The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification

Abstract

Defining all sites for a post-translational modification in the cell, and identifying their upstream modifying enzymes, is essential for a complete understanding of a modification’s function. However, the complete mapping of a modification in the proteome and definition of its associated enzyme–substrate network is rarely achieved. Here, we present the protein methylation network for Saccharomyces cerevisiae. Through a formal process of defining and quantifying all potential sources of incompleteness, for both the methylation sites in the proteome and also protein methyltransferases, we prove that this protein methylation network is now near-complete. It contains 33 methylated proteins and 28 methyltransferases, comprising 44 enzyme-substrate relationships, and a predicted further three enzymes. While the precise molecular function of most methylation sites is unknown, and it remains possible that other sites and enzymes remain undiscovered, the completeness of this protein modification network is unprecedented and allows us to holistically explore the role and evolution of protein methylation in the eukaryotic cell. We show that while no single protein methylation event is essential in yeast, the vast majority of methylated proteins are themselves essential, being primarily involved in the core cellular processes of transcription, RNA processing, and translation. This suggests that protein methylation in lower eukaryotes exists to fine-tune proteins whose sequences are evolutionarily constrained, providing an improvement in the efficiency of their cognate processes. The approach described here, for the construction and evaluation of post-translational modification networks and their constituent enzymes and substrates, defines a formal process of utility for other post-translational modifications.

Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance

“…Set5p, a histone methyltransferase, is known to perform the function of monomethylation modification at histone H4 lysine residues 5, 8, and 12 in yeast. , Set5p regulates gene transcription and the cellular DNA damage response and has overlapping functions with the COMPASS complex and NuA4 histone acetyltransferase complex . Meanwhile, Set5p along with histone H3K4 methyltransferase Set1p also play an important role in both telomere maintenance and transcription of Ty transposable elements in yeast .…”

Methylosome and SMN complexes are dispensable for snRNP assembly in Arabidopsis

“…However, BRR1P is required in presence of specific perturbations, such as weak sm mutant alleles (Schwer et al, 2017). The contribution of arginine methylation to snRNP biogenesis and RNA splicing in yeast has not been studied extensively (Low and Wilkins, 2012; Hamey and Wilkins, 2023).…”