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Sabalette KB, Campo VA, De Gaudenzi JG. Proteomic data of the Trypanosoma cruzi insect-dwelling epimastigotes overexpressing the RNA-binding protein UBP1. Data Brief 2024; 53:110085. [PMID: 38348324 PMCID: PMC10859248 DOI: 10.1016/j.dib.2024.110085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
We present data on the proteome of the Trypanosoma cruzi epimastigote cells overexpressing the U-rich RNA-binding protein 1 (UBP1). The role of this regulatory protein during the epimastigote-to-metacyclic trypomastigote stage transition was clearly established by our group at the transcriptome level; nevertheless, the impact of UBP1 overexpression on protein synthesis is not known. To address this question, we performed shotgun label-free quantification proteomics using an in vitro system based on the tetracycline-inducible expression of TcUBP1 and epimastigote wildtype cells. Using tryptic peptide digestion and LC-MS/MS analysis with Orbitrap technology, this data file describes the proteome of three biological samples per condition and yields 1637 correctly quantified proteins. The statistical comparisons of the two analyzed groups within the Proteome Discoverer platform identified 379 differentially expressed proteins, with 207 being up-regulated and 172 being down-regulated. In addition, profile plots and heatmap analysis to visualize the distribution of protein abundances within replicates are also presented. Data are available via ProteomeXchange with identifier PXD047761.
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Affiliation(s)
- Karina B. Sabalette
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A. Campo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
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Romagnoli BAA, Lucena ACR, Freire ER, Munhoz da Rocha IF, Alves LR, Goldenberg S. TcZC3HTTP, a regulatory element that contributes to Trypanosoma cruzi cell proliferation. Microbiol Spectr 2024; 12:e0288023. [PMID: 38270449 PMCID: PMC10913370 DOI: 10.1128/spectrum.02880-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024] Open
Abstract
Post-transcriptional regulation of gene expression is a critical process for adapting to and surviving Trypanosoma cruzi, a parasite with a complex life cycle. RNA-binding proteins (RBPs) are key players in this regulation, forming ribonucleoprotein complexes (messenger ribonucleoproteins) and RNA granules that control transcript stability, localization, degradation, and translation modulation. Understanding the specific roles of individual RBPs is crucial for unraveling the details of this regulatory network. In this study, we generated null mutants of the TcZC3HTTP gene, a specific RBP in the Trypanosoma family characterized by a C3H zinc finger and a DNAJ domain associated with RNA and protein binding, respectively. Through cell growth assays, we demonstrated that the absence of TcZC3HTTP or the expression of an additional tagged version impacted epimastigote growth, indicating its contribution to cell proliferation. TcZC3HTTP was found to associate with mRNAs involved in cell cycle and division in epimastigotes, while in nutritionally stressed parasites it exhibited associations with mRNAs coding for other RBPs and rRNA. Furthermore, our analysis identified that TcZC3HTTP protein partners were different during normal growth conditions compared to starvation conditions, with the latter showing enrichment of ribosomal proteins and other RBPs. Therefore, this study provides insights into TcZC3HTTP's role in the post-transcriptional regulation of gene expression during normal growth and nutritional stress in T. cruzi, uncovering its versatile functions in different cellular contexts.IMPORTANCEUnderstanding how Trypanosoma cruzi, the causative agent of Chagas disease, regulates gene expression is crucial for developing targeted interventions. In this study, we investigated the role of TcZC3HTTP, an RNA-binding protein, in post-transcriptional regulation. Our findings demonstrate that TcZC3HTTP is relevant for the growth and proliferation of epimastigotes, a stage of the parasite's life cycle. We identified its associations with specific mRNAs involved in cell cycle and division and its interactions with enzymes and other RNA-binding proteins (RBPs) under normal and starvation conditions. These insights shed light on the regulatory network underlying gene expression in T. cruzi and reveal the multifaceted functions of RBPs in this parasite. Such knowledge enhances our understanding of the parasite's biology and opens avenues for developing novel therapeutic strategies targeting post-transcriptional gene regulation in T. cruzi.
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Affiliation(s)
| | - Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | - Eden Ribeiro Freire
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | | | - Lysangela Ronalte. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity, CHU de Quebec Research Center, University Laval, Quebec, Canada
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
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Ceballos-Pérez G, Rico-Jiménez M, Gómez-Liñán C, Estévez AM. Role of the RNA-binding protein ZC3H41 in the regulation of ribosomal protein messenger RNAs in trypanosomes. Parasit Vectors 2023; 16:118. [PMID: 37004055 PMCID: PMC10064699 DOI: 10.1186/s13071-023-05728-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/03/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Trypanosomes are single-celled eukaryotes that rely heavily on post-transcriptional mechanisms to regulate gene expression. RNA-binding proteins play essential roles in regulating the fate, abundance and translation of messenger RNAs (mRNAs). Among these, zinc finger proteins of the cysteine3histidine (CCCH) class have been shown to be key players in cellular processes as diverse as differentiation, regulation of the cell cycle and translation. ZC3H41 is an essential zinc finger protein that has been described as a component of spliced leader RNA granules and nutritional stress granules, but its role in RNA metabolism is unknown. METHODS Cell cycle analysis in ZC3H41- and Z41AP-depleted cells was carried out using 4',6-diamidino-2-phenylindole staining, microscopic examination and flow cytometry. The identification of ZC3H41 protein partners was done using tandem affinity purification and mass spectrometry. Next-generation sequencing was used to evaluate the effect of ZC3H41 depletion on the transcriptome of procyclic Trypanosoma brucei cells, and also to identify the cohort of mRNAs associated with the ZC3H41/Z41AP complex. Levels of 5S ribosomal RNA (rRNA) species in ZC3H41- and Z41AP-depleted cells were assessed by quantitative reverse transcription-polymerase chain reaction. Surface sensing of translation assays were used to monitor global translation. RESULTS We showed that depletion of the zinc finger protein ZC3H41 resulted in marked cell cycle defects and abnormal cell morphologies. ZC3H41 was found associated with an essential protein, which we named Z41AP, forming a stable heterodimer, and also with proteins of the poly(A)-binding protein 1 complex. The identification of mRNAs associated with the ZC3H41/Z41AP complex revealed that it is primarily composed of ribosomal protein mRNAs, and that binding to target transcripts is diminished upon nutritional stress. In addition, we observed that mRNAs encoding several proteins involved in the maturation of 5S rRNA are also associated with the ZC3H41/Z41AP complex. Finally, we showed that depletion of either ZC3H41 or Z41AP led to the accumulation of 5S rRNA precursors and a decrease of protein translation. CONCLUSIONS We propose that ZC3H41 and Z41AP play important roles in controlling the fate of ribosomal components in response to environmental cues.
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Affiliation(s)
- Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Miriam Rico-Jiménez
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
- Estación Experimental del Zaidín (EEZ), CSIC, Prof. Albareda 1, 18008, Granada, Spain
| | - Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Antonio M Estévez
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain.
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Oliveira C, Holetz FB, Alves LR, Ávila AR. Modulation of Virulence Factors during Trypanosoma cruzi Differentiation. Pathogens 2022; 12:pathogens12010032. [PMID: 36678380 PMCID: PMC9865030 DOI: 10.3390/pathogens12010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi. This protozoan developed several mechanisms to infect, propagate, and survive in different hosts. The specific expression of proteins is responsible for morphological and metabolic changes in different parasite stages along the parasite life cycle. The virulence strategies at the cellular and molecular levels consist of molecules responsible for mediating resistance mechanisms to oxidative damage, cellular invasion, and immune evasion, performed mainly by surface proteins. Since parasite surface coat remodeling is crucial to invasion and infectivity, surface proteins are essential virulence elements. Understanding the factors involved in these processes improves the knowledge of parasite pathogenesis. Genome sequencing has opened the door to high-throughput technologies, allowing us to obtain a deeper understanding of gene reprogramming along the parasite life cycle and identify critical molecules for survival. This review therefore focuses on proteins regulated during differentiation into infective forms considered virulence factors and addresses the current known mechanisms acting in the modulation of gene expression, emphasizing mRNA signals, regulatory factors, and protein complexes.
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Affiliation(s)
- Camila Oliveira
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Centre de Recherche CERVO, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Fabíola Barbieri Holetz
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
| | - Lysangela Ronalte Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center, University Laval, Québec City, QC G1V 4G2, Canada
| | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Correspondence: ; Tel.: +55-41-33163230
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Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics. mSphere 2021; 6:e0036621. [PMID: 34468164 PMCID: PMC8550152 DOI: 10.1128/msphere.00366-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Trypanosoma cruzi is the etiological agent for Chagas disease, a neglected parasitic disease in Latin America. Gene transcription control governs the eukaryotic cell replication but is absent in trypanosomatids; thus, it must be replaced by posttranscriptional regulatory events. We investigated the entrance into the T. cruzi replicative cycle using ribosome profiling and proteomics on G1/S epimastigote cultures synchronized with hydroxyurea. We identified 1,784 translationally regulated genes (change > 2, false-discovery rate [FDR] < 0.05) and 653 differentially expressed proteins (change > 1.5, FDR < 0.05), respectively. A major translational remodeling accompanied by an extensive proteome change is found, while the transcriptome remains largely unperturbed at the replicative entrance of the cell cycle. The differentially expressed genes comprise specific cell cycle processes, confirming previous findings while revealing candidate cell cycle regulators that undergo previously unnoticed translational regulation. Clusters of genes showing a coordinated regulation at translation and protein abundance share related biological functions such as cytoskeleton organization and mitochondrial metabolism; thus, they may represent posttranscriptional regulons. The translatome and proteome of the coregulated clusters change in both coupled and uncoupled directions, suggesting that complex cross talk between the two processes is required to achieve adequate protein levels of different regulons. This is the first simultaneous assessment of the transcriptome, translatome, and proteome of trypanosomatids, which represent a paradigm for the absence of transcriptional control. The findings suggest that gene expression chronology along the T. cruzi cell cycle is controlled mainly by translatome and proteome changes coordinated using different mechanisms for specific gene groups. IMPORTANCE Trypanosoma cruzi is an ancient eukaryotic unicellular parasite causing Chagas disease, a potentially life-threatening illness that affects 6 to 7 million people, mostly in Latin America. The antiparasitic treatments for the disease have incomplete efficacy and adverse reactions; thus, improved drugs are needed. We study the mechanisms governing the replication of the parasite, aiming to find differences with the human host, valuable for the development of parasite-specific antiproliferative drugs. Transcriptional regulation is essential for replication in most eukaryotes, but in trypanosomatids, it must be replaced by subsequent gene regulation steps since they lack transcription initiation control. We identified the genome-wide remodeling of mRNA translation and protein abundance during the entrance to the replicative phase of the cell cycle. We found that translation is strongly regulated, causing variation in protein levels of specific cell cycle processes, representing the first simultaneous study of the translatome and proteome in trypanosomatids.
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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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A Trypanosoma cruzi zinc finger protein that is implicated in the control of epimastigote-specific gene expression and metacyclogenesis. Parasitology 2020; 148:1171-1185. [PMID: 33190649 PMCID: PMC8312218 DOI: 10.1017/s0031182020002176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Trypanosoma cruzi has three biochemically and morphologically distinct developmental stages that are programmed to rapidly respond to environmental changes the parasite faces during its life cycle. Unlike other eukaryotes, Trypanosomatid genomes contain protein coding genes that are transcribed into polycistronic pre-mRNAs and have their expression controlled by post-transcriptional mechanisms. Transcriptome analyses comparing three stages of the T. cruzi life cycle revealed changes in gene expression that reflect the parasite adaptation to distinct environments. Several genes encoding RNA binding proteins (RBPs), known to act as key post-transcriptional regulatory factors, were also differentially expressed. We characterized one T. cruzi RBP, named TcZH3H12, which contains a zinc finger domain and is up-regulated in epimastigotes compared to trypomastigotes and amastigotes. TcZC3H12 knockout (KO) epimastigotes showed decreased growth rates and increased capacity to differentiate into metacyclic trypomastigotes. Transcriptome analyses comparing wild type and TcZC3H12 KOs revealed a TcZC3H12-dependent expression of epimastigote-specific genes such as genes encoding amino acid transporters and proteins associated with differentiation (PADs). RNA immunoprecipitation assays showed that transcripts from the PAD family interact with TcZC3H12. Taken together, these findings suggest that TcZC3H12 positively regulates the expression of genes involved in epimastigote proliferation and also acts as a negative regulator of metacyclogenesis.
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Romagnoli BAA, Holetz FB, Alves LR, Goldenberg S. RNA Binding Proteins and Gene Expression Regulation in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:56. [PMID: 32154189 PMCID: PMC7045066 DOI: 10.3389/fcimb.2020.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. In the case of Trypanosoma cruzi, the characterization of messenger ribonucleoprotein (mRNP) particles has allowed the identification of several classes of RNA binding proteins (RBPs), as well as non-canonical RBPs, associated with mRNA molecules. The protein composition of the mRNPs as well as the localization and functionality of the mRNAs depend on their associated proteins. mRNPs can also be organized into larger complexes forming RNA granules, which function as stress granules or P-bodies depending on the associated proteins. The fate of mRNAs in the cell, and consequently the genes expressed, depends on the set of proteins associated with the messenger molecule. These proteins allow the coordinated expression of mRNAs encoding proteins that are related in function, resulting in the formation of post-transcriptional operons. However, the puzzle posed by the combinatorial association of sets of RBPs with mRNAs and how this relates to the expressed genes remain to be elucidated. One important tool in this endeavor is the use of the CRISPR/CAS system to delete genes encoding RBPs, allowing the evaluation of their effect on the formation of mRNP complexes and associated mRNAs in the different compartments of the translation machinery. Accordingly, we recently established this methodology for T. cruzi and deleted the genes encoding RBPs containing zinc finger domains. In this manuscript, we will discuss the data obtained and the potential of the CRISPR/CAS methodology to unveil the role of RBPs in T. cruzi gene expression regulation.
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Affiliation(s)
- Bruno A A Romagnoli
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Fabiola B Holetz
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Lysangela R Alves
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
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Trenaman A, Glover L, Hutchinson S, Horn D. A post-transcriptional respiratome regulon in trypanosomes. Nucleic Acids Res 2019; 47:7063-7077. [PMID: 31127277 PMCID: PMC6648352 DOI: 10.1093/nar/gkz455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/25/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional regulons coordinate the expression of groups of genes in eukaryotic cells, yet relatively few have been characterized. Parasitic trypanosomatids are particularly good models for studies on such mechanisms because they exhibit almost exclusive polycistronic, and unregulated, transcription. Here, we identify the Trypanosoma brucei ZC3H39/40 RNA-binding proteins as regulators of the respiratome; the mitochondrial electron transport chain (complexes I-IV) and the FoF1-ATP synthase (complex V). A high-throughput RNAi screen initially implicated both ZC3H proteins in variant surface glycoprotein (VSG) gene silencing. This link was confirmed and both proteins were shown to form a cytoplasmic ZC3H39/40 complex. Transcriptome and mRNA-interactome analyses indicated that the impact on VSG silencing was indirect, while the ZC3H39/40 complex specifically bound and stabilized transcripts encoding respiratome-complexes. Quantitative proteomic analyses revealed specific positive control of >20 components from complexes I, II and V. Our findings establish a link between the mitochondrial respiratome and VSG gene silencing in bloodstream form T. brucei. They also reveal a major respiratome regulon controlled by the conserved trypanosomatid ZC3H39/40 RNA-binding proteins.
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Affiliation(s)
- Anna Trenaman
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lucy Glover
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sebastian Hutchinson
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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11
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Sabalette KB, Romaniuk MA, Noé G, Cassola A, Campo VA, De Gaudenzi JG. The RNA-binding protein TcUBP1 up-regulates an RNA regulon for a cell surface-associated Trypanosoma cruzi glycoprotein and promotes parasite infectivity. J Biol Chem 2019; 294:10349-10364. [PMID: 31113862 DOI: 10.1074/jbc.ra118.007123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/06/2019] [Indexed: 11/06/2022] Open
Abstract
The regulation of transcription in trypanosomes is unusual. To modulate protein synthesis during their complex developmental stages, these unicellular microorganisms rely largely on post-transcriptional gene expression pathways. These pathways include a plethora of RNA-binding proteins (RBPs) that modulate all steps of the mRNA life cycle in trypanosomes and help organize transcriptomes into clusters of post-transcriptional regulons. The aim of this work was to characterize an RNA regulon comprising numerous transcripts of trypomastigote-associated cell-surface glycoproteins that are preferentially expressed in the infective stages of the human parasite Trypanosoma cruzi. In vitro and in vivo RNA-binding assays disclosed that these glycoprotein mRNAs are targeted by the small trypanosomatid-exclusive RBP in T. cruzi, U-rich RBP 1 (TcUBP1). Overexpression of a GFP-tagged TcUBP1 in replicative parasites resulted in >10 times up-regulated expression of transcripts encoding surface proteins and in changes in their subcellular localization from the posterior region to the perinuclear region of the cytoplasm, as is typically observed in the infective parasite stages. Moreover, RT-quantitative PCR analysis of actively translated mRNAs by sucrose cushion fractionation revealed an increased abundance of these target transcripts in the polysome fraction of TcUBP1-induced samples. Because these surface proteins are involved in cell adherence or invasion during host infection, we also carried out in vitro infections with TcUBP1-transgenic trypomastigotes and observed that TcUBP1 overexpression significantly increases parasite infectivity. Our findings provide evidence for a role of TcUBP1 in trypomastigote stage-specific gene regulation important for T. cruzi virulence.
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Affiliation(s)
- Karina B Sabalette
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
| | - María Albertina Romaniuk
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
| | - Griselda Noé
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
| | - Alejandro Cassola
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
| | - Vanina A Campo
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
| | - Javier G De Gaudenzi
- From the Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, 1650 San Martín, Buenos Aires, Argentina
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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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Kulandaisamy A, Srivastava A, Kumar P, Nagarajan R, Priya SB, Gromiha MM. Identification and Analysis of Key Residues in Protein-RNA Complexes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1436-1444. [PMID: 29993582 DOI: 10.1109/tcbb.2018.2834387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein-RNA complexes play important roles in various biological processes. The functions of protein-RNA complexes are dictated by their interactions, binding, stability, and affinity. In this work, we have identified the key residues (KRs), which are involved in both stability and binding. We found that 42 percent of considered proteins share common binding and stabilizing residues, whereas these residues are distinct in 58 percent of the proteins. Overall, 5 percent of stabilizing and 3 percent of binding residues serve as key residues. These residues are enriched with the combination of polar, charged, aliphatic, and aromatic residues. Analysis on subclasses of protein-RNA complexes based on protein structural class, function and RNA type showed that regulatory proteins, and complexes with single stranded RNA and rRNA have appreciable number of key residues. Specifically, Arg, Tyr, and Thr are preferred in most of the subclasses of protein-RNA complexes. In addition, residues with similar chemical behavior have different preferences to be KRs, such that Arg, Tyr, Val, and Thr are preferred over Lys, Trp, Ile, and Ser, respectively. Atomic level contacts revealed that charged and polar-nonpolar contacts are dominant in enzymes, polar in structural, and nonpolar in regulatory proteins. On the other hand, polar-nonpolar contacts are enriched in all these classes of protein-RNA complexes. Further, the influence of sequence and structural features such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long-range order in key residues are also discussed. We envisage that the present study provides insights to understand the structural and functional aspects of protein-RNA complexes.
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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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15
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Santos CMBD, Ludwig A, Kessler RL, Rampazzo RDCP, Inoue AH, Krieger MA, Pavoni DP, Probst CM. Trypanosoma cruzi transcriptome during axenic epimastigote growth curve. Mem Inst Oswaldo Cruz 2018; 113:e170404. [PMID: 29668769 PMCID: PMC5907844 DOI: 10.1590/0074-02760170404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/29/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi is an important protozoan parasite and the causative agent of Chagas disease. A critical step in understanding T. cruzi biology is the study of cellular and molecular features exhibited during its growth curve. OBJECTIVES We aimed to acquire a global view of the gene expression profile of T. cruzi during epimastigote growth. METHODS RNA-Seq analysis of total and polysomal/granular RNA fractions was performed along the 10 days T. cruzi epimastigote growth curve in vitro, in addition to cell viability and cell cycle analyses. We also analysed the polysome profile and investigated the presence of granular RNA by FISH and western blotting. FINDINGS We identified 1082 differentially expressed genes (DEGs), of which 220 were modulated in both fractions. According to the modulation pattern, DEGs were grouped into 12 clusters and showed enrichment of important gene ontology (GO) terms. Moreover, we showed that by the sixth day of the growth curve, polysomal content declined greatly and the RNA granules content appeared to increase, suggesting that a portion of mRNAs isolated from the sucrose gradient during late growth stages was associated with RNA granules and not only polyribosomes. Furthermore, we discuss several modulated genes possibly involved in T. cruzi growth, mainly during the stationary phase, such as genes related to cell cycle, pathogenesis, metabolic processes and RNA-binding proteins.
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Affiliation(s)
| | - Adriana Ludwig
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, PR, Brasil
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16
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Knockout of the CCCH zinc finger protein TcZC3H31 blocks Trypanosoma cruzi differentiation into the infective metacyclic form. Mol Biochem Parasitol 2018; 221:1-9. [DOI: 10.1016/j.molbiopara.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/21/2018] [Accepted: 01/29/2018] [Indexed: 01/23/2023]
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Erben ED. High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks. Curr Genomics 2018; 19:78-86. [PMID: 29491736 PMCID: PMC5814965 DOI: 10.2174/1389202918666170815125336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/22/2016] [Accepted: 02/03/2017] [Indexed: 12/24/2022] Open
Abstract
From synthesis to decay, mRNA associates with RNA-binding proteins (RBPs) establishing dynamic ribonucleoprotein particles (RNPs). Understanding the composition and function of RNPs is fundamental to understanding how eukaryotic mRNAs are controlled. This is especially relevant for trypanosomes and related kinetoplastid parasites, which mostly rely on post-transcriptional mechanisms to control gene expression. Crucial for trypanosome differentiation, development, or even response to heat shock, RBPs are known to be essential modulators of diverse molecular processes. The recent application of large-scale quantitative methods, such as Next-Generation Sequencing (NGS) and quantitative mass spectrometry, has revealed new exciting features about the parasite RNA-related metabolism. Novel proteins carrying RNA-binding activity, including many proteins without RNA-related ontology were discovered setting a necessary groundwork to get in insights into RNA biology. Conclusion: This review aims to give the reader an understanding of current trypanosome RNP research, highlighting the progress made using high-throughput approaches.
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Affiliation(s)
- Esteban D Erben
- Zentrum fur Molekulare Biologie der Universitet Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120Heidelberg, Germany
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18
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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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20
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Li Y, Shah-Simpson S, Okrah K, Belew AT, Choi J, Caradonna KL, Padmanabhan P, Ndegwa DM, Temanni MR, Corrada Bravo H, El-Sayed NM, Burleigh BA. Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection. PLoS Pathog 2016; 12:e1005511. [PMID: 27046031 PMCID: PMC4821583 DOI: 10.1371/journal.ppat.1005511] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/28/2016] [Indexed: 01/22/2023] Open
Abstract
Intracellular colonization and persistent infection by the kinetoplastid protozoan parasite, Trypanosoma cruzi, underlie the pathogenesis of human Chagas disease. To obtain global insights into the T. cruzi infective process, transcriptome dynamics were simultaneously captured in the parasite and host cells in an infection time course of human fibroblasts. Extensive remodeling of the T. cruzi transcriptome was observed during the early establishment of intracellular infection, coincident with a major developmental transition in the parasite. Contrasting this early response, few additional changes in steady state mRNA levels were detected once mature T. cruzi amastigotes were formed. Our findings suggest that transcriptome remodeling is required to establish a modified template to guide developmental transitions in the parasite, whereas homeostatic functions are regulated independently of transcriptomic changes, similar to that reported in related trypanosomatids. Despite complex mechanisms for regulation of phenotypic expression in T. cruzi, transcriptomic signatures derived from distinct developmental stages mirror known or projected characteristics of T. cruzi biology. Focusing on energy metabolism, we were able to validate predictions forecast in the mRNA expression profiles. We demonstrate measurable differences in the bioenergetic properties of the different mammalian-infective stages of T. cruzi and present additional findings that underscore the importance of mitochondrial electron transport in T. cruzi amastigote growth and survival. Consequences of T. cruzi colonization for the host include dynamic expression of immune response genes and cell cycle regulators with upregulation of host cholesterol and lipid synthesis pathways, which may serve to fuel intracellular T. cruzi growth. Thus, in addition to the biological inferences gained from gene ontology and functional enrichment analysis of differentially expressed genes in parasite and host, our comprehensive, high resolution transcriptomic dataset provides a substantially more detailed interpretation of T. cruzi infection biology and offers a basis for future drug and vaccine discovery efforts. In-depth knowledge of the functional processes governing host colonization and transmission of pathogenic microorganisms is essential for the advancement of effective intervention strategies. This study focuses on Trypanosoma cruzi, the vector-borne protozoan parasite responsible for human Chagas disease and the leading cause of infectious myocarditis worldwide. To gain global insights into the biology of this parasite and its interaction with mammalian host cells, we have exploited a deep-sequencing approach to generate comprehensive, high-resolution transcriptomic maps for mammalian-infective stages of T. cruzi with the simultaneous interrogation of the human host cell transcriptome across an infection time course. We demonstrate that the establishment of intracellular T. cruzi infection in mammalian host cells is accompanied by extensive remodeling of the parasite and host cell transcriptomes. Despite the lack of transcriptional control mechanisms in trypanosomatids, our analyses identified functionally-enriched processes within sets of developmentally-regulated transcripts in T. cruzi that align with known or predicted biological features of the parasite. The novel insights into the biology of intracellular T. cruzi infection and the regulation of amastigote development gained in this study establish a unique foundation for functional network analyses that will be instrumental in providing functional links between parasite dependencies and host functional pathways that have the potential to be exploited for intervention.
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Affiliation(s)
- Yuan Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Sheena Shah-Simpson
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Kwame Okrah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - A Trey Belew
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jungmin Choi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Kacey L Caradonna
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Prasad Padmanabhan
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David M Ndegwa
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - M Ramzi Temanni
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Héctor Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America.,Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Barbara A Burleigh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED. Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome. Mol Microbiol 2016; 100:457-71. [PMID: 26784394 DOI: 10.1111/mmi.13328] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2016] [Indexed: 12/11/2022]
Abstract
Control of gene expression at the post-transcriptional level is essential in all organisms, and RNA-binding proteins play critical roles from mRNA synthesis to decay. To fully understand this process, it is necessary to identify the complete set of RNA-binding proteins and the functional consequences of the protein-mRNA interactions. Here, we provide an overview of the proteins that bind to mRNAs and their functions in the pathogenic bloodstream form of Trypanosoma brucei. We describe the production of a small collection of open-reading frames encoding proteins potentially involved in mRNA metabolism. With this ORFeome collection, we used tethering to screen for proteins that play a role in post-transcriptional control. A yeast two-hybrid screen showed that several of the discovered repressors interact with components of the CAF1/NOT1 deadenylation complex. To identify the RNA-binding proteins, we obtained the mRNA-bound proteome. We identified 155 high-confidence candidates, including many not previously annotated as RNA-binding proteins. Twenty seven of these proteins affected reporter expression in the tethering screen. Our study provides novel insights into the potential trypanosome mRNPs composition, architecture and function.
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Affiliation(s)
- Smiths Lueong
- Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Clementine Merce
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282
| | - Bernd Fischer
- Computational Genome Biology, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Esteban D Erben
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282
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22
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Alves LR, Goldenberg S. RNA-binding proteins related to stress response and differentiation in protozoa. World J Biol Chem 2016; 7:78-87. [PMID: 26981197 PMCID: PMC4768126 DOI: 10.4331/wjbc.v7.i1.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/23/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell death. The RBPs can differentially combine with RNA molecules and form ribonucleoprotein (RNP) complexes, defining the function and fate of RNA molecules in the cell. RBPs display diverse domains that allow them to be categorized into distinct families. They play important roles in the cellular response to physiological stress, in cell differentiation, and, it is believed, in the cellular localization of certain mRNAs. In several protozoa, a physiological stress (nutritional, temperature or pH) triggers differentiation to a distinct developmental stage. Most of the RBPs characterized in protozoa arise from trypanosomatids. In these protozoa gene expression regulation is mostly post-transcriptional, which suggests that some RBPs might display regulatory functions distinct from those described for other eukaryotes. mRNA stability can be altered as a response to stress. Transcripts are sequestered to RNA granules that ultimately modulate their availability to the translation machinery, storage or degradation, depending on the associated proteins. These aggregates of mRNPs containing mRNAs that are not being translated colocalize in cytoplasmic foci, and their numbers and size vary according to cell conditions such as oxidative stress, nutritional status and treatment with drugs that inhibit translation.
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Fritz M, Vanselow J, Sauer N, Lamer S, Goos C, Siegel TN, Subota I, Schlosser A, Carrington M, Kramer S. Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve. Nucleic Acids Res 2015; 43:8013-32. [PMID: 26187993 PMCID: PMC4652759 DOI: 10.1093/nar/gkv731] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/07/2015] [Indexed: 02/07/2023] Open
Abstract
RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly understood, one reason for this is that RNP granule purification has not yet been achieved. We have exploited a unique feature of trypanosomes to prepare a cellular fraction highly enriched in starvation stress granules. First, granules remain trapped within the cage-like, subpellicular microtubule array of the trypanosome cytoskeleton while soluble proteins are washed away. Second, the microtubules are depolymerized and the granules are released. RNA sequencing combined with single molecule mRNA FISH identified the short and highly abundant mRNAs encoding ribosomal mRNAs as being excluded from granules. By mass spectrometry we have identified 463 stress granule candidate proteins. For 17/49 proteins tested by eYFP tagging we have confirmed the localization to granules, including one phosphatase, one methyltransferase and two proteins with a function in trypanosome life-cycle regulation. The novel method presented here enables the unbiased identification of novel RNP granule components, paving the way towards an understanding of RNP granule function.
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Affiliation(s)
- Melanie Fritz
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jens Vanselow
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Nadja Sauer
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stephanie Lamer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Ines Subota
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Mark Carrington
- Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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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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Lott K, Mukhopadhyay S, Li J, Wang J, Yao J, Sun Y, Qu J, Read LK. Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome. Nucleic Acids Res 2015; 43:5501-23. [PMID: 25940618 PMCID: PMC4477658 DOI: 10.1093/nar/gkv428] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/22/2015] [Indexed: 12/30/2022] Open
Abstract
Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei. Here, we report the effects of arginine methylation on the functions of the essential and previously uncharacterized T. brucei RBP, DRBD18. RNAseq analysis shows that DRBD18 depletion causes extensive rearrangement of the T. brucei transcriptome, with increases and decreases in hundreds of mRNAs. DRBD18 contains three methylated arginines, and we used complementation of DRBD18 knockdown cells with methylmimic or hypomethylated DRBD18 to assess the functions of these methylmarks. Methylmimic and hypomethylated DRBD18 associate with different ribonucleoprotein complexes. These altered macromolecular interactions translate into differential impacts on the T. brucei transcriptome. Methylmimic DRBD18 preferentially stabilizes target RNAs, while hypomethylated DRBD18 is more efficient at destabilizing RNA. The protein arginine methyltransferase, TbPRMT1, interacts with DRBD18 and knockdown of TbPRMT1 recapitulates the effects of hypomethylated DRBD18 on mRNA levels. Together, these data support a model in which arginine methylation acts as a switch that regulates T. brucei gene expression.
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Affiliation(s)
- Kaylen Lott
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shreya Mukhopadhyay
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jin Yao
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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