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de Lima LP, Poubel SB, Yuan ZF, Rosón JN, Vitorino FNDL, Holetz FB, Garcia BA, da Cunha JPC. Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite's metacyclogenesis and life cycle. J Proteomics 2020; 225:103847. [PMID: 32480077 DOI: 10.1016/j.jprot.2020.103847] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/26/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Trypanosome histone N-terminal sequences are very divergent from the other eukaryotes, although they are still decorated by post-translational modifications (PTMs). Here, we used a highly robust workflow to analyze histone PTMs in the parasite Trypanosoma cruzi using mass spectrometry-based (MS-based) data-independent acquisition (DIA). We adapted the workflow for the analysis of the parasite's histone sequences by modifying the software EpiProfile 2.0, improving peptide and PTM quantification accuracy. This workflow could now be applied to the study of 141 T. cruzi modified histone peptides, which we used to investigate the dynamics of histone PTMs along the metacyclogenesis and the life cycle of T. cruzi. Global levels of histone acetylation and methylation fluctuates along metacyclogenesis, however most critical differences were observed between parasite life forms. More than 66 histone PTM changes were detected. Strikingly, the histone PTM pattern of metacyclic trypomastigotes is more similar to epimastigotes than to cellular trypomastigotes. Finally, we highlighted changes at the H4 N-terminus and at H3K76 discussing their impact on the trypanosome biology. Altogether, we have optimized a workflow easily applicable to the analysis of histone PTMs in T. cruzi and generated a dataset that may shed lights on the role of chromatin modifications in this parasite. SIGNIFICANCE: Trypanosomes are unicellular parasites that have divergent histone sequences, no chromosome condensation and a peculiar genome/gene regulation. Genes are transcribed from divergent polycistronic regions and post-transcriptional gene regulation play major role on the establishment of transcripts and protein levels. In this regard, the fact that their histones are decorated with multiple PTMs raises interesting questions about their role. Besides, this digenetic organism must adapt to different environments changing its metabolism accordingly. As metabolism and epigenetics are closely related, the study of histone PTMs in trypanosomes may enlighten this strikingly, and not yet fully understood, interplay. From a biomedical perspective, the comprehensive study of molecular mechanisms associated to the metacyclogenesis process is essential to create better strategies for controlling Chagas disease.
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Affiliation(s)
- Loyze P de Lima
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Saloe Bispo Poubel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil; Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR 81350-010, Brazil
| | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana Nunes Rosón
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Francisca Nathalia de Luna Vitorino
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Fabiola Barbieri Holetz
- Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR 81350-010, Brazil
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil.
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Malvezzi AM, Aricó M, Souza-Melo N, Dos Santos GP, Bittencourt-Cunha P, Holetz FB, Schenkman S. GCN2-Like Kinase Modulates Stress Granule Formation During Nutritional Stress in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:149. [PMID: 32373547 PMCID: PMC7176912 DOI: 10.3389/fcimb.2020.00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
The integrated stress response in eukaryotic cells is an orchestrated pathway that leads to eukaryotic Initiation Factor 2 alpha subunit (eIF2α) phosphorylation at ser51 and ultimately activates pathways to mitigate cellular damages. Three putative kinases (Tck1, Tck2, and Tck3) are found in the Trypanosoma cruzi genome, the flagellated parasite that causes Chagas disease. These kinases present similarities to other eukaryotic eIF2α kinases, exhibiting a typical insertion loop in the kinase domain of the protein. We found that this insertion loop is conserved among kinase 1 of several T. cruzi strains but differs among various Kinetoplastidae species, suggesting unique roles. Kinase 1 is orthologous of GCN2 of several eukaryotes, which have been implicated in the eIF2α ser51 phosphorylation in situations that mainly affects the nutrients levels. Therefore, we further investigated the responses to nutritional stress of T. cruzi devoid of TcK1 generated by CRISPR/Cas9 gene replacement. In nutrient-rich conditions, replicative T. cruzi epimastigotes depleted of TcK1 proliferate as wild type cells but showed increased levels of polysomes relative to monosomes. Upon nutritional deprivation, the polysomes decreased more than in TcK1 depleted line. However, eIF2α is still phosphorylated in TcK1 depleted line, as in wild type parasites. eIF2α phosphorylation increased at longer incubations times, but KO parasites showed less accumulation of ribonucleoprotein granules containing ATP-dependent RNA helicase involved in mRNA turnover (DHH1) and Poly-A binding protein (PABP1). Additionally, the formation of metacyclic-trypomastigotes is increased in the absence of Tck1 compared to controls. These metacyclics, as well as tissue culture trypomastigotes derived from the TcK1 knockout line, were less infective to mammalian host cells, although replicated faster inside mammalian cells. These results indicate that GCN2-like kinase in T. cruzi affects stress granule formation, independently of eIF2α phosphorylation upon nutrient deprivation. It also modulates the fate of the parasites during differentiation, invasion, and intracellular proliferation.
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Affiliation(s)
- Amaranta Muniz Malvezzi
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mirella Aricó
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Normanda Souza-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gregory Pedroso Dos Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Paula Bittencourt-Cunha
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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