Protein and mRNA content of TcDHH1-containingmRNPs in Trypanosoma cruziFabıola B. Holetz1, Lysangela R. Alves1, Christian M. Probst1, Bruno Dallagiovanna1, Fabricio K. Marchini1,Patricio Manque2,3, Gregory Buck2, Marco A. Krieger1, Alejandro Correa1 and Samuel Goldenberg1

1 Instituto Carlos Chagas ⁄ FIOCRUZ, Curitiba, Brazil

2 Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA

3 Instituto de Biotecnologia, Universidad Mayor, Santiago, Chile

Keywords

differentiation; P-bodies; stress granules;

translation control; Trypanosoma

Correspondence

S. Goldenberg, Instituto Carlos

Chagas ⁄ FIOCRUZ, Rua Professor Algacyr

Munhoz Mader 3775, Curitiba 81350-010

PR, Brazil

Fax: (55) 41 3316 3230

Tel: (55) 41 3316 3230

E-mail: sgoldenb@fiocruz.br

(Received 29 January 2010, revised 3 June

2010, accepted 23 June 2010)

doi:10.1111/j.1742-4658.2010.07747.x

In trypanosomatids, the regulation of gene expression occurs mainly at thepost-transcriptional level. Previous studies have revealed nontranslatedmRNA in the Trypanosoma cruzi cytoplasm. Previously, we have identifiedand cloned the TcDHH1 protein, a DEAD box RNA helicase. It has beenreported that Dhh1 is involved in multiple RNA-related processes in vari-ous eukaryotes. It has also been reported to accumulate in stress granulesand processing bodies of yeast, animal cells, Trypanosoma brucei andT. cruzi. TcDHH1 is localized to discrete cytoplasmic foci that varydepending on the life cycle status and nutritional conditions. To study thecomposition of mRNPs containing TcDHH1, we carried out immunopre-cipitation assays with anti-TcDHH1 using epimastigote lysates. The proteincontent of mRNPs was determined by MS and pre-immune serum wasused as control. We also carried out a ribonomic approach to identify themRNAs present within the TcDHH1 immunoprecipitated complexes. Forthis purpose, competitive microarray hybridizations were performed againstnegative controls, the nonprecipitated fraction. Our results showed thatmRNAs associated with TcDHH1 in the epimastigote stage are thosemainly expressed in the other forms of the T. cruzi life cycle. These datasuggest that mRNPs containing TcDHH1 are involved in mRNA metabo-lism, regulating the expression of at least epimastigote-specific genes.

Structured digital abstractl MINT-7909478: DHH1 (uniprotkb:Q4DIE1) physically interacts (MI:0915) with PABP2 (uni-

protkb:Q27335) by anti bait coimmunoprecipitation (MI:0006)l MINT-7909338: DHH1 (uniprotkb:Q4DIE1) physically interacts (MI:0914) with ATP-depen-

dent DEAD ⁄ H RNA helicase, putative (uniprotkb:Q4DIE1), Actin, putative (uniprotkb:

Q4D7A6), Actin, putative (uniprotkb:Q4CLA9), Chaperonin HSP60, mitochondrial (uni-

protkb:Q4DYP6), ATP-dependent Clp protease subunit, heat shock protein 100 (HSP100),

putative (uniprotkb:Q4CNM5), Elongation factor 2, putative (uniprotkb:Q4D5X0), Elonga-

tion factor 1-alpha (EF-1-alpha), putative (uniprotkb:Q4CU73), Heat shock protein 85,

putative (uniprotkb:Q4CQS6), Glutamate dehydrogenase, putative (uniprotkb:Q4DWV8),

Putative uncharacterized protein (uniprotkb:Q4CNI8), 40S ribosomal protein S11, putative

(uniprotkb:Q4CRH9), Sterol 24-c-methyltransferase, putative (uniprotkb:Q4CMB7), Heat

shock protein 70 (HSP70), putative (uniprotkb:Q4DTM9), Glutamate dehydrogenase, puta-

tive (uniprotkb:Q4D5C2) and Calpain-like cysteine peptidase, putative (uniprotkb:Q4CYU3)

by anti bait coimmunoprecipitation (MI:0006)l MINT-7909469: DHH1 (uniprotkb:Q4DIE1) physically interacts (MI:0915) with PABP1

(uniprotkb:Q4E4I9) by anti bait coimmunoprecipitation (MI:0006)

Abbreviations

eIF, eukaryotic initiation factor; IP, immunoprecipitated; MASP, mucin-associated surface protein; PABP, poly(A)-binding protein; P-bodies,

processing bodies; SG, stress granule; SP, supernatant.

FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS 1

Introduction

The life cycle of the three trypanosomatid parasites

pathogenic to humans involves the alternation

between a mammal and an arthropod host. The two

main developmental stages of Trypanosoma brucei are

extracellular, in both mammalian host blood and the

tsetse fly intestine [1]. Trypanosoma cruzi exists in its

amastigote form in the cytoplasm of the mammal

infected cell, or as an epimastigote in the kissing bug

intestine [2]. Protozoans of the Leishmania genus, in

turn, multiply in the form of amastigotes within mac-

rophages and as extracellular promastigotes in the

insect vector [3]. The regulation of gene expression

thus plays a major role in determining the adaptation

and differentiation of these parasites throughout their

life cycle.

Trypanosomatids diverge from other eukaryotes in

several aspects, including the editing of mitochondrial

RNA molecules, trans-splicing, genes almost never

interrupted by introns and a lack of typical promoter

sequences for the transcription of protein-encoding

genes. In addition, transcription by RNA polymer-

ase II is constitutive and genes in the same polycis-

tronic unit display different levels of processed mRNA

[4–6]. Consequently, the regulation of gene expression

in trypanosomatids seems to occurs mainly post-trans-

criptionally [6,7].

When mRNAs enter the cytoplasm, they can be

translated, stored for later translation or degradation,

degraded or subjected to a combination of these

processes. In mammalian cells, mRNAs that are not

translated or destined for degradation are compart-

mentalized in distinct cytoplasmic structures, known as

‘processing bodies’ (‘P-bodies’) and stress granules [8–

10]. These RNA granules are key structures in the reg-

ulation of gene expression at the post-transcriptional

level [11–13]. Recently, we have identified the protein

TcDHH1, a putative DEAD box RNA helicase, in

T. cruzi, homologous to Dhh1 (yeast) and Rck ⁄p54(mammals) proteins [14]. It has been reported that

Dhh1 is involved in multiple RNA-related processes in

various eukaryotes, and accumulates in stress granules

and P-bodies of yeast, animal cells and T. brucei

(reviewed in [15–21]). Trypanosoma cruzi DHH1 is pres-

ent in polysome-independent complexes and is located

diffusely in the cytoplasm and in cytoplasmic granules,

which vary in number when the parasite is subjected to

nutritional stress or conditions interfering with the

translation process, e.g. treatment with cycloheximide

or puromycin [14].

In this article, we show that TcDHH1-containing

foci are present throughout the T. cruzi life cycle; how-

ever, they are less well defined in the infective metacy-

clic trypomastigote form. We also show that proteins

directly or indirectly associated with TcDHH1 include

those of diverse function, e.g. translation-related fac-

tors, cytoskeleton proteins, heat shock proteins and

metabolic proteins. We use a ribonomic approach to

identify the mRNA content of the TcDHH1-contain-

ing complexes. Microarray analyses reveal that the

mRNAs associated with TcDHH1 in the epimastigote

stage are some of those mainly expressed in the other

forms of the T. cruzi life cycle. These data suggest that

mRNPs containing TcDHH1 are involved in mRNA

metabolism, regulating the expression of, at least,

epimastigote-specific genes.

Results

TcDHH1-containing granules are present in all

developmental forms of T. cruzi

We have shown previously that, in epimastigotes,

TcDHH1 proteins are localized in discrete cytoplasmic

foci during the logarithmic growth phase and increase

in number under nutritional stress [14]. In this study,

we confirmed our previous data and also showed that

TcDHH1 is localized to cytoplasmic foci in adherent

parasites differentiating into metacyclic trypomastig-

otes and amastigotes. TcDHH1-containing granules

were not readily observed in trypomastigotes. This is

evident in microscopic fields in which terminally differ-

entiated metacyclic trypomastigotes and intermediate

forms are present (Fig. 1D). However, when the expo-

sure time for the photograph was at least doubled, a

few TcDHH1-containing granules were observed in

metacyclic trypomastigotes (data not shown). To a les-

ser extent, TcDHH1 was also observed diffusely in the

cytoplasm in all forms analyzed (Fig. 1). At least 10

random fields of each developmental form were ana-

lyzed, and more than 95% of the parasites had the

appearance described above.

Protein composition of TcDHH1-containing

complexes

Cytoplasmic complexes containing the protein

TcDHH1 in logarithmic growth phase epimastigotes

were immunoprecipitated with specific antiserum. As

seen by western blot analysis, the antiserum recognizes

a unique band of the expected mass size in a cyto-

plasmic extract of T. cruzi (Fig. 2). Pre-immune serum

was used as an experimental control. Three different

DHH1-mRNPs in Trypanosoma cruzi F. B. Holetz et al.

2 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS

immunoprecipitation experiments were performed.

Proteins associated with immunoprecipitated (IP) com-

plexes and proteins not associated with TcDHH1 from

the supernatant (SP) were resolved by SDS ⁄PAGE and

visualized by silver staining (Fig. 3A). The IP and SP

samples obtained with pre-immune serum were pro-

cessed in the same way and are shown in Fig. 3C. To

provide a measure of the efficiency of TcDHH1 immu-

noprecipitation, IP and SP samples were loaded onto

an SDS ⁄PAGE gel, transferred to a nitrocellulose

membrane, and immunoblotted with the TcDHH1

antibody (Fig. 3B). The results showed that different

protein profiles were obtained for the IP and SP silver-

stained gels (Fig. 3A, C). Western blot analysis using

the TcDHH1 antiserum allowed the identification of

the band corresponding to TcDHH1 (Fig. 3B), which

was not detected in the IP fraction obtained with the

pre-immune serum (Fig. 3D). The fact that TcDHH1

could also be detected in the SP fraction is probably a

A

B

Fig. 2. Western blot analysis of T. cruzi protein extracts using

anti-TcDHH1. (A) Western blot analysis of protein extracts from

epimastigotes (Epi), epimastigotes under nutritional stress (Stress),

differentiating epimastigotes (cells adherent after 24 h) (Ad24h),

metacyclic trypomastigotes (Meta) and amastigotes (Ama), probed

with antiserum against TcDHH1 protein (1 : 100 dilution). The

extracts were standardized and all lanes were loaded with 10 lg of

protein. (B) SDS ⁄ PAGE stained with Coomassie brilliant blue to

control protein load. TcDHH1 has an expected molecular mass of

46.7 kDa. The molecular mass marker (in kDa) is the Benchmark

Protein Ladder (Gibco, Grand Island, NY, USA).

A

B

C

D

E

Fig. 1. Localization of TcDHH1 during the life cycle of T. cruzi. (A)

Epimastigotes in logarithmic growth phase. (B) Epimastigotes under

nutritional stress. (C) Differentiating epimastigotes (24 h adherent

cells). (D) Metacyclic trypomastigotes. (E) Amastigotes. Cells were

incubated with antiserum against TcDHH1 and the immune com-

plexes were reacted with Alexa-labeled goat anti-mouse antibodies.

Kinetoplasts and nuclei were stained with propidium iodide. Open

arrowheads indicate an epimastigote form in the metacyclic trypo-

mastigote population. Filled arrowheads point to a trypomastigote

among the amastigotes. Bar, 10 lm.

F. B. Holetz et al. DHH1-mRNPs in Trypanosoma cruzi

FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS 3

result of the abundance of TcDHH1, as inferred from

recent data from T. brucei [22].

IP proteins were digested with trypsin and

subjected to analysis by two-dimensional nano

LC-MS ⁄MS. The mass spectra obtained were compared

with spectra deduced from protein sequences in the

T. cruzi data bank. We used the following criteria to

reliably select proteins from the database for further

analysis: (a) proteins with probability values equal

to or < 0.001; (b) proteins present in at least two

experiments using TcDHH1 antiserum; and (c) pro-

teins that did not appear in any of the three control

samples. Proteins that fulfilled the above criteria are

listed in Table 1 (for a complete list with all proteins

reliably identified in the immunoprecipitation assays,

but not meeting the selection criteria, see Table S1).

These complexes contain various proteins in addition

to TcDHH1, including heat shock proteins, mRNA-

binding proteins, initiation and elongation translation

factors, ribosomal proteins and metabolic proteins.

Abundant proteins, such as heat shock proteins and

elongation factor 1a, were present in the TcDHH1

immunoprecipitates, whereas other highly abundant

proteins, such as the cysteine proteinase cruzipain,

epimastigote-specific mucins and paraflagellar rod

proteins, were not detected in any of the experi-

ments.

TcDHH1 granules contain poly(A)-binding

proteins (PABPs)

As described previously, PABP1 is a core component

of stress granules in mammals [23]. Two PABPs with a

high similarity to other eukaryotic PABPs have been

identified previously in T. cruzi, TcPABP1 and

TcPABP2, with molecular masses of 63.8 and

61.4 kDa, respectively [24,25]. To test for the presence

of these proteins in TcDHH1 granules, epimastigotes

in the exponentially growing phase or under nutri-

tional stress were used for colocalization analyses.

PABP2 antiserum showed a punctate distribution in

the cytoplasm of epimastigotes and stressed epimastig-

otes. Most granules in these cells seemed to colocalize

with granules containing TcDHH1; those that did not

colocalize were grouped in defined regions of the cyto-

plasm lying next to each other (Fig. 4). Colocalization

assays with PABP1 antiserum showed a slightly differ-

ent staining pattern, with diffuse fluorescence and

some more intense fluorescent foci throughout the

cytoplasm. These foci partially colocalized with

TcDHH1 in both epimastigotes and epimastigotes

under nutritional stress (Fig. 4). In parallel with the

colocalization experiments, we carried out immunopre-

cipitation assays using mouse TcDHH1 antiserum, and

the presence of TcPABP1 and TcPABP2 proteins in

the precipitated complex was determined using western

blot analysis with rabbit LmPABP1 and LmPABP2

antisera (Fig. 5). Both antibodies specifically recog-

nized a single band with the expected molecular mass

in western blots, confirming that TcPABPs are part of

the TcDHH1 protein complex.

mRNAs present in TcDHH1-containing complexes

are regulated in a stage-specific manner

We used a ribonomic approach to identify the mRNAs

associated with TcDHH1, and thus to infer the role

C D

A B

Fig. 3. Analysis of TcDHH1 immunoprecipitation. (A) Epimastigote

proteins immunoprecipitated with TcDHH1 antibody (IP) and

proteins from the supernatant fraction (SP) were resolved by

SDS ⁄ PAGE and visualized by silver staining. (B) Western blot analy-

sis of IP and SP samples probed with antiserum against TcDHH1

protein (1 : 100 dilution), showing the efficiency of TcDHH1 immu-

noprecipitation. (C) Epimastigote proteins immunoprecipitated with

pre-immune serum (IP) and proteins from the supernatant fraction

(SP) were resolved by SDS ⁄ PAGE and visualized by silver staining.

(D) Western blot analysis of IP and SP samples, obtained with

pre-immune serum, and probed with serum against TcDHH1 pro-

tein (1 : 100 dilution). It should be noted that tracks in (C) and (D)

have a higher IgG background when compared with those in (A)

and (B) as pre-immune serum was used at a lower dilution in order

to discard the spurious recognition of TcDHH1. The molecular mass

marker (in kDa) is the Benchmark Protein Ladder (Gibco).

DHH1-mRNPs in Trypanosoma cruzi F. B. Holetz et al.

4 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS

played by this protein in the regulation of gene expres-

sion in T. cruzi. The mRNAs associated with IP com-

plexes from epimastigotes were compared with the

mRNAs not associated with TcDHH1 from SP. IP

and SP samples were obtained from six experiments,

and were compared using competitive hybridization

assays in oligo-DNA microarrays. The amount of

RNA extracted from IP samples was generally smaller

than that from SP samples. This was expected, as the

mRNA population associated directly or indirectly

with TcDHH1 is likely to represent only a fraction of

the total RNA.

We identified mRNAs that were present in IP and

SP samples in different amounts, based on a two-fold

difference in mRNA levels and a 5% false discovery

rate. For epimastigote forms in the logarithmic growth

phase, 203 distinct mRNAs displayed higher levels in

the IP than SP fraction, with 265 mRNAs present at

lower levels in the SP sample. Most of the mRNAs

associated with TcDHH1 were from mucin-associated

surface protein (MASP) and mucin protein families,

with others corresponding to several hypothetical and

hypothetical conserved proteins. We also observed

mRNAs corresponding to metabolic proteins, mRNA-

binding proteins, amastin and cyclin, among others

(Fig. 6A, Table 2) (for a detailed list of mRNAs, see

Table S2). A semi-quantitative approach, RT-PCR

and densitometry analysis of gel bands for five

mRNAs with different distribution patterns between

IP and SP samples confirmed these results (Fig. 6B).

Surface proteins (MASP and mucins) are encoded by

multigene families. Although these gene families were

the largest in the T. cruzi genome, we did not identify

any of the corresponding mRNAs in the SP sample,

demonstrating the specific presence of these mRNAs in

the IP sample. Moreover, mRNAs from other large

gene families in T. cruzi, e.g. those encoding trans-siali-

dase and cysteine protease, were not found in the IP

sample.

Discussion

Recently, we have identified a putative RNA helicase

(TcDHH1), which is similar to its eukaryotic orthologs

[14]. Members of this protein family are involved in

several aspects of mRNA metabolism and localize to

distinct foci in the cytoplasm [26]. We compared the

replicative, nutritionally stressed, differentiating and

infective forms of T. cruzi, and showed that these

T. cruzi life cycle stages display distinct granular pat-

terns of cytoplasmic TcDHH1-containing foci (Fig. 1).

These granules were not as clearly visible in trypom-

astigotes as in the other forms, but TcDHH1 protein

levels remained similar for all T. cruzi developmental

stages [14]. Thus, the variation in the number of

TcDHH1-containing granules does not seem to be

related to changes in gene expression levels, but is

probably related to diffuse or foci-like distributions. In

a recent study, Cassola et al. [20] showed that epim-

astigotes in culture and parasites at different time

points during in vitro differentiation did not display

mRNA granules. Although, at first, these findings

seem to disagree with our work, it is not possible to

compare these studies because different experimental

approaches were used to investigate the presence of

mRNA granules in developmental forms of T. cruzi.

Table 1. Protein composition of TcDHH1-containing complexes. IP, complexes immunoprecipitated with anti-TcDHH1 antibody; C, complexes

immunoprecipitated with pre-immune serum; 1, 2, 3, biological replicates; •, indicates the presence of a protein in that fraction.

Protein description IP1 IP2 IP3 C1 C2 C3

Tc00.1047053510127.79 actin, putative • •Tc00.1047053510573.10 actin, putative • •Tc00.1047053507641.280 Cnp60 chaperonin HSP60, mitochondrial precursor; groELprotein; heats • •Tc00.1047053508665.14 ATP-dependent Clp protease subunit, heat shock protein 100,putative • •Tc00.1047053508169.20 elongation factor 2, putative • • •Tc00.1047053508949.4 elongation factor 1a (EF-1a), putative • • •Tc00.1047053507713.30 heat shock protein 85, putative • • •Tc00.1047053507875.20 glutamate dehydrogenase, putative • •Tc00.1047053508111.30 glutamate dehydrogenase, putative • •Tc00.1047053509139.10 hypothetical protein, conserved • •Tc00.1047053511139.20 40S ribosomal protein S11, putative • •Tc00.1047053506983.39 calpain-like cysteine peptidase, putative • •Tc00.1047053504191.10 sterol 24-c-methyltransferase, putative • •Tc00.1047053511211.160 heat shock protein 70 (HSP70), putative • •Tc00.1047053506959.30 ATP-dependent DEAD ⁄ H RNA helicase, putative • •

F. B. Holetz et al. DHH1-mRNPs in Trypanosoma cruzi

FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS 5

In yeast, the Dhh1 protein interacts with decapping

and deadenylation complexes, stimulating mRNA

decapping [15–18]. Dhh1p homologs from Caenorhabd-

itis elegans (Cgh1), Drosophila (Me31b) and Xenopus

(Xp54) are involved in the storage of translationally

repressed maternal mRNAs [16,17]. In addition, the

RNA helicase DOZI, involved in the storage and

silencing of certain mRNA species, has been identified

recently in Plasmodium berghei and is localized to cyto-

plasmic granules in female gametocytes [19].

Dhh1 ⁄Rckp54 is common to both P-bodies and stress

granules [10–13]; both of these types of granule may

therefore exist in T. cruzi. Therefore, we studied

mRNPs containing TcDHH1 and investigated their

potential similarity with mRNPs in other organisms.

We have shown previously that TcDHH1 is present in

cytoplasmic complexes containing mRNA and pro-

teins. TcDHH1-containing complexes have been puri-

fied previously from polysome and polysome-free

fractions [27]. TcDHH1 must therefore be, at least

partly, associated with mRNAs that are independent

of the translation machinery.

Our analysis of IP complexes showed that TcDHH1

interacts with proteins that are described as stress

granule components (SGs). We identified TcDHH1, as

expected, and proteins previously identified in stress

granules, such as heat shock proteins and 40S ribo-

somal subunit proteins. Translation initiation factors

(eukaryotic initiation factors 3 and 4, eIF3 and eIF4),

also typical of SGs, were observed in one of the three

A

B

Fig. 4. Colocalization assays of PABP

proteins with TcDHH1. (A) Logarithmic

growth phase epimastigotes. (B) Epimastig-

otes under nutritional stress. Antibodies

against PABP1 and PABP2 were produced

in rabbit and tested at 1 : 100 dilutions.

Antibodies against TcDHH1 protein were

produced in mouse and used at 1 : 100

dilution. Immune complexes reacted with

Alexa-labeled 546 goat anti-rabbit and

Alexa-labeled 488 goat anti-mouse antibod-

ies (1 : 400). Bar, 10 lm.

DHH1-mRNPs in Trypanosoma cruzi F. B. Holetz et al.

6 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS

biological replicates (Table S1). Although abundant

proteins, such as heat shock proteins and eIF1a, are

present in these complexes, other proteins highly abun-

dant in epimastigotes, such as the cysteine proteinase

cruzipain, the family of GP63 metalloproteases, many

ribosomal proteins, epimastigote-specific mucins and

the epimastigote-specific metabolic protein histidine

ammonia-lyase, were not detected in any of the experi-

ments [28–30]. Nonetheless, it remains to be elucidated

whether these proteins indeed interact with TcDHH1

or are fraction contaminants. Interestingly, Pare et al.

[31] have revealed recently that a heat shock protein

(Hsp90) is important for recruiting the argonaute

protein (hAgo2) to SGs and for efficient biogenesis and ⁄or stability of P-bodies in mammals. Thus, it seems

probable that the heat shock proteins identified in our

study might interact with TcDHH1. We also identified

proteins that are not characteristic of these structures,

such as translation elongation factors, metabolic

proteins and actin (Table 1). Although actin is not a

A B

Fig. 6. mRNAs present in TcDHH1-containing complexes in epimastigotes. (A) Pie chart diagram displaying the percentage representation of

the most abundant mRNAs present in TcDhh1-containing complexes. (B) RT-PCR analysis of five mRNAs with different distribution patterns

between IP and SP fractions. Putative glucose-regulated protein 78, more represented in the SP fraction, showed an IP ⁄ SP ratio of 0.51.

Putative (H+)-ATPase G subunit, equally represented in both fractions, resulted in an IP ⁄ SP ratio of 0.98. Putative cyclin, putative mucin

TcMUCII and hypothetical protein were more represented in the IP fraction, with IP ⁄ SP ratios of 2.0, 6.7 and 1.8, respectively.

A B

Fig. 5. Co-immunoprecipitation assays of TcDHH1 with PABP pro-

teins. Epimastigote proteins were immunoprecipitated with mouse

TcDHH1 antibody (I) or pre-immune serum (PI), resolved by

SDS ⁄ PAGE, electrotransferred onto Hybond-C membranes and

probed with rabbit anti-LmPABP1 (A) and anti-LmPABP2 (B) anti-

sera (1 : 100 dilution), showing that PABPs are part of the TcDHH1

protein complex. The molecular mass marker (in kDa) is the Bench-

mark Protein Ladder (Gibco).

Table 2. mRNAs present in TcDHH1-containing complexes in

epimastigotes.

Gene description No. of genes

Mucin-associated surface protein (MASP), putative 61

Mucin-associated surface protein (MASP,

pseudogene), putative

4

Mucin TcMUCII, putative 52

Mucin TcMUCII (pseudogene), putative 3

Mucin TcSMUGS, putative 1

Hypothetical protein, conserved 31

Hypothetical protein 34

ADP-ribosylation factor family, putative 1

Amastin, putative 1

Cyclin, putative 1

Expression site-associated gene (ESAG-like)

protein, putative

1

Meiotic recombination protein SPO11, putative 1

Mitochondrial carrier protein, putative 1

Nucleoside transporter 1, putative 1

Phosphatidic acid phosphatase, putative 1

Protein kinase, putative 1

Ras-related GTP-binding protein, putative 1

RNA-binding protein 5, putative 1

RNA-binding protein, putative 1

Serine acetyltransferase, putative 1

Serine ⁄ threonine protein phosphatase, putative 1

Serine ⁄ threonine protein phosphatase 2A,

catalytic subunit, putative

1

Serine-, alanine- and proline-rich protein, putative 1

Trypanothione synthetase, putative 1

F. B. Holetz et al. DHH1-mRNPs in Trypanosoma cruzi

FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS 7

typical SG, there seems to be a close interaction

between cytoplasmic mRNA granules and the cytoskel-

eton. Indeed, granules remaining motionless are associ-

ated with actin filaments, whereas those that move in

the cytoplasm remain associated with microtubules

[32]. Thus, it is possible that actin is indeed a compo-

nent of TcDHH1-containing complexes and not a

putative contaminant. The fact that other abundant

proteins were not detected in this fraction would be

consistent with this. Interestingly, we did not identify

P-body core proteins, such as LSMs and exonuclease

5¢–3¢ XRN1. These findings suggest that TcDHH1-

containing complexes are more likely to be compo-

nents of SGs than of P-bodies. We cannot rule out the

possibility that the identified proteins of TcDHH1-con-

taining complexes also correspond to the cytoplasmic

granule-free fraction of TcDHH1.

We tested for the colocalization of TcDHH1 with

PABP present in stress granules to extend our findings

from the immunoprecipitation experiments and to gain

further insight into the function of TcDHH1-contain-

ing granules. Our results suggest that TcDHH1-

containing granules contain PABPs. Indeed, PABP2

seemed to colocalize with most granules containing

TcDHH1 in both unstressed epimastigotes and epi-

mastigotes subjected to nutritional stress. Granules

appearing to contain only PABPs remained adjacent

to these TcDHH1-containing granules (Fig. 4).

Our findings are in agreement with the data pub-

lished by Cassola et al. [20], who demonstrated that, in

starved parasites, TcPABP1 and TcPABP2 showed

strong accumulation in mRNA granules. However, in

contrast with our study, these authors showed that

TcPABP1 and TcPABP2 were not recruited to mRNA

granules in parasites not subjected to starvation. One

possible explanation for this difference is the fact that

these authors used parasites overexpressing green fluo-

rescent protein fusions, in contrast with the native pro-

teins evaluated here. PABP1 is used as a marker for

stress granules and is absent from P-bodies in mam-

mals. However, Brengues and Parker [33] showed that

PABP1 is present in the P-bodies of Saccharomyces

cerevisiae, and that mRNPs containing poly(A)+

mRNA, PABP1, eIF4E and eIF4G enter these struc-

tures, possibly representing a transitional state during

mRNA exchange between P-bodies and the translation

machinery. These authors also demonstrated that

PABP1 may be present in P-bodies even in the absence

of stress. Another study demonstrated that granules

containing PABP1 in S. cerevisiae were distinct from

the P-bodies formed specifically under stress caused by

glucose deprivation, and that these two types of gran-

ule partially colocalize. These granules may function as

mRNA storage compartments, called EGP-bodies,

allowing mRNA translation to resume when cell

growth conditions are restored, and are analogous to

the stress granules observed in mammals [34].

The characterization of mRNAs from mRNP com-

plexes immunoprecipitated with TcDHH1 antiserum

revealed the presence of several mRNA species, with

overrepresentation of those encoding MASP, mucins,

hypothetical proteins and amastin. In general, mRNAs

associated with TcDHH1 are not translated into pro-

teins in epimastigotes, but are predominantly trans-

lated during other stages of the parasitic life cycle. For

example, TcMUCII proteins are specific to, and

MASP proteins are mostly produced in, the trypomas-

tigote forms [35,36]. The mRNA encoding amastin, a

protein predominantly produced in amastigotes [37],

was also present in the TcDHH1-containing complexes

from epimastigotes. These findings suggest that epi-

mastigote TcDHH1-associated mRNAs are either

stored for later use or are present in the initial steps to

degradation, given that their poly(A) tails are mostly

intact. Accordingly, recent work using an ATPase-defi-

cient dhh1 mutant provided evidence that a pathway

including Dhh1 has a selective role in the destabiliza-

tion of many regulated mRNAs in procyclic forms of

T. brucei [22].

It should be noted that the ribonomic approach used

in this study favors the identification of polyadenylated

mRNAs present in IP complexes; deadenylated mRNAs

destined for, or in the initial stages of, degradation

would not be detected by these microarray analyses.

Materials and methods

Parasites

The T. cruzi clone Dm28c [38] was maintained at 28 �C in

liver infusion tryptose medium supplemented with 10%

heat-inactivated fetal bovine serum. Epimastigotes under

nutritional stress, metacyclic trypomastigotes and amastig-

otes were obtained in vitro as described previously [39,40].

Immunofluorescence and imaging

Immunofluorescence assays were carried out using a proto-

col described previously [14], which was modified slightly to

ensure that parasites were resuspended and washed in

NaCl ⁄Pi for only 5 min before being fixed.

Mouse polyclonal anti-TcDHH1 antibody was produced

as described previously [14]; the antiserum was affinity puri-

fied and stored in aliquots at )20 �C prior to use. Rabbit

polyclonal antibodies against PABP1 and PABP2 were

kindly provided by Dr Osvaldo P. de Melo Neto (Centro

DHH1-mRNPs in Trypanosoma cruzi F. B. Holetz et al.

8 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS

de Pesquisas Aggeu Magalhaes, Fiocruz, Recife, Brazil).

Serum dilutions of antibodies were as follows: rabbit

anti-LmPABP1 and anti-LmPABP2, 1 : 100; mouse anti-

TcDHH1, 1 : 100. Alexa Fluor-488 and Alexa Fluor-546

were used as conjugated secondary antibodies (1 : 400;

Molecular Probes, Invitrogen, Eugene, OR, USA). Images

showing subcellular localization were acquired using a

Nikon Eclipse E600 microscope (Nikon Corporation,

Tokyo, Japan) coupled to a Cool SNAP-PRO color camera

(Media Cybernetics, Bethesda, MD, USA). Merged images

were obtained by superimposing image files with image-pro

plus software (Media Cybernetics).

DHH1 immunoprecipitation assays: protein

content

Immunoprecipitation assays with the anti-TcDHH1 anti-

body were carried out in cytoplasmic extracts from loga-

rithmic growth phase epimastigotes. Mouse anti-TcDHH1

(50 lL) was incubated with 150 lL of resin containing pro-

tein G Sepharose (Sigma) for 8 h at 4 �C, with moderate

stirring. Pre-immune serum was incubated with resin under

the same conditions and used as a control for immunopre-

cipitation reaction specificity. After incubation, the resin

was collected by centrifugation at 600 g for 2 min, the

supernatant was discarded and the resin was incubated with

5% nonfat milk in NaCl ⁄Pi for 30 min. The resin was then

washed twice with NaCl ⁄Pi.

To obtain T. cruzi cytoplasmic extracts, 2 · 109 parasites

were washed with NaCl ⁄Pi and incubated in 2 mL of IMP1

buffer (KCl, 100 mm; MgCl2, 5 mm; Hepes, 10 mm,

pH 7.0; protease inhibitor, 1 : 100; RNase OUT,

200 UÆmL)1; Nonidet P40, 0.5%) for 2 h on ice, with mod-

erate agitation. Parasite lysis was monitored with a light

microscope. Cytoplasmic extracts were obtained by centri-

fugation at 7000 g for 20 min at 4 �C; 1 mL of this extract,

corresponding to the lysis of 1 · 109 parasites, was incu-

bated with resin previously coupled to anti-TcDHH1 anti-

body or to the pre-immune serum, as described above, for

16 h at 4 �C, with moderate agitation.

The IP complexes were collected by centrifugation at

600 g for 2 min and SPs were saved. The resin was washed

three times with IMP2 buffer (KCl, 100 mm; MgCl2, 5 mm;

Hepes, 10 mm, pH 7.0; protease inhibitor, 1 : 100; RNase

OUT, 200 UÆmL)1; Nonidet P40, 1%), followed by the

same centrifugation step. Proteins linked to the resin were

eluted with 150 lL of glycine (0.1 m, pH 2.0) and the pH

was adjusted to 7.5–8.0. Next, 150 lL of buffer (urea, 7 m;

thiourea, 2 m; Chaps, 2%; Triton, 2%; dithiothreitol, 1%;

nuclease, 1 : 100; protease inhibitor, 1 : 100) was added to

the sample and proteins were analyzed by two-dimensional

nano LC-MS ⁄MS. Fifty micrograms of protein were puri-

fied before analysis using a two-dimensional clean-up kit,

following the manufacturer’s instructions (GE Healthcare,

Buckinghamshire, UK). Proteins were reduced with dith-

iothreitol, alkylated with iodoacetamide and digested over-

night with trypsin. The resulting tryptic peptides were

desalted on C8 cartridges (Michrom BioResources, Auburn,

CA, USA) and subjected to two-dimensional nano

LC ⁄MS ⁄MS analyses on a Michrom BioResources Paradigm

MS4 Multi-Dimensional Separations Module, a Michrom

NanoTrap Platform and an LCQ Deca XP plus ion trap mass

spectrometer. The mass spectrometer was used in data-depen-

dent mode, and the four most abundant ions in each mass

spectrum were selected and fragmented to produce tandem

mass spectra. The MS ⁄MS spectra were recorded in the pro-

file mode. Proteins were identified by comparing the MS ⁄MS

spectra obtained with our T. cruzi database and its reversed

complement using Bioworks v3.2. Peptide and protein hits

were scored and ranked using the probability-based scoring

algorithm incorporated in Bioworks v3.2 and adjusted to a

false positive rate of less than 1%. Only peptides showing

fully tryptic termini, with cross-correlation scores (Xcorr)

greater than 1.9 for single-charged peptides, 2.3 for double-

charged peptides and 3.75 for triple-charged peptides, were

used for peptide identification. In addition, delta correlation

scores (DCn) were set to be > 0.1 and, for increased strin-

gency, proteins were accepted only if their probability score

was less than 0.001. The following search parameters were

used: taxonomy, eukaryota; monoisotopic mass tolerance,

0.1 Da; partial methionine oxidation; and one missed tryptic

cleavage allowed. Criteria for positive protein identification

included Mascot scores and sequence coverage.

Parallel to MS, IP and SP samples were analyzed by

SDS ⁄PAGE. Gels were silver stained according to the

following protocol: incubation in fixing solution (50%

ethanol, 12% acetic acid, 0.02% formaldehyde) for 1 h,

three washes in 50% ethanol for 15 min and sensibilization

in 0.02% sodium thiosulfate for 1 min, followed by an

extensive wash in distilled water. Staining was performed

by incubating the gel for 30 min in silver nitrate solution

(0.2% silver nitrate, 0.02% formaldehyde), followed by

washing three times in distilled water for 1 min. The gel

was developed in 3% sodium carbonate and 0.05% formal-

dehyde. Staining was stopped in 50% ethanol and 12% ace-

tic acid for 5 min. For western blot analysis, IP and SP

samples were separated on a 13% SDS ⁄PAGE gel and

transferred to a nitrocellulose membrane. Nonspecific bind-

ing sites were blocked by incubating the membrane with

5% nonfat milk powder and 0.1% Tween-20 in NaCl ⁄Pi

for 30 min. For analysis of the efficiency of TcDHH1

immunoprecipitation, membranes were incubated for 1 h

with anti-TcDHH1 antibody (1 : 100 dilution) or with pre-

immune serum. For co-immunoprecipitation analysis of

TcDHH1 and TcPABPs, membranes were incubated for

1 h with rabbit anti-LmPABP1 and anti-LmPABP2 (1 : 100

dilution). The membranes were then extensively washed in

NaCl ⁄Pi and incubated with goat phosphatase-conjugated

anti-rabbit IgG (Sigma) diluted 1 : 10 000. The color

reaction was developed with 5-bromo-4-chloro-3-indolyl

F. B. Holetz et al. DHH1-mRNPs in Trypanosoma cruzi

FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS 9

phosphate and nitroblue tetrazolium (Promega, Fitchburg,

WI, USA).

DHH1 immunoprecipitation assays: ribonomics

To determine which mRNAs were associated with the

TcDHH1 protein ⁄ complexes, anti-TcDHH1 was incubated

with resin containing protein A Sepharose (Sigma) for

16 h at 4 �C with agitation. Antiserum (150 lL) was

mixed with 150 lL of resin and 1 lL of RNAse OUT

(Invitrogen). After incubation, the resin was collected by

centrifugation and processed as described above. Cyto-

plasmic extract, corresponding to 2 · 109 cells, was incu-

bated with resin previously linked to anti-TcDHH1

antibodies for 2 h in an ice bath, with agitation. The

resin was then collected by centrifugation and SP was

retained for a control. Resin was washed three times with

IMP2 buffer. The RNAs from the SP or resin (IP) were

purified with an RNeasy� (Qiagen, Hilden, Germany) kit

using the ‘Animal Cells I’ protocol in the manufacturer’s

manual, with the additional step of DNase treatment in

a column. Linearly amplified RNA was generated from

1 lg of total RNA (single round) using a MessageAmp

amplified RNA kit (Ambion, Austin, TX, USA), follow-

ing the manufacturer’s instructions. cDNA was synthe-

sized from 1 lg of total or affinity-purified RNA using

an oligo(dT) primer (US Biochemical Corporation, Cleve-

land, OH, USA) and reverse transcriptase (IMPROM II;

Promega), as recommended.

Oligonucleotide DNA microarrays

The microarray was constructed with 70-mer oligonucleo-

tides. As a result of the hybrid and repetitive nature of the

sequenced T. cruzi strain (CL Brener), all coding regions

(CDS) identified in the genome (version 3) were retrieved

and clustered using the blastclust program, with 40%

coverage and 75% identity. For the probe design, array-

oligoselector software (v. 3.8.1) was used, with 50% GC

content; 10 359 probes were designed to the longest T. cruzi

CDS of each cluster; 393 probes correspond to genes of an

external group (Cryptosporidium hominis) and 64 spots con-

tain only spotting solution (NaCl ⁄Cit, 3 ·), totaling 10 816

spots. These oligonucleotides were spotted from a 50 lm

solution onto poly-l-lysine-coated slides and cross-linked

with 600 mJ UV. Each probe corresponding to T. cruzi

genes was identified following the T. cruzi Genome Consor-

tium annotation (http://www.genedb.org). The microarray

slides were produced at Virginia Commonwealth Univer-

sity, Richmond, VA, USA.

Microarray hybridization and analysis

Fluorescent cyanin (Cy) dyes, Cy3 or Cy5 as appropriate,

were incorporated into second-strand cDNA synthesis using

2 lg of amplified RNA as the starting material for each

sample. Labeled cDNA was purified with a Microcom 30

device (Millipore, Carrigtwohill, Ireland). Microarray

hybridizations and washes were carried out in a GeneTac

automated hybridization station (Genomic Solutions,

Chelmsford, MA, USA). The Cy3- and Cy5-labeled cDNAs

were mixed and added to 120 lL of hybridization solution

and allowed to hybridize for 14–16 h at 42 �C. The micro-

array slides were then washed in buffer of increasing strin-

gency (0.5 · and 0.05 · NaCl ⁄Cit) and dried by

centrifugation at 280 g for 5 min. The dried slides were

scanned in a 428 Array Scanner (Affymetrix, Santa Clara,

CA, USA). The images were analyzed with spot software.

The resulting data were corrected for background and nor-

malized, using the normexp and PrintTip-Loess methods,

respectively, within the Limma package [41].

A total of six individual IP and SP pairs was hybridized

in a semi-balanced dye design; overrepresented genes from

both fractions were selected using sam software [42]. Genes

were thus selected on the basis of at least a two-fold differ-

ence in mRNA levels and a 5% false discovery rate. Micro-

array data were submitted to ArrayExpress accession

number E-MEXP-2448.

RT-PCR

cDNA was synthesized from 1 lg of total RNA using 1 lLof 10 lm random primers (USB Corporation, Cleveland,

OH, USA) and 1 lL of reverse transcriptase (IMPROM II;

Promega), according to the manufacturer’s instructions.

PCR was carried out with 20 ng of cDNA as template,

20 mm Tris-HCl (pH 8.4), 10 pmol of primers, 2.5 mm

MgCl2, 0.0625 mm dNTPs and 1 U Taq polymerase

(Invitrogen). The oligonucleotide primer sets used for PCR

were as follows: putative cyclin (Tc00.1047053506945.270),

F, 5¢-TGGGGAGGATTATAGCGATG-3¢; R, 5¢-ACTTC

GGCAGAGCACTTCAT-3¢; putative mucin TcMUCII

(Tc00.1047053506131.20), F, 5¢-GCGGAGAACAAGATG

AGGA-3¢; R, 5¢-TCGCTTTTGAAATAGGCACC-3¢;hypothetical protein (Tc00.1047053509891.40), F, 5¢-GCCG

TCATGCAAAAATATCC-3¢; R, 5¢-CCTTTTCAGCCAA

AAAGCTG-3¢; putative glucose-regulated protein 78

(Tc00.1047053506585.40), F, 5¢-TGGCGGTAAGAAGAA

GCAGT-3¢; R, 5¢-CCGAGGTCAAACACAAGGAT-3¢;putative (H+)-ATPase G subunit (Tc00.1047053510993.

10), F, 5¢-ACAACGTGCAAAGGCTTCTT-3¢; R, 5¢-CTCGTGCCAACTCCAAGTTT-3¢.

PCR, using a Bio-Cycler II thermocycler (Peltier Thermal

Cycler; Bio-Rad, Hercules, CA, USA), included heating at

94 �C for 2 min, followed by 25 cycles of 94 �C for 15 s,

58 �C for 30 s and 72 �C for 30 s, with a final extension of

72 �C for 3 min. Ten microliters of RT-PCR products were

resolved by 2% agarose gel electrophoresis, visualized by

ethidium bromide staining. Gel photographs were taken

using a UVP Bioimaging System (UVP, Upland, CA,

DHH1-mRNPs in Trypanosoma cruzi F. B. Holetz et al.

10 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS

USA), and densitometry analysis of bands was performed

using the Kodak 1D Scientific Imaging System v.3.5.2

program (Kodak, Rochester, NY, USA). The ratio of the

densitometric values of the bands containing amplified

cDNA between IP and SP samples was determined.

Acknowledgements

We thank Andreia Dallabona, Nilson Fidencio and

Crisciele Kuligovski for skillful technical assistance, Dr

Osvaldo Pompilio de Melo Neto for PABP antibodies

and Dr Andrea Rodrigues Avila for helpful suggestions

and discussion of the manuscript. This investigation

received financial support from Conselho Nacional de

Desenvolvimento Cientıfico e Tecnologico (CNPq) and

Fundacao Oswaldo Cruz (PAPES-CNPq-Fiocruz).

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Supporting information

The following supplementary material is available:

Table S1. Protein composition of TcDHH1-containing

complexes.

Table S2. mRNAs present in TcDHH1-containing

complexes in epimastigotes.

This supplementary material can be found in the

online version of this article.

Please note: As a service to our authors and readers,

this journal provides supporting information supplied

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should be addressed to the authors.

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12 FEBS Journal (2010) ª 2010 The Authors Journal compilation ª 2010 FEBS