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RNA-seq reveals that overexpression of TcUBP1 switches the gene expression pattern towards that of the infective form of Trypanosoma cruzi. J Biol Chem 2023; 299:104623. [PMID: 36935010 PMCID: PMC10141520 DOI: 10.1016/j.jbc.2023.104623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
Trypanosomes regulate gene expression mainly by using post-transcriptional mechanisms. Key factors responsible for carrying out this regulation are RNA-binding proteins (RBPs), affecting subcellular localization, translation, and/or transcript stability. Trypanosoma cruzi U-rich RBP 1 (TcUBP1) is a small protein that modulates the expression of several surface glycoproteins of the trypomastigote infective stage of the parasite. Its mRNA targets are known but the impact of its overexpression at the transcriptome level in the insect-dwelling epimastigote cells has not yet been investigated. Thus, in the present study, by using a tetracycline-inducible system, we generated a population of TcUBP1-overexpressing parasites and analyzed its effect by RNA-seq methodology. This allowed us to identify 793 up- and 371 down-regulated genes with respect to the wild-type control sample. Among the up-regulated genes, it was possible to identify members coding for the TcS superfamily, MASP, MUCI/II, and protein kinases, whereas among the down-regulated transcripts, we found mainly genes coding for ribosomal, mitochondrial, and synthetic pathway proteins. RNA-seq comparison with two previously published datasets revealed that the expression profile of this TcUBP1-overexpressing replicative epimastigote form resembles the transition to the infective metacyclic trypomastigote stage. We identified novel cis-regulatory elements in the 3'-untranslated region of the affected transcripts and confirmed that UBP1m -a signature TcUBP1 binding element previously characterized in our lab- is enriched in the list of stabilized genes. We can conclude that the overall effect of TcUBP1 overexpression on the epimastigote transcriptome is mainly the stabilization of mRNAs coding for proteins that are important for parasite infection.
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Inoue AH, Domingues PF, Serpeloni M, Hiraiwa PM, Vidal NM, Butterfield ER, Del Pino RC, Ludwig A, Boehm C, Field MC, Ávila AR. Proteomics Uncovers Novel Components of an Interactive Protein Network Supporting RNA Export in Trypanosomes. Mol Cell Proteomics 2022; 21:100208. [PMID: 35091090 PMCID: PMC8938319 DOI: 10.1016/j.mcpro.2022.100208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022] Open
Abstract
In trypanosomatids, transcription is polycistronic and all mRNAs are processed by trans-splicing, with export mediated by noncanonical mechanisms. Although mRNA export is central to gene regulation and expression, few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components. We previously described conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII (previously Hel45), a core component of the exon junction complex (EJC). Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry. Significant overlap between TcSub2 and TceIF4AIII-interacting protein cohorts suggests that both proteins associate with similar machinery. We identified several interactions with conserved core components of the EJC and multiple additional complexes, together with proteins specific to trypanosomatids. Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events. We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of mRNA metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome mRNA maturation.
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Affiliation(s)
| | | | | | | | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Adriana Ludwig
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Cordula Boehm
- School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland, UK; Biology Centre, University of South Bohemia, České Budějovice, Czech Republic.
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3
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Gao J, Xiao C, Liao S, Tu X. Crystal structure of TbAlba1 from Trypanosoma brucei. J Struct Biol 2021; 213:107751. [PMID: 34107324 DOI: 10.1016/j.jsb.2021.107751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
Alba (Acetylation lowers binding affinity) domain is a small, dimeric nucleic acid-binding domain, which is widely distributed in archaea and numbers of eukaryotes. Alba domain containing proteins have been reported to be involved in many cellular processes, such as regulation of translation, maintaining genome stability, regulation of RNA processing and so on. In Trypanosoma brucei (T. brucei), there are four Alba proteins identified, which are named TbAlba1 to TbAlba4. However, the structure and function of TbAlba proteins are still unknown. Here, we solved the crystal structure of TbAlba1 to a resolution of 2.46 Å. TbAlba1 adopts a similar Alba-fold, which comprises of four β-strands (β1-β4) and three long α-helices (α1-α3). Furthermore, TbAlba1 displays some structural features quite different from other Alba proteins. These differences may imply the diverse biological roles of Alba family members.
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Affiliation(s)
- Jie Gao
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China; Department of Ophthalmology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, PR China
| | - Cong Xiao
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China.
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Characterization of the RNA-Binding Protein TcSgn1 in Trypanosoma cruzi. Microorganisms 2021; 9:microorganisms9050986. [PMID: 34063193 PMCID: PMC8147501 DOI: 10.3390/microorganisms9050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
RNA-binding proteins (RBPs) participate in several steps of post-transcriptional regulation of gene expression, such as splicing, messenger RNA transport, mRNA localization, and translation. Gene-expression regulation in trypanosomatids occurs primarily at the post-transcriptional level, and RBPs play important roles in the process. Here, we characterized the RBP TcSgn1, which contains one RNA recognition motif (RRM). TcSgn1 is a close ortholog of yeast Saccharomyces cerevisiae protein ScSgn1, which plays a role in translational regulation in the cytoplasm. We found that TcSgn1 in Trypanosoma cruzi is localized in the nucleus in exponentially growing epimastigotes. By performing immunoprecipitation assays of TcSgn1, we identified hundreds of mRNAs associated with the protein, a significant fraction of them coding for nucleic acids binding, transcription, and endocytosis proteins. In addition, we show that TcSgn1 is capable of interacting directly with the poly(A) tail of the mRNAs. The study of parasites under nutritional stress showed that TcSgn1 was localized in cytoplasmic granules in addition to localizing in the nucleus. Similar to ScSgn1, we observed that TcSgn1 also interacts with the PABP1 protein, suggesting that this protein may play a role in regulating gene expression in T. cruzi. Taken together, our results show that RNA-binding protein TcSgn1 is part of ribonucleoprotein complexes associated with nuclear functions, stress response, and RNA metabolism.
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Wippel HH, Malgarin JS, Inoue AH, Leprevost FDV, Carvalho PC, Goldenberg S, Alves LR. Unveiling the partners of the DRBD2-mRNP complex, an RBP in Trypanosoma cruzi and ortholog to the yeast SR-protein Gbp2. BMC Microbiol 2019; 19:128. [PMID: 31185899 PMCID: PMC6560856 DOI: 10.1186/s12866-019-1505-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/31/2019] [Indexed: 12/12/2022] Open
Abstract
Background RNA-binding proteins (RBPs) are well known as key factors in gene expression regulation in eukaryotes. These proteins associate with mRNAs and other proteins to form mRNP complexes that ultimately determine the fate of target transcripts in the cell. This association is usually mediated by an RNA-recognition motif (RRM). In the case of trypanosomatids, these proteins play a paramount role, as gene expression regulation is mostly posttranscriptional. Despite their relevance in the life cycle of Trypanosoma cruzi, the causative agent of Chagas’ disease, to date, few RBPs have been characterized in this parasite. Results We investigated the role of DRBD2 in T. cruzi, an RBP with two RRM domains that is associated with cytoplasmic translational complexes. We show that DRBD2 is an ortholog of the Gbp2 in yeast, an SR-rich protein involved in mRNA quality control and export. We used an immunoprecipitation assay followed by shotgun proteomics and RNA-seq to assess the interaction partners of the DRBD2-mRNP complex in epimastigotes. The analysis identified mostly proteins involved in RNA metabolism and regulation, such as ALBA1, ALBA3, ALBA4, UBP1, UBP2, DRBD3, and PABP2. The RNA-seq results showed that most of the transcripts regulated by the DRBD2 complex mapped to hypothetical proteins related to multiple processes, such as to biosynthetic process, DNA metabolic process, protein modification, and response to stress. Conclusions The identification of regulatory proteins in the DRBD2-mRNP complex corroborates the important role of DRBD2 in gene expression regulation in T. cruzi. We consider these results an important contribution to future studies regarding gene expression regulation in T. cruzi, especially in the field of RNA-binding proteins. Electronic supplementary material The online version of this article (10.1186/s12866-019-1505-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helisa Helena Wippel
- Carlos Chagas Institute-Fiocruz, Professor Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | | | - Alexandre Haruo Inoue
- Carlos Chagas Institute-Fiocruz, Professor Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil.,Molecular Biology Institute-Paraná, Curitiba, Brazil
| | - Felipe da Veiga Leprevost
- Medical Science Unit I, Department of Pathology, University of Michigan, EUA, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Paulo Costa Carvalho
- Carlos Chagas Institute-Fiocruz, Professor Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | - Samuel Goldenberg
- Carlos Chagas Institute-Fiocruz, Professor Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil
| | - Lysangela Ronalte Alves
- Carlos Chagas Institute-Fiocruz, Professor Algacyr Munhoz Mader, 3775, Curitiba, Paraná, Brazil.
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Wippel HH, Inoue AH, Vidal NM, da Costa JF, Marcon BH, Romagnoli BAA, Santos MDM, Carvalho PC, Goldenberg S, Alves LR. Assessing the partners of the RBP9-mRNP complex in Trypanosoma cruzi using shotgun proteomics and RNA-seq. RNA Biol 2018; 15:1106-1118. [PMID: 30146924 PMCID: PMC6161725 DOI: 10.1080/15476286.2018.1509660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/01/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in Trypanosoma cruzi with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation. Taking this result as a motivation, we used shotgun proteomics and RNA-seq approaches to assess the core of the RBP9-mRNP complex. In epimastigotes in exponential growth, the complex was composed mostly by RBPs involved in RNA metabolism, such as ZC3H39, UBP1/2, NRBD1, and ALBA3/4. When parasites were subjected to nutritional stress, our analysis identified regulatory RBPs and the translation initiation factors eIF4E5, eIF4G5, eIF4G1, and eIF4G4. The RNA-seq results showed that RBP9-mRNP complex regulates transcripts encoding some RBPs - e.g. RBP5, RBP6, and RBP10 -, and proteins involved in metabolic processes. Therefore, we argue that RBP9 is part of cytoplasmic mRNPs complexes associated with mRNA metabolism and translation regulation in T. cruzi.
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Affiliation(s)
- Helisa Helena Wippel
- Carlos Chagas Institute, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
| | - Alexandre Haruo Inoue
- Carlos Chagas Institute, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
- Molecular Biology Institute of Paraná, IBMP, Curitiba, PR, Brazil
| | | | | | | | | | | | - Paulo Costa Carvalho
- Carlos Chagas Institute, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
| | - Samuel Goldenberg
- Carlos Chagas Institute, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
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Wippel HH, Malgarin JS, Martins SDT, Vidal NM, Marcon BH, Miot HT, Marchini FK, Goldenberg S, Alves LR. The Nuclear RNA-binding Protein RBSR1 Interactome in Trypanosoma cruzi. J Eukaryot Microbiol 2018; 66:244-253. [PMID: 29984450 DOI: 10.1111/jeu.12666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022]
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, has been widely studied, reflecting both its medical importance and the particular features that make this pathogen an attractive model for basic biological studies. The repression of transcripts by messenger ribonucleoprotein (mRNP) complexes is an important pathway of post-transcriptional regulation in eukaryotes, including T. cruzi. RBSR1 is a serine-arginine (SR)-rich RNA-binding protein (RBP) in T. cruzi that contains one RNA-recognition motif (RRM); this protein has a primarily nuclear localization and is developmentally regulated, not being detected in metacyclic trypomastigotes. RBSR1 interacts with other RBPs, such as UBP1 and UBP2, and the nuclear SR-protein TRRM1. Phylogenetic analysis indicated that RBSR1 is orthologous to the human splicing factor SRSF7, what might indicate its possible involvement in pre-RNA processing. Accordingly, ribonomics data showed the enrichment of snoRNAs and snRNAs in the RBSR1 immunoprecipiatation complex, hence reinforcing the supposition that this protein might be involved in RNA processing in the nucleus.
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Affiliation(s)
- Helisa H Wippel
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Juliane S Malgarin
- Molecular Biology Institute of Paraná, IBMP, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Sharon de Toledo Martins
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Newton M Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland, 20894
| | - Bruna H Marcon
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Hálisson T Miot
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Fabricio K Marchini
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Samuel Goldenberg
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Lysangela R Alves
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
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8
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Costa JFD, Ferrarini MG, Nardelli SC, Goldenberg S, Ávila AR, Holetz FB. Trypanosoma cruzi XRNA granules colocalise with distinct mRNP granules at the nuclear periphery. Mem Inst Oswaldo Cruz 2018; 113:e170531. [PMID: 29924141 PMCID: PMC6001583 DOI: 10.1590/0074-02760170531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/10/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Eukaryotic ribonucleoprotein (RNP) granules are important for the regulation of RNA fate. RNP granules exist in trypanosomatids; however, their roles in controlling gene expression are still not understood. XRNA is a component of granules in Trypanosoma brucei but has not been investigated in Trypanosoma cruzi. OBJECTIVES This study aimed to investigate the TcXRNA dynamic assembly and its interaction with RNP components under conditions that affect the mRNA availability. METHODS We used in vitro metacyclogenesis of T. cruzi to observe changes in RNP granules during the differentiation process. TcXRNA expression was analysed by Western blot and immunofluorescence. Colocalisation assays were performed to investigate the interaction of TcXRNA with other RNP components. FINDINGS TcXRNA is constantly present during metacyclogenesis and is localised in cytoplasmic granules. TcXRNA does not colocalise with TcDHH1 and TcCAF1 granules in the cytoplasm. However, TcXRNA granules colocalise with mRNP granules at the nuclear periphery when mRNA processing is inhibited. MAIN CONCLUSIONS TcXRNA plays a role in mRNA metabolism as a component of mRNP granules whose assembly is dependent on mRNA availability. TcXRNA granules colocalise with distinct RNP granules at the nuclear periphery, suggesting that the perinuclear region is a regulatory compartment in T. cruzi mRNA metabolism.
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Affiliation(s)
| | | | | | - Samuel Goldenberg
- Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brasil
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9
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Brito Querido J, Mancera-Martínez E, Vicens Q, Bochler A, Chicher J, Simonetti A, Hashem Y. The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein. Structure 2017; 25:1785-1794.e3. [DOI: 10.1016/j.str.2017.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/20/2017] [Accepted: 09/20/2017] [Indexed: 12/01/2022]
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Oliveira C, Faoro H, Alves LR, Goldenberg S. RNA-binding proteins and their role in the regulation of gene expression in Trypanosoma cruzi and Saccharomyces cerevisiae. Genet Mol Biol 2017; 40:22-30. [PMID: 28463381 PMCID: PMC5409782 DOI: 10.1590/1678-4685-gmb-2016-0258] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) have important functions in the regulation of gene
expression. RBPs play key roles in post-transcriptional processes in all eukaryotes,
such as splicing regulation, mRNA transport and modulation of mRNA translation and
decay. RBPs assemble into different mRNA-protein complexes, which form messenger
ribonucleoprotein complexes (mRNPs). Gene expression regulation in trypanosomatids
occurs mainly at the post-transcriptional level and RBPs play a key role in all
processes. However, the functional characterization of RBPs in Trypanosoma
cruzi has been impaired due to the lack of reliable reverse genetic
manipulation tools. The comparison of RBPs from Saccharomyces
cerevisiae and T. cruzi might allow inferring on the
function of these proteins based on the information available for the orthologous
RNA-binding proteins from the S. cerevisiae model organism. In this
review, we discuss the role of some RBPs from T. cruzi and their
homologues in regulating gene expression in yeast.
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Affiliation(s)
- Camila Oliveira
- Instituto Carlos Chagas, Fiocruz-Paraná, Curitiba, PR, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fiocruz-Paraná, Curitiba, PR, Brazil
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Oliveira C, Carvalho PC, Alves LR, Goldenberg S. The Role of the Trypanosoma cruzi TcNRBD1 Protein in Translation. PLoS One 2016; 11:e0164650. [PMID: 27760165 PMCID: PMC5070865 DOI: 10.1371/journal.pone.0164650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 11/28/2022] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. Despite the importance of this type of control in Trypanosoma cruzi, few RNA binding proteins have been characterized. The RRM domain (RNA Recognition Motif) is one of the most abundant domains found in RNA-binding proteins in higher eukaryotes. Proteins containing the RRM domain are involved in the majority of post-transcriptional processes regulating gene expression. In this work, we aimed to characterize the protein TcNRBD1 from T. cruzi. TcNRBD1 is an RNA-binding protein that contains 2 RRM domains and is the ortholog of the P34 and P37 proteins from Trypanosoma brucei. The TcNRBD1 protein is expressed in all developmental stages of T. cruzi, and its localization pattern is concentrated at the perinuclear region. TcNRBD1 is associated with polysomes and with the 80S monosomes. Furthermore, sequencing of the mRNAs bound to TcNRBD1 allowed the identification of several transcripts that encode ribosomal proteins. Immunoprecipitation assays followed by mass spectrometry showed that the protein complexes with several ribosomal proteins from both the 40S and 60S subunits. In summary, the results indicate that TcNRBD1 is associated with different parts of the translation process, either by regulating mRNAs that encode ribosomal proteins or by acting in some step of ribosome assembly in T. cruzi.
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Affiliation(s)
- Camila Oliveira
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Cidade Industrial de Curitiba–CIC, 81350–010, Curitiba, Brasil
| | - Paulo Costa Carvalho
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Cidade Industrial de Curitiba–CIC, 81350–010, Curitiba, Brasil
| | - Lysangela Ronalte Alves
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Cidade Industrial de Curitiba–CIC, 81350–010, Curitiba, Brasil
- * E-mail: (SG); (LRA)
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fiocruz-Paraná, Rua Professor Algacyr Munhoz Mader, 3775, Cidade Industrial de Curitiba–CIC, 81350–010, Curitiba, Brasil
- * E-mail: (SG); (LRA)
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12
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Goyal M, Banerjee C, Nag S, Bandyopadhyay U. The Alba protein family: Structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:570-83. [PMID: 26900088 DOI: 10.1016/j.bbapap.2016.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/06/2016] [Accepted: 02/16/2016] [Indexed: 01/05/2023]
Abstract
Alba family proteins are small, basic, dimeric nucleic acid-binding proteins, which are widely distributed in archaea and a number of eukaryotes. This family of proteins bears the distinct features of regulation through acetylation/deacetylation, hence named as acetylation lowers binding affinity (Alba). Alba family proteins bind DNA cooperatively with no apparent sequence specificity. Besides DNA, Alba proteins also interact with diverse RNA species and associate with ribonucleo-protein complexes. Initially, Alba proteins were recognized as chromosomal proteins and supposed to be involved in the maintenance of chromatin architecture and transcription repression. However, recent studies have shown increasing evidence of functional plasticity among Alba family of proteins that widely range from genome packaging and organization, transcriptional and translational regulation, RNA metabolism, and development and differentiation processes. In recent years, Alba family proteins have attracted growing interest due to their widespread occurrence in large number of organisms. Presence in multiple copies, functional crosstalk, differential binding affinity, and posttranslational modifications are some of the key factors that might regulate the biological functions of Alba family proteins. In this review article, we present an overview of the Alba family proteins, their salient features and emphasize their functional role in different organisms reported so far.
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Affiliation(s)
- Manish Goyal
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India.
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Differential Subcellular Localization of Leishmania Alba-Domain Proteins throughout the Parasite Development. PLoS One 2015; 10:e0137243. [PMID: 26334886 PMCID: PMC4559404 DOI: 10.1371/journal.pone.0137243] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/14/2015] [Indexed: 12/15/2022] Open
Abstract
Alba-domain proteins are RNA-binding proteins found in archaea and eukaryotes and recently studied in protozoan parasites where they play a role in the regulation of virulence factors and stage-specific proteins. This work describes in silico structural characterization, cellular localization and biochemical analyses of Alba-domain proteins in Leishmania infantum. We show that in contrast to other protozoa, Leishmania have two Alba-domain proteins, LiAlba1 and LiAlba3, representative of the Rpp20- and the Rpp25-like eukaryotic subfamilies, respectively, which share several sequence and structural similarities but also important differences with orthologs in other protozoa, especially in sequences targeted for post-translational modifications. LiAlba1 and LiAlba3 proteins form a complex interacting with other RNA-binding proteins, ribosomal subunits, and translation factors as supported by co-immunoprecipitation and sucrose gradient sedimentation analysis. A higher co-sedimentation of Alba proteins with ribosomal subunits was seen upon conditions of decreased translation, suggesting a role of these proteins in translational repression. The Leishmania Alba-domain proteins display differential cellular localization throughout the parasite development. In the insect promastigote stage, Alba proteins co-localize predominantly to the cytoplasm but they translocate to the nucleolus and the flagellum upon amastigote differentiation in the mammalian host and are found back to the cytoplasm once amastigote differentiation is completed. Heat-shock, a major signal of amastigote differentiation, triggers Alba translocation to the nucleolus and the flagellum. Purification of the Leishmania flagellum confirmed LiAlba3 enrichment in this organelle during amastigote differentiation. Moreover, partial characterization of the Leishmania flagellum proteome of promastigotes and differentiating amastigotes revealed the presence of other RNA-binding proteins, as well as differences in the flagellum composition between these two parasite lifestages. Shuttling of Alba-domain proteins between the cytoplasm and the nucleolus or the flagellum throughout the parasite life cycle suggests that these RNA-binding proteins participate in several distinct regulatory pathways controlling developmental gene expression in Leishmania.
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Smircich P, Eastman G, Bispo S, Duhagon MA, Guerra-Slompo EP, Garat B, Goldenberg S, Munroe DJ, Dallagiovanna B, Holetz F, Sotelo-Silveira JR. Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi. BMC Genomics 2015; 16:443. [PMID: 26054634 PMCID: PMC4460968 DOI: 10.1186/s12864-015-1563-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 04/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background Due to the absence of transcription initiation regulation of protein coding genes transcribed by RNA polymerase II, posttranscriptional regulation is responsible for the majority of gene expression changes in trypanosomatids. Therefore, cataloging the abundance of mRNAs (transcriptome) and the level of their translation (translatome) is a key step to understand control of gene expression in these organisms. Results Here we assess the extent of regulation of the transcriptome and the translatome in the Chagas disease causing agent, Trypanosoma cruzi, in both the non-infective (epimastigote) and infective (metacyclic trypomastigote) insect’s life stages using RNA-seq and ribosome profiling. The observed steady state transcript levels support constitutive transcription and maturation implying the existence of distinctive posttranscriptional regulatory mechanisms controlling gene expression levels at those parasite stages. Meanwhile, the downregulation of a large proportion of the translatome indicates a key role of translation control in differentiation into the infective form. The previously described proteomic data correlate better with the translatomes than with the transcriptomes and translational efficiency analysis shows a wide dynamic range, reinforcing the importance of translatability as a regulatory step. Translation efficiencies for protein families like ribosomal components are diminished while translation of the transialidase virulence factors is upregulated in the quiescent infective metacyclic trypomastigote stage. Conclusions A large subset of genes is modulated at the translation level in two different stages of Trypanosoma cruzi life cycle. Translation upregulation of virulence factors and downregulation of ribosomal proteins indicates different degrees of control operating to prepare the parasite for an infective life form. Taking together our results show that translational regulation, in addition to regulation of steady state level of mRNA, is a major factor playing a role during the parasite differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1563-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pablo Smircich
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay. .,Department of Genetics. School of Medicine, Universidad de la República, Montevideo, Uruguay.
| | - Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay.
| | - Saloe Bispo
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - María Ana Duhagon
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay. .,Department of Genetics. School of Medicine, Universidad de la República, Montevideo, Uruguay.
| | - Eloise P Guerra-Slompo
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Beatriz Garat
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay.
| | - Samuel Goldenberg
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - David J Munroe
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Bruno Dallagiovanna
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Fabiola Holetz
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Jose R Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay. .,Department of Cell and Molecular Biology, School of Sciences, Universidad de la Republica, Montevideo, Uruguay.
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Alves LR, Oliveira C, Goldenberg S. Eukaryotic translation elongation factor-1 alpha is associated with a specific subset of mRNAs in Trypanosoma cruzi. BMC Microbiol 2015; 15:104. [PMID: 25986694 PMCID: PMC4436862 DOI: 10.1186/s12866-015-0436-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/05/2015] [Indexed: 11/17/2022] Open
Abstract
Background Regulation of gene expression in trypanosomatids is mainly posttranscriptional. Tight regulation of mRNA stability and access to polysomes allows Trypanosoma cruzi to adapt to different environmental conditions during its life cycle. Posttranscriptional regulation requires association between mRNAs and specific proteins to form mRNP complexes. Proteins that lack a canonical RNA-binding domain, such as eukaryotic elongation factor-1α (EF-1α), may also associate with mRNPs. EF-1α is conserved in many organisms, and it plays roles in many cellular processes other than translation, including RNA transport, the cell cycle, and apoptosis. Results In a previous study, EF-1α was found associated with mRNP-forming mRNAs in polysome-free fractions both in epimastigotes growing under normal conditions and in nutritionally stressed parasites. This finding suggested the possibility that EF-1α has a non-canonical function. Thus, we investigated the dynamics of EF-1α in association with T. cruzi epimastigote mRNAs under normal and stressed nutritional conditions. EF-1α is expressed throughout the parasite life cycle, but it shows a slight decrease in protein levels in the metacyclic trypomastigote form. The protein is cytoplasmically localized with a granular pattern in all forms analyzed. Following puromycin treatment, EF-1α migrated with the heaviest gradient fractions in a sucrose polysome profile, indicating that its association with large protein complexes was independent of the translation machinery. We next characterized the EF-1α-associated mRNAs in unstressed and stressed epimastigotes. We observed that specific subsets of mRNAs were associated with EF-1α-mRNPs in unstressed or stressed epimastigotes. Some mRNAs were identified in both physiological conditions, whereas others were condition-specific. Gene ontology analysis identified enrichment of gene sets involved in single-organism metabolic processes, amino acid metabolic processes, ATP and metal ion binding, glycolysis, glutamine metabolic processes, and cobalt and iron ion binding. Conclusion These results indicate that in T. cruzi, as in other eukaryotes, EF-1α may play a non-canonical cellular role. We observed the enrichment of functionally related transcripts bound to EF-1α in normal growth conditions as well as in nutritionally stressed cell indicating a potential role of EF-1α mRNP in stress response. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0436-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Camila Oliveira
- Instituto Carlos Chagas, Fiocruz - PR, Curitiba, Parana, Brazil
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Inoue AH, Serpeloni M, Hiraiwa PM, Yamada-Ogatta SF, Muniz JRC, Motta MCM, Vidal NM, Goldenberg S, Ávila AR. Identification of a novel nucleocytoplasmic shuttling RNA helicase of trypanosomes. PLoS One 2014; 9:e109521. [PMID: 25313564 PMCID: PMC4196910 DOI: 10.1371/journal.pone.0109521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression in trypanosomes is controlled mostly by post-transcriptional pathways. Little is known about the components of mRNA nucleocytoplasmic export routes in these parasites. Comparative genomics has shown that the mRNA transport pathway is the least conserved pathway among eukaryotes. Nonetheless, we identified a RNA helicase (Hel45) that is conserved across eukaryotes and similar to shuttling proteins involved in mRNA export. We used in silico analysis to predict the structure of Trypanosoma cruzi Hel45, including the N-terminal domain and the C-terminal domain, and our findings suggest that this RNA helicase can form complexes with mRNA. Hel45 was present in both nucleus and cytoplasm. Electron microscopy showed that Hel45 is clustered close to the cytoplasmic side of nuclear pore complexes, and is also present in the nucleus where it is associated with peripheral compact chromatin. Deletion of a predicted Nuclear Export Signal motif led to the accumulation of Hel45ΔNES in the nucleus, indicating that Hel45 shuttles between the nucleus and the cytoplasm. This transport was dependent on active transcription but did not depend on the exportin Crm1. Knockdown of Mex67 in T. brucei caused the nuclear accumulation of the T. brucei ortholog of Hel45. Indeed, Hel45 is present in mRNA ribonucleoprotein complexes that are not associated with polysomes. It is still necessary to confirm the precise function of Hel45. However, this RNA helicase is associated with mRNA metabolism and its nucleocytoplasmic shuttling is dependent on an mRNA export route involving Mex67 receptor.
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Affiliation(s)
| | - Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | | | - Maria Cristina Machado Motta
- Departamento de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Newton Medeiros Vidal
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Alves LR, Oliveira C, Mörking PA, Kessler RL, Martins ST, Romagnoli BAA, Marchini FK, Goldenberg S. The mRNAs associated to a zinc finger protein from Trypanosoma cruzi shift during stress conditions. RNA Biol 2014; 11:921-33. [PMID: 25180711 PMCID: PMC4179965 DOI: 10.4161/rna.29622] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Trypanosome gene expression is regulated almost exclusively at the posttranscriptional level, through mRNA stability, storage and degradation. Here, we characterize the ribonucleoprotein complex (mRNPs) corresponding to the zinc finger protein TcZC3H39 from T. cruzi comparing cells growing in normal conditions and under nutritional stress. The nutritional stress is a key step during T. cruzi differentiation from epimastigote form to human infective metacyclic trypomastigote form. The mechanisms by which the stress, altogether with other stimuli, triggers differentiation is not well understood. This work aims to characterize the TcZC3H39 protein during stress response. Using cells cultured in normal and stress conditions, we observed a dynamic change in TcZC3H39 granule distribution, which appeared broader in stressed epimastigotes. The protein core of the TcZC3H39-mRNP is composed of ribosomes, translation factors and RBPs. The TcZC3H39-mRNP could act sequestering highly expressed mRNAs and their associated ribosomes, potentially slowing translation in stress conditions. A shift were observed in the mRNAs associated with TcZC3H39: the number of targets in unstressed epimastigotes was smaller than that in stressed parasites, with no clear functional clustering in normal conditions. By contrast, in stressed parasites, the targets of TcZC3H39 were mRNAs encoding ribosomal proteins and a remarkable enrichment in mRNAs for the cytochrome c complex (COX), highly expressed mRNAs in the replicative form. This identification of a new component of RNA granules in T. cruzi, the TcZC3H39 protein, provides new insight into the mechanisms involved in parasite stress responses and the regulation of gene expression during T. cruzi differentiation.
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Gupta SK, Chikne V, Eliaz D, Tkacz ID, Naboishchikov I, Carmi S, Waldman Ben-Asher H, Michaeli S. Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol 2014; 11:715-31. [PMID: 24922194 DOI: 10.4161/rna.29143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In trypanosomes, mRNAs are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNAs from a small RNA donor, the spliced leader RNA (SL RNA). However, little is known regarding how this process is regulated. In this study we investigated the function of two serine-arginine-rich proteins, TSR1 and TSR1IP, implicated in trans-splicing in Trypanosoma brucei. Depletion of these factors by RNAi suggested their role in both cis- and trans-splicing. Microarray was used to examine the transcriptome of the silenced cells. The level of hundreds of mRNAs was changed, suggesting that these proteins have a role in regulating only a subset of T. brucei mRNAs. Mass-spectrometry analyses of complexes associated with these proteins suggest that these factors function in mRNA stability, translation, and rRNA processing. We further demonstrate changes in the stability of mRNA as a result of depletion of the two TSR proteins. In addition, rRNA defects were observed under the depletion of U2AF35, TSR1, and TSR1IP, but not SF1, suggesting involvement of SR proteins in rRNA processing.
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Affiliation(s)
- Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Dror Eliaz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Itai Dov Tkacz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Ilana Naboishchikov
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
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Chung J, Rocha AA, Tonelli RR, Castilho BA, Schenkman S. Eukaryotic initiation factor 5A dephosphorylation is required for translational arrest in stationary phase cells. Biochem J 2013; 451:257-67. [PMID: 23368777 DOI: 10.1042/bj20121553] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The protein known as eIF5A (eukaryotic initiation factor 5A) has an elusive role in translation. It has a unique and essential hypusine modification at a conserved lysine residue in most eukaryotes. In addition, this protein is modified by phosphorylation with unknown functions. In the present study we show that a phosphorylated state of eIF5A predominates in exponentially growing Trypanosoma cruzi cells, and extensive dephosphorylation occurs in cells in stationary phase. Phosphorylation occurs mainly at Ser(2), as shown in yeast eIF5A. In addition, a novel phosphorylation site was identified at Tyr(21). In exponential cells, T. cruzi eIF5A is partially associated with polysomes, compatible with a proposed function as an elongation factor, and becomes relatively enriched in polysomal fractions in stationary phase. Overexpression of the wild-type eIF5A, or eIF5A with Ser(2) replaced by an aspartate residue, but not by alanine, increases the rate of cell proliferation and protein synthesis. However, the presence of an aspartate residue instead of Ser(2) is toxic for cells reaching the stationary phase, which show a less-pronounced protein synthesis arrest and a decreased amount of eIF5A in dense fractions of sucrose gradients. We conclude that eIF5A phosphorylation and dephosphorylation cycles regulate translation according to the growth conditions.
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Affiliation(s)
- Janete Chung
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Pedro de Toledo 669 L6A, São Paulo, S.P. 04039-032, Brazil
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20
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Gupta SK, Carmi S, Waldman Ben-Asher H, Tkacz ID, Naboishchikov I, Michaeli S. Basal splicing factors regulate the stability of mature mRNAs in trypanosomes. J Biol Chem 2013; 288:4991-5006. [PMID: 23283975 DOI: 10.1074/jbc.m112.416578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene expression in trypanosomes is mainly regulated post-transcriptionally. Genes are transcribed as polycistronic mRNAs that are dissected by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common exon, the spliced leader, is added to all mRNAs from a small RNA. In this study, we examined by microarray analysis the transcriptome following RNAi silencing of the basal splicing factors U2AF65, SF1, and U2AF35. The transcriptome data revealed correlations between the affected genes and their splicing and polyadenylation signaling properties, suggesting that differential binding of these factors to pre-mRNA regulates trans-splicing and hence expression of specific genes. Surprisingly, all these factors were shown to affect not only splicing but also mRNA stability. Affinity purification of SF1 and U2AF35 complexes supported their role in mRNA stability. U2AF35 but not SF1 was shown to bind to ribosomes. To examine the role of splicing factors in mRNA stability, mutations were introduced into the polypyrimidine tract located in the 3' UTR of a mini-gene, and the results demonstrate that U2AF65 binds to such a site and controls the mRNA stability. We propose that transcripts carrying splicing signals in their 3' UTR bind the splicing factors and control their stability.
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Affiliation(s)
- Sachin Kumar Gupta
- Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
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21
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Teixeira PC, Frade AF, Nogueira LG, Kalil J, Chevillard C, Cunha-Neto E. Pathogenesis of Chagas disease cardiomyopathy. World J Clin Infect Dis 2012; 2:39-53. [DOI: 10.5495/wjcid.v2.i3.39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chagas disease, or American trypanosomiasis, is a parasitic infection caused by the flagellate protozoan Trypanosoma cruzi. Chagas disease is mainly affecting rural populations in Mexico and Central and South America. The World Health Organization estimates that 300 000 new cases of Chagas disease occur every year and approximately 20 000 deaths are attributable to Chagas. However, this organisation classified Chagas disease as a neglected tropical disease. The economic burden of this disease is significant. In many Latin American countries, the direct and indirect costs, including the cost of health care in dollars and loss of productivity, attributable to Chagas disease ranges from $40 million to in excess of $800 million per nation per annum. So, it remains a contemporary public health concern. In chronic phase, mortality is primarily due to the rhythm disturbances and congestive heart failure that result from the chronic inflammatory cardiomyopathy (CCC) due to the persistence presence of parasites in the heart tissue. Mechanisms underlying differential progression to CCC are still incompletely understood. In the last decades immunological proteomic genetic approaches lead to significant results which help to disperse the veil covering the knowledge of the pathogenic process. Here, we reported these significant progresses.
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Teixeira SM, de Paiva RMC, Kangussu-Marcolino MM, Darocha WD. Trypanosomatid comparative genomics: Contributions to the study of parasite biology and different parasitic diseases. Genet Mol Biol 2012; 35:1-17. [PMID: 22481868 PMCID: PMC3313497 DOI: 10.1590/s1415-47572012005000008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/18/2011] [Indexed: 01/23/2023] Open
Abstract
In 2005, draft sequences of the genomes of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major, also known as the Tri-Tryp genomes, were published. These protozoan parasites are the causative agents of three distinct insect-borne diseases, namely sleeping sickness, Chagas disease and leishmaniasis, all with a worldwide distribution. Despite the large estimated evolutionary distance among them, a conserved core of ~6,200 trypanosomatid genes was found among the Tri-Tryp genomes. Extensive analysis of these genomic sequences has greatly increased our understanding of the biology of these parasites and their host-parasite interactions. In this article, we review the recent advances in the comparative genomics of these three species. This analysis also includes data on additional sequences derived from other trypanosmatid species, as well as recent data on gene expression and functional genomics. In addition to facilitating the identification of key parasite molecules that may provide a better understanding of these complex diseases, genome studies offer a rich source of new information that can be used to define potential new drug targets and vaccine candidates for controlling these parasitic infections.
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Affiliation(s)
- Santuza M Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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23
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24
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Tonelli RR, Augusto LDS, Castilho BA, Schenkman S. Protein synthesis attenuation by phosphorylation of eIF2α is required for the differentiation of Trypanosoma cruzi into infective forms. PLoS One 2011; 6:e27904. [PMID: 22114724 PMCID: PMC3218062 DOI: 10.1371/journal.pone.0027904] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 10/27/2011] [Indexed: 01/13/2023] Open
Abstract
Chagas' disease is a potentially life-threatening illness caused by the unicellular protozoan parasite Trypanosoma cruzi. It is transmitted to humans by triatomine bugs where T. cruzi multiplies and differentiates in the digestive tract. The differentiation of proliferative and non-infective epimastigotes into infective metacyclic trypomastigotes (metacyclogenesis) can be correlated to nutrient exhaustion in the gut of the insect vector. In vitro, metacyclic-trypomastigotes can be obtained when epimastigotes are submitted to nutritional stress suggesting that metacyclogenesis is triggered by nutrient starvation. The molecular mechanism underlying such event is not understood. Here, we investigated the role of one of the key signaling responses elicited by nutritional stress in all other eukaryotes, the inhibition of translation initiation by the phosphorylation of the eukaryotic initiation factor 2α (eIF2α), during the in vitro differentiation of T. cruzi. Monospecific antibodies that recognize the phosphorylated Tc-eIF2α form were generated and used to demonstrate that parasites subjected to nutritional stress show increased levels of Tc-eIF2α phosphorylation. This was accompanied by a drastic inhibition of global translation initiation, as determined by polysomal profiles. A strain of T. cruzi overexpressing a mutant Tc-eIF2α, incapable of being phosphorylated, showed a block on translation initiation, indicating that such a nutritional stress in trypanosomatids induces the conserved translation inhibition response. In addition, Tc-eIF2α phosphorylation is critical for parasite differentiation since the overexpression of the mutant eIF2α in epimastigotes abolished metacyclogenesis. This work defines the role of eIF2α phosphorylation as a key step in T. cruzi differentiation.
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Affiliation(s)
- Renata R Tonelli
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brasil
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Araújo PR, Teixeira SM. Regulatory elements involved in the post-transcriptional control of stage-specific gene expression in Trypanosoma cruzi: a review. Mem Inst Oswaldo Cruz 2011; 106:257-66. [PMID: 21655811 DOI: 10.1590/s0074-02762011000300002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/07/2011] [Indexed: 11/22/2022] Open
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26
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Holetz FB, Alves LR, Probst CM, Dallagiovanna B, Marchini FK, Manque P, Buck G, Krieger MA, Correa A, Goldenberg S. Protein and mRNA content of TcDHH1-containing mRNPs in Trypanosoma cruzi. FEBS J 2010; 277:3415-26. [PMID: 20629747 DOI: 10.1111/j.1742-4658.2010.07747.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In trypanosomatids, the regulation of gene expression occurs mainly at the post-transcriptional level. Previous studies have revealed nontranslated mRNA in the Trypanosoma cruzi cytoplasm. Previously, we have identified and cloned the TcDHH1 protein, a DEAD box RNA helicase. It has been reported that Dhh1 is involved in multiple RNA-related processes in various eukaryotes. It has also been reported to accumulate in stress granules and processing bodies of yeast, animal cells, Trypanosoma brucei and T. cruzi. TcDHH1 is localized to discrete cytoplasmic foci that vary depending on the life cycle status and nutritional conditions. To study the composition of mRNPs containing TcDHH1, we carried out immunoprecipitation assays with anti-TcDHH1 using epimastigote lysates. The protein content of mRNPs was determined by MS and pre-immune serum was used as control. We also carried out a ribonomic approach to identify the mRNAs present within the TcDHH1 immunoprecipitated complexes. For this purpose, competitive microarray hybridizations were performed against negative controls, the nonprecipitated fraction. Our results showed that mRNAs associated with TcDHH1 in the epimastigote stage are 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.
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