Deep,Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow

Introduction of antibodies specific for acetylated lysine has significantly improved the detection of endogenous acetylation sites by mass spectrometry. Here, we describe a new, commercially available mixture of anti-lysine acetylation (Kac) antibodies and show its utility for in-depth profiling of the acetylome. Specifically, seven complementary monoclones with high specificity for Kac were combined into a final anti-Kac reagent which results in at least a twofold increase in identification of Kac peptides over a commonly used Kac antibody. We outline optimal antibody usage conditions, effective offline basic reversed phase separation, and use of state-of-the-art LC-MS technology for achieving unprecedented coverage of the acetylome. The methods were applied to quantify acetylation sites in suberoylanilide hydroxamic acid-treated Jurkat cells. Over 10,000 Kac peptides from over 3000 Kac proteins were quantified from a single stable isotope labeling by amino acids in cell culture labeled sample using 7.5 mg of peptide input per state. This constitutes the deepest coverage of acetylation sites in quantitative experiments obtained to-date. The approach was also applied to breast tumor xenograft samples using isobaric mass tag labeling of peptides (iTRAQ4, TMT6 and TMT10-plex reagents) for quantification. Greater than 6700 Kac peptides from over 2300 Kac proteins were quantified using 1 mg of tumor protein per iTRAQ 4-plex channel. The novel reagents and methods we describe here enable quantitative, global acetylome analyses with depth and sensitivity approaching that obtained for other well-studied post-translational modifications such as phosphorylation and ubiquitylation, and should have widespread application in biological and clinical studies employing mass spectrometry-based proteomics.Lysine acetylation (Kac)¹ is a well conserved, reversible post-translational modification (PTM) involved in multiple cellular processes (1). Acetylation is regulated by two classes of enzymes: lysine acetyltransferases (KATs) and histone deacetylases (HDACs) (2–4). This modification was originally identified as a nuclear event on histone proteins and has been long appreciated for its role in epigenetic and DNA-dependent processes. With the help of a growing number of large-scale acetylation studies, it has become evident that lysine acetylation is ubiquitous, also occurring on cytoplasmic and mitochondrial proteins and has a role in signaling, metabolism, and immunity (1, 4–6). Therefore, the examination of lysine acetylation on nonhistone proteins has gained a prominent role in PTM analysis.To date, the identification of large numbers of acetylation sites has been challenging because of the substoichiometric nature of this modification (7, 8). Additionally, global acetylation is generally less abundant than phosphorylation and ubiquitylation (1). The introduction of antibodies specific for lysine acetylation has significantly improved the ability to enrich and identify thousands of sites (9–14). A landmark study by Choudhary et al. used anti-Kac antibodies to globally map 3600 lysine acetylation sites on 1750 proteins, thereby demonstrating the feasibility of profiling the acetylome (10). A more recent study by Lundby et al. investigated the function and distribution of acetylation sites in 16 different rat tissues, and identified, in aggregate, 15,474 acetylation sites from 4541 proteins (12).Although anti-acetyl lysine antibodies have been a breakthrough for globally mapping acetylation sites (9–12), it remains a challenge to identify large numbers of lysine acetylation sites from a single sample, as is now routinely possible for phosphorylation and ubiquitylation (13, 15–18). To improve the depth-of-coverage in acetylation profiling experiments there is a clear need for (1) alternative anti-acetyl lysine antibodies with higher specificity, (2) optimized antibody usage parameters, and (3) robust proteomic workflows that permit low to moderate protein input. In this study, we describe a newly commercialized mixture of anti-Kac antibodies and detail a complete proteomic workflow for achieving unprecedented coverage of the acetylome from a single stable isotope labeling by amino acids in cell culture (SILAC) labeled sample as well as isobaric tags for relative and absolute quantitation (iTRAQ)- and tandem mass tag (TMT)-labeled samples.     

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

Post-translational 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 contains 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 4000 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 with nonacetylated 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 is 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.Lysine acetylation is a dynamic and reversible post-translational modification. Acetylation of lysines on their ε-amino group is catalyzed by lysine acetyltransferases (KATs¹, also known as histone acetyltrasferases (HATs)), and reversed by lysine deacetylases (KDACs, also known as histone deacetylases (HDACs)) (1). The enzymatic machinery involved in lysine acetylation is evolutionary conserved in all forms of life (2–4). The role of acetylation has been extensively studied in the regulation of gene expression via modification of histones (5). Acetylation also plays important roles in controlling cellular metabolism (6–10), protein folding (11), and sister chromatid cohesion (12). Furthermore, acetylation has been implicated in regulating the beneficial effects of calorie restriction (13), a low nutrient diet without starvation, and aging. Based on these findings, it is proposed that the functional roles of acetylation in these processes are evolutionary conserved from yeast to mammals.Advancements in mass spectrometry (MS)-based proteomics have greatly facilitated identification of thousands of post-translational modification (PTM) sites in eukaryotic cells (14–18). Proteome-wide mapping of PTM sites can provide important leads for analyzing the functional relevance of individual sites and a systems-wide view of the regulatory scope of post-translational modifications. Also, large-scale PTM datasets are an important resource for the in silico analysis of PTMs, which can broaden the understanding of modification site properties and their evolutionary trajectories.The budding yeast Saccharomyces cerevisiae is a commonly used unicellular eukaryotic model organism. Yeast has been used in many pioneering “-omics” studies, including sequencing of the first eukaryotic genome (19), systems-wide genetic interactions analysis (20, 21), MS-based comprehensive mapping of a eukaryotic proteome (22), and proteome-wide analysis of protein-protein interactions (23, 24). In addition, S. cerevisiae has been extensively used to study the molecular mechanisms of acetylation. Many lysine acetyltransferases and deacetylases were discovered in this organism (2, 25), and their orthologs were subsequently identified in higher eukaryotes. Furthermore, the functional roles of many well-studied acetylation sites on histones are conserved from yeast to mammals. Recent data from human and Drosophila cells show that acetylation is present on many highly conserved metabolic enzymes (26–28). However, only a few dozen yeast acetylation sites are annotated in the Uniprot database. Given the presence of a well-conserved and elaborate acetylation machinery in yeast, we reasoned that many more acetylation sites exist in this organism that remained to be identified.Here we used high resolution mass spectrometry-based proteomics to investigate the scope of acetylation in S. cerevisiae. We identified about 4000 unique acetylation sites in this important model organism. Bioinformatic analysis of yeast acetylation sites and comparison with previously identified human and Drosophila acetylation sites indicates that many acetylation sites are evolutionary conserved. Furthermore, quantitative analysis of the Rpd3-regulated acetylation sites identified several nuclear proteins that showed increased acetylation in rpd3 knockout cells. Our results provide a systems-wide view of acetylation in budding yeast, and a rich dataset for functional analysis of acetylation sites in this organism.     

Acetylome Analysis Reveals Diverse Functions of Lysine Acetylation in Mycobacterium tuberculosis

The lysine acetylation of proteins is a reversible post-translational modification that plays a critical regulatory role in both eukaryotes and prokaryotes. Mycobacterium tuberculosis is a facultative intracellular pathogen and the causative agent of tuberculosis. Increasing evidence shows that lysine acetylation may play an important role in the pathogenesis of M. tuberculosis. However, only a few acetylated proteins of M. tuberculosis are known, presenting a major obstacle to understanding the functional roles of reversible lysine acetylation in this pathogen. We performed a global acetylome analysis of M. tuberculosis H37Ra by combining protein/peptide prefractionation, antibody enrichment, and LC-MS/MS. In total, we identified 226 acetylation sites in 137 proteins of M. tuberculosis H37Ra. The identified acetylated proteins were functionally categorized into an interaction map and shown to be involved in various biological processes. Consistent with previous reports, a large proportion of the acetylation sites were present on proteins involved in glycolysis/gluconeogenesis, the citrate cycle, and fatty acid metabolism. A NAD⁺-dependent deacetylase (MRA_1161) deletion mutant of M. tuberculosis H37Ra was constructed and its characterization showed a different colony morphology, reduced biofilm formation, and increased tolerance of heat stress. Interestingly, lysine acetylation was found, for the first time, to block the immunogenicity of a peptide derived from a known immunogen, HspX, suggesting that lysine acetylation plays a regulatory role in immunogenicity. Our data provide the first global survey of lysine acetylation in M. tuberculosis. The dataset should be an important resource for the functional analysis of lysine acetylation in M. tuberculosis and facilitate the clarification of the entire metabolic networks of this life-threatening pathogen.Mycobacterium tuberculosis was responsible for 1.3 million deaths and 8.6 million new cases of tuberculosis (TB)¹ worldwide in 2012 (1). This global public health crisis remains a serious problem, with the emergence of drug-resistant M. tuberculosis, especially multidrug-resistant and extensively drug-resistant M. tuberculosis, and also the emergence of coinfections of TB and human immunodeficiency virus (2, 3). To counter the increasing threat of TB, it is critical to understand fundamental aspects of TB-related biology. Such studies will not only provide new drug targets for the design of novel therapeutic agents, but also facilitate the development of novel diagnostic tools and new vaccines.Acetylation is one of the important protein modifications and occurs both co- and post-translationally on the α-amino group at the N terminus of the protein, so-called “N-terminal acetylation,” or on the ε-amino group on the side chain of lysine (4). Lysine acetylation is one of the most common post-translational modifications to proteins in both eukaryotes and prokaryotes. As a dynamic and reversible process, protein acetylation plays important roles in many cellular physiological processes, including cell-cycle regulation and apoptosis, cell morphology (5), metabolic pathways (6–8), protein interactions (9), and enzymatic activity (8, 10). In recent years, great advances have been made in proteomic studies, and a large number of lysine-acetylated proteins have been identified in many eukaryotes, including human (5, 11, 12), rat (13), mouse (11), Drosophila (14), Arabidopsis (15, 16), Saccharomyces cerevisiae (17), and protozoans (18, 19). The global analysis of lysine acetylation has also been reported in bacteria, including Escherichia coli (20–22), Erwinia amylovora (23), Bacillus subtilis (24), and Salmonella enterica (6). These acetylome studies have generated large datasets of bacterial proteins acetylated on lysine residues and have demonstrated the diverse cellular functions of lysine acetylation in bacteria.Increasing evidence shows that protein acetylation occurs and plays an important regulatory role in mycobacteria (8, 25–31). For example, Lange et al. reported the N-terminal acetylation of early secreted antigenic target 6 (ESAT-6) protein (31). Rv1151c is reported to be an NAD⁺-dependent protein deacetylase in M. tuberculosis that deacetylates and thus regulates the activity of acetyl-CoA synthase (25, 32). Two cyclic adenosine monophosphate (cAMP)-binding proteins in M. smegmatis and M. tuberculosis (MSMEG_5458 and Rv0998, respectively) show similarity to the GNAT family of acetyltransferases and could acetylate a universal stress protein (USP, MSMEG_4207) (30). Subsequent structural studies revealed the fine mechanisms of how cAMP regulates the protein lysine acetyltransferase in mycobacteria (27, 28). Very recently, reversible lysine acetylation was shown to regulate the activity of several fatty acyl-CoA synthetases in M. tuberculosis (8, 26), and also to regulate acetate and propionate metabolism in M. smegmatis (8, 26). However, to the best of our knowledge, only a few acetylated proteins in M. tuberculosis have been identified, presenting a major obstacle to further understanding the regulatory roles of reversible lysine acetylation in this life-threatening pathogen.To fill this gap in our knowledge, we undertook a systematic study of the functional roles of lysine acetylation in M. tuberculosis. We performed an acetylomic analysis of M. tuberculosis H37Ra using high-accuracy MS combined with the identification of 226 unique lysine acetylation sites on 137 proteins. This set of M. tuberculosis proteins acetylated on lysine residues supports the emerging view that lysine acetylation is a general and fundamental regulatory process, and is not restricted to eukaryotes. It also opens the way for its detailed functional and evolutionary analysis of lysine acetylation in M. tuberculosis. The identified acetylated proteins that are involved in several important biological processes were functionally categorized into an interaction map. This is the first time that an interaction network of acetylated proteins in M. tuberculosis has been constructed, and should allow us to better understand the significance of acetylation in key cellular mechanisms in M. tuberculosis. To further explore the effects of lysine acetylation on the physiology of M. tuberculosis H37Ra, MRA_1161, the gene encoding the only known protein deacetylase in this bacterium, was deleted. The roles of MRA_1161 in the colony morphology, carbon source utilization, heat stress tolerance, and biofilm formation of M. tuberculosis were analyzed. The effect of lysine acetylation on the immunogenicity of a known immunogen, HspX, was also tested.