551
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PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc Natl Acad Sci U S A 2009; 106:761-6. [PMID: 19136633 DOI: 10.1073/pnas.0811739106] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present sequence alignment software, called PTMap, for the accurate identification of full-spectrum protein post-translational modifications (PTMs) and polymorphisms. The software incorporates several features to improve searching speed and accuracy, including peak selection, adjustment of inaccurate mass shifts, and precise localization of PTM sites. PTMap also automates rules, based mainly on unmatched peaks, for manual verification of identified peptides. To evaluate the quality of sequence alignment, we developed a scoring system that takes into account both matched and unmatched peaks in the mass spectrum. Incorporation of these features dramatically increased both accuracy and sensitivity of the peptide- and PTM-identifications. To our knowledge, PTMap is the first algorithm that emphasizes unmatched peaks to eliminate false positives. The superior performance and reliability of PTMap were demonstrated by confident identification of PTMs on 156 peptides from four proteins and validated by MS/MS of the synthetic peptides. Our results demonstrate that PTMap is a powerful algorithm capable of identification of all possible protein PTMs with high confidence.
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552
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Smith BC, Denu JM. Chemical mechanisms of histone lysine and arginine modifications. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:45-57. [PMID: 18603028 PMCID: PMC2642981 DOI: 10.1016/j.bbagrm.2008.06.005] [Citation(s) in RCA: 277] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
Abstract
Histone lysine and arginine residues are subject to a wide array of post-translational modifications including methylation, citrullination, acetylation, ubiquitination, and sumoylation. The combinatorial action of these modifications regulates critical DNA processes including replication, repair, and transcription. In addition, enzymes that modify histone lysine and arginine residues have been correlated with a variety of human diseases including arthritis, cancer, heart disease, diabetes, and neurodegenerative disorders. Thus, it is important to fully understand the detailed kinetic and chemical mechanisms of these enzymes. Here, we review recent progress towards determining the mechanisms of histone lysine and arginine modifying enzymes. In particular, the mechanisms of S-adenosyl-methionine (AdoMet) dependent methyltransferases, FAD-dependent demethylases, iron dependent demethylases, acetyl-CoA dependent acetyltransferases, zinc dependent deacetylases, NAD(+) dependent deacetylases, and protein arginine deiminases are covered. Particular attention is paid to the conserved active-site residues necessary for catalysis and the individual chemical steps along the catalytic pathway. When appropriate, areas requiring further work are discussed.
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Affiliation(s)
- Brian C. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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553
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Taouatas N, Altelaar AFM, Drugan MM, Helbig AO, Mohammed S, Heck AJ. Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications. Mol Cell Proteomics 2009; 8:190-200. [DOI: 10.1074/mcp.m800285-mcp200] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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554
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Berndsen CE, Denu JM. Catalysis and substrate selection by histone/protein lysine acetyltransferases. Curr Opin Struct Biol 2008; 18:682-9. [PMID: 19056256 PMCID: PMC2723715 DOI: 10.1016/j.sbi.2008.11.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 11/03/2008] [Indexed: 01/28/2023]
Abstract
Reversible protein acetylation is controlled by the opposing actions of protein lysine acetyltransferases and deacetylations. Recent developments on the structure and biochemical mechanisms of histone acetyltransferases (HATs) have provided new insight into catalysis and substrate selection. Diverse families of HATs appear to perform a conserved mechanism of acetyl transfer, where the lysine-containing substrate directly attacks enzyme-bound acetyl-CoA. The ability of HATs to form distinct multi-subunit complexes provides a means to regulate HAT activity by altering substrate specificity, targeting to specific loci, enhancing acetyltransferase activity, restricting access of non-target proteins, and coordinating the multiple enzyme activities of the complex. In the case of newly discovered Rtt109 HAT, association with distinct histone chaperones directs substrate selection between N-terminal lysines (H3K9, H3K23) and those (H3K56) within the histone fold domain. Moreover, the ability of some HATs to utilize longer chain acyl-CoA (i.e. propionyl-CoA) as alternative substrates suggests a potential direct link between the metabolic state of the cell and transcriptional regulation.
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Affiliation(s)
- Christopher E. Berndsen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Ave, Madison, WI 53706
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Ave, Madison, WI 53706
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555
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Pelletier N, Grégoire S, Yang XJ. Analysis of protein lysine acetylation in vitro and in vivo. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2008; Chapter 14:14.11.1-14.11.17. [PMID: 19016432 DOI: 10.1002/0471140864.ps1411s54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein lysine acetylation, referring to acetylation of the epsilon-amino group of a lysine residue, has recently emerged as an important post-translational modification for regulating protein functions in various organisms. Like phosphorylation, lysine acetylation is a rapidly reversible and precisely controlled covalent modification that serves as a simple on/off switch or participates in a codified manner with other post-translational modifications to regulate protein functions in different cellular and developmental processes. This unit describes and discusses methods used for in vitro and in vivo determination of lysine acetylation.
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Affiliation(s)
- Nadine Pelletier
- Rosalind and Morris Goodman Cancer Center and Department of Medicine, McGill University, Montreal, Canada
| | - Serge Grégoire
- Rosalind and Morris Goodman Cancer Center and Department of Medicine, McGill University, Montreal, Canada
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Center and Department of Medicine, McGill University, Montreal, Canada
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556
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Smith BC, Hallows WC, Denu JM. Mechanisms and molecular probes of sirtuins. CHEMISTRY & BIOLOGY 2008; 15:1002-13. [PMID: 18940661 PMCID: PMC2626554 DOI: 10.1016/j.chembiol.2008.09.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 09/08/2008] [Accepted: 09/17/2008] [Indexed: 12/12/2022]
Abstract
Sirtuins are critical regulators of many cellular processes, including insulin secretion, the cell cycle, and apoptosis. Sirtuins are associated with a variety of age-associated diseases such as type II diabetes, obesity, and Alzheimer's disease. A thorough understanding of sirtuin chemical mechanisms will aid toward developing novel therapeutics that regulate metabolic disorders and combat associated diseases. In this review, we discuss the unique deacetylase mechanism of sirtuins and how this information might be employed to develop inhibitors and other molecular probes for therapeutic and basic research applications. We also cover physiological regulation of sirtuin activity and how these modes of regulation may be exploited to manipulate sirtuin activity in live cells. Development of molecular probes and drugs that specifically target sirtuins will further understanding of sirtuin biology and potentially afford new treatments of several human diseases.
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Affiliation(s)
- Brian C. Smith
- Department of Biomolecular Chemistry; University of Wisconsin, Medical School; Madison, WI 53706; USA
| | - William C. Hallows
- Department of Biomolecular Chemistry; University of Wisconsin, Medical School; Madison, WI 53706; USA
| | - John M. Denu
- Department of Biomolecular Chemistry; University of Wisconsin, Medical School; Madison, WI 53706; USA
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557
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Garcia BA, Thomas CE, Kelleher NL, Mizzen CA. Tissue-specific expression and post-translational modification of histone H3 variants. J Proteome Res 2008; 7:4225-36. [PMID: 18700791 PMCID: PMC2615678 DOI: 10.1021/pr800044q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analyses of histone H3 from 10 rat tissues using a Middle Down proteomics platform revealed tissue-specific differences in their expression and global PTM abundance. ESI/FTMS with electron capture dissociation showed that, in general, these proteins were hypomodified in heart, liver and testes. H3.3 was hypermodified compared to H3.2 in some, but not all tissues. In addition, a novel rat testes-specific H3 protein was identified with this approach.
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Affiliation(s)
- Benjamin A Garcia
- Institute for Genomic Biology, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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558
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Cheng Z, Tang Y, Chen Y, Kim S, Liu H, Li SSC, Gu W, Zhao Y. Molecular characterization of propionyllysines in non-histone proteins. Mol Cell Proteomics 2008; 8:45-52. [PMID: 18753126 DOI: 10.1074/mcp.m800224-mcp200] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine propionylation and butyrylation are protein modifications that were recently identified in histones. The molecular components involved in the two protein modification pathways are unknown, hindering further functional studies. Here we report identification of the first three in vivo non-histone protein substrates of lysine propionylation in eukaryotic cells: p53, p300, and CREB-binding protein. We used mass spectrometry to map lysine propionylation sites within these three proteins. We also identified the first two in vivo eukaryotic lysine propionyltransferases, p300 and CREB-binding protein, and the first eukaryotic depropionylase, Sirt1. p300 was able to perform autopropionylation on lysine residues in cells. Our results suggest that lysine propionylation, like lysine acetylation, is a dynamic and regulatory post-translational modification. Based on these observations, it appears that some enzymes are common to the lysine propionylation and lysine acetylation regulatory pathways. Our studies therefore identified first several important players in lysine propionylation pathway.
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Affiliation(s)
- Zhongyi Cheng
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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559
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Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 2008; 8:215-25. [PMID: 18723842 DOI: 10.1074/mcp.m800187-mcp200] [Citation(s) in RCA: 397] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine acetylation and its regulatory enzymes are known to have pivotal roles in mammalian cellular physiology. However, the extent and function of this modification in prokaryotic cells remain largely unexplored, thereby presenting a hurdle to further functional study of this modification in prokaryotic systems. Here we report the first global screening of lysine acetylation, identifying 138 modification sites in 91 proteins from Escherichia coli. None of the proteins has been previously associated with this modification. Among the identified proteins are transcriptional regulators, as well as others with diverse functions. Interestingly, more than 70% of the acetylated proteins are metabolic enzymes and translation regulators, suggesting an intimate link of this modification to energy metabolism. The new dataset suggests that lysine acetylation could be abundant in prokaryotic cells. In addition, these results also imply that functions of lysine acetylation beyond regulation of gene expression are evolutionarily conserved from bacteria to mammals. Furthermore, we demonstrate that bacterial lysine acetylation is regulated in response to stress stimuli.
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Affiliation(s)
- Junmei Zhang
- Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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560
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Ishino K, Shibata T, Ishii T, Liu YT, Toyokuni S, Zhu X, Sayre LM, Uchida K. Protein N-acylation: H2O2-mediated covalent modification of protein by lipid peroxidation-derived saturated aldehydes. Chem Res Toxicol 2008; 21:1261-70. [PMID: 18512967 DOI: 10.1021/tx800080x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various lines of evidence indicate that the oxidative modification of protein and the subsequent accumulation of the degenerated proteins have been found in cells and tissues during aging, oxidative stress, and in a variety of pathological states. The critical agents that give rise to this protein degeneration may be represented by aldehydes. Although the covalent modification of proteins by aldehydes alone has been well-studied, the effect of reactive oxygen species, such as H2O2, upon aldehyde modification of the protein has received little attention. We have now established a unique protein modification in which H2O2 and, to a lesser extent, alkyl hydroperoxides mediate the binding of alkanals to the lysine residues of protein to generate structurally unusual N-acylation products. Upon the reaction of a lysine-containing peptide, N(alpha)-benzoylglycyl-lysine, with hexanal in the presence of H2O2, a product containing one molecule of hexanal per peptide was detected. On the basis of the chemical and spectroscopic evidence, the product was identified to be the acylation product, N(epsilon)-hexanoyllysine. H2O2 mediated the N-acylation of the lysine derivative by the saturated aldehydes of 1-6 carbons in length. The H2O2-mediated acylation of the protein was immunochemically confirmed by reaction of the proteins with hexanal in the presence of H2O2. Furthermore, the enhanced N-acylations (N-acetylation and N-hexanoylation) were also observed in the kidney of rats exposed to ferric nitrilotriacetate, a well-characterized inducer of oxidative stress. Mechanistic studies using a phosphonium lysine derivative suggest a Baeyer-Villiger-like reaction proceeding through peroxide addition to the aldehyde Schiff base. These data suggest that the hydroperoxides, including H2O2, might be involved not only in the oxidative modification of protein but also in the covalent binding of the saturated aldehydes to proteins under oxidative stress.
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Affiliation(s)
- Kousuke Ishino
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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561
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Leemhuis H, Packman LC, Nightingale KP, Hollfelder F. The human histone acetyltransferase P/CAF is a promiscuous histone propionyltransferase. Chembiochem 2008; 9:499-503. [PMID: 18247445 DOI: 10.1002/cbic.200700556] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Indexed: 11/06/2022]
Affiliation(s)
- Hans Leemhuis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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562
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Yang XJ, Seto E. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 2008; 9:206-18. [PMID: 18292778 PMCID: PMC2667380 DOI: 10.1038/nrm2346] [Citation(s) in RCA: 947] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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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Affiliation(s)
- Xiang-Jiao Yang
- Molecular Oncology Group, Department of Medicine, McGill University Health Center, Montréal, Québec, H3A 1A1, Canada.
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563
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Jones P, Altamura S, De Francesco R, Gallinari P, Lahm A, Neddermann P, Rowley M, Serafini S, Steinkühler C. Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases. Bioorg Med Chem Lett 2008; 18:1814-9. [PMID: 18308563 DOI: 10.1016/j.bmcl.2008.02.025] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Revised: 02/07/2008] [Accepted: 02/09/2008] [Indexed: 10/22/2022]
Abstract
It has been widely debated whether class IIa HDACs have catalytic deacetylase activity, and whether this plays any part in controlling gene expression. Herein, it has been demonstrated that class IIa HDACs isolated from mammalian cells are contaminated with other deacetylases, but can be prepared cleanly in Escherichia coli. These bacteria preparations have weak but measurable deacetylase activity. The low efficiency can be restored either by: mutation of an active site histidine to tyrosine, or by the use of a non-acetylated lysine substrate, allowing the development of assays to identify class IIa HDAC inhibitors.
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Affiliation(s)
- Philip Jones
- IRBM/Merck Research Laboratories, Via Pontina km 30,600, 00040 Pomezia, Italy.
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564
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Smith BC, Denu JM. Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. J Biol Chem 2007; 282:37256-65. [PMID: 17951578 DOI: 10.1074/jbc.m707878200] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Class III histone deacetylases (Sir2 or sirtuins) catalyze the NAD+-dependent conversion of acetyl-lysine residues to nicotinamide, 2'-O-acetyl-ADP-ribose (OAADPr), and deacetylated lysine. Class I and II HDACs utilize a different deacetylation mechanism, utilizing an active site zinc to direct hydrolysis of acetyl-lysine residues to lysine and acetate. Here, using ten acetyl-lysine analog peptides, we have probed the substrate binding pockets of sirtuins and investigated the catalytic differences among sirtuins and class I and II deacetylases. For the sirtuin Hst2, acetyl-lysine analog peptide binding correlated with the hydrophobic substituent parameter pi with a slope of -0.35 from a plot of log Kd versus pi. Interestingly, propionyl- and butyryl-lysine peptides were found to bind tighter to Hst2 compared with acetyl-lysine peptide and showed measurable rates of catalysis with Hst2, Sirt1, Sirt2, and Sirt3, suggesting propionyl- and butyryl-lysine proteins may be sirtuin substrates in vivo. Unique among the acetyl-lysine analog peptides examined, homocitrulline peptide produced ADP-ribose instead of the corresponding OAADPr analog. The electron-withdrawing nature of each acetyl analog had a profound impact on the deacylation rate between deacetylase classes. The rate of catalysis with the acetyl-lysine analog peptides varied over five orders of magnitude with the class III deacetylase Hst2, revealing a linear free energy relationship with a slope of -1.57 when plotted versus the Taft constant, sigma*. HDAC8, a class I deacetylase, displayed the opposite trend with a slope of +0.79. These results are applicable toward the development of selective substrates and other mechanistic probes of protein deacetylases.
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Affiliation(s)
- Brian C Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1532, USA
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565
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Dormeyer W, Mohammed S, Breukelen BV, Krijgsveld J, Heck AJR. Targeted analysis of protein termini. J Proteome Res 2007; 6:4634-45. [PMID: 17927228 DOI: 10.1021/pr070375k] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a targeted analysis of protein isoforms by selective enrichment and identification of in vivo acetylated protein N-termini and protein C-termini. Our method allows the characterization of these protein termini regardless of their annotation in protein databases and requires no chemical derivatization. Using an iterative database search strategy that takes account of the enrichment protocol, 263 IPI annotated and 87 unpredicted acetylated N-termini were identified in the crude membrane fraction of human embryonic carcinoma cells. The N-acetylated peptides conform to the reported criteria for in vivo modification. In addition, 168 IPI annotated and 193 unpredicted C-termini were identified. Additionally, and for the first time, we also report on in vivo N-terminal propionylation. The significant number of unknown protein N- and C-termini suggests a high degree of novel transcription independent of annotated gene boundaries and/or specific protein processing. Biological relevance of several of these unpredicted protein termini could be curated from the literature, adding further weight to the argument to go beyond routine database search strategies. Our method will improve the correct annotation of genes and proteins in databases.
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Affiliation(s)
- Wilma Dormeyer
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, the Netherlands
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566
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Witze ES, Old WM, Resing KA, Ahn NG. Mapping protein post-translational modifications with mass spectrometry. Nat Methods 2007; 4:798-806. [PMID: 17901869 DOI: 10.1038/nmeth1100] [Citation(s) in RCA: 575] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Post-translational modifications of proteins control many biological processes, and examining their diversity is critical for understanding mechanisms of cell regulation. Mass spectrometry is a fundamental tool for detecting and mapping covalent modifications and quantifying their changes. Modern approaches have made large-scale experiments possible, screening complex mixtures of proteins for alterations in chemical modifications. By profiling protein chemistries, biologists can gain deeper insight into biological control. The aim of this review is introduce biologists to current strategies in mass spectrometry-based proteomics that are used to characterize protein post-translational modifications, noting strengths and shortcomings of various approaches.
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Affiliation(s)
- Eric S Witze
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
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567
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Yang XJ, Seto E. HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 2007; 26:5310-8. [PMID: 17694074 DOI: 10.1038/sj.onc.1210599] [Citation(s) in RCA: 742] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acetylation of the epsilon-amino group of a lysine residue was first discovered with histones in 1968, but the responsible enzymes, histone acetyltransferases and deacetylases, were not identified until the mid-1990s. In the past decade, knowledge about this modification has exploded, with targets rapidly expanding from histones to transcription factors and other nuclear proteins, and then to cytoskeleton, metabolic enzymes, and signaling regulators in the cytoplasm. Thus, protein lysine acetylation has emerged as a major post-translational modification to rival phosphorylation. In this issue of Oncogene, 19 articles review various aspects of the enzymes governing lysine acetylation, especially about their intimate links to cancer. To introduce the articles, we highlight here four central themes: (i) multisubunit enzymatic complexes; (ii) non-histone substrates in diverse cellular processes; (iii) interplay of lysine acetylation with other regulatory mechanisms, such as noncoding RNA-mediated gene silencing and activation; and (iv) novel therapeutic strategies and preventive measures to combat cancer and other human diseases.
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Affiliation(s)
- X-J Yang
- Molecular Oncology Group, Department of Medicine, McGill University Health Center, Montréal, Québec, Canada.
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568
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Hildmann C, Riester D, Schwienhorst A. Histone deacetylases—an important class of cellular regulators with a variety of functions. Appl Microbiol Biotechnol 2007; 75:487-97. [PMID: 17377789 DOI: 10.1007/s00253-007-0911-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 02/26/2007] [Accepted: 02/26/2007] [Indexed: 12/25/2022]
Abstract
The elucidation of mechanisms of chromatin remodeling, particular transcriptional activation, and repression by histone acetylation and deacetylation has shed light on the role of histone deacetylases (HDAC) as a new kind of therapeutic target for human cancer treatment. HDACs, in general, act as components of large corepressor complexes that prevent the transcription of several tumor suppression genes. In addition, they appear to be also involved in the deacetylation of nonhistone proteins. This paper reviews the most recent insights into the diverse biological roles of HDACs as well as the evolution of this important protein family.
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Affiliation(s)
- Christian Hildmann
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, Grisebachstr. 8, 37077, Göttingen, Germany
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