A global analysis of low-complexity regions in the Trypanosoma brucei proteome reveals enrichment in the C-terminus of nucleic acid binding proteins providing potential targets of phosphorylation

• Published in: Wellcome open research Vol. 5; p. 219
• Main Authors: Cayla, Mathieu, Matthews, Keith R, Ivens, Alasdair C
• Format: Journal Article
• Language: English
• Published: England Wellcome Trust Limited 2020; F1000 Research Limited; Wellcome
• Subjects: Algorithms; Amino acids; Bias; Expected values; Gene expression; Ontology; Peer review; Phosphorylation; Proteins; Statistical analysis; Web sites; nucleic acid binding proteins; liquid-liquid phase separation; Low-complexity regions (LCRs); phosphorylation; granules; proteome
• ISSN: 2398-502X; 2398-502X
• DOI: 10.12688/wellcomeopenres.16286.2

Low-complexity regions (LCRs) on proteins have attracted increasing attention recently due to their role in the assembly of membraneless organelles or granules by liquid-liquid phase separation. Several examples of such granules have been shown to sequester RNA and proteins in an inactive state, providing an important mechanism for dynamic post-transcriptional gene regulation. In trypanosome parasites, post-transcriptional control overwhelmingly dominates gene regulation due to the organisation of their genome into polycistronic transcription units. The purpose of the current study was to generate a substantially more comprehensive genome-wide survey of LCRs on trypanosome proteins than currently available Using the Shannon's entropy method, provided in the R package 'entropy', we identified LCRs in the proteome of . Our analysis predicts LCRs and their positional enrichment in distinct protein cohorts and superimposes on this a range of post-translational modifications derived from available experimental datasets. We have identified 8162 LCRs present on 4914 proteins, representing 42% of the proteome, placing among the eukaryotes with the highest percentage of LCRs Our results highlight the enrichment of LCRs in the C-terminal region of predicted nucleic acid binding proteins, these acting as favoured sites for potential phosphorylation. Phosphorylation represents 51% of the post-translational modifications present on LCRs compared to 16% on the rest of the proteome. The post-translational modifications of LCRs, and in particular phosphorylation events, could contribute to post-transcriptional gene expression control and the dynamics of protein targeting to membraneless organelles in kinetoplastid parasites.