TY - JOUR
T1 - Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications
T2 - Study of changes in epigenetic marks through the parasite's metacyclogenesis and life cycle
AU - de Lima, Loyze P.
AU - Poubel, Saloe Bispo
AU - Yuan, Zuo Fei
AU - Rosón, Juliana Nunes
AU - Vitorino, Francisca Nathalia de Luna
AU - Holetz, Fabiola Barbieri
AU - Garcia, Benjamin A.
AU - da Cunha, Julia Pinheiro Chagas
N1 - Funding Information:
We thank Karin Cruz, Ivan Novaski Avino and Ismael Feitosa Lima for technical assistance. We thank Dr. Andrea Avila, Dr. Ariel Silber, Dr. Maria Carolina Elias and Dr. Simone Sidoli for reading this manuscript and providing critical comments. This work was supported by fellowships from CNPq , and by grants ( #18/15553-9 , #17/18344-9 , #17/06104-3 , #18/14432-3 , #18/21785-0 and #13/07467-1 ) from Sao Paulo Research Foundation (FAPESP) and by the Serrapilheira Institute (grant number Serra- 1709-16865 ). LPL, FNLV were supported by fellowships from FAPESP; SBP was supported by fellowship from Serrapilheira Institute ; JNR was supported by CAPES .
Funding Information:
We thank Karin Cruz, Ivan Novaski Avino and Ismael Feitosa Lima for technical assistance. We thank Dr. Andrea Avila, Dr. Ariel Silber, Dr. Maria Carolina Elias and Dr. Simone Sidoli for reading this manuscript and providing critical comments. This work was supported by fellowships from CNPq, and by grants (#18/15553-9, #17/18344-9, #17/06104-3, #18/14432-3, #18/21785-0 and #13/07467-1) from Sao Paulo Research Foundation (FAPESP) and by the Serrapilheira Institute (grant number Serra-1709-16865). LPL, FNLV were supported by fellowships from FAPESP; SBP was supported by fellowship from Serrapilheira Institute; JNR was supported by CAPES. LPL, SBP, FBH, ZFY, BAG, JPCC -Conceptualization; LPL, SBP, ZFY, JNR, FNLV and FBH - Formal analysis; BAG, JPCC - Funding acquisition; ZFY, BAG - Software; BAG, JPCC -Supervision; LPL, JPCC - Writing - original draft with comments from all authors.
Publisher Copyright:
© 2020 Elsevier B.V.
PY - 2020/8/15
Y1 - 2020/8/15
N2 - 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.
AB - 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.
KW - EpiProfile
KW - Histone PTM
KW - Life cycle
KW - Metacyclogenesis
KW - Trypanosoma cruzi
UR - http://www.scopus.com/inward/record.url?scp=85085989950&partnerID=8YFLogxK
U2 - 10.1016/j.jprot.2020.103847
DO - 10.1016/j.jprot.2020.103847
M3 - Article
C2 - 32480077
AN - SCOPUS:85085989950
SN - 1874-3919
VL - 225
JO - Journal of Proteomics
JF - Journal of Proteomics
M1 - 103847
ER -