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Antioxidants & Redox Signaling Jul 2015The expression and/or activity of histone deacetylases (HDACs) can be regulated by a variety of environmental conditions, including inflammation and oxidative stress.... (Review)
Review
SIGNIFICANCE
The expression and/or activity of histone deacetylases (HDACs) can be regulated by a variety of environmental conditions, including inflammation and oxidative stress. These events result in diminished or exaggerated protein acetylation, both of which can be causative for many ailments. While the anti-inflammatory activity of HDAC inhibitors (HDACis) is well known, recent studies started unraveling details of the molecular mechanisms underlying the pro-inflammatory function of HDACs.
RECENT ADVANCES
Recent evidence shows that HDACs are found in association with transcribed regions and ensure proper transcription by maintaining acetylation homeostasis. We also discuss current insights in the molecular mechanisms mediating acetylation-dependent inhibition of pro-inflammatory transcription factors of the NF-κB, HIF-1, IRF, and STAT families.
CRITICAL ISSUES
The high number of acetylations and the complexity of the regulatory consequences make it difficult to assign biological effects directly to a single acetylation event. The vast majority of acetylated proteins are nonhistone proteins, and it remains to be shown whether the therapeutic effects of HDACis are attributable to altered histone acetylation.
FUTURE DIRECTIONS
In the traditional view, only exaggerated acetylation is harmful and causative for diseases. Recent data show the relevance of acetylation homeostasis and suggest that both diminished and inflated acetylation can enable the development of ailments. Since acetylation of nonhistone proteins is essential for the induction of a substantial part of the inflammatory gene expression program, HDACis are more than "epigenetic drugs." The identification of substrates for individual HDACs will be the prerequisite for the adequate use of highly specific HDACis.
Topics: Acetylation; Animals; Epigenesis, Genetic; Gene Expression; Histone Acetyltransferases; Histone Deacetylases; Humans; Inflammation; Transcription Factors
PubMed: 24359078
DOI: 10.1089/ars.2013.5750 -
Cell Reports Nov 2021Acetyl ligation to the amino acids in a protein is an important posttranslational modification. However, in contrast to lysine acetylation, N-terminal acetylation is...
Acetyl ligation to the amino acids in a protein is an important posttranslational modification. However, in contrast to lysine acetylation, N-terminal acetylation is elusive in terms of its cellular functions. Here, we identify Nat3 as an N-terminal acetyltransferase essential for autophagy, a catabolic pathway for bulk transport and degradation of cytoplasmic components. We identify the actin cytoskeleton constituent Act1 and dynamin-like GTPase Vps1 (vacuolar protein sorting 1) as substrates for Nat3-mediated N-terminal acetylation of the first methionine. Acetylated Act1 forms actin filaments and therefore promotes the transport of Atg9 vesicles for autophagosome formation; acetylated Vps1 recruits and facilitates bundling of the SNARE (soluble N-ethylmaleimide-sensitive factor activating protein receptor) complex for autophagosome fusion with vacuoles. Abolishment of the N-terminal acetylation of Act1 and Vps1 is associated with blockage of upstream and downstream steps of the autophagy process. Therefore, our work shows that protein N-terminal acetylation plays a critical role in controlling autophagy by fine-tuning multiple steps in the process.
Topics: Acetylation; Actin Cytoskeleton; Actins; Autophagosomes; Autophagy; Carrier Proteins; China; GTP-Binding Proteins; N-Terminal Acetyltransferase B; N-Terminal Acetyltransferases; Phagosomes; Protein Processing, Post-Translational; Protein Transport; SNARE Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Vacuoles; Vesicular Transport Proteins
PubMed: 34788606
DOI: 10.1016/j.celrep.2021.109937 -
Science Advances Apr 2020About 80% of human proteins are amino-terminally acetylated (Nt-acetylated) by one of seven Nt-acetyltransferases (NATs). Actin, the most abundant protein in the...
About 80% of human proteins are amino-terminally acetylated (Nt-acetylated) by one of seven Nt-acetyltransferases (NATs). Actin, the most abundant protein in the cytoplasm, has its own dedicated NAT, NAA80, which acts posttranslationally and affects cytoskeleton assembly and cell motility. Here, we show that NAA80 does not associate with filamentous actin in cells, and its natural substrate is the monomeric actin-profilin complex, consistent with Nt-acetylation preceding polymerization. NAA80 Nt-acetylates actin-profilin much more efficiently than actin alone, suggesting that profilin acts as a chaperone for actin Nt-acetylation. We determined crystal structures of the NAA80-actin-profilin ternary complex, representing different actin isoforms and different states of the catalytic reaction and revealing the first structure of NAT-substrate complex at atomic resolution. The structural, biochemical, and cellular analysis of mutants shows how NAA80 has evolved to specifically recognize actin among all cellular proteins while targeting all six actin isoforms, which differ the most at the amino terminus.
Topics: Acetylation; Acetyltransferases; Actins; Amino Acid Sequence; Binding Sites; Fluorescent Antibody Technique; Humans; Models, Molecular; Molecular Conformation; Profilins; Protein Binding; Protein Domains; Protein Isoforms; Protein Multimerization; Structure-Activity Relationship; Substrate Specificity
PubMed: 32284999
DOI: 10.1126/sciadv.aay8793 -
FASEB Journal : Official Publication of... Oct 2020Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in... (Review)
Review
Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal-dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large-scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC-substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non-catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell-based experimental strategies used to identify KDAC-substrate pairs and evaluate each for the purpose of directly identifying non-histone substrates of metal-dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non-histone substrate-KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well-established, while another thirteen pairs have both cell-based and in vitro evidence but lack independent replication and/or sufficient cell-based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
Topics: Acetylation; Animals; Chromosomal Proteins, Non-Histone; Humans; Protein Processing, Post-Translational; Proteome; Transcription Factors; Tubulin; Zinc
PubMed: 32862458
DOI: 10.1096/fj.202001301RR -
Methods in Enzymology 2023Protein acetylation is a vital biological process that regulates myriad cellular events. Despite its profound effects on protein function, there are limited research...
Protein acetylation is a vital biological process that regulates myriad cellular events. Despite its profound effects on protein function, there are limited research tools to dynamically and selectively regulate protein acetylation. To address this, we developed an acetylation tagging system, called AceTAG, to target proteins for chemically induced acetylation directly in live cells. AceTAG uses heterobifunctional molecules composed of a ligand for the lysine acetyltransferase p300/CBP and a FKBP12 ligand. Target proteins are genetically tagged with FKBP12 and brought in proximity with p300/CBP by AceTAG molecules to subsequently undergo protein-specific acetylation. Targeted acetylation of proteins in cells using AceTAG is selective, rapid, and can be modulated in a dose-dependent fashion, enabling controlled investigations of acetylated protein targets directly in cells. In this protocol, we focus on (1) generation of AceTAG constructs and cell lines, (2) in vitro characterization of AceTAG mediated ternary complex formation and cellular target engagement studies; and (3) in situ characterization of AceTAG induced acetylation of targeted proteins by immunoblotting and quantitative proteomics. The robust procedures described herein should enable the use of AceTAG to explore the roles of acetylation for a variety of protein targets.
Topics: Acetylation; Tacrolimus Binding Protein 1A; Ligands; Cell Line
PubMed: 36764762
DOI: 10.1016/bs.mie.2022.08.014 -
Nature Communications Oct 2023Lysine acetylation has been discovered in thousands of non-histone human proteins, including most metabolic enzymes. Deciphering the functions of acetylation is key to...
Lysine acetylation has been discovered in thousands of non-histone human proteins, including most metabolic enzymes. Deciphering the functions of acetylation is key to understanding how metabolic cues mediate metabolic enzyme regulation and cellular signaling. Glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme in the pentose phosphate pathway, is acetylated on multiple lysine residues. Using site-specifically acetylated G6PD, we show that acetylation can activate (AcK89) and inhibit (AcK403) G6PD. Acetylation-dependent inactivation is explained by structural studies showing distortion of the dimeric structure and active site of G6PD. We provide evidence for acetylation-dependent K95/97 ubiquitylation of G6PD and Y503 phosphorylation, as well as interaction with p53 and induction of early apoptotic events. Notably, we found that the acetylation of a single lysine residue coordinates diverse acetylation-dependent processes. Our data provide an example of the complex roles of acetylation as a posttranslational modification that orchestrates the regulation of enzymatic activity, posttranslational modifications, and apoptotic signaling.
Topics: Humans; Lysine; Acetylation; Protein Processing, Post-Translational
PubMed: 37798264
DOI: 10.1038/s41467-023-41895-2 -
Genes Feb 2021Acetylation on lysine 56 of histone H3 of the yeast has been implicated in many cellular processes that affect genome stability. Despite being the object of much... (Review)
Review
Acetylation on lysine 56 of histone H3 of the yeast has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.
Topics: Acetylation; DNA Repair; DNA Replication; Genomic Instability; Histone Deacetylases; Histones; S Phase; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 33668997
DOI: 10.3390/genes12030342 -
Methods in Molecular Biology (Clifton,... 2022Lysine acetylation is a widespread posttranslational modification (PTM) in all kingdoms of live. A large number of proteins involved in most of biological pathways are...
Lysine acetylation is a widespread posttranslational modification (PTM) in all kingdoms of live. A large number of proteins involved in most of biological pathways are targets of this PTM. The lysine acetylation is a reversible modification controlled by two main groups of enzymes, lysine acetyltransferases responsible for transferring the acetyl group of acetylCoA to the side chain of lysine residues and lysine deacetylases which effectively remove the acetyl tag. Dysregulation of enzymes that control acetylation and/or target proteins have been associated with a growing number of human pathologies. Lysine acetylation is largely a modification that occurs at low stoichiometry at its target sites. Here we describe a method to identify lysine acetylation sites and estimate their site occupancy at the proteome scale. The method relies on a high-resolution mass spectrometry-based proteomics approach, which includes a specific chemical acetylation reaction on unmodified lysine residues that carry heavy isotopes. The procedures described here have been applied to cell line cultures and to clinically relevant samples stored as both snap-frozen and formalin-fixed paraffin-embedded (FFPE) tissues.
Topics: Acetylation; Humans; Lysine; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 34905167
DOI: 10.1007/978-1-0716-1936-0_7 -
Microbiology Spectrum Feb 2023The success of Mycobacterium tuberculosis () as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP...
The success of Mycobacterium tuberculosis () as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP (cAMP) receptor protein (CRP) is closely related to the pathogenicity of and plays an important role in this process. However, the molecular mechanisms guiding the autoregulation and downstream target genes of CRP while responds to its environment are not fully understood. Here, it is demonstrated that the acetylation of conserved lysine 193 (K193) within the C-terminal DNA-binding domain of CRP reduces its DNA-binding ability and inhibits transcriptional activity. The reversible acetylation status of CRP K193 was shown to significantly affect mycobacterial growth phenotype, alter the stress response, and regulate the expression of biologically relevant genes using a CRP K193 site-specific mutation. Notably, the acetylation level of K193 decreases under CRP-activating conditions, including the presence of cAMP, low pH, high temperature, and oxidative stress, suggesting that microenvironmental signals can directly regulate CRP K193 acetylation. Both cell- and murine-based infection assays confirmed that CRP K193 is critical to the regulation of virulence. Furthermore, the acetylation of CRP K193 was shown to be dependent on the intracellular metabolic intermediate acetyl phosphate (AcP), and deacetylation was mediated by NAD-dependent deacetylases. These findings indicate that AcP-mediated acetylation of CRP K193 decreases CRP activity and negatively regulates the pathogenicity of . We believe that the underlying mechanisms of cross talk between transcription, posttranslational modifications, and metabolites are a common regulatory mechanism for pathogenic bacteria. Mycobacterium tuberculosis () is the causative agent of tuberculosis, and the ability of to survive harsh host conditions has been the subject of intensive research. As a result, we explored the molecular mechanisms guiding downstream target genes of CRP when responds to its environment. Our study makes a contribution to the literature because we describe the role of acetylated K193 in regulating its binding affinity to target DNA and influencing the virulence of mycobacteria. We discovered that mycobacteria can regulate their pathogenicity through the reversible acetylation of CRP K193 and that this reversible acetylation is mediated by AcP and a NAD-dependent deacetylase. The regulation of CRP by posttranslational modifications, at the transcriptional level, and by metabolic intermediates contribute to a better understanding of its role in the survival and pathogenicity of mycobacteria.
Topics: Animals; Mice; Virulence; Cyclic AMP Receptor Protein; Acetylation; NAD; Mycobacterium tuberculosis; Protein Processing, Post-Translational; Bacterial Proteins; Gene Expression Regulation, Bacterial
PubMed: 36700638
DOI: 10.1128/spectrum.04002-22 -
Artificial Cells, Nanomedicine, and... Dec 2019JHDM1A participates in cancer development via demethylate dimethyl histone H3 lysine 36 (H3K36me2). p300 is an intrinsic acetyltransferase. This study explored the...
JHDM1A participates in cancer development via demethylate dimethyl histone H3 lysine 36 (H3K36me2). p300 is an intrinsic acetyltransferase. This study explored the acetyltransferase activity of p300 on JHDM1A and analyzed the JHDM1A acetylation on H3K36me2 demethylation in osteosarcoma. Co-immunoprecipitation (CoIP) and immunoblotting assay found that p300 directly acetylated JHDM1A at K409 residue in osteosarcoma MG-63 and HOS cells. Nucleosomes and mononucleosomes were prepared and found that acetylation of JHDMIA disrupted its association with nucleosomes and thereby impaired its capability to induce H3K36me2 demethylation. Moreover, chromatin immunoprecipitation (ChIP) assay discovered that the input levels of H3K36me2 in the promoter regions of and were increased after acetylation of JHDM1A, which raised the and mRNA levels in the cells. Finally, the analysis of JHDM1A acetylation on osteosarcoma cell proliferation and invasion, along with tumor growth pointed out that acetylation of JHDMIA inhibited the proliferation and invasion of osteosarcoma HOS cells, as well as suppressed the tumor growth of osteosarcoma. In conclusion, the outcomes of our research verified that p300 could directly acetylate JHDM1A at K409 site, which reduces the demethylation of H3K36me2, enhanced the transcription of and , and thereby inhibited the growth and metastasis of osteosarcoma.
Topics: Acetylation; Animals; Apoptosis Regulatory Proteins; Carcinogenesis; Cyclin-Dependent Kinase Inhibitor p21; E1A-Associated p300 Protein; F-Box Proteins; Histones; Humans; Jumonji Domain-Containing Histone Demethylases; Lysine; Methylation; Mice; Nucleosomes; Osteosarcoma; Proto-Oncogene Proteins; Transcription, Genetic
PubMed: 31307234
DOI: 10.1080/21691401.2019.1638790