Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential

Abstract

Edited by John Denu This article contains supporting information.

Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast

“…For ease of visualisation, only a single copy of histones H3 and H4 have been illustrated, while both copies of histones H2A and H2B have been omitted. PTM sites were from a recent systematic characterisation of yeast histone methyltransferases and demethylases (316) and high-throughput phosphoproteomic and acetylomic studies (247,. For each modification type, the number of residues within each protein that has been shown to be post-translationally modified in at least one study has been graphed as a bar chart.…”

“…The vast majority of these PTM sites have been identified through high-throughput proteomic screens that typically involve affinity-based enrichment for specific modification types and their subsequent analysis by high-resolution, bottom-up mass spectrometry of peptides. To canvass the PTM topology of histone methylation proteins, we mined several publicly available proteomic datasets ( 246 , 301 , 302 , 303 , 304 , 305 , 306 , 307 , 308 , 309 , 310 , 311 , 312 , 313 , 314 , 315 , 316 , 317 , 318 , 319 , 320 , 321 ) and PTM databases (including UniProt ( 322 ), PhosphoGRID ( 323 ), and YAAM ( 324 )), including one study that achieved near-complete characterization of the purified enzymes ( 315 ). Our collation of PTMs comprises a total of 251 modification sites, of which phosphorylation (143 sites), acetylation (101 sites), and ubiquitination (seven sites) were the most commonly found ( Fig.…”

“…These PTMs represent those identified in a range of yeast cellular growth states and under different growth conditions. Despite efforts to identify other PTM types ( e.g., protein methylation, acylation, crotonylation, ADP-ribosylation) on this family of enzymes ( 315 ), no such sites have been observed to date. This does not, however, definitively rule out the possibility of their occurrence in vivo.…”

“…

Figure 4 Post - translational modifications on yeast histone methylation enzymes . PTM sites were from a recent systematic characterization of yeast histone methyltransferases and demethylases ( 315 ) and high-throughput phosphoproteomic and acetylomic studies ( 246 , 301 , 302 , 303 , 304 , 305 , 306 , 307 , 308 , 309 , 310 , 311 , 312 , 313 , 314 , 315 , 316 , 317 , 318 , 319 , 320 , 321 ). For each modification type, the number of residues within each protein that has been shown to be post-translationally modified in at least one study has been graphed as a bar chart.

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“…The histone lysine methylation network in budding yeast receives substantial input from upstream signaling pathways. A recent systematic characterization of all S. cerevisiae histone methyltransferases and demethylases defined a comprehensive set of phosphosites occurring on these enzymes in vivo for mid–log phase yeast cells grown under standard laboratory conditions ( 315 ). This study, in conjunction with previous high-throughput phosphoproteomic analyses, identified a total of 107 and 35 phosphosites on serine and threonine residues, respectively.…”