA sequence were identical except for a
proline 3 1 4 (CCT) in the gene compared to a serine residue (TCT) in the cDNA sequence.
Results / 101
5. Transciption Initiation Site of the Factor XII Gene
The site of transciption initiation was determined by primer extension and nuclease SI
mapping analysis of the 5' end of the gene. The primers used in these experiments are
indicated in Fig. 14 and the reaction products are shown in Figs. 15 and 16. The nucleotide
sequences of the templates from which the primers were prepared are also given in Figs. 15
and 16. The furthest extension product is a weak band seen with a long exposure of the gel
(7 days) and corresponds to position +1 in Fig. 14. This extension product corresponds to
the longest nuclease Sl-resistant fragment. Other nuclease SI and primer extension
products were observed and could be aligned within 1 nucleotide of each other. These
positions in the 5' end of the gene are: +14 and + 22, represented by two strong bands in
the primer extension reactions, and +27 and +33, represented by weak bands in the
autoradiograms of both the primer extension and nuclease SI reactions. Higher molecular
weight bands were not observed even with prolonged exposures (two weeks) of the gels (Fig.
15). Since the nuclease S l and primer extension products correspond to one another, it
appears that there is no intron within the 5' untranslated region of the factor XII gene. The
primer extension experiment was repeated three times resulting in the identical banding
pattern seen in Fig. 15. Furthermore, longer (220 bp) and shorter (50 bp) primers were
used in the extension reaction; the longer primer folded upon itself and could not prime
RNA, and the shorter primer resulted in only a few nucleotides of extension. No extended
product was observed when oligonucleotide primers (17 to 20 bp in length) were used in the
primer extension reaction. In separate experiments, the primer extension and nuclease S l
reactions of the primer without mRNA showed no extended product and no protected
fragments, respectively (data not shown).
/ 102
Figure 15: Nuclease S l Mapping of the 5' End of the FXII Gene.
A 450 bp Hpall fragment containing all of exon 1 and 5' flanking sequence was used to
obtain a 228 bp probe for the nuclease S l mapping reaction. The probe begins at the
position 90 and extends to position -120 (Fig. 15). The 3 2P-labeled fragment was
hybridized to 18 ug Poly A + mRNA and was digested with 200 units nuclease S l for 1 hour
at 3 7 ° C . The reaction was electrophoresed in a 6% polyacrylamide-8M urea gel along with
a D N A sequencing ladder of the probe D N A (Lanes GATC). The gel was autoradiographed
for 18 hours (Lanes GATC) and 3 days with an intensifier screen and - 7 0 ° C (Lane 1). Lanes
GATC are Sanger sequencing reactions of the probe DNA. Lane 1 is the nuclease S l
reaction of poly A + mRNA from liver. The wide arrows show the nuclease S l digestion
products and the narrow arrows, the exact nucleotide to which the nuclease S l band
corresponds.
/ 104
Figure 16: Primer Extension Analysis of the 5' End of the FXII Gene.
A 180 bp 3 zP-labelled fragment of sequence complementary to FXII mRNA was hybridized
to 18 Mg of poly A + mRNA from liver and extended from the Hindll site at position 96 bp
(Fig. 15). The reaction products were electrophoresed in a 6% polyacrylamide-8M urea gel
along with Sanger sequencing reactions performed on the pcHXII-WF7 used in preparation
of the primer. Lanes 1 and 2 are primer extension products of mRNA from liver reacted
with reverse transcriptase at 3 7 ° C and 4 5 ° C for 1 hour. The gel was exposed for 18 hours
[Lanes GATC) and for 7 days at - 7 0 ° C with an intensifying screen {Lanes 1 and 2). Lanes
G A T C are the sequencing reations of the primer DNA. P indicates the primer before
extension and wide arrows indicate the extended products. Met indicates the A T G initiator
methionine sequence. Hell is the Hindi restriction site used to generate the single stranded
primer used in the primer extention reaction. The numbers beside the sequencing gel
correspond to the extended product sizes counted from the Met (ATG) (as "CAT" in the gel
shown) sequence.
Results / 106
The position of the nuclease Sl-protected product was verified further by hybridizing an
oligonucleotide complementary to nucleotides -23 to -6 (Fig. 14) to a Northern blot (Fig. 17)
of human liver polyA + mRNA. This oligonucleotide did not hybridize to the mRNA although
another oligonucleotide complementary to the region +89 to +106 did hybridize.
Therefore, the sequence immediately upstream of the putative transcriptional start site does
not contain coding sequence.
The D N A sequence of the 5' flanking region to the transcription initiation site was
determined and was analyzed for the characteristic recognition sequences " T A T A " and
"CAAT". The closest sequences to these consensus sequences were a " C T A T T T C " at -26
and a " C C A A G " at -105. The SV40 enhancer core consensus TGG(A/T)(A/T)(A/T) was
found at position -330 (ATGGTAGT). A similar sequence, A T G G T A T G , was observed at
position -123 in the promoter region of the albumin gene (Gorski et al., 1986).
/ 107
Figure 17: Northern Blot Analysis of the 5' End of the FXII Gene
Human liver poly A + mRNA (10 Mg) was electrophoresed in a denaturing
agarose-formaldehyde gel. The gel also contained BamtLVHindUI digestion product of a
subcloned fragment (pB/H76-5.5) of XHXII-76 representing the 5.5 BamHI/ffmaTII
fragment at its 5' end (see Fig. 14). The nucleic acids were transferred to nitrocellulose and
hybridized with two 3 2P-labeled oligonucleotides ("a" and "b") representing -23 to -6 (oligo
"a") and +89 to +106 (oligo "b")(Fig.l5) of the gene. The filter was autoradiographed for
24 hours at - 7 0 ° C with an intensifying screen. Lane A, pB/H76-5.5 digested with
BamHI/HindlU and hybridized with the "b" oligo; Lane B, poly A + mRNA hybridized with
oligo "b"; Lane C, polyA* mRNA hybridized with oligo "a"; Lane D, pB/H76-5.5 digested
with BamHI/i/mdIII and hybridized with the "a" oligo. The numbers indicate the lengths of
the XDNA-Hmdll l marker fragments.
IV. DISCUSSION
A. CHARACTERIZATION OF THE HUMAN FACTOR XII CDNA
1. Characterization of Factor XII cDNA Clones
A factor XII'cDNA of 1959 bp was isolated from a cDNA library prepared from human liver
mRNA. This cDNA (pcHXII-501) codes for part of a leader peptide followed by the entire
coding region of plasma factor XII, a T G A stop codon, a 150 bp non-coding region at the 3'
end and a poly A + tail of at least 75 bp. A second human liver cDNA library was screened
and two identical clones (pcWFHXII-WF7,-WF9) were isolated that contained cDNA
sequence coding for the signal peptide region, the putative initiator methionine residue of
factor XII and three nucleotides of 5' untranslated end of the message.
The cDNA sequence data have enabled us to locate the kallikrein cleavage sites (solid
arrows, Fig. 8) that produce a- and 0-factor X l l a during zymogen activation (Cochrane et
al., 1973; Revak et al., 1977; Dunn et al., 1982). The three cleavage sites occur carboxy-
terminal to arginine residues in the sequences: Leu-Thr-Arg, Gly-Gln-Arg and Met-Thr-Arg.
Because kallikrein does not recognize a unique sequence, however, the locations of other
kallikrein cleavage sites in the M r 52,000 fragment of a-factor X l l a cannot be determined
from the cDNA sequence data.
109
Discussion / 110
2. Factor XII Is Synthesized as a Prescursor
Factor XII is a secreted protein and would be expected to contain a signal peptide which
functions in the transport of the protein across the rough endoplasmic reticulum membrane
(Blobel etal., 1979). The cDNA sequence predicts that factor XII is synthesized as a
precursor containing an amino-terminal extension of at least 19 amino acid residues
(encoded by nucleotides 1-18, Fig.D and nucleotides 3-40, Fig.9). Cleavage of a Ser-Ile bond
(encoded by nucleotides 16-21, Fig.8) in the precursor would give rise to plasma factor XII.
This bond cleavage is consistent with the specificity of signal peptidase (Watson, 1984).
Several clotting factors require vitamin K for their biosynthesis, including prothrombin,
factor X , factor IX, factor VII and protein C (Jackson and Nemerson, 1980; Suttie, 1985).
Each of these proteins undergoes a post-translational modification of 10-12 glutamic acid
residues by a vitamin K-dependent carboxylase. The resulting 7-carboxyglutamate
residues bind calcium ions. In contrast to factor XII, the vitamin K-dependent blood clotting
factors are synthesized as prepro-proteins (Kurachi et al, 1982; Degen et al., 1983; Jaye et
al, 1983; Long et al, 1984; MacGillivray and Davie, 1984; Fung et al, 1984; 1985). In
each of these proteins, formation of the plasma protein results from the cleavage of a bond
carboxy-terminal to an arginyl residue. Since signal peptidase does not cleave such bonds
(Strauss et al, 1978; Gordon et al, 1983) it has been proposed that the leader peptides of
these proteins may be cleaved by signal peptidase to form proproteins, and a second
protease(s) then converts the proproteins to the forms found in plasma. Other plasma
proteins are also synthesized as prepro-proteins, including albumin (Straus et al, 1977;
MacGillivray et al, 1979; Lawn et al, 1981), apolipoprotein A-II (Gordon et al, 1983) and
PAs (Pennica etal, 1983; Freizner-Degen etal, 1986; Riccio et al, 1985). The pro-proteins
Discussion / 111
of prothrombin, factor X, factor IX, and protein C share a high level of sequence homology
(Fung et al., 1985) that is not found in the pro-regions of albumin, apolipoprotein A-II or
plasminogen activators. The pro region has now been shown to be important for
carboxylation of the vitamin K-dependent proteins (Jorgensen et al., 1987).
B. HOMOLOGIES WITH OTHER PROTEINS
Comparison of residues 1-276 of factor XII with protein sequences in the National
Biomedical Research Foundation (Washington, D.C.) Protein Data Base reveals extensive
sequence homology with both fibronectin and plasminogen activators. Based on these
sequence homologies, a schematic representation of the structure of factor XII is shown in
Fig. 18. This structure is based on five different regions that share homology with regions
of both fibronectin and plasminogen activators. In addition, factor XII contains a
proline-rich region that does not share sequence homology with any known protein
sequence. Each of these six regions of factor XII are discussed in detail in the following
sections.
1. Amino-Terminal End of the Zymogen Form of Factor XII
The amino terminal region of factor XII (region N H 2 - A , Fig. 18) contains the signal peptide
amino acid sequence with its characteristic hydrophobic core (Blobel et al., 1979). The
signal peptide sequence is followed by a region that is rich in charged amino acids (amino
acids 1-20, Fig. 8). There are 9/19 amino acids that are charged at neutral pH, five of
which have a positive charge and four of them appear clustered near the middle of the
domain. This region is a candidate for the anionic surface binding property of factor XII
/ 112
Figure 18: Proposed Model for Factor XII
The model was based on amino acid sequence homologies with tPA (Pennica et al., 1983; Ny
et al., 1984) and bovine fibronectin (Petersen et al., 1983). Thin arrows demarcate the
proposed protein structural domains found in human factor XII. Regions A-B represents a
fibronectin typell homology; B-C and D-E are growth factor-like reigons; C-D region is a
fibronectin type I homology; region E - F is a kringle structure and F - G is a proline rich
region whose structure is undefined, and G-COOH represents the catalytic region (see text
for details). Disulfide bonds have been inserted according to their arrangement in the
homologous domains of other proteins; the disulfide bond arrangement of the fibronectin
type II region has been determined by Patthy et al. (1984). The disulfide bonds in the
catalytic region were based on the proposed model of 0-factor X l l a (see Discussion).
Kallikrein cleavage sites that give rise to /3-factor X l l a are indicated by the heavy arrows.
Discussion / 114
although both positively and negatively charged amino acids are represented.
2. Fibronectin Homology
The next region of factor XII (region A-B, Fig. 18) shares sequence homology with the type
II homology regions of fibronectin. The type II homologies are each composed of about 60
residues including four half-cysteine residues (Petersen et al., 1983), and share
approximately 54% sequence identity with each other (31/57 residues in corresponding
positions are identical). Residues 13-69 of factor XII share 39% sequence identity (22/57
residues are identical) and 40% sequence identity (23/57 residues are identical) with the two
fibronectin sequences, respectively, including the four half-cysteine residues (Fig. 19-A).
The type II homologies are present in a M r 45,000 fragment of fibronectin that binds to
collagen (see Yamada, 1983; Hermans, 1985); by analogy, the region of factor XII that
shares sequence homology to the type II regions may be responsible for the putative
collagen-binding properties of factor XII (Wilner et al., 1968). Evidence for collagen
activation of factor XII has been strongly disputed, however, since purified collagen added to
plasma does not initiate coagulation as expected for surface-dependent activation of the
cascade (Griffin et al., 1975; Fujikawa et al., 1980a). The proposed disulfide-bridging
pattern shown in the model for factor XII corresponds to that described by Patthy et al.
(1984) for fibronectin and has a kringle-like structure in which the first and third and the
second and fourth cysteine residues form disulfide bridges.
Separating the two growth factor-like regions of factor XII (described below) is a 43 amino
acid peptide (regions C-D, Fig. 18) that shares limited sequence homology with the type I
regions of fibronectin (Fig. 19-C). This domain in fibronectin is characterized by two
/ 115
Figure 19: Homologies Between the Amino Acid Sequence of Factor XII, Bovine
Fibronectin (Petersen et al., 1983) and Human tPA (Pennica et al., 1983)
Identical residues in corresponding positions are boxed; gaps have been inserted in the
sequences to maximize homology. A: Comparison of Segment S3, residues 14-73 (type
II-1), and residues 74-130 (type II-2) of fibronectin with residues 13-69 of factor XII (FXII).
B: Comparison of residues 51-84 of tissue-type plasminogen activator (tPA) and residues
79-111 (FXII-1) and residues 159-190 (FXII-2) of factor XII. Arrows denote glycine and
cysteine residues that are invariant in this type of homology. C: Comparison of segment
S l , residues 17-57 (type 1-1) and segment S l residues 66-104 (type 1-2) of fibronectin with
residues 116-151 of factor XII (FXII). D: Comparison of residues 87-173 of tissue-type
plasminogen activator (tPA) with residues 193-276 of factor XII (FXII).
A Fibronectin Type II Homology:
Type I I - l Type II -2 FXII
Type I I - l Type II -2 FXII
T T T T T T
G E P C|V L|P F G|A L|C H F P F
V T|G E P C H F P F
t T T l E j Q D Q K N Y D ( A ) D Q K
N { T | D Q D QpTw
Y N I G K T F Y S
Y N J N H N [ 7 | T D
Y ( H R Q L | Y | H K
C T C T C T G P
H L W c M K W c Q P w c
|3 Growth Factor Homology:
tPA FXII -2 FXII -1
E P •si F N G G 1 P C Q Q A L Y F S D F V C Q C P E G F A G K C C T N P c L H G G [ | Oc L E V E G H R L - - C H C P v G . Y T G P F C H S P c Q K G G 1 ? c V N M P S G P H - - £ L C P Q H L T G N H C_
t t t t t t t t
C Fibronectin Type I Homology
SD N
- T T Y P E I - l
T Y P E 1-2
FXII : 0
P G D
E Q -
K H Y Q I
N T [ Y J R V
R F F H K
7 J Y L G S A ] L - V C T c Y G G S R G - F N C
P K D S - - M _ I W D C T c I G A G R G R I S C
T ) E Q - A Aj V A R cjol |c| K G _ P D A H - - - £_
Q Kringle Homology:
tPA FXII
tPA FXII
D T D T
P D R N
A I R W - -
E D
D G
L G L G
R [ G J L
N " H J N
G _HjA
R G R G
T W L A
Y C R N P D
F C R N P D
R I D " S
N [ D J I
S G A
S G A
K P W C
R P W c CTi
Discussion / 117
disulfide bonds giving a two loop structure that has been named a "finger" domain (Petersen
et al., 1983). The functions of the finger domains in fibronectin may be varied and involve
the fibrin, heparin and perhaps gelatin binding properties of the protein (see Yamada, 1983;
Petersen and Skorstengaard, 1985).
Fibronectin is a macromolecular dimer of nearly identical polypeptide chains ( M r
220,000-250,000) which are held together at their carboxy termini by two disulfide bonds
(Petersen and Skorstengaard, 1985). The protein is found inside the cell, in the
extracellular matrix and in plasma (McDonagh et al., 1985). Plasma fibronectin is
synthesized in the liver and is secreted. Fibronectin is also synthesized by megakaryocytes
and found in platelets (Plow et al., 1979). A single gene codes for human fibronectin
although three different proteins have been described which result from alternative splicing
of the mRNA transcript (Schwarzbauer et al., 1983). The protein is comprised of multiple
structural and functional domains consisting of three repeated units, 12 with type I
homology, two with type II homlogy and 15 with type III homology (Petersen and
Skorstengaard, 1985). As determined by electron microscopy studies (Hirano et al., 1983)
the chicken fibronectin gene consists of at least 48 exons with each being about 150 bp in
length and correspond to the lengths of the type I and type II homologies.
The functions of fibronectin are varied due to its binding to many different biological
substances, especially to those on cell surfaces (Petersen and Skorstengaard, 1985).
Interactions with collagen, fibrin and cells implicates fibronectin in the process of wound
repair (Clark and Colvin, 1985) either as a result of severe injury or in inflammation. After
fibrin, fibronectin is the major protein found in the blood clot (4-5% of the total protein) and
has been shown to be cross-linked to fibrin by factor XHIa in vitro (Mosher, 1975).
Discussion / 118
Fibronectin also binds to collagen as well as being chemotactic for fibroblasts, neutrophils
and macrophages. Therefore, it appears to be associated with various stages of tissue
repair in organisms including the initial stage, cellular infiltration and the phagocytic
removal of debris (McDonagh et al., 1985). Importantly, fibronectin may be a central
component in cell migration, attachment and differentiation although formal proof is lacking
(Clark and Colvin, 1985).
3. Epidermal Growth Factor Homology
Two regions of factor XII (regions B-C and D-E , Fig. 18) are homologous to an epidermal
growth factor-like sequence that has been found in many proteins including the 19K protein
from Vaccina virus, transforming growth factor type 1, tPA, and several clotting factors
(Blomquist et al., 1984; Doolittle et al., 1984). In each of these proteins, there is a highly
conserved region of 50 amino acids with nine invariant cysteine and glycine residues. After
the insertion of three gaps in the factor XII sequences, all cysteine residues align perfectly
(Fig.l9-B). The carboxy-terminal growth factor domain also contains the invariant glycine
residues; in the amino-terminal domain, however, one invariant glycine residue has been
replaced with a histidine.
4. Kringle Homology
Another type of homology found in factor XII is the kringle domain (region E - F , Fig. 18).
Kringle domains are typically 80 amino acids in length and form three characteristic
disulfide bonds. Kringles have been found in prothrombin (Magnusson et al., 1975),
plasminogen (Sottrup-Jensen et al., 1978), tPA (Pennica et al., 1983) and urokinase
Discussion / 119
(Gunzler et al., 1982) and share approximately 40% sequence identity with each other
including six invariant half-cysteine residues (see Jackson and Nemerson, 1980). An
alignment of one of the kringle regions of tPA with factor XII is shown in Fig.l9-D. If three
gaps are inserted into the factor XII sequence, the kringles share 41% sequence identity (36
out of 87 residues are identical). The function of the kringle regions is unclear but it may be
involved in binding factor XII to fibrinogen and fibrin as has been described for a tPA
kringle (van Zonneveld et al., 1986). The presence of both a finger domain and a kringle
suggests that the fibrin binding capacity of factor XII may be important in vivo.
5. Proline-Rich Domain
The kringle structure is followed by a region (residues 279-330, Fig 8; region F - G , Fig. 18)
in which 33% of the residues are proline (17 out of 52). Despite the high proline content,
this region does not share any sequence homology with other proline-rich proteins such as
those from salivary glands (Ziemer et al., 1984). However, residues 299-308 of the
proline-rich region of factor XII share sequence homology with residues 29-38 of calf
thymus HMG-17 (Walker et al., 1977) in which eight out of ten residues in corresponding
positions are identical. The significance of this homology and the function of the proline-rich
region of factor Xn are unclear.
6. Serine Protease Domain
Downstream of the proline-rich region in factor XII is the catalytic region (region G to the
COOH-terminus, Fig. 18) that shares amino acid sequence homology with other serine
proteases. A n alignment of the amino acid sequences of the catalytic regions of /3-factor
Discussion / 120
X l l a , plasminogen activators and the three pancreatic serine proteases is given in Figure
20. An analysis of the sequence homology between these enzymes is summarized in Table
V. It is notable that the sequence identity between /3-factor X l l a and the pancreatic
enzymes (average value of 35%) is comparable to the identity present between the
pancreatic enzymes themselves (average value of 42%).
A computer generated structural model of /3-factor X l l a was developed by Dr. Brayer and
G.V. Louie (Department of Biochemistry,University of British Columbia) (see Cool et al.,
1985), based on the known three dimensional structures of the pancreatic enzymes. The
model provided structural information about factor XII which may affect its catalytic
activity. For example, it is known that all 14 cysteine residues of /3-factor X l l a are involved
in disulfide bridging (Fujikawa and McMullen, 1983). From the sequence alignment of
/3-factor X l l a (Figure 20), it is apparent that four disulfide bridges (involving residues
42-58, 136-201, 168-182 and 191-220) are conserved in all three pancreatic enzymes, and a
further homologous disulfide bridge is shared with chymotrypsin (residues 1-122). The
disulfide bridging pattern of the remaining four cysteine residues of /3-factor X l l a cannot be
determined from primary structure alignments alone. Within the tertiary structure model
of /3-factor X l l a , however, pairing of these remaining cysteines residues were proposed and
are Cys-50 to Cys-111 and Cys-77 to Cys-80. This accounts for the seven possible disulfide
bonds in the serine protease domain.
Also evident from the tertiary structural model of /3-factor X l l a are the positions of major
insertions that occur in the amino acid sequence of /3-factor X l l a [residues 61 A - C , 109 A - E
and 205 A-C (Figure 20)]. All three of these insertions occur towards the end of existing
surface /3-loops in the pancreatic enzymes; two insertions are positioned on the forward
/ 121
Figure 20: Amino Acid Sequence Alignment of the Catalytic Regions of 0-Factor
Xlla (FXII), Bovine Trypsin (TRYP), Porcine Elastase (ELAS), bovine chymotrypsin
(CHYM) and Human tPA
The sequences of trypsin, elastase, chymotrypsin and tPA are taken from Marquart et al.
(1983), Sawyer et al. (1978), Cohen et al. (1981) and Pennica et al. (1983), respectively.
The numbering system used is based on that of chymotrypsinogen A (Hartley and
Kauffman, 1966), with insertions in the sequences of related enzymes denoted by letters
(36A, 36B, etc.). Deletions are indicated by dashed lines. Identical residues in
corresponding positions of all five proteins are boxed. The standard single letter code for
amino acids is used.
F X I I TRYP ELAS CHYM tPA
10 11 12 13
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 36 36 36 36 F X I I V V G G L V A L R G A H P Y I A A L Y TRYP I V G G Y T C G A N T V P Y Q V S L N ELAS V V G G T E A Q R N S w P S Q I S L Q Y R S G S -CHVH I V N G E E A V P c s w P W Q V s L C 0 X - - - -tPA I K G G L r A 0 1 A S H P W Q A A I F A X H R R S
E 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
F X I I W G H S F C A G S L 1 A P c W V L T A A H C L Q TRYP - S G Y H F c G G S L I N S Q W V V S A A H C Y K ELAS - 5 W A H T c G G T L I R 0 H w V M T A A H C V D CH KM - T G r K F c G G S L I N E H M V V T A A H c G V CPA P G E R F L c G G I L I S S C W I L S A A H c P Q
A B C A 61 61 61 61 62 63 64 65 65 66 67 6B 69 70 71 72 73 74 75 76 77 78 79 80 81
r X I I D R P A P E D h T V V L G 0 B R R N H S C E P c Q TRYP S - - . - G I Q V R L - - G E 0 N I H V V E G N E Q ELAS R - - E L T F, R V V V G E H N L N Q 14 N G T Z Q CHYM T • - - T S D V - V V A G E F D Q G S S S E X I Q tPA E R F P P H . H L T V I L G R T Y R V V P G E E E Q
62 83 84 85 86 87 38 89 , .90 91 92 93 94 95 96 97 98 99 A B
99 99 100 101 102 103 104 r x i i T L A V R S Y R L H E A F S P V S Y - - Q H D L A TRYP F 1 S A 5 X S I V H P S Y N S N T L - - N N D X H ELAS Y V G V Q K X V V H P Y W N T D D V A A G Y D I A CHYM K L K I A K V F K N s X Y . N S L T I - - N N D I T tPA K r E V e .K Y I V H X E F D D D T t D N D 1 A
r X I I TRYP. ELAS CHYM tPA
105 106 107 108 109 109 109 109 109 109 110 111 112 113 114 115 116 117 118 119 120" 121 122 123 124 I E D A D G S C A L L S P '
125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 F X I I S G A A R P S E T T L C Q V A G H G H Q F E G A E TRYP T - S c A S - A G T 0 C L I S G N G N T X S S G T ELAS R A G T I L A N N S P c Y I T G W G L T R T N G CHYM S A S 0 D F A A G T T c V T T G H G L T R Y T N A tPA P A D L C L P D W T E c E L S G Y G K H E A L S P
F X I I TRYP ELAS CHYM tPA
150.151 152 153 154 155 156 157 15B 159 160 161 162 163 164 165 166.167 168 169 170 170 170 171 172
F X I I TRYP ELAS CHYM tPA
173 174 175 176 177 178 179 180 181 182 183 184 184 185 186 187 188 168 166 188 168 168 168 188 169 L E G G T - - - - - - D
F XII TRYP ELAS CHYM tPA
190 191 192 193 194 195 196 197 196 199 200 201 202 203 204 205 205 205 205 206 207 208 209 210 211 C " ] E D Q A A E R R L T L Q
- ' - - C K L f i V N G - - - Q Y A V H
: K N G - - - A W T L V N . D G - - - R M T L V
F XII TRYP ELAS CHYM tPA
F XII TRYP ELAS CHYM tPA
212 213 214 215 216 217 217 218 219 220 221 221 222 223 224 225 226 227 228 229 230 231 232 233 234 C
Cj G 0. 235 236 23J 238 239 240 241 242 243 244 245
123
0 - f a c t or X l l a
Chymo t r yp s In
E l a s t a s e
Chymo t r y p s i n
(243 )
86 (35%)
E l a s t a s e
( 240)
79 (33%)
94 (41%)
T r yp s In
( 223 )
84 (38%)
101 (45%)
87 (39%)
T a b l e V . C o m p a r a t i v e A n a l y s i s o f the Amino A c i d S e q u e n c e A l i g n m e n t
Between the C a t a l y t i c R e g i o n s of / 3 - F a c t o r X l l a and the
P a n c r e a t i c S e r i n e P r o t e a s e s .
The t o t a l number of r e s i d u e s in each p r o t e i n Is g i v e n in p a r e n t h e s e s be l ow
i t s name in the h e a d i n g . Fo r each p a i r o f p r o t e i n s a l i g n e d in F i g u r e 20 , the
m a t r i x c o n t a i n s the number of i d e n t i c a l r e s i d u e s f o l l o w e d by the o v e r a l l
s e q u e n c e homology ( g i v e n as a p e r c e n t a g e of the s m a l l e r p r o t e i n ) in
p a r e n t h e s e s .
Discussion / 124
active site face of the enzyme (residues 61 A-C and 109 A-E), and the other is positioned
towards the back surface of the enzyme (residues 205 A-C). Thus, the insertions observed
for /3-factor X l l a occur at sites easily accommodated within the overall structural
framework of the pancreatic enzymes.
The insertion of five residues at position 109 is found in a region in other proteases which
shows no amino acid sequence variability amongst them and includes the pancreatic
proteases, thrombin, factor Xa and factor IXa (Furie et al., 1982). Interestingly, this insert
is also found in tPA (Figure 20). Since the insertion occurs on the surface of the enzyme it
is most probably related to the ability of /3-factor X l l a to recognize the physiological
molecular surfaces with which it must interact. It is notable that the carbohydrate moiety
of /3-factor X l l a (bound to Asn-74; Fujikawa and McMullen, 1983) is positioned near this
insertion and according to the teritiary structural model, is on the substrate binding surface
of the enzyme. Specialized surface features such as these and the variable regions already
discussed provide a mechanism by which complex cascade pathways like those involved in
blood coagulation and fibrinolysis can occur by the specific recognition of substrate molecules
(Jackson and Nemerson; Nemerson and Furie, 1980).
7. Plasminogen Activator Homology
From these sequence comparisons, it can be seen that factor XII shares remarkable
sequence homology with tPA (Ny et al., 1984), a protease that converts plasminogen to
plasmin in the fibrinolytic pathway (see Collen, 1980). The complete amino acid sequence
of human tPA has been predicted from the cDNA sequence (Pennica et al., 1983; Fisher et
al., 1985) and shows that tPA consists of a finger domain, a growth factor-like domain, two
Discussion / 125
kringle structures and the catalytic serine protease domain. This organization is similar to
regions C to the COOH-terminus of factor XII except that one of the tPA kringles is replaced
by the proline-rich region (Fig. 18). However, the tPA transcript contains a leader sequence
with not only the signal peptide sequence but also a pro-region which is removed prior to
secretion (Ny et al., 1984). No corresponding pro-region is found in factor XII but it is
present in other proteases involved in coagulation such as, prothrombin, factor X , factor IX
and protein C (discussed above).
8. Physiological Significance of the Homologous Protein Domains
Complex proteins such as the coagulation and fibrinolysis serine proteases and fibronectin
consist of multiple structural and functional domains which have been assembled during
evolution to produce the molecules found today. When a function has been defined for a
particular domain such the epidermal growth factor homology, it is tempting to attribute an
EGF-like function to the acceptor protein. This argument is flawed, however, since proteins
with homologous structures can possess different functions [for example, hemoglobin, a
protein in red blood cells and myoglobin (Blanchetot et al., 1983) have homologous domains;
or, a-crystallin which is an eye lens protein, is similar to a Drosophila heat shock protein
(Doolittle, 1985)]. Evidence for functionality of a protein domain within a particular protein
will have to be obtained directly. For example, functional assays have been performed on
the kringle domains of tPA (van Zonneveld et al., 1986). These studies showed that the
kringle binds to fibrin which would be important in the degradation of fibrin by plasmin (see
Collen, 1980). However, similar studies have not been performed on the putative functional
domains of FXII.
Discussion / 126
C. A PERSPECTIVE ON THE ROLE OF THE CONTACT SYSTEM IN
HOMEOSTASIS
Our understanding of the complex process of wound repair and the regenerative process
(reviewed in Clark and Colvin, 1985) is becoming clearer as the components of the plasma
systems involved are being defined. The plasma systems, blood coagulation, fibrinolysis
and inflammation have already been described in detail (see "Introduction"). Other plasma
systems involved in wound repair include the complement system and the immunoglobulin
molecules and are described elsewhere (Bennett and Ogston, 1981; Pesce and Dosekun,
1983). Also important to the healing process is the regeneration of new tissue at the site of
injury. Epithelium cells at the wound margin are stimulated to elongate and divide and
migrate to cover the thick mat of fibrin and fibronectin. Blood vessels sprout branches and
migrate to the wound bed and also begin to divide. Fibroblasts and macrophages are
summoned to the wound and newly synthesized glycosaminoglycans (GAG), fibronectin and
collagen, probably supplied by the fibroblasts are used to form the new extracellular matrix.
Central to these events is fibronectin which binds to fibrin, G A G , collagen, can stimulate cell
migration (epithelium) and is chemotactic for neutrophils and macrophages.
The convergence of the plasma systems involved in wound repair and the regenerative
process occurs as a result of the assembly of the essential components at the site of injury.
Plasma and tissue factors initiate the coagulation cascade producing a network of fibrin.
Trapped in this mesh are the molecules that are vital for repair. These include plasminogen
activators, plasminogen, fibronectin and perhaps factor XII. The proteins are all related
structurally although it is not known if each homologous domain exhibits similar function.
The plasminogen activator, factor XII and plasminogen have homologous kringles (possible
Discussion / 127
fibrin binding property) and serine protease domains. Plasminogen activator, factor XII
and fibronectin are related through the type I homology (possible fibrin binding property).
Factor XII also contains a type II homology (possible collagen binding property) found in
fibronectin.
Interestingly, like fibronectin, factor XII appears central in the processes of wound repair
(see "Introduction") in that factor XII is important in the contact activation of coagulation,
fibrinolysis, inflammation and kinin generation through the activation of prekallikrein.
Also, the epidermal growth factor domains in factor XII may be premordial growth factors
which may still have stimulatory properties since at the site of injury, cell proliferation
takes place and it may be possible that these regions in factor XII (and tissue-type
plasminogen activator) may play a minor role. Factor XII and fibronectin are structurally
unalike except in the fibronectin type I and type II homologous domains found in factor XII.
It is possible that during the process of evolution, factor XII acquired these two domains (see
below), and since factor XII was also functional in wound repair, the newly acquired
domains may have assumed similar function. The amino acid sequence of the factor XII
protein has changed during the process of evolution but may still have retained essential
amino acids required for the binding of collagen or fibrin. Finally, this evolutionary
strategy may also be applied to the other proteins important in wound repair (plasminogen
and tissue-type plasminogen activator) which have also acquired the homologous domains
(kringles and type I homology).
It should be emphasized that there is only circumstantial evidence to implicate fibronectin in
the wound repair and the regenerative processes. In addition, factor XII and prekallikrein
are not essential for wound repair since individuals deficient in either of these proteins are
Discussion / 128
assymptomatic. However, it is likely that the plasma systems are interrelated in such a
way that if an initiation factor is not present then the reaction will still occur via another,
perhaps less efficient, mechanism. Secondary activation mechanisms of any one of these
plasma systems involved in wound repair are crucial since inactivation of the system would
probably be lethal to the organism.
An understanding of the mechanism of gene evolution may elucidate the importance and
relevance of the exchange of protein domains within a family and between families of
proteins. This study of the factor XII gene structure has provided more data concerning the
evolution of the serine proteases and their structural and functional relationships.
D. DNA SEQUENCE ANALYSIS OF THE HUMAN FACTOR XII GENE
Two recombinant phage containing the entire factor XII gene were isolated from a human
genomic phage library. The gene is approximately 12 kb in length and consists of 13
introns and 14 exons. Restriction enzyme mapping and D N A sequence analysis were used
to localize all exon sequence for factor XII mRNA in the gene (Fig. 12). An A A T A A A
sequence is often found approximately 20 bp 5' to the polyadenylation site in eukaryotic
genes (Birnstiel et al., 1985). This sequence was located at nucleotides 11693-11699 in the
FXII gene. A consensus sequence C A Y T G is another possible recognition site downstream
of the polyadenylation site (Berget, 1984). A similar sequence was found at position 11703
as C T T T G . Al l the splice junction sequences agree with the consensus sequence of Mount
(1982) except for the splice donor of intron J which has a G C instead of a G T dinucleotide.
However, other genes have been described with similar junction sequences (Wieringa et al.,
1984; Dush et al, 1985; Irwin, 1986) and Aebi et al. (1986) have shown that GC is a
Discussion / 129
reasonable splice donor sequence which is spliced accurately in vivo.
An unusual feature of the FXII gene is that it has many very small introns such that exons
3 through 14 are contained in a 4.2 kbp fragment of genomic D N A with three introns less
than 100 bp in length. However, due to the presence of the first two large introns, the total
length of the gene is 12 kb which is an expected size when compared to other genes with
similar lengths of coding sequence (Naora and Deacon, 1982).
E. ANALYSIS OF THE PROMOTER REGION IN THE HUMAN FXII GENE
Promoters of many genes have a C C A A T or a T A T A element (reviewed in Corden et al.,
1980; Breathnach and Chambon, 1981; Hansen and Sharp, 1984; Dynan and Tjian, 1985;
Bucher and Trifonov, 1986) which are positioned at -70 to -80 bp and -27 to -34 bp from the
transcriptional start site, respectively. The primer extension and nuclease S i mapping
results for the human FXII gene show that these elements are not present in the 5' end of
the gene although a C C A A G sequence at -105 and a C T A T T T C at -26 bp are present (see
Table VI for frequency of nucleotides at each position).
1. The C A A T Element
These promoter elements are not essential for the expression of all R N A Polymerase
II-transcribed genes. For example, the C C A A T region in the globin gene family is required
for expression but there is no corresponding sequence in many genes expressed in the liver
such as the blood clotting factors, retinol binding protein (Laurent et al., 1985) and a-1
antitrypsin (Table VI). Deletion studies on the a-1 antitrypsin (Ciliberto et al., 1985) and
130
C o n s e n s u s (Cor den et a l . , 1980)
( -33 to - 2 7 ) ( -27 to - 2 1 )
T ( 3 7 ) A ( 3 9 ) T ( 3 7 ) A ( 3 5 ) A ( 2 3 ) A ( 3 7 ) T ( 2 0 ) C (3) T (1) A (4) T (3) T ( 1 8 ) T (4) A ( 1 4 )
G (6) C (1)
a -1 An t I t r yp s i n - 2 6 (CI l i b e r to et a l . 1 985 ) T T A A A T A
B o v i n e P r o t h r o m b i n - 2 9 ( I r w i n , 1986) C A T T A A C
F a c t o r V I I I - 2 8 ( G i t s c h l e r et a l . , 1984) TAAAAAG
F a c t o r IX - 4 4 ( Y o s h i t a k e et a l . , 1985) TAAATAC
P r o t e l n C - 3 4 ( P l u t z k y et a l . , 1986) CAAATAT
E - a Immune R e s p o n s e - 3 0 ( M a t h i s et a l . , 1983) T T T T A A T
F a c t o r XI I - 2 6 C T A T T T C
T a b l e V I . Summary o f T A T A - 1 Ike E l e m e n t s F o u n d In L i v e r S p e c i f i c
G e n e s , C o a g u l a t i o n F a c t o r G e n e s and the E - a Immune R e s p o n s e G e n e .
The c o n s e n s u s s e q u e n c e f o r TATA l i k e s e q u e n c e s was d e t e r m i n e d f r o m
40 e u k a r y o t i c P o l y m e r a s e II t r a n s c r i b e d genes and were s u m m a r i z e d
in C o r d e n et a l . The numbers a b o v e the s e q u e n c e e l e m e n t s d e s c r i b e
the p o s i t i o n in the gene f r o m the t r a n s c r i p t i o n a l s t a r t s i t e s in
where t h e s e e l e m e n t s a re commonly f o u n d .
Discussion / 131
albumin (Gorski et al., 1986) promoter regions have shown that both genes have strong
promoters upstream of C A A T or T A T A regions. Albumin has a C C A A T element at -89 bp,
but it was shown that deletion of this region reduced the transcription rate by only 10%
whereas sequences further 5' reduced the rate by 85%. In addition, promotion of both the
albumin and a-1 antitrypsin genes required liver specific factors since the promoters did not
function significantly when the deletion mutants were expressed in tissues that did not
normally produce the gene products. Therefore, it appears that there are strong promoters
in these liver genes that are independent of the C A A T regions. Although similar studies
have not been described in the literature for clotting factor promoters, it is possible that the
genes which are highly expressed (prothrombin and antithrombin III) probably will also
have non-CAAT-like promoter sequences recognized by liver specific factors.
2. The TATA Box
The blood clotting factor genes as well as many others have atypical or no canonical T A T A
elements (Table VI). Other genes such as the housekeeping genes
[3-hydroxy-3-methylglutaryl CoA (Reynolds et al., (1984); dihydrofolate reductase (Crouse
et al., (1982); hypoxanthine-guanine phosphoribosyl transferase (Melton et al., 1984), and
adenosine deaminase (Valerio et al., (1985)], Thy-1 (Giguere et al., (1985), E G F receptor
(Ishii et al., 1985) and viral promoters (Baker et al., 1979; Ghosh et al., 1979) do not have
T A T A elements but do have G + C rich regions 5' to the transcriptional start site. These
genes also often have S p l binding sequences (GGGCGG) (reviewed in Dynan and Tjian,
1985). Another class of non-TATA like promoters includes those which have no apparent
D N A features that are particularly distinguishable. These genes are human ^-tubulin (Lee
et al., 1983), T-cell receptor/T3 complex (van den Elsen et al., 1986) and perhaps factor XII .
Discussion / 132
In most of the cases listed, all the mRNA transcripts appear to have heterogeneous 5' ends
suggesting that the major role of the T A T A sequence in these genes is to direct the position
of the 5' end of the transcript.
Variability in the nature and function of the T A T A sequence is demonstrated in in vivo
deletion studies. The T A T A sequences in the SV40 (Benoist and Chambon, 1980) and sea
urchin H2A (Grosschedl et al., 1980) gene promoters showed that the T A T A sequence was
required for precision in transcript initiation but did not affect transcription rates.
Sequences around the mRNA capping site may also contribute to the determination of the
transcription initiation site as illustrated in a mutant rabbit 0 globin gene which lacks a
proper T A T A sequence (Charnay et al., 1985; Dierks et al, 1983) and yet the majority of
mRNA transcripts contained the correct 5'end. On the other hand, both rate and placement
of transcript initiation required T A T A sequence elements in expression of the thymidine
kinase and globin genes (McKnight and Kingsbury, 1982; Charnay et al., 1985; reviewed in
Hansen and Sharp, 1984). Certainly the lack of T A T A or presence of weaker TATA-like
sequences (Table VI) is exceptional as most eukaryotic RNA Polymerase II genes do have
the consensus sequence (Breathnach and Chambon, 1981). However, many genes function
normally without the T A T A sequence and probably possess other factors pertinent to
transcription initiation and regulation.
Until further studies are performed with the FXII 5' flanking region, the identity of the
regulatory sequence(s) of the factor XII gene remains unknown. The nuclease S l and
primer extension products for FXII strongly suggest that FXII is lacking a typical T A T A
sequence possibly resulting in transcription initiation at more than one site. However,
analysis of the 5' flanking regions of the genes listed in Table VI and those discussed above
Discussion / 133
indicates that many genes are lacking or have atypical T A T A sequences. The absence of
true C A A T or T A T A sequences may be a means of maintaining a low level of transcription
for those genes coding for low abundant mRNAs (Bucher and Trifonov, 1986). Genes which
require stronger promotion but do not have typical promoter sequences (for example, a-1
antitrypsin and prothrombin, Table VI) may possess unique promoter elements such as
those recognized by liver specific factors (Ciliberto et al., 1985; Gorski et al., 1986) resulting
in high levels of gene expression.
F. PUTATIVE PROTEIN DOMAINS ARE FOUND ON SEPARATE EXONS
The positions of the introns in the factor XII gene divide the coding region into discrete
protein modular units (demarcated by arrows in Fig. 18) which share amino acid sequence
identity with similar regions in tPA (Ny et al., 1984) and fibronectin (Peterson etal., 1983).
Comparisons of the FXII amino acid sequence with those of tPA and fibronectin show that
there is only approximately 30-40% (Figure 19) sequence identity but the positions of
half-cysteine residues in each unit are conserved.
The schematic representation of the FXII coding sequence, shown in Fig. 21, was based on
sequence homologies found in tPA and fibronectin. The lengths of each exon are given in
Table IV. A putative signal peptide sequence (Blobel et al., 1979) at the N-terminus of the
zymogen is located on the first exon (NH2-A, Fig. 21) followed by a region of unknown
homology (A-B, Fig. 21) that is encoded by the second exon. A "type II" homology with
apparent collagen binding properties in fibronectin (Petersen et al., 1983; Yamada, 1983) is
represented by exons three and four (B-D, Fig. 21). Next is the EGF-like domain (D-E,
Fig.21) on exon five (Blomquist et al, 1984; Doolittle et al., 1984) followed by the "type I"
/ 134
Figure 21: Schematic Diagram of the FXII Protein Coding Domains and the
Positions of Introns.
The standard one-letter code of each amino acid is given in the open circles. The solid black
bars, indicating possible disulfide bonding between cysteine residues is based on protein
homologies of other proteins (Magnusson et al., 1975; Yamada, 1983; Blomquist et al.,
1984; Patthy et al, 1984; Cool et al., 1985). The arrows A - M indicate the positions of
introns in the coding sequence. He at position 1 indicates the first residue of the zymogen
and is marked by a curved arrow. The short, closed arrows show cleavage activation sites
by kallikrein which produce j3-factor Xl la .
Discussion / 136
homology, or, the fibrin finger in fibronectin (E-F, Fig. 21) (Petersen et al., 1983) found on
exon six. Exon seven encodes another EGF-like domain (F-G, Fig.21) preceeding a kringle
structure and a proline rich region (G-I, Fig. 21) on exons eight and nine.
FXII activation requires cleavage by kallikrein, carboxy terminal to two Arg residues (thick
arrows in Fig. 21), generating one form of the serine protease, (3-FXIIa (I-COOH, Fig. 21).
The serine protease consists of five exons with the catalytic triad residues, His, Asp and Ser
separated by introns. Exon 14 is the largest (320 bp) and encodes 55 amino acid residues of
the serine protease and 150 bp of the 3' untranslated end of the mRNA.
Although the protein domains described above may be functional in other proteins, it is not
yet known whether similar functions can be attributed to FXII or tPA. It has been
speculated that exons may represent functional building blocks in a protein and that these
elements can be exchanged between existing genes and generate new kinds of proteins
(Gilbert, 1978; Blake, 1978). Patthy (1985) has suggested that the proteins involved in
coagulation and fibrinolysis may have been altered through this action of exon shuffling to
account for their present day structures.
G. EVOLUTION OF THE FACTOR XII GENE
The number and position of introns can be used to describe the evolutionary relatedness of
proteins (Craik et al., 1983) since proteins with conserved structure and function have
common gene organizations and have probably arisen through gene duplication events
(Patthy, 1985; Rogers, 1985). The urokinase and tPA genes have been described (Ny et al.,
1984; Riccio, et al., 1985; Friezner Degen et al., 1986) and are a family of serine proteases
Discussion / 137
separate from the clotting factors (Patthy, 1985; Rogers, 1985; Irwin, 1986). It was
anticipated that since FXII and tPA had many regions of protein homology which were
organized in the same manner in both proteins and that half-cysteine residues were
conserved, then the number and position of introns within their genes would likely be
similar. The positions of introns of the plasminogen activators were compared to those of
FXII and were found to be more conserved in the carboxy terminal half of the molecules
than in the amino terminal region of the proteins (Figs. 22 and 23).
1. Evolution of the Amino Terminal Half of Factor XII
Protein coding sequences of the amino terminal regions of the plasminogen activators and
FXII are interrupted by introns in identical codon reading phases although there is
considerable variation in the coding sequence itself. For example, there are only two exons
(those encoding the EGF-like domain and the kringle) which are common to all three
proteins but the lengths of each exon is conserved and varies by only 10 bp. These exons,
whose functions have been described above, have similar sequence identity and conserved
half-cysteine residues (Fig. 22). The fibronectin type I homology is found amino terminal to
the EGF-like domain in FXII and tPA but not in human urokinase. The fibronectin
homology appears in the FXII and tPA genes on separate exons of almost identical length
and with conserved half-cysteine residues.
Further variation in gene organization was found in the connecting regions in which there is
a kringle in tPA (85 amino acids), a proline-rich region in FXII (55 amino acids), but no
corresponding region in urokinase. The porcine urokinase protein has a 27 bp insert at this
position relative to the human urokinase protein (Nagamine et al., 1984). Analysis of the
/ 138
Figure 22: Comparison of the Exon Organization in the ^N-Terminal Chains of
Human FXII, tPA (Ny et al., 1984) and uPA (Riccio et al., 1985).
Exons are represented by open bars; 5' untranslated regions are represented by solid bars
and signal or pre-regions by dotted bars. The sizes of exons are drawn to scale. Triplet
codon phase in which the exon is interrupted by the intron is designated as 0, I or II. The
sizes of the introns are not to scale. The vertical lines below the open bars represent
positions of cysteine residues in the exons. The lettering in the open boxes refer to the type
homology encoded by the exon: Fnl l , type II homology in fibronectin; E G F , epidermal
growth factor; F F , type I homology in fibronectin, the "fibrin finger"; K , kringle; and P,
proline-rich region. The scale represents 50 bp.
Urokinase ••B-ll-jM^~J-0-£2> EGF h H [ K h l H ^ ( H
tPA HIIIIHhl-BIIEiKKISh 1-̂ Fnl H - ^ j & F ^ I - T K HH ^ HH K r- l l -fg-yi
Factor XII sssTT̂ r̂C-J h H FnllT-lHTnTTr-H EGF H H Fnt h H EGF h I H K >IH K r~P~r-l
1 JI i 111 II i T r i i i r I—I 50 bp
Discussion / 140
gene shows that the intron/exon junction has shifted downstream 27 bp keeping the protein
in the correct reading frame (Nagamine et al., 1985). The insert is not long enough to be a
result of an inserted exon with subsequent loss of an intron in the porcine gene (Blake,
1983).
Kringles are encoded by two exons (reviewed in Patthy, 1985), interrupted by an intron in
the II codon reading frame. The second exon does not usually contain more than about 30
amino acids of coding sequence in the plasminogen activators, plasminogen or prothrombin
(Patthy, 1985). Unlike these genes, the FXII gene contains a 55 amino acid proline-rich
region attached to the second exon of the kringle. However, the length of the first exon of
the FXII kringle and the placement of the middle intron are almost identical to the
plasminogen activator kringles and therefore, the kringle in the FXII gene was probably
present prior to the time of FXII and plasminogen activator divergence. It is possible that,
by exon shuffling or another mechanism of gene evolution, FXII acquired a proline-rich exon
between the second exon of the kringle and the first exon of the serine protease domain with
subsequent loss of an intron. Other genes such as collagen, insulin and actin exhibit loss of
introns when their intron/exon gene organzitions are compared to other members in their
respective families (see Blake, 1983).
Sequences amino terminal to the fibronectin type I homology domain in the plasminogen
activators and FXII share no common homologies although codon phase interruption is
conserved (Fig. 2 2). The FXII gene has two exons which bear amino acid sequence
homology to the type II collagen binding domain in fibronectin and an E G F domain. These
domains are not present in the plasminogen activators. However, the plasminogen
activators have a prepro region which is cleaved prior to secretion, generating the single
Discussion / 141
chain form of the plasminogen activators found in plasma (Ny et al., 1984). This region is
found in the gene as part of the second exon which also contains 26 bp of the 5' untranslated
end of the transcript and nucleotide sequence for the signal peptide domain. The prepro
region is interrupted by an intron in the plasminogen activators and shares the third exon
with amino acid sequence of the zymogens. This third exon is very small (27 nucleotides) in
urokinase and (45 nucleotides) in tPA, and is flanked by O and I triplet codon intron
insertions in both genes. The second exon of FXII encodes the first 19 amino acids of the
zymogen, which follows the signal peptide domain and is flanked by introns in the 0 and I
reading frames, similar to the third exon of the plasminogen activator genes. Since it is not
known whether exons are lost or are acquired through mechanisms such as exon shuffling
in the genome, it is difficult to assess the actual structure of the ancestral gene prior to the
divergence of the plasminogen activator and FXII genes.
The untranslated 5' end of the plasminogen activators and FXII genes are also different.
There is an intron in the plasminogen acitivators which is not found in FXII. Urokinase and
tPA differ also in that the intron is inserted in different reading frames in the genes and the
lengths of the first exons vary. The first exon of FXII contains coding sequence for the 5'
untranslated end (47 bp) and the signal peptide sequence. Interestingly, the first intron in
the FXII gene is positioned immediately following the last residue of the signal peptide in
the O triplet codon reading frame. The 5' untranslated region of the gene is subject to more
variation than the coding regions as observed in the plasminogen activators themselves.
Furthermore, the clotting factors, human FIX (Yoshitake et al., 1985), bovine prothrombin
(Irwin, 1986) and human protein C (Foster et al., 1985; Plutzky et al., 1986) which belong to
the same family of serine proteases (Rogers, 1985; Irwin, 1986) also exhibit variation in
that there is an intron in the 5' untranslated region of the protein C gene but not in the
corresponding regions of the FIX or prothrombin genes.
Discussion / 142
2. Evolution of the Serine Protease Domain of Factor XII
The serine protease domains of FXII, tPA and uPA consist of five exons, four of which are
flanked by introns that have inserted into the same triplet codon reading frame in all three
genes (Fig. 23). This organization was compared to other serine proteases (Fig. 23) in order
to determine the evolutionary history of the FXII gene. Serine proteases can be divided into
five different families of genes based on their intron/exon gene organization (Rogers, 1985;
Irwin, 1986). Three of these families are shown in Figure 23 and are: first, the pancreatic,
kallikrein, nerve growth factors, plasminogen activators and factor XII family; second, the
factor IX and protein C family; and third (but closely related to the FIX and Protein C
family), the prothrombin family. Two other distantly related families belonging to the
serine protease superfamily of proteins (not shown in the figure) are represented by
haptoglobin and complement factor B (Rogers, 1985). Haptoglobin has lost its serine
protease activity although it has retained its activation by proteolysis property common to
the serine proteases. Also, the haptoglobin gene does not have introns in the equivalent
domain (Doolittle, 1985; Rogers, 1985). Complement factor B has serine protease activity
upon activation by proteolysis and has two more introns compared to the FXII/PA family of
proteins.
Although there are differences, FXII is closely related to the plasminogen activator,
pancreatic, nerve growth factor and kallikrein family of serine proteases since each of these
genes contain introns 3' to codons for both the active site histidine and aspartate and a 5'
intron to the codon for the active site serine (Fig. 23). However, the placement of all four
/ 143
Figure 23: Comparison of the Serine Protease Exon Organization in the
Trypsinogen (Craik et al., 1984), Chymotrypsinogen (Bell et al., 1984), Proelastase
(Swift et al., 1984), Kallikrein (Mason et al., 1983; van Leeuwen, 1986), a and 7
Subunits of Nerve Growth Factor (Evans and Richards, 1985), Tissue-type
Plasminogen Activator (Ny et al., 1984; Degen et al., 1986), Urokinase (Nagamine et
al., 1984; Riccio et al., 1985), Factor IX (Anson et al., 1984; Yoshitake et al., 1985),
Protein C (Foster et ah, 1985; Plutzky et al., 1986), Prothrombin (Irwin, 1986) and
Factor XII genes.
Exons are shown as open boxes; the scale at the bottom represents 100 bp. Triplet codon
phase in which the intron is positioned is represented as 0, I or II. The activation sites of
the zymogens are shown by an arrow (the gamma subunit of nerve growth factor is not
activated this way). The codons for the histidine, aspartic acid and serine residues
comprising the catalytic triad are indicated by H , D and S, respectively. The 3'
untranslated ends of factor IX, tPA and urokinase have been abbreviated and are 1935, 914
and 1119 bp in length, respectively. Dotted bars represent exons coding for signal peptides
and slashed bars represent 3' untranslated regions of the mRNAs.
H D s Trypsinogen D - 1 H V ll H h i H r-O-t
Chymotrypsinogen • H D s Chymotrypsinogen ILJ-i-l _ _ r - o - L J - i i H \o\ r • H hCH
Proelastase • H
i D s
Proelastase D H H H lol h i H rO-T
Kallikrein H D S
Kallikrein N h 1 H H H h i H r-0-i' V/A H 1,
D s « N G F Rv| h 1 H H H h i H rOH VA « N G F
H 0 S T N G F N h 1 H ' h l H h i H 1-0-.' VA T N G F
1 H I
D s tPA H H H 'HH T H r-0-T V///AY/////////A
H D s Urokinase H V i H r H H H l-OH V//AV/////////A Urokinase
It H D s Factor XII H ' H H Vi H •hlH Factor XII
H •
D s Factor IX H • ^ o r H V//AV////////X
• H t
D s Protein C H 3 o - r h 1 A V////////////A Protein C
H •
D s • _ Prothrombin 1 H HH h ' H V///A
5' —-3 ' 100 bp
1 ^
Discussion / 145
introns in almost identical locations and in the same codon phase in the plasminogen
activators and FXII genes suggests that these genes may be more closely related to one
another than to the other serine proteases of this family. Figure 23 also shows that the
intron/exon gene organization of FXII and the plasminogen activators is unlike that found in
the FIX and protein C family and the prothrombin gene.
The evolution of the serine protease family of genes has been intensively studied as the
amino acid sequence and tertiary structure of many of the proteins involved have been
determined as well as their respective intron/exon gene organizations. In addition, these
proteins represent a very old family of genes, present in both prokaryotic and eukaryotic
species. The presence of the blood proteins probably arose in organisms when the
vertebrates evolved (Doolittle, 1984). At this time a primordial protease gene was
amplified by gene duplication events and the family was generated (Young et al., 1978;
Doolittle, 1984a; Neurath, 1984; Doolittle, 1985; Patthy, 1985).
Important to gene evolution is the emergence of introns. It is not known and is heavily
debated as to whether introns invaded coding sequences or introns from ancient genes were
lost during the evolution of gene families (Blake, 1983; Gilbert, 1979; Rogers, 1985).
Analysis of the serine proteases in Figure 23 shows that the introns could have been present
prior to gene duplication and subsequently lost. Thus, the older the protein, the fewer
introns which are present. For example, the most distantly related protein is haptoglobin
which has no introns and may have been present in invertebrate species prior to the clotting
factors. Also, invertebrates generally have fewer introns (Gilbert, 1985; Gilbert et al.,
1986) due to loss of introns or less insertion. The role of introns is not known but may be
important in providing raw genetic material (as in intron/exon sliding events observed in the
Discussion / 146
porcine gene and described below) or they allow recombination to occur between genes but
not within coding sequences so that important protein domains are not interrupted (Gilbert,
1979). Evidence for insertion of introns or loss of introns will be provided as we gain more
information about the intron/exon organization of related proteins in lower species and a
time scale of intron loss or gain in a protein family can be assigned.
3. Intron/Exon Sliding
The mechanism of intron/exon junction sliding could explain any small variation in lengths
of exons found in homologous domains (Craik et al., 1983; Nagamine et al., 1985) in the
plasminogen activators and FXII (Fig. 23). According to the tertiary structural model
proposed for /3-FXIIa (Cool et al., 1985), there are three insertions in the serine protease
domain which occur on the surface of the molecule. Two of these inserts (also found in tPA)
appear at or close to a junction (positions A r g 3 , 8 to A l a 4 0 0 and G l u 4 5 0 to G l y 4 5 4 , Fig. 14)
and are at positions 61 and 109 of the serine protease domain (Figure 20). Craik et al.
(1983) proposed that intron/exon sliding, which generates new coding sequence occurs on
the surfaces of molecules. Such modifications in 0-factor X l l a also map to the surface of the
molecule (Cool et al., 1985). However, the third insertion at position 205 is 13 amino acids
away from the junction (position A l a 5 5 s to A r g 5 5 7 , Fig. 14) and could be acquired through
other mechanisms. These length variations could confer new function to a molecule since
the insert at 109 is near an Asn-74 residue to which a carbohydrate moeity is bound
(Fujikawa and McMullen, 1983) and, according to the tertiary structural model, the insert is
on the substrate binding face of the enzyme.
Discussion / 147
H. A MODEL FOR THE EVOLUTION OF THE HUMAN FACTOR XII GENE
According to the model of evolution of the serine proteases proposed by Platthy (1985) and
based on the amino acid sequence homology in the serine protease domain, FXII and the
plasminogen activators evolved separately from the coagulation family of proteins (Figure
24). The model also illustrates that the plasminogen activator family diverged from the
clotting members after the EGF(A) domains were acquired but before the kringles. It is
interesting that after this divergence, both the FXII and the clotting factor genes were
invaded by another E G F domain of the B type but the plasminogen activators were not,
unless this exon was lost during evolution. The uPA and tPA/FXII genes separated at some
time prior to the acquisition of the fibrin finger domain in tPA and FXII. Since the amino
terminal region of the plasminogen activators and FXII proteins are remarkably different in
terms of their structure and function, it is very difficult to apply the model of exon shuffling
completely to the evolution of the FXII gene as it relates to either the plasminogen activator
or the family of coagulation proteins. Perhaps by some recombination event, all or parts of
the amino terminal region of an ancient gene (represented by the 5' untranslated end, signal
peptide sequence, fibronectin type II homology and possibly the E G F domains in FXII) were
spliced onto or fused with a primordial plasminogen activator gene (Doolittle, 1985) followed
by the insertion of exon domains as described in the exon shuffling model. A recombination
event involving gene fusion has also been proposed for the generation of the FXI and
prekallikrein genes (Chung et al., 1986). The model suggests that the amino terminal chain
(heavy chain consisting of the four tandem repeat units) was fused with the serine protease
domain of a FIX related ancestral gene (Chung et al., 1986) producing FXI or prekallikrein.
Analysis. of plasminogen activators and clotting factors of lower vertebrates and
invertebrates may verify this model and provide a time scale to the events.
/ 148
Figure 24: A Model for the Evolution of the Plasminogen Activators and FXII.
Rectangles with S represent the serine protease domain. Triangles with Gg or G ^
represent the epidermal growth factor type B or type A homology, respectively. Diamonds
with I or II represent fibronectin homologies with the fibrin finger or collagen properties,
respectively. Circles with a K indicates a kringle domain or with an N , the amino terminal
domains for the plasminogen activators. Circles with an X represents the unknown
homology in FXII with possible surface binding properties. A rectangle with N indicates the
factor XII amino terminus or with Pro, the proline-rich domain, (see text for details)
149
gene fusion
© A c .0
N w u v r K
Duplication
uPA gene f u s i o n ^ - <^>
©Oz^©CZJ Duplication
©<i>A©i—§1 © gene fusion
00<O> gene fusioiW^
gene fusion
©<£^©©CZI tPA
gene fusion
EK^><0>7^<I>7M^ p - S
intron loss
-i s
FXII
CONCLUDING REMARKS
The complete amino acid sequence of human factor XII, including the signal peptide
sequence, has been predicted from the D N A sequence of the cDNA and the gene. The
human gene has been identified and the intron/exon gene organization and the 5' and 3'
flanking regions determined. Complete characterization of the human factor XII protein
and its gene has expanded our understanding of the role of factor XII in the contact system.
The presence of putative functional domains which bear homology with fibronectin and
plasminogen activators suggests that the overlapping functions in wound repair for all these
proteins may be a result of these common protein domains. The major plasma systems
involved in wound repair, coagulation, fibrinolysis, complement and regeneration require the
components of the contact system (factor XII, prekallikrein, H M W kininogen), plasminogen
activator and fibronectin. Since the components involved have overlapping functions (at
least in vitro) they may be the means through which the plasma systems are interrelated
and homeostasis maintained during injury.
Analysis of the gene for factor XII shows that it is a member of the plasminogen activator
gene family. Residual function may still be present in the modern factor XII molecule so
that it can act, perhaps weakly, in plasma systems other than coagulation. The complexity
of these serine protease and fibronectin molecules seems to depend on the acquisition of
multiple protein domains. Whether this mechanism is merely an evolutionary strategy to
rapidly increase sequence variation in proteins or whether it is a strategy to confer new
function as well on a protein remains to be determined for human factor XII.
150
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