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

Abstract

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.