de Godoy, L. M. F. | bioRxiv Science

bioRxiv2026

Proteomic Profiling of Enriched Nuclei Provides a Nuclear Proteome Resource and Protein Interaction Landscape for Trypanosoma cruzi

The processes such as DNA replication, transcription, and repair are often modulated by specific nuclear proteins, protein-protein interactions (PPIs), and post-translational modifications (PTMs). In Trypanosoma cruzi, however, the nuclear proteome and interactome have not been systematically mapped, limiting the interpretation of nuclear regulatory processes. Here, we report a nuclear proteome resource generated from intact nuclei isolated from T. cruzi and analyzed by high-resolution Orbitrap LC-MS/MS, integrating proteome profiling, computational interaction network inference, and exploratory crosslinking mass spectrometry (XL-MS). Proteome profiling identified 1,734 proteins in the nuclear fraction, including 316 proteins identified with PTM-containing peptides. Subcellular localization prediction and Gene Ontology analysis support nuclear enrichment and highlight functions related to transcription, RNA metabolism, and genome maintenance. The in silico interaction network derived from STRINGDB organizes the proteins into functional clusters, including a histone-associated interaction neighborhood. In parallel, XL-MS identified 26 residue-resolved interprotein crosslinks involving 36 proteins and detected PTMs at or near linked residues. Together, these data support reuse for comparative nuclear proteomics, multi-omics integration, and prioritization of candidates for future functional studies.

microbiology↗

bioRxiv2022

Protein arginine and lysine methylation in Trypanosoma cruzi

Post-translational methylation of proteins, which occurs in arginines and lysines, modulates several biological processes at different levels of cell signaling. Recently, methylation has been demonstrated in the regulation beyond histones, for example, in the dynamics of protein-protein and protein-nucleic acid interactions. However, the presence and role of non-histone methylation in Trypanosoma cruzi, the etiologic agent of Chagas disease, has not yet been elucidated. Here, we applied mass spectrometry-based-proteomics (LC-MS/MS) to describe the methylproteome of T. cruzi epimastigotes. A total of 1253 methyl sites in 824 methylated proteins were identified, of these, 712 (86.4%) proteins were identified in two or more biological replicates. Our results of functional enrichment analysis, protein-protein interaction, and co-occurrence with other PTMs, show that protein methylation impacts different levels of biological processes, such translation, RNA and DNA binding, amino acid and carbohydrate metabolism. In addition, 171 methylated proteins were previously reported with phosphorylation sites in T. cruzi, including flagellar proteins and RNA binding proteins, indicating that there may be an interplay between these different modifications in non-histone proteins. Our results show that a broad spectrum of functions are affected by methylation indicating its potential to impact important processes in the biology of the parasite and other trypanosomes. Statement of the significanceTrypanosoma cruzi is a protozoan parasite that causes Chagas disease in humans and faces different environmental changes throughout its life cycle. Protein methylation is an important post-translational modification by which cells respond and adapt to the environment. We applied mass spectrometry-based proteomics and reported the first proteomic analysis of arginine and lysine methylation in T. cruzi. Our data demonstrate that protein methylation is broad and impacts different cellular processes in T. cruzi. This study represents a significant advance in the investigation of the importance of protein methylation in trypanosomes.

genomics↗