Cell Cycle 9:20, 4228-4235; October 15, 2010; © 2010 Landes Bioscience

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4228 Cell Cycle Volume 9 Issue 20

*Correspondence to: Narendra Tuteja; Email: narendra@icgeb.res.inSubmitted: 07/10/10; Revised: 09/01/10; Accepted: 09/13/10Previously published online: www.landesbioscience.com/journals/cc/article/13635DOI: 10.4161/cc.9.20.13635

Introduction

Helicase was first discovered from E. coli in 1976 and classified as “DNA unwinding enzyme”.1 Basically helicases break hydro-gen bonding between the duplex helix. Mostly all helicases con-tain some conserved signature motifs, which act as an engine to power DNA unwinding. Multiple helicases are known to be present in individual cells because of a variety of different needs for the duplex nucleic acids to be unwound in different DNA or RNA metabolism.2 The DEAD-box RNA helicases which are found in all eukaryotes and most prokaryotes constitutes a large family of proteins. These proteins are characterized by the pres-ence of nine conserved motifs.2,3 The hydrolysis of ATP through Walker motifs of the DEAD (Asp-Glu-Ala-Asp) box family of proteins is necessary for the nucleic acid unwinding activity of these enzymes. The motifs I (AxxGxGKT) and II (VLDEAD) are characteristic of NTP hydrolyzing proteins, the motif III (SAT) is involved in coupling of ATP hydrolysis and unwind-ing. The motifs IV (FVNT) and V (RGxD) are involved in RNA binding, and the motif VI (HRIGRxxR) is required for the nucleic acid-dependent NTP hydrolysis.4,5 The RNA helicase families are named as DEAD (DDX), DEAH or DExH (DHX) according to the conserved motif II. The genetic and biochemi-cal experiments in yeast suggests that DEAD-box helicases could be involved in processes that involve RNA metabolism,

Helicases are motor proteins of biological system, which catalyze the opening of energetically stable duplex nucleic acids in an ATP-dependent manner and thereby are involved in almost all aspects of nucleic acid metabolism including cell cycle progression. They contain several conserved domains including the DEAD-box and also several unique domains associated with these. The Pfam database (pfam.janelia.org/) is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). A diverse range of proteins are found in nature, and the functional specificity to each protein, to a greater extent, is imparted by its domain architecture. To this extent, a DEAD-box ATP-dependent RNA helicase (LOC_Os01g36890; Genomic sequence length: 6284 nucleotides; CDS length: 1,299 nucleotides; protein length: 432 amino acids) was studied. The protein sequence was imported for domain search on Pfam. This particular Pfam entry after covering a large proportion of sequences in the underlying database has generated a more comprehensive coverage across a wide range of phyla of the known domains that are associated with the typical DEAD-box helicase motif. A total of 362 domain architectures were recollected from the Pfam database for the Family: DEAD (PF00270). We have therefore systematically analyzed the domains closely associated with DEAD-motif, which occur in a variety of proteins and can provide insights into their function.

Architectures of the unique domains associated with the DEAD-box helicase motif

Pavan Umate, Renu Tuteja and Narendra Tuteja*

International Center for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg, New Delhi India

Key words: DEAD motif, PAZ domain, Pfam database, rice, RQC domain

RNA splicing, nuclear export, transcription initiation, mRNA translation and regulation of RNA stability.3,6,7 It has been sug-gested that RNA helicases have some nontraditional roles as well and can regulate gene silencing at nearly every level of the RNA interference (RNAi) pathways.8 Xeroderma pigmentosum group B (XPB) and Xeroderma pigmentosum group D (XPD) are DEAH box helicases, which play specific and distinct roles in mamma-lian nucleotide excision repair (NER) pathway by opening the damaged DNA.9

The information on characterized protein domains is essen-tially required for accurate assessment of the function of a pro-tein. Further, the evolution of functional diversity in proteins depends on the presence of domains, motifs and repeats which forms the basic structural unit of a protein. Moreover, the assem-bly of several structural domains, motifs or repeats constitutes the tertiary structure of larger proteins. For this reason, we have analyzed the unique domains which occur in tandem with the DEAD-motif of the helicase family of proteins.

Results and Discussion

A diversity of pivotal functions is undertaken by a large group of helicases in eukaryotic cells. Many individual helicases are ‘putative’ which are partially or completely uncharacterized in the databases. Much of information is available on the helicase

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describe 22 such unique domains and their functional significance.

Helicase conserved C-terminal (Helic C) domain. [Pfam: Family: Helicase_C (PF00271)]. This family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase-related proteins (Fig. 1a). The eukaryotic translation initiation factor 4A (eIF4A) is a prototype member of the DEA(D/H)-box RNA helicase fam-ily. This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding.10-12 The structure of the carboxyl-terminal (C-terminal) domain of eIF4A has been deter-mined to 1.75 Å resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases.13

CarD-like/TRCF (transcription repair coupling factor) domain. [Pfam: Family: CarD_TRCF (PF02559)]. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes.14 This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in M. xanthus.15 This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins (Fig. 1b). TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription.16 This domain is involved in binding to the stalled RNA polymerase (Table 1).

DEAD-box protein A (DbpA) RNA binding domain. [Pfam: Family: DbpA (PF03880)]. This RNA binding domain is found at the C-terminus of a number of DEAD-box helicase proteins (Fig. 1c).17 It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA.

RecQ C-terminal (RQC) domain. [Pfam: Family: RQC (PF09382)]. This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family of enzymes, is a high affinity G4 DNA binding domain (Table 1).18 This domain has a helix-turn-helix structure.18 RecQ helicases are essential for the maintenance of genome stability.19 In both human and mouse, five members of RecQ family have been identified and muta-tions in some such as Bloom (BLM), Werner (WRN) and RecQ4 are associated with human diseases.20 It has been suggested that the genomic instability of WRN-/- cells results from a defect in the response of replication forks to DNA damage or arrest.21 In human cells WRN helicase has been shown to be involved in the repair of a specific class of double-strand breaks.22 RecQ fam-ily helicases can unwind G4 DNA, and play important role at G-rich domains of the genome, including the telomeres, rDNA and immunoglobulin switch regions. It has been proposed that the DNA-PKcs (protein kinase catalytic subunit) and WRN cooperation plays an important role in the maintenance of telomere length and structure in proliferating cells.23 Binding of RecQ to Holliday junctions involve both the RQC and the HRDC domains (Fig. 1d).

domain containing motifs Q, I, Ia, Ib and from II to VI found in SF1 and SF2 superfamilies of helicases. Motif I and II are also called as Walker motifs A and B respectively, and they are mainly involved in nucleic acid binding and/or NTP hydrolysis. The Q-motif is identified in DEAD-box helicases is devoted for ATP binding and hydrolysis. Concomitantly, there is no information available on the occurrence of DEAD-box domain in association with other unique protein domains. For this reason, we have ini-tiated a study to understand the architectures of various domains which occur together with the DEAD-box domain. Interestingly, a total of 362 domain architectures in a variety of organisms and protein sequences were recollected from the Pfam database for the Family: DEAD (PF00270). The functional significance of some of these unique domains is given in Table 1. Below we

Table 1. Summary of function(s) of the unique domains which occur in close proximity with the DEAD-box motif in several protein sequences

S. no. Domain Function(s)

1 DEAD unwind nucleic acids

2 CarD-like/TRCF binds to stalled RNA polymerase

3 HelicC integral part of the helicase

4 DbpA RNA-binding confers specificity for 23S rRNA

5 RQCG4 DNA binding domain (RecQ

members)

6 HRDC nucleic acid binding

7 HA2 unknown; nucleic acid binding

8 DUF1605 unknown

9 OB-foldnucleic acid binding; anti-codon

binding

10 DSHCTDOB1/SK12/helY-like DEAD-box

helicases

11 Potyvirus P1 proteaseRNA viruses; serine-type protease;

virus-host interactions

12 DEAD_2 RAD3-like DNA-binding helicases

13Cold shock protein

DEAD-box Aexpressed in bacteria under cold

shock

14 DBP10CTC-terminal domain of Dbp10p

subfamily RNA helicases

15 Sec63 Brlassembly of functional ER

translocons

16 S1 RNA bindingstructurally similar to cold shock

protein; binds nucleic acids

17 HDmetal-dependent

phosphohydrolases

18 Toprim conserved region from DNA primase

19 Topoisomerase relax negatively supercoiled DNA

20 GUCT RNA helicase II/Gu protein family

21 RWDidentified in WD40 repeat proteins;

unknown function

22 SPRY unknown

23 PAZnamed after proteins Piwi, Argonaut

and Zwille; role in PTGS

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Figure 1 (Part 1). The figure shows diagrammatic representations of the Pfam domain organization and the occurrence of DEAD-motif. For each category, the organism and the number of sequences with the typical pattern of domain organization is shown. Of the total 362 profiles obtained on Pfam, domain architectures for 20 are shown below.

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Helicase associated (HA2) domain. [(Pfam: Family: HA2 (PF04408)]. This presumed domain is about 90 amino acid residues in length. It is found in a diverse set of RNA helicases (Fig. 1e). Its function is unknown; however it seems likely to be involved in nucleic acid binding (Table 1). The importance of this domain has been shown in a recent study. It has been reported that human DHX9 and DHX36 are localized within cytosol and are bound directly to the Toll-interleukin receptor domain of myeloid differentiation primary response gene 88 via their HA2 domain.27

Domain of unknown function (DUF1605). [Pfam: Family: DUF1605 (PF07717)]. This domain is found towards the C-terminus of the DEAD-box helicases. In these helicases it apparently is always found in association with HA2 (Fig. 1e). There do seem to be a couple of instances where it occurs by

Helicase and RNase D C-terminal (HRDC) domain. [(Pfam: Family: HRDC (PF00570)]. The HRDC domain has a putative role in nucleic acid binding (Fig. 1d). Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterized by proportionate pre- and postnatal growth deficiency; sun-sensitiv-ity, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability.24 BLM helicase has been identified as a new substrate for cdc2 kinase and this obser-vation suggests that BLM helicase plays a role in mitosis.25 It was shown that both N- and C-terminal domains including HRDC domain were phosphorylated at multiple sites by this kinase and two new phosphorylation sites at Ser-714 and Thr-766 were also identified.25 It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.26

Figure 1 (Part 2). The figure shows diagrammatic representations of the Pfam domain organization and the occurrence of DEAD-motif. For each category, the organism and the number of sequences with the typical pattern of domain organization is shown. Of the total 362 profiles obtained on Pfam, domain architectures for 20 are shown below.

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(Fig. 1l). Dbp10 encodes an essential putative RNA helicase that is required for accurate ribosome biogenesis.38 Genetic deple-tion of Dbp10 results in a deficit in 60S ribosomal subunits.38 Consistent with a direct role in ribosome biogenesis, Dbp10 was found to be located predominantly in the nucleolus.38

Sec63/Brl domain. [Pfam: Family: Sec63 (PF02889)]. The Sec63 domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum (ER) translo-cons.39 This domain was named after the yeast Sec63 (or NPL1) protein in which it was found (Fig. 1j and m).40 SEC63 encodes a protein required for secretory protein translocation into the ER of Saccharomyces cerevisiae (Fig. 1m).40 Mutations in the SEC63 gene are associated with defects in protein translocation into the ER as well as in nuclear protein localization in yeast.41 It was demonstrated that a conserved Brl (Brr2-like) domain in the COOH-terminal cytosolic region of Sec63p is essential for func-tion both in vivo and in vitro.39 Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases.39

S1 RNA binding domain. [Pfam: Family: S1 (PF00575)]. The S1 domain is structurally similar to cold shock protein which binds nucleic acids (Fig. 1n). The S1 domain has an OB-fold structure.42 The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins.42 The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been deter-mined using NMR methods and consists of a five-stranded anti-parallel beta barrel.42 The S1 domain also occurs in RNase E, RNase II, NusA, EMB-5 and other proteins.42

Histidine-aspartate (HD) domain. [Pfam: Family: HD (PF01966)]. HD domains are metal-dependent phosphohy-drolases found in a superfamily of enzymes with a predicted or known phosphohydrolase activity.43 The HD motif defines a superfamily that includes a variety of uncharacterized proteins and domains associated with nucleotidyltransferases and heli-cases from bacteria, archaea and eukaryotes (Fig. 1o).44 In all mature tRNAs, the 3'-terminal CCA sequence is synthesized or repaired by a template-independent nucleotidyltransferase.44 The E. coli enzyme comprises of two domains: an N-terminal domain containing the nucleotidyltransferase activity and an uncharac-terized C-terminal HD domain.44 Mutations at the conserved His-255 and Asp-256 residues comprising the C-terminal HD domain of this protein inactivated both phosphodiesterase and phosphatase activities, indicating that these activities are associ-ated with the HD domain.44 The data also suggested that the phosphohydrolase activities of the HD domain of the E. coli tRNA nucleotidyltransferase are involved in the repair of the 3'-CCA end of tRNA.44

Topoisomerase-primase (Toprim) domain. [Pfam: Family: Toprim (PF01751)]. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins (Fig. 1p).45 The DxD (motif-V) of DnaG may be involved in Mg2+ binding and mutations to the conserved gluta-mate (motif-IV) completely abolish DnaG type primase activ-ity.45 DNA primase is a nucleotidyltransferase. It synthesizes the

itself—e.g., Q84VZ2 (At1g58060) [see (PF00270)]. As sug-gested by its name the function of this domain was not known earlier. In a recent interesting study it has been shown that this DUF1605 domain of human DHX9 was required for binding to unmethylated C-phosphate-G (CpG) DNA in human plasma-cytoid dendritic cells.27 These observations suggest that human DHX9 and DHX36 are essential for sensing viral DNA patho-gens which in turn triggers differential cytokine responses.

OB-fold nucleic acid binding domain. [Pfam: Family: tRNA_anti (PF01336)]. This family contains oligonucleotide/oligosaccharide-binding fold (OB-fold) domains that bind to nucleic acids (Fig. 1f and Table 1).28 The family includes the anti-codon binding domain of lysyl, aspartyl and asparaginyl-tRNA synthetases [See (PF00152)]. Aminoacyl-tRNA synthe-tases catalyse the addition of an amino acid to the appropriate tRNA molecule. This family also includes part of RecG helicase involved in DNA repair.29 Replication factor A is a heterotrimeric complex, which contains a subunit in this family.30 This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.31

DOB1/SK12/helY C-terminal (DSHCT) domain. [Pfam: Family: DSHCT (PF08148)]. This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases (Fig. 1g).32 Dob1 (dietary obesity 1) is an essential putative ATP-dependent RNA helicase. Polysome analyses revealed an under accumulation of 60S ribosomal subunits in the dob1-1 mutant. It was proposed that Dob1p functions as a cofactor for the exosome complex that unwinds secondary structures in the pre-rRNA that otherwise block the progression of the 3'-5' exonucleases.33

Potyvirus P1 protease. [Pfam: Family: Peptidase_S30 (PF01577)]. The potyviridae family includes positive stand RNA viruses with genome encoding a polyprotein. Members include zucchini yellow mosaic virus and turnip mosaic viruses which cause considerable losses of crops worldwide. This family con-sists of a C-terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein) (Fig. 1h). The C-terminus of P1 is a serine-type protease responsible for autocatalytic cleavage between P1 and the helper component pro-tease (see PF00851).34,35 The entire P1 protein may be involved in virus-host interactions.35

DEAD_2 domain. [Pfam: Family: DEAD_2 (PF06733)]. This domain represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiqui-tous (Fig. 1i). The members include proteins of eukaryotic, bac-terial and archaeal origin. RAD3 is involved in NER, and forms part of the transcription factor TFIIH in yeast.36

Cold shock protein DEAD box A. [Pfam: Family: DEADboxA (PF12343)]. This domain family is found in bacte-ria, and is typically between 68 and 89 amino acids in length.37 This family is the C-terminal region of DEAD-box A, a protein expressed under conditions of cold shock which is involved in various cellular processes such as transcription, translation and recombination (Fig. 1k).37

DEAD-box protein 10 C-terminal (DBP10CT) domain. [Pfam: Family: DBP10CT (PF08147)]. This C-terminal domain is found in the Dbp10 subfamily of hypothetical RNA helicases

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proteins, and yeast DEAD (DExD)-like helicases.54 Seven WD repeats were found in beta subunit of G-protein which are sug-gested to be involved in protein-protein interaction.55

SPla-RYanodine (SPRY) domain. [Pfam: Family: SPRY (PF00622)]. SPRY domain is named from SPla and the RYanodine receptor (Fig. 1s).56 The SPRY domain is of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin.56 Calcium ion (Ca2+)-release from the sarcoplasmic or ER, the intracellular Ca2+ store, is mediated by the ryanodine receptor (RyR) and/or the inositol trisphosphate receptor (IP3R).56 The predicted amino acid sequence of chicken DDX1 was 93% iden-tical to that of human DDX1.57 All DEAD-box motifs, as well as a SPRY domain, were present in chicken DDX1.57 SPRY and B30.2 are homologous domains which can be identified in 11 pro-tein families encoded in the human genome.58 These include cell surface receptors of the immunoglobulin super-family (BTNs), negative regulators of the JAK/STAT pathway (SOCS-box SSB1-4) and proteins encoded by the numerous TRIM genes.58 Collectively, proteins containing SPRY and B30.2 domains cover a wide range of functions, including regulation of cytokine sig-nalling (SOCS), RNA metabolism (DDX1, hnRNPs), intracel-lular calcium release (RyR receptors), immunity to retroviruses (TRIM5alpha) as well as regulatory and developmental processes (HERC1, Ash2L).58

Piwi-Argonaut-Zwille (PAZ) domain. [Pfam: Family: PAZ (PF02170)]. This domain is named PAZ after the proteins Piwi, Argonaut and Zwille (Fig. 1t).59 This domain is found in two families of proteins that are involved in post-transcriptional gene silencing (PTGS).60 These are the Piwi family and the Dicer fam-ily, that includes the Carpel factory protein.60 The biochemical function of PAZ domain is unknown.61 It was shown that PAZ domains from different human Argonaute proteins can bind RNA.61 Apparently, the PAZ domain may contribute to the spe-cific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.62

Materials and Methods

Screening of database. A putative function search was con-ducted for helicase genes in the Rice Genome Annotation Project (RAP) database (rice.plantbiology.msu.edu/) and a list of 115 genes was compiled.3 A DEAD-box ATP-dependent RNA heli-case (LOC_Os01g36890) was selected for further in silico analysis.

Identification of conserved helicase motifs. The Basic Local Alignment Search Tool (BLAST) has identified all the conserved signature motifs on LOC_Os01g36890 which are typical for the helicase family members.

Sequence analysis. The genomic sequence length, CDS length and protein sequence for LOC_Os01g36890 were retrieved using rice.plantbiology.msu.edu/.

Conserved domains and DEAD-box associated domains search. The protein sequence was imported in the Pfam data-base (pfam.janelia.org/) for conserved domain search analysis. Through iterated searches for DEAD-associated domains was conducted in Pfam database.

oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the lead-ing stand and has been implicated in cell division.46 This family also includes the atypical archaeal A subunit from type II DNA topoisomerases.47

DNA topoisomerase. [Pfam: Family: Topoisom_bac (PF01131)]. This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho-tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA (Fig. 1p).48 DNA topoisomerases regu-late the number of topological links between two DNA strands (i.e., change the number of superhelical turns) by catalyzing tran-sient single- or double-strand breaks, crossing the strands through one another, and then resealing the breaks.49 These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis.49,50 DNA topoisomerases are divided into two classes: type I enzymes (topoisomerases I, III and V) break single-strand DNA and type II enzymes (topoisomerases II, IV and VI) break double-strand DNA.51 It has been shown that WRN helicase genetically interacts with topoisomerase III and restores the top3 slow growth phenotype of sgs1 top3.52 The pea topoisomerase I was reported to interact with pea DNA helicase 45 (PDH45; homologous to eIF4A), as a result of interaction the topoisomerase I activity was stimulated.10

Gu C-terminal (GUCT) domain. [Pfam: Family: GUCT (PF08152)]. This is the C-terminal domain found in the RNA helicase II / Gu protein family (Fig. 1q). Human RNA helicase II/Gu alpha (RH-II/Gu alpha) and RNA helicase II/Gubeta (RH-II/Gu beta) are paralogues that share the same domain structure, consisting of the DEAD-box domain, the helicase conserved C-terminal domain (helicase_C) and the GUCT domain.53 The N-terminal regions of the RH-II/Gu proteins, including the DEAD domain and the helicase_C domain, unwind double-stranded RNAs.53 The C-terminal tail of RH-II/Gu alpha, which follows the GUCT domain, folds a single RNA strand, while that of RH-II/Gu beta does not, and the GUCT domain is not essen-tial for either the RNA helicase or foldase activity.53 The GUCT domain has not been studied widely. The solution structure of the RH-II/Gu beta GUCT domain was determined.53 A study on structural homology search revealed that the GUCT domain has the RNA recognition motif (RRM) fold, which is typically found in RNA-interacting proteins.53

RWD (RING finger and WD repeats) domain. [Pfam: Family: RWD (PF05773)]. The function of this domain is unknown. The RWD eukaryotic domain is found in RING fin-ger and WD repeats (Trp-Asp repeats) containing proteins and DExD-like helicase subfamily related to the ubiquitin-conju-gating enzymes domain (Fig. 1r).54 GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) kinase that appears in all eukaryotes.54 Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing pro-teins: RING finger-containing proteins, WD-repeat-containing

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Likewise the majority of core protein domains are defined while the functions of some remain more enigmatic. Most of these domains play a functional role in the regulation of protein activity and also confer structural and functional advantages. The present study elucidates the biological functions of such domains which are associated with the DEAD-motif of the helicase family of proteins with potential implications to understanding the complex protein regulatory networks in different organisms. This study should also make a significant contribution to our better understanding of the nucleic acid transactions in both the eukaryotes and prokaryotes.

Acknowledgements

This mauscript is dedicated to the memory of Professor Arturo Falaschi. Work on helicases and plant stress tolerance in N.T.’s laboratory is supported partially by the Department of Science and Technology (DST), Government of India and Department of Biotechnology (DBT), Government of India.

Conclusions

Helicases are involved in almost every aspect of DNA and RNA metabolisms, which makes them a very important molecule of the cell, and thereby have several implications of general interest. Despite the diversity of their functions and a large range of organ-isms in which these proteins have been identified, high sequence conservation has been maintained in the large group of helicases, suggesting that all these helicase genes evolved from a common ancestor. In general, the protein sequences contain invariably one or several large domain(s) with distinct functions. Helicases contain conserved core domains and also several unique domains associated with these. The helicase core of DEAD-box proteins exhibits almost no substrate specificity in terms of nucleic acid binding.63 The N- and C-terminal regions are poorly conserved in helicase proteins. However these regions that usually flank the core catalytic helicase domain might provide binding sites for pro-tein-protein interaction or add novel functional specificities.63,64

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