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      Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes

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          Abstract

          Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation.

          ABSTRACT

          Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.

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          Most cited references198

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          Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

          Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins. Mammalian cell lines are grown in media lacking a standard essential amino acid but supplemented with a non-radioactive, isotopically labeled form of that amino acid, in this case deuterated leucine (Leu-d3). We find that growth of cells maintained in these media is no different from growth in normal media as evidenced by cell morphology, doubling time, and ability to differentiate. Complete incorporation of Leu-d3 occurred after five doublings in the cell lines and proteins studied. Protein populations from experimental and control samples are mixed directly after harvesting, and mass spectrometric identification is straightforward as every leucine-containing peptide incorporates either all normal leucine or all Leu-d3. We have applied this technique to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Proteins that were found to be up-regulated during this process include glyceraldehyde-3-phosphate dehydrogenase, fibronectin, and pyruvate kinase M2. SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system.
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            The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men.

            Protein lysine deacetylases have a pivotal role in numerous biological processes and can be divided into the Rpd3/Hda1 and sirtuin families, each having members in diverse organisms including prokaryotes. In vertebrates, the Rpd3/Hda1 family contains 11 members, traditionally referred to as histone deacetylases (HDAC) 1-11, which are further grouped into classes I, II and IV. Whereas most class I HDACs are subunits of multiprotein nuclear complexes that are crucial for transcriptional repression and epigenetic landscaping, class II members regulate cytoplasmic processes or function as signal transducers that shuttle between the cytoplasm and the nucleus. Little is known about class IV HDAC11, although its evolutionary conservation implies a fundamental role in various organisms.
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              The Sir2 family of protein deacetylases.

              The yeast SIR protein complex has been implicated in transcription silencing and suppression of recombination. The Sir complex represses transcription at telomeres, mating-type loci, and ribosomal DNA. Unlike SIR3 and SIR4, the SIR2 gene is highly conserved in organisms ranging from archaea to humans. Interestingly, Sir2 is active as an NAD+-dependent deacetylase, which is broadly conserved from bacteria to higher eukaryotes. In this review, we discuss the role of NAD+, the unusual products of the deacetylation reaction, the Sir2 structure, and the Sir2 chemical inhibitors and activators that were recently identified. We summarize the current knowledge of the Sir2 homologs from different organisms, and finally we discuss the role of Sir2 in caloric restriction and aging.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                mBio
                MBio
                mbio
                mbio
                mBio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                9 April 2019
                Mar-Apr 2019
                : 10
                : 2
                : e02708-18
                Affiliations
                [a ]Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
                [b ]Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
                [c ]Buck Institute for Research on Aging, Novato, California, USA
                University of Texas Health Science Center at Houston
                Author notes
                Address correspondence to M. L. Kuhn, mkuhn@ 123456sfsu.edu , or A. J. Wolfe, awolfe@ 123456luc.edu .
                Author information
                https://orcid.org/0000-0002-9704-9665
                https://orcid.org/0000-0002-7951-9141
                Article
                mBio02708-18
                10.1128/mBio.02708-18
                6456759
                30967470
                db14acab-c423-42bc-bf06-63fbadd6754a
                Copyright © 2019 Christensen et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 227, Pages: 20, Words: 14863
                Funding
                Funded by: HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID), https://doi.org/10.13039/100000060;
                Award ID: AI108255
                Award Recipient : Award Recipient :
                Funded by: National Science Foundation (NSF), https://doi.org/10.13039/100000001;
                Award ID: CHE-1708863
                Award Recipient :
                Funded by: HHS | NIH | National Center for Research Resources (NCRR), https://doi.org/10.13039/100000097;
                Award ID: 1S10 OD016281
                Award Recipient :
                Funded by: HHS | NIH | National Institute of General Medical Sciences (NIGMS), https://doi.org/10.13039/100000057;
                Award ID: GM066130
                Award Recipient :
                Categories
                Minireview
                Molecular Biology and Physiology
                Custom metadata
                March/April 2019

                Life sciences
                acetylation,acetylome,bacteria,lysine acetyltransferase,mass spectrometry,proteomics
                Life sciences
                acetylation, acetylome, bacteria, lysine acetyltransferase, mass spectrometry, proteomics

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