Biology subjects

Wallis, D. C.

Publications and source records attributed to Wallis, D. C..

3 recordsLinked to original sources

bioRxiv2026

LC-MS profiling of prmt-1 and prmt-5 knockout C. elegans reveals PRMT-1 substrates and global proteome remodeling

Although protein arginine methylation regulates diverse biological processes, it remains understudied relative to other post-translational modifications. Here, we analyzed C. elegans prmt-1 and prmt-5 null mutants using LC-MS proteomics to map PRMT methylation substrates and to quantify the effects of PRMT knockout on global protein abundance. High-pH strong cation exchange fractionation was used to enrich methylated peptides, and parallel analysis of whole cell lysates was used to measure global protein abundance. Quantitative methyl-proteomics identified 31 PRMT-1-dependent methyl-arginine peptides from 15 proteins with several arginine residues demonstrating dramatic decrease in both monomethyl- and asymmetric dimethyl-arginine abundance. Whole-proteome profiling revealed that prmt-1 knockout caused broad remodeling of the worm proteome with changes linked to DNA replication/cell-cycle programs, protein folding, and amino acid metabolism. Although prmt-5 knockout affected similar biological pathways to prmt-1 knockout, the effects on the C. elegans proteome were more modest. Together, these data connect PRMT-dependent methylation changes to proteome remodeling in a whole-animal model, support previous work suggesting that PRMT-1 is the dominant Type I PRMT in C. elegans, and provide a resource for studying how PRMT-1 and PRMT-5 shape protein regulation in vivo. All raw data have been deposited in the PRIDE database with accession number PXD074042.

systems biology↗

bioRxiv2025

RG motifs promote piRNA-mediated gene silencing in C. elegans

Argonaute proteins are essential players in RNA silencing pathways, and their N-terminal extensions, particularly in the PIWI clade, often harbor conserved sequences like RG motifs. Despite their prevalence in Argonaute proteins, the role of these motifs remains poorly understood. In this study, we focus on the RG motifs within the N-terminal region of Caenorhabditis elegans PRG-1, a PIWI clade Argonaute. Using sequence alignment across Caenorhabditis species, we identify three conserved RG motifs that are methylated, as confirmed by mass spectrometry. The region surrounding these motifs is intrinsically disordered, as predicted by disorder algorithms and structural modeling. While the RG motifs are critical for fertility, germline morphology, and piRNA silencing, they are not required for PRG-1 expression, localization, or piRNA loading. Notably, mutation of the RG motifs results in defects in downstream small RNA production, specifically the depletion of mutator class siRNAs, without affecting piRNA biogenesis. These findings suggest that the RG motifs of PRG-1 play a crucial role in linking piRNA-mediated silencing to siRNA production, and that their function is critical for fertility and germline maintenance in C. elegans. Despite these defects, the phenotypic severity in the RG mutant is milder than in a PRG-1 null mutant, highlighting the complexity of PRG-1 function and its post-translational modifications.

molecular biology↗

bioRxiv2020

Mutator foci are regulated by developmental stage, RNA, and the germline cell cycle in Caenorhabditis elegans

RNA interference is a crucial gene regulatory mechanism in Caenorhabditis elegans. Phase-separated perinuclear germline compartments called Mutator foci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance, Mutator foci regulation is not well understood, and observations of Mutator foci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctate Mutator foci arise in the progenitor germ cells of early embryos and persist throughout all larval stages. They are additionally present throughout the male germline and in the cytoplasm of post-meiotic spermatids, suggestive of a role in paternal epigenetic inheritance. In the adult germline, transcriptional inhibition results in a pachytene-specific loss of Mutator foci, indicating that Mutator foci are partially reliant on RNA for their stability. Finally, we demonstrate that Mutator foci intensity is modulated by the stage of the germline cell cycle and specifically, that Mutator foci are brightest and most robust in the mitotic cells, transition zone, and late pachytene of adult germlines. Thus, our data defines several new factors that modulate Mutator foci morphology which may ultimately have implications for efficacy of RNAi in certain cell stages or environments.

genetics↗