1
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Lima ARJ, Silva HGD, Poubel S, Rosón JN, de Lima LPO, Costa-Silva HM, Gonçalves CS, Galante PAF, Holetz F, Motta MCMM, Silber AM, Elias MC, da Cunha JPC. Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci. Epigenetics Chromatin 2022; 15:22. [PMID: 35650626 PMCID: PMC9158160 DOI: 10.1186/s13072-022-00450-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into codirectional gene clusters with unrelated functions. Moreover, there is no dedicated promoter for each gene, resulting in polycistronic gene transcription, with posttranscriptional control playing a major role. Nonetheless, these parasites harbor epigenetic modifications at critical regulatory genome features that dynamically change among parasite stages, which are not fully understood. RESULTS Here, we investigated the impact of chromatin changes in a scenario commanded by posttranscriptional control exploring the parasite Trypanosoma cruzi and its differentiation program using FAIRE-seq approach supported by transmission electron microscopy. We identified differences in T. cruzi genome compartments, putative transcriptional start regions, and virulence factors. In addition, we also detected a developmental chromatin regulation at tRNA loci (tDNA), which could be linked to the intense chromatin remodeling and/or the translation regulatory mechanism required for parasite differentiation. We further integrated the open chromatin profile with public transcriptomic and MNase-seq datasets. Strikingly, a positive correlation was observed between active chromatin and steady-state transcription levels. CONCLUSION Taken together, our results indicate that chromatin changes reflect the unusual gene expression regulation of trypanosomes and the differences among parasite developmental stages, even in the context of a lack of canonical transcriptional control of protein-coding genes.
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Affiliation(s)
- Alex Ranieri Jerônimo Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Herbert Guimarães de
Sousa Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Saloe Poubel
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Juliana Nunes Rosón
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Loyze Paola Oliveira de Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Héllida Marina Costa-Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Camila Silva Gonçalves
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Pedro A. F. Galante
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, SP Brazil
| | - Fabiola Holetz
- grid.418068.30000 0001 0723 0931Instituto Carlos Chagas, Fiocruz, Curitiba, PR Brazil
| | - Maria Cristina Machado M. Motta
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Ariel M. Silber
- grid.11899.380000 0004 1937 0722Universidade de São Paulo, São Paulo, SP Brazil
| | - M. Carolina Elias
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil. .,Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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2
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Lima ARJ, de Araujo CB, Bispo S, Patané J, Silber AM, Elias MC, da Cunha JPC. Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms. PLoS Pathog 2021; 17:e1009272. [PMID: 33497423 PMCID: PMC7864430 DOI: 10.1371/journal.ppat.1009272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/05/2021] [Accepted: 01/04/2021] [Indexed: 11/25/2022] Open
Abstract
Trypanosoma cruzi alternates between replicative and nonreplicative life forms, accompanied by a shift in global transcription levels and by changes in the nuclear architecture, the chromatin proteome and histone posttranslational modifications. To gain further insights into the epigenetic regulation that accompanies life form changes, we performed genome-wide high-resolution nucleosome mapping using two T. cruzi life forms (epimastigotes and cellular trypomastigotes). By combining a powerful pipeline that allowed us to faithfully compare nucleosome positioning and occupancy, more than 125 thousand nucleosomes were mapped, and approximately 20% of them differed between replicative and nonreplicative forms. The nonreplicative forms have less dynamic nucleosomes, possibly reflecting their lower global transcription levels and DNA replication arrest. However, dynamic nucleosomes are enriched at nonreplicative regulatory transcription initiation regions and at multigenic family members, which are associated with infective-stage and virulence factors. Strikingly, dynamic nucleosome regions are associated with GO terms related to nuclear division, translation, gene regulation and metabolism and, notably, associated with transcripts with different expression levels among life forms. Finally, the nucleosome landscape reflects the steady-state transcription expression: more abundant genes have a more deeply nucleosome-depleted region at putative 5' splice sites, likely associated with trans-splicing efficiency. Taken together, our results indicate that chromatin architecture, defined primarily by nucleosome positioning and occupancy, reflects the phenotypic differences found among T. cruzi life forms despite the lack of a canonical transcriptional control context.
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Affiliation(s)
- Alex R. J. Lima
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Christiane B. de Araujo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Saloe Bispo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - José Patané
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel M. Silber
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - M. Carolina Elias
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
- * E-mail: (MCE); (JPCC)
| | - Julia P. C. da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
- * E-mail: (MCE); (JPCC)
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3
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Dos Santos GP, Abukawa FM, Souza-Melo N, Alcântara LM, Bittencourt-Cunha P, Moraes CB, Jha BK, McGwire BS, Moretti NS, Schenkman S. Cyclophilin 19 secreted in the host cell cytosol by Trypanosoma cruzi promotes ROS production required for parasite growth. Cell Microbiol 2020; 23:e13295. [PMID: 33222354 DOI: 10.1111/cmi.13295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 01/06/2023]
Abstract
Infection by Trypanosoma cruzi, the protozoan parasite that causes Chagas disease, depends on reactive oxygen species (ROS), which has been described to induce parasite proliferation in mammalian host cells. It is unknown how the parasite manages to increase host ROS levels. Here, we found that intracellular T. cruzi forms release in the host cytosol its major cyclophilin of 19 kDa (TcCyp19). Parasites depleted of TcCyp19 by using CRISPR/Cas9 gene replacement proliferate inefficiently and fail to increase ROS, compared to wild type parasites or parasites with restored TcCyp19 gene expression. Expression of TcCyp19 in L6 rat myoblast increased ROS levels and restored the proliferation of TcCyp19 depleted parasites. These events could also be inhibited by cyclosporin A, (a cyclophilin inhibitor), and by polyethylene glycol-linked to antioxidant enzymes. TcCyp19 was found more concentrated in the membrane leading edges of the host cells in regions that also accumulate phosphorylated p47phox , as observed to the endogenous cyclophilin A, suggesting some mechanisms involved with the translocation process of the regulatory subunit p47phox in the activation of the NADPH oxidase enzymatic complex. We concluded that cyclophilin released in the host cell cytosol by T. cruzi mediates the increase of ROS, required to boost parasite proliferation in mammalian hosts.
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Affiliation(s)
- Gregory Pedroso Dos Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Midori Abukawa
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Normanda Souza-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Laura Maria Alcântara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Paula Bittencourt-Cunha
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Carolina Borsoi Moraes
- Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Bijay Kumar Jha
- Division of Infectious Diseases/Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Bradford S McGwire
- Division of Infectious Diseases/Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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4
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Castro Machado F, Bittencourt-Cunha P, Malvezzi AM, Arico M, Radio S, Smircich P, Zoltner M, Field MC, Schenkman S. EIF2α phosphorylation is regulated in intracellular amastigotes for the generation of infective Trypanosoma cruzi trypomastigote forms. Cell Microbiol 2020; 22:e13243. [PMID: 32597009 DOI: 10.1111/cmi.13243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
Trypanosomatids regulate gene expression mainly at the post-transcriptional level through processing, exporting and stabilising mRNA and control of translation. In most eukaryotes, protein synthesis is regulated by phosphorylation of eukaryotic initiation factor 2 (eIF2) at serine 51. Phosphorylation halts overall translation by decreasing availability of initiator tRNAmet to form translating ribosomes. In trypanosomatids, the N-terminus of eIF2α is extended with threonine 169 the homologous phosphorylated residue. Here, we evaluated whether eIF2α phosphorylation varies during the Trypanosoma cruzi life cycle, the etiological agent of Chagas' disease. Total levels of eIF2α are diminished in infective and non-replicative trypomastigotes compared with proliferative forms from the intestine of the insect vector or amastigotes from mammalian cells, consistent with decreased protein synthesis reported in infective forms. eIF2α phosphorylation increases in proliferative intracellular forms prior to differentiation into trypomastigotes. Parasites overexpressing eIF2αT169A or with an endogenous CRISPR/Cas9-generated eIF2αT169A mutation were created and analysis revealed alterations to the proteome, largely unrelated to the presence of μORF in epimastigotes. eIF2αT169A mutant parasites produced fewer trypomastigotes with lower infectivity than wild type, with increased levels of sialylated mucins and oligomannose glycoproteins, and decreased galactofuranose epitopes and the surface protease GP63 on the cell surface. We conclude that eIF2α expression and phosphorylation levels affect proteins relevant for intracellular progression of T. cruzi.
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Affiliation(s)
- Fabricio Castro Machado
- Departmento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Paula Bittencourt-Cunha
- Departmento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Amaranta Muniz Malvezzi
- Departmento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mirella Arico
- Departmento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Santiago Radio
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Martin Zoltner
- Drug Discovery and Evaluation, Centre for Research of Pathogenicity and Virulence of Parasites, Charles University, Prague, Czech Republic
| | - Mark C Field
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK.,Institute of Parasitology, Czech Academy of Sciences, Prague, Czech Republic
| | - Sergio Schenkman
- Departmento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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5
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Pavani RS, Lima LP, Lima AA, Fernandes CAH, Fragoso SP, Calderano SG, Elias MC. Nuclear export of replication protein A in the nonreplicative infective forms of
Trypanosoma cruzi. FEBS Lett 2020; 594:1596-1607. [DOI: 10.1002/1873-3468.13755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Raphael S. Pavani
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - Loyze P. Lima
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - André A. Lima
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - Carlos A. H. Fernandes
- Departamento de Física e Biofísica Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) Botucatu Brazil
- Laboratorie de Biologie et Pharmacologie Appliquée Ecole Normale Supérieure Paris‐Saclay Cachan France
| | | | - Simone G. Calderano
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
- Laboratório de Parasitologia Instituto Butantan São Paulo Brazil
| | - Maria Carolina Elias
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
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6
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Meng QB, Peng JJ, Qu ZW, Zhu XM, Wen Z, Kang WM. Eukaryotic initiation factor 5A2 and human digestive system neoplasms. World J Gastrointest Oncol 2019; 11:449-458. [PMID: 31236196 PMCID: PMC6580320 DOI: 10.4251/wjgo.v11.i6.449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/17/2019] [Accepted: 05/04/2019] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic initiation factor 5A2 (eIF5A2), as one of the two isoforms in the family, is reported to be a novel oncogenic protein that is involved in multiple aspects of many types of human cancer. Overexpression or gene amplification of EIF5A2 has been demonstrated in many cancers. Accumulated evidence shows that eIF5A2 initiates tumor formation, enhances cancer cell growth, increases cancer cell metastasis, and promotes treatment resistance through multiple means, including inducing epithelial–mesenchymal transition, cytoskeletal rearrangement, angiogenesis, and metabolic reprogramming. Expression of eIF5A2 in cancer correlates with poor survival, advanced disease stage, as well as metastasis, suggesting that eIF5A2 function is crucial for tumor development and maintenance but not for normal tissue homeostasis. All these studies suggest that eIF5A2 is a useful biomarker in the prediction of cancer prognosis and serves as an anticancer molecular target. This review focuses on the expression, subcellular localization, post-translational modifications, and regulatory networks of eIF5A2, as well as its biochemical functions and evolving clinical applications in cancer, especially in human digestive system neoplasms.
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Affiliation(s)
- Qing-Bin Meng
- Department of Gastrointestinal Surgery, the First Hospital of Wuhan City, Wuhan 430022, Hubei Province, China
| | - Jing-Jing Peng
- Department of Gastroenterology, General Hospital of the Yangtze River Shipping, Wuhan 430015, Hubei Province, China
| | - Zi-Wei Qu
- Department of Gastrointestinal Surgery, the First Hospital of Wuhan City, Wuhan 430022, Hubei Province, China
| | | | - Zhang Wen
- Department of Hepato-Biliary-Pancreatic Surgery and Liver Transplantation, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Wei-Ming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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7
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Moreira DDS, Duarte AP, Pais FSM, da Silva-Pereira RA, Romanha AJ, Schenkman S, Murta SMF. Overexpression of eukaryotic initiation factor 5A (eIF5A) affects susceptibility to benznidazole in Trypanosoma cruzi populations. Mem Inst Oswaldo Cruz 2018; 113:e180162. [PMID: 30066751 PMCID: PMC6060400 DOI: 10.1590/0074-02760180162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022] Open
Abstract
Eukaryotic initiation factor 5A (eIF5A) is a conserved protein with an essential role in translation elongation. Using one and two-dimensional western blotting, we showed that the eIF5A protein level was 2-fold lower in benznidazole (BZ)-resistant (BZR and 17LER) Trypanosoma cruzi populations than in their respective susceptible counterparts (BZS and 17WTS). To confirm the role of eIF5A in BZ resistance, we transfected BZS and 17WTS with the wild-type eIF5A or mutant eIF5A-S2A (in which serine 2 was replaced by alanine). Upon overexpressing eIF5A, both susceptible lines became approximately 3- and 5-fold more sensitive to BZ. In contrast, the eIF5A-S2A mutant did not alter its susceptibility to BZ. These data suggest that BZ resistance might arise from either decreasing the translation of proteins that require eIF5A, or as a consequence of differential levels of precursors for the hypusination reactions (e.g., spermidine and trypanothione), both of which alter BZ's effects in the parasite.
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Affiliation(s)
| | - Ana Paula Duarte
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Belo Horizonte, MG, Brasil
| | | | | | - Alvaro José Romanha
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Belo Horizonte, MG, Brasil
| | - Sergio Schenkman
- Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brasil
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8
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Moretti NS, Cestari I, Anupama A, Stuart K, Schenkman S. Comparative Proteomic Analysis of Lysine Acetylation in Trypanosomes. J Proteome Res 2018; 17:374-385. [PMID: 29168382 DOI: 10.1021/acs.jproteome.7b00603] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Protein acetylation is a post-translational modification regulating diverse cellular processes. By using proteomic approaches, we identified N-terminal and ε-lysine acetylated proteins in Trypanosoma cruzi and Trypanosoma brucei, which are protozoan parasites that cause significant human and animal diseases. We detected 288 lysine acetylation sites in 210 proteins of procyclic form, an insect stage of T. brucei, and 380 acetylation sites in 285 proteins in the form of the parasite that replicates in mammalian bloodstream. In T. cruzi insect proliferative form we found 389 ε-lysine-acetylated sites in 235 proteins. Notably, we found distinct acetylation profiles according to the developmental stage and species, with only 44 common proteins between T. brucei stages and 18 in common between the two species. While K-ac proteins from T. cruzi are enriched in enzymes involved in oxidation/reduction balance, required for the parasite survival in the host, in T. brucei, most K-ac proteins are enriched in metabolic processes, essential for its adaptation in its hosts. We also identified in both parasites a quite variable N-terminal acetylation sites. Our results suggest that protein acetylation is involved in differential regulation of multiple cellular processes in Trypanosomes, contributing to our understanding of the essential mechanisms for parasite infection and survival.
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Affiliation(s)
- Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo , R. Pedro de Toledo 669 L6A, 04039-032 São Paulo, SP, Brazil.,Center for Infectious Disease Research , 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Igor Cestari
- Center for Infectious Disease Research , 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Atashi Anupama
- Center for Infectious Disease Research , 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Ken Stuart
- Center for Infectious Disease Research , 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo , R. Pedro de Toledo 669 L6A, 04039-032 São Paulo, SP, Brazil
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9
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de Lima Stein ML, Icimoto MY, de Castro Levatti EV, Oliveira V, Straus AH, Schenkman S. Characterization and role of the 3-methylglutaconyl coenzyme A hidratase in Trypanosoma brucei. Mol Biochem Parasitol 2017; 214:36-46. [PMID: 28366667 DOI: 10.1016/j.molbiopara.2017.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 01/30/2023]
Abstract
Trypanosoma brucei, the agent of African Trypanosomiasis, is a flagellated protozoan parasite that develops in tsetse flies and in the blood of various mammals. The parasite acquires nutrients such as sugars, lipids and amino acids from their hosts. Amino acids are used to generate energy and for protein and lipid synthesis. However, it is still unknown how T. brucei catabolizes most of the acquired amino acids. Here we explored the role of an enzyme of the leucine catabolism, the 3-methylglutaconyl-Coenzyme A hydratase (3-MGCoA-H). It catalyzes the hydration of 3-methylglutaconyl-Coenzyme A (3-MGCoA) into 3-hydroxymethylglutaryl-Coenzyme A (3-HMGCoA). We found that 3-MGCoA-H localizes in the mitochondrial matrix and is expressed in both insect and mammalian bloodstream forms of the parasite. The depletion of 3-MGCoA-H by RNA interference affected minimally the proliferation of both forms. However, an excess of leucine in the culture medium caused growth defects in cells depleted of 3-MGCoA-H, which could be reestablished by mevalonate, a precursor of isoprenoids and steroids. Indeed, procyclics depleted of the 3-MGCoA-H presented reduced levels of synthesized steroids relative to cholesterol that is scavenged by the parasite, and these levels were also reestablished by mevalonate. These results suggest that accumulation of leucine catabolites could affect the level of mevalonate and consequently inhibit the sterol biosynthesis, required for T. brucei growth.
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Affiliation(s)
- Mariana Leão de Lima Stein
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo Yudi Icimoto
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | - Vitor Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Anita Hilda Straus
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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10
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Pereira KD, Tamborlin L, Meneguello L, de Proença ARG, Almeida ICDPA, Lourenço RF, Luchessi AD. Alternative Start Codon Connects eIF5A to Mitochondria. J Cell Physiol 2016; 231:2682-9. [PMID: 27414022 DOI: 10.1002/jcp.25370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/04/2016] [Indexed: 01/02/2023]
Abstract
Eukaryotic translation initiation factor 5A (eIF5A), a protein containing the amino acid residue hypusine required for its activity, is involved in a number of physiological and pathological cellular processes. In humans, several EIF5A1 transcript variants encode the canonical eIF5A1 isoform B, whereas the hitherto uncharacterized variant A is expected to code for a hypothetical eIF5A1 isoform, referred to as isoform A, which has an additional N-terminal extension. Herein, we validate the existence of eIF5A1 isoform A and its production from transcript variant A. In fact, variant A was shown to encode both eIF5A1 isoforms A and B. Mutagenic assays revealed different efficiencies in the start codons present in variant A, contributing to the production of isoform B at higher levels than isoform A. Immunoblotting and mass spectrometric analyses showed that isoform A can undergo hypusination and acetylation at specific lysine residues, as observed for isoform B. Examination of the N-terminal extension suggested that it might confer mitochondrial targeting. Correspondingly, we found that isoform A, but not isoform B, co-purified with mitochondria when the proteins were overproduced. These findings suggest that eIF5A1 isoform A has a role in mitochondrial function. J. Cell. Physiol. 231: 2682-2689, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Karina Danielle Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Letícia Tamborlin
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Letícia Meneguello
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, Brazil
| | | | | | - Rogério Ferreira Lourenço
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Augusto Ducati Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, Brazil
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11
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Leandro de Jesus TC, Calderano SG, Vitorino FNDL, Llanos RP, Lopes MDC, de Araújo CB, Thiemann OH, Reis MDS, Elias MC, Chagas da Cunha JP. Quantitative Proteomic Analysis of Replicative and Nonreplicative Forms Reveals Important Insights into Chromatin Biology of Trypanosoma cruzi. Mol Cell Proteomics 2016; 16:23-38. [PMID: 27852749 DOI: 10.1074/mcp.m116.061200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/02/2016] [Indexed: 01/02/2023] Open
Abstract
Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and nonreplicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and nonreplicative (trypomastigote) forms by high-resolution mass spectrometry. More than 2000 proteins were identified and quantified both in chromatin and nonchromatin extracts. Besides histones and other known nuclear proteins, trypanosomes chromatin also contains metabolic (mainly from carbohydrate pathway), cytoskeleton and many other proteins with unknown functions. Strikingly, the two parasite forms differ greatly regarding their chromatin-associated factors composition and amount. Although the nucleosome content is the same for both life forms (as seen by MNase digestion), the remaining proteins were much less detected in nonreplicative forms, suggesting that they have a naked chromatin. Proteins associated to DNA proliferation, such as PCNA, RPA, and DNA topoisomerases were exclusively found in the chromatin of replicative stages. On the other hand, the nonreplicative stages have an enrichment of a histone H2B variant. Furthermore, almost 20% of replicative stages chromatin-associated proteins are expressed in nonreplicative forms, but located at nonchromatin space. We identified different classes of proteins including phosphatases and a Ran-binding protein, that may shuttle between chromatin and nonchromatin space during differentiation. Seven proteins, including those with unknown functions, were selected for further validation. We confirmed their location in chromatin and their differential expression, using Western blotting assays and chromatin immunoprecipitation (ChIP). Our results indicate that the replicative state in trypanosomes involves an increase of chromatin associated proteins content. We discuss in details, the qualitative and quantitative implication of this chromatin set in trypanosome chromatin biology. Because trypanosomes are early-branching organisms, this data can boost our understanding of chromatin-associated processes in other cell types.
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Affiliation(s)
- Teresa Cristina Leandro de Jesus
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,§Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo - USP, São Carlos, SP, 13563-120, Brazil
| | - Simone Guedes Calderano
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,¶Laboratório de Parasitologia, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Francisca Nathalia de Luna Vitorino
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Ricardo Pariona Llanos
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Mariana de Camargo Lopes
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Christiane Bezerra de Araújo
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Otavio Henrique Thiemann
- §Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo - USP, São Carlos, SP, 13563-120, Brazil
| | - Marcelo da Silva Reis
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Maria Carolina Elias
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Julia Pinheiro Chagas da Cunha
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil;
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12
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Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. Sci Rep 2016; 6:31697. [PMID: 27545962 PMCID: PMC4992866 DOI: 10.1038/srep31697] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/25/2016] [Indexed: 01/11/2023] Open
Abstract
Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.
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Avila CCDC, Peacock L, Machado FC, Gibson W, Schenkman S, Carrington M, Castilho BA. Phosphorylation of eIF2α on Threonine 169 is not required for Trypanosoma brucei cell cycle arrest during differentiation. Mol Biochem Parasitol 2016; 205:16-21. [PMID: 26996431 PMCID: PMC4850487 DOI: 10.1016/j.molbiopara.2016.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 11/17/2022]
Abstract
Pleomorphic T. brucei expressing an eIF2α phosphorylation site mutant were made. The mutation did not prevent normal arrest and differentiation into stumpy forms. Mutants differentiate into procyclic forms in vitro and in tsetse flies.
The trypanosome life cycle consists of a series of developmental forms each adapted to an environment in the relevant insect and/or mammalian host. The differentiation process from the mammalian bloodstream form to the insect-midgut procyclic form in Trypanosoma brucei occurs in two steps in vivo. First proliferating ‘slender' bloodstream forms differentiate to non-dividing ‘stumpy' forms arrested in G1. Second, in response to environmental cues, stumpy bloodstream forms re-enter the cell cycle and start to proliferate as procyclic forms after a lag during which both cell morphology and gene expression are modified. Nearly all arrested cells have lower rates of protein synthesis when compared to the proliferating equivalent. In eukaryotes, one mechanism used to regulate the overall rate of protein synthesis involves phosphorylation of the alpha subunit of initiation factor eIF2 (eIF2α). The effect of eIF2α phosphorylation is to prevent the action of eIF2B, the guanine nucleotide exchange factor that activates eIF2 for the next rounds of initiation. To investigate the role of the phosphorylation of eIF2α in the life cycle of T. brucei, a cell line was made with a single eIF2α gene that contained the phosphorylation site, threonine 169, mutated to alanine. These cells were capable of differentiating from proliferating bloodstream form cells into arrested stumpy forms in mice and into procyclic forms in vitro and in tsetse flies. These results indicate that translation attenuation mediated by the phosphorylation of eIF2α on threonine 169 is not necessary for the cell cycle arrest associated with these differentiation processes.
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Affiliation(s)
- Carla Cristi D C Avila
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Lori Peacock
- Department of Clinical Veterinary Science, University of Bristol, Langford, Bristol BS40 5DU, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Fabricio Castro Machado
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Sergio Schenkman
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Beatriz A Castilho
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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14
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Cassola A, Romaniuk MA, Primrose D, Cervini G, D'Orso I, Frasch AC. Association of UBP1 to ribonucleoprotein complexes is regulated by interaction with the trypanosome ortholog of the human multifunctional P32 protein. Mol Microbiol 2015; 97:1079-96. [PMID: 26096620 DOI: 10.1111/mmi.13090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 12/30/2022]
Abstract
Regulation of gene expression in trypanosomatid parasitic protozoa is mainly achieved posttranscriptionally. RNA-binding proteins (RBPs) associate to 3' untranslated regions in mRNAs through dedicated domains such as the RNA recognition motif (RRM). Trypanosoma cruzi UBP1 (TcUBP1) is an RRM-type RBP involved in stabilization/degradation of mRNAs. TcUBP1 uses its RRM to associate with cytoplasmic mRNA and to mRNA granules under starvation stress. Here, we show that under starvation stress, TcUBP1 is tightly associated with condensed cytoplasmic mRNA granules. Conversely, under high nutrient/low density-growing conditions, TcUBP1 ribonucleoprotein (RNP) complexes are lax and permeable to mRNA degradation and disassembly. After dissociating from mRNA, TcUBP1 can be phosphorylated only in unstressed parasites. We have identified TcP22, the ortholog of mammalian P32/C1QBP, as an interactor of TcUBP1 RRM. Overexpression of TcP22 decreased the number of TcUBP1 granules in starved parasites in vivo. Endogenous TcUBP1 RNP complexes could be dissociated in vitro by addition of recombinant TcP22, a condition stimulating TcUBP1 phosphorylation. Biochemical and in silico analysis revealed that TcP22 interacts with the RNA-binding surface of TcUBP1 RRM. We propose a model for the decondensation of TcUBP1 RNP complexes in T. cruzi through direct interaction with TcP22 and phosphorylation.
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Affiliation(s)
- Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - María Albertina Romaniuk
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Debora Primrose
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Gabriela Cervini
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Iván D'Orso
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Alberto Carlos Frasch
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
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15
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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: 93] [Impact Index Per Article: 10.3] [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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16
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Igarashi K, Kashiwagi K. Modulation of protein synthesis by polyamines. IUBMB Life 2015; 67:160-9. [PMID: 25906835 DOI: 10.1002/iub.1363] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 11/09/2022]
Abstract
Polyamines are ubiquitous small basic molecules that play important roles in cell growth and viability. Since polyamines mainly exist as a polyamine-RNA complex, we looked for proteins whose synthesis is preferentially stimulated by polyamines at the level of translation, and thus far identified 17 proteins in Escherichia coli and 6 proteins in eukaryotes. The mechanisms of polyamine stimulation of synthesis of these proteins were investigated. In addition, the role of eIF5A, containing hypusine formed from spermidine, on protein synthesis is described. These results clearly indicate that polyamines and eIF5A contribute to cell growth and viability through modulation of protein synthesis.
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Affiliation(s)
- Kazuei Igarashi
- Department of Clinical Biochemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-Ku, Chiba, Japan; Amine Pharma Research Institute, Chuo-Ku, Chiba, Japan
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17
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da Silva Augusto L, Moretti NS, Ramos TCP, de Jesus TCL, Zhang M, Castilho BA, Schenkman S. A membrane-bound eIF2 alpha kinase located in endosomes is regulated by heme and controls differentiation and ROS levels in Trypanosoma cruzi. PLoS Pathog 2015; 11:e1004618. [PMID: 25658109 PMCID: PMC4450062 DOI: 10.1371/journal.ppat.1004618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/10/2014] [Indexed: 12/29/2022] Open
Abstract
Translation initiation has been described as a key step for the control of growth and differentiation of several protozoan parasites in response to environmental changes. This occurs by the activation of protein kinases that phosphorylate the alpha subunit of the translation initiation factor 2 (eIF2α), which decreases translation, and in higher eukaryotes favors the expression of stress remedial response genes. However, very little is known about the signals that activate eIF2α kinases in protozoan parasites. Here, we characterized an eIF2α kinase of Trypanosoma cruzi (TcK2), the agent of Chagas’ disease, as a transmembrane protein located in organelles that accumulate nutrients in proliferating parasite forms. We found that heme binds specifically to the catalytic domain of the kinase, inhibiting its activity. In the absence of heme, TcK2 is activated, arresting cell growth and inducing differentiation of proliferative into infective and non-proliferative forms. Parasites lacking TcK2 lose this differentiation capacity and heme is not stored in reserve organelles, remaining in the cytosol. TcK2 null cells display growth deficiencies, accumulating hydrogen peroxide that drives the generation of reactive oxygen species. The augmented level of hydrogen peroxide occurs as a consequence of increased superoxide dismutase activity and decreased peroxide activity. These phenotypes could be reverted by the re-expression of the wild type but not of a TcK2 dead mutant. These findings indicate that heme is a key factor for the growth control and differentiation through regulation of an unusual type of eIF2α kinase in T. cruzi. Trypanosoma cruzi proliferates as epimastigotes in the midgut of the insect vector filled with blood meal. There, it accumulates nutrients in specific endosomal organelles. The parasite moves towards the hindgut and when the blood is completely digested, these organelles are consumed. At this moment, the insect is ready for a new feeding cycle that promotes the release of infective metacyclic-trypomastigote forms. We have previously found that such differentiation involves protein synthesis arrest through the phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α). Now, we show that one of the kinases (TCK2) that phosphorylate eIF2α is localized in these endosomes. TcK2 binds and is specifically inhibited by heme derived from blood hemoglobin. We also found that heme inhibits differentiation, suggesting that it is an important signal for differentiation. By generating knockouts of TcK2, we observed an increased accumulation of heme in the cytosol, which induced cellular damage by affecting the reactive oxygen metabolism in the parasite. We conclude that this eIF2α kinase senses cytosolic heme obtained from the blood meal, promoting its storage in the cytosolic organelles. When heme levels are decreased in the cytosol, TcK2 activation can then arrest protein synthesis that is followed by the induction of the differentiation of proliferative epimastigote forms to infective metacyclic-trypomastigotes.
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Affiliation(s)
- Leonardo da Silva Augusto
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Thiago Cesar Prata Ramos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Teresa Cristina Leandro de Jesus
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Min Zhang
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Beatriz A. Castilho
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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18
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Stress induces changes in the phosphorylation of Trypanosoma cruzi RNA polymerase II, affecting its association with chromatin and RNA processing. EUKARYOTIC CELL 2014; 13:855-65. [PMID: 24813189 DOI: 10.1128/ec.00066-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the trans-splicing of all mRNAs transcribed on long polycistronic units. We found that Trypanosoma cruzi RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing.
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19
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Shang Y, Zhao X, Tian B, Wang Y, Ren F, Jia B, Zhai Y, Chen W, He D, Chang Z. CHIP/Stub1 interacts with eIF5A and mediates its degradation. Cell Signal 2014; 26:1098-104. [PMID: 24509416 DOI: 10.1016/j.cellsig.2014.01.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/09/2014] [Accepted: 01/26/2014] [Indexed: 12/12/2022]
Abstract
eIF5A, containing the unusual amino acid hypusine, is a highly conserved protein essential for the proliferation of eukaryotic cells. Previous studies have demonstrated that the activity of eIF5A was regulated through modification of hypusine, phosphorylation and acetylation. However, no study was documented for regulation of the protein stability. Here, we report that eIF5A is a target of CHIP (the carboxyl terminus of Hsc70-interacting protein, also named Stub1), an E3 ligase with a U-box domain, through a proteomics analysis. CHIP directly interacted with eIF5A, preferably through the U-box domain, to mediate eIF5A ubiquitination and degradation. Simultaneously, we investigated that CHIP expression inversely correlated with eIF5A levels in colorectal cancers, consistent with the fact that the protein level of eIF5A was increased in the CHIP knock-out MEF cells. Taken together, we propose that CHIP regulates the eIF5A protein stability via a protein degradation mechanism. This study provides a new insight into understanding the regulation of the eIF5A stability.
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Affiliation(s)
- Yu Shang
- The Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Xinghui Zhao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China; State Key Laboratory of Pathogens and Biosecurity, Laboratory of Applied Molecular Biology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Bo Tian
- Department of Surgical Oncology, Affiliated Hospital of Shaanxi University of Chinese Medicine, Shaanxi, Xianyang 712083, China
| | - Yinyin Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fangli Ren
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Baoqing Jia
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Yonggong Zhai
- The Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Wei Chen
- State Key Laboratory of Pathogens and Biosecurity, Laboratory of Applied Molecular Biology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Dacheng He
- The Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhijie Chang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China.
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Rossi D, Kuroshu R, Zanelli CF, Valentini SR. eIF5A and EF-P: two unique translation factors are now traveling the same road. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:209-22. [PMID: 24402910 DOI: 10.1002/wrna.1211] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 11/09/2022]
Abstract
Translational control is extremely important in all organisms, and some of its aspects are highly conserved among all primary kingdoms, such as those related to the translation elongation step. The previously classified translation initiation factor 5A (eIF5A) and its bacterial homologue elongation factor P (EF-P) were discovered in the late 70's and have recently been the object of many studies. eIF5A and EF-P are the only cellular proteins that undergo hypusination and lysinylation, respectively, both of which are unique posttranslational modifications. Herein, we review all the important discoveries related to the biochemical and functional characterization of these factors, highlighting the implication of eIF5A in translation elongation instead of initiation. The findings that eIF5A and EF-P are important for specific cellular processes and play a role in the relief of ribosome stalling caused by specific amino acid sequences, such as those containing prolines reinforce the hypothesis that these factors are involved in specialized translation. Although there are some divergences between these unique factors, recent studies have clarified that they act similarly during protein synthesis. Further studies may reveal their precise mechanism of ribosome activity modulation as well as the mRNA targets that require eIF5A and EF-P for their proper translation.
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Affiliation(s)
- Danuza Rossi
- Department of Biological Sciences, School of Pharmaceutical Sciences, Univ Estadual Paulista (UNESP), Araraquara, SP, Brazil
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Pascoalino B, Dindar G, Vieira-da-Rocha JP, Machado CR, Janzen CJ, Schenkman S. Characterization of two different Asf1 histone chaperones with distinct cellular localizations and functions in Trypanosoma brucei. Nucleic Acids Res 2013; 42:2906-18. [PMID: 24322299 PMCID: PMC3950673 DOI: 10.1093/nar/gkt1267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The anti-silencing function protein 1 (Asf1) is a chaperone that forms a complex with histones H3 and H4 facilitating dimer deposition and removal from chromatin. Most eukaryotes possess two different Asf1 chaperones but their specific functions are still unknown. Trypanosomes, a group of early-diverged eukaryotes, also have two, but more divergent Asf1 paralogs than Asf1 of higher eukaryotes. To unravel possible different functions, we characterized the two Asf1 proteins in Trypanosoma brucei. Asf1A is mainly localized in the cytosol but translocates to the nucleus in S phase. In contrast, Asf1B is predominantly localized in the nucleus, as described for other organisms. Cytosolic Asf1 knockdown results in accumulation of cells in early S phase of the cell cycle, whereas nuclear Asf1 knockdown arrests cells in S/G2 phase. Overexpression of cytosolic Asf1 increases the levels of histone H3 and H4 acetylation. In contrast to cytosolic Asf1, overexpression of nuclear Asf1 causes less pronounced growth defects in parasites exposed to genotoxic agents, prompting a function in chromatin remodeling in response to DNA damage. Only the cytosolic Asf1 interacts with recombinant H3/H4 dimers in vitro. These findings denote the early appearance in evolution of distinguishable functions for the two Asf1 chaperons in trypanosomes.
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Affiliation(s)
- Bruno Pascoalino
- Depto. de Microbiologia, Imunologia e Parasitologia, UNIFESP, Rua Pedro de Toledo 669 L6A, São Paulo, São Paulo 04039-032, Brazil, Lehrstuhl für Zell- und Entwicklungsbiologie, Theodor-Boveri-Institut, Biozentrum der Universität Würzburg, Am Hubland, 97074 Würzburg, Germany and Depto. de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CP 4861, 30161-970, Belo Horizonte, Minas Gerais, Brazil
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