Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

University of Copenhagen, Denmark
Molecular & Cellular Proteomics (Impact Factor: 6.56). 08/2012; 11(11). DOI: 10.1074/mcp.M112.017251
Source: PubMed


Summary Posttranslational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contain several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4,000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared to non-acetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes.

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    • "Protein (de)acetylation plays critical roles in many key biological processes, for example, transcriptional regulation, aging, and metabolism (Cohen et al., 2004; Grunstein, 1997; Lin et al., 2009; Lu et al., 2011). Recent mass spectrometry (MS) efforts have revealed that many proteins are acetylated in Escherichia coli, although only a single E. coli lysine deacetylase (KDAC), CobB, has been identified so far (Choudhary et al., 2009; Henriksen et al., 2012; Zhang et al., 2013a). The fact that induction of CobB only had a limited impact on reducing the global protein acetylation level suggests that additional KDACs may exist. "
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    ABSTRACT: Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a 'clip-chip' strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD(+) or Zn(2+) like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC's bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs.
    Preview · Article · Dec 2015 · eLife Sciences
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    • "Saccharomyces cerevisiae 2878/1059 a,b,e 17.9 N [80] Salmonella enterica 235/191 a,e 4.2 Y [9] "
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    ABSTRACT: Post-translational modification of proteins is a reversible mechanism of cellular adaptation to changing environmental conditions. In eukaryotes, the physiological relevance of N-ɛ-lysine protein acetylation is well demonstrated. In recent times, important roles in the regulation of metabolic processes in bacteria are being uncovered, adding complexity to cellular regulatory networks. The aim of this mini-review is to sum up the current state-of-the-art in the regulation of bacterial physiology by protein acetylation. Current knowledge on the molecular biology aspects of known bacterial protein acetyltransferases and deacetylases will be summarized. Protein acetylation in Escherichia coli, Salmonella enterica, Bacillus subtilis, Rhodopseudomonas palustris and Mycobacterium tuberculosis, will be explained in the light of their physiological relevance. Progress in the elucidation of bacterial acetylomes and the emerging understanding of chemical acylation mechanisms will be discussed together with their regulatory and evolutionary implications. Fundamental molecular studies detailing this recently discovered regulatory mechanism pave the way for their prospective application for the construction of synthetic regulation networks.
    Full-text · Article · Dec 2014 · New Biotechnology
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    • "Proteins from every functional class are subject to acetylation (e.g., RNA processing, protein synthesis ) while almost every enzyme participating in major metabolic pathways (e.g., glycolysis, gluconeogenesis) is acetylated in yeast (Henriksen et al., 2012). The evolutionary conservation of acetylated lysines is higher than non-acetylated lysines (Weinert et al., 2011; Henriksen et al., 2012) and sites of lysine acetylation are more tightly conserved than sites of phosphorylation (Weinert et al., 2011). Nevertheless, the stoichiometry of phosphorylation in yeast is significantly higher than acetylation, where the majority of acetylated sites have stoichiometries lower than 1% (Weinert et al., 2013b). "
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    ABSTRACT: Lysine modifications have been studied extensively in the nucleus, where they play pivotal roles in gene regulation and constitute one of the pillars of epigenetics. In the cytoplasm, they are critical to proteostasis. However, in the last decade we have also witnessed the emergence of mitochondria as a prime locus for post-translational modification (PTM) of lysine thanks, in large measure, to evolving proteomic techniques. Here, we review recent work on evolving set of PTM that arise from the direct reaction of lysine residues with energized metabolic thioester-coenzyme A intermediates, including acetylation, succinylation, malonylation, and glutarylation. We highlight the evolutionary conservation, kinetics, stoichiometry, and cross-talk between members of this emerging family of PTMs. We examine the impact on target protein function and regulation by mitochondrial sirtuins. Finally, we spotlight work in the heart and cardiac mitochondria, and consider the roles acetylation and other newly-found modifications may play in heart disease.
    Full-text · Article · Sep 2014 · Frontiers in Physiology
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