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Non-histone protein acetylation by the evolutionarily conserved GCN5 and PCAF acetyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194608. [PMID: 32711095 DOI: 10.1016/j.bbagrm.2020.194608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
GCN5, conserved from yeast to humans, and the vertebrate specific PCAF, are lysine acetyltransferase enzymes found in large protein complexes. Both enzymes have well documented roles in the histone acetylation and the concomitant regulation of transcription. However, these enzymes also acetylate non-histone substrates to impact diverse aspects of cell physiology. Here, I review our current understanding of non-histone acetylation by GCN5 and PCAF across eukaryotes, from target identification to molecular mechanism and regulation. I focus mainly on budding yeast, where Gcn5 was first discovered, and mammalian systems, where the bulk of non-histone substrates have been characterized. I end the review by defining critical caveats and open questions that apply to all models.
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Lu Q, Helm S, Rödiger A, Baginsky S. On the Extent of Tyrosine Phosphorylation in Chloroplasts. PLANT PHYSIOLOGY 2015; 169:996-1000. [PMID: 26243617 PMCID: PMC4587464 DOI: 10.1104/pp.15.00921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 07/29/2015] [Indexed: 05/20/2023]
Abstract
Reanalysis of published mass spectrometry data on Tyr-phosphorylated chloroplast proteins indicates that the majority of peptide spectrum matches reporting Tyr phosphorylation are ambiguous.
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Affiliation(s)
- Qintao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Stefan Helm
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Anja Rödiger
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
| | - Sacha Baginsky
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (Q.L.); andInstitute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.H., A.R., S.B.)
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Rohe A, Platzer C, Masch A, Greiner S, Henze C, Ihling C, Erdmann F, Schutkowski M, Sippl W, Schmidt M. Identification of peptidic substrates for the human kinase Myt1 using peptide microarrays. Bioorg Med Chem 2015; 23:4936-4942. [DOI: 10.1016/j.bmc.2015.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 01/25/2023]
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Small GTP-binding protein Ran is regulated by posttranslational lysine acetylation. Proc Natl Acad Sci U S A 2015; 112:E3679-88. [PMID: 26124124 DOI: 10.1073/pnas.1505995112] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ran is a small GTP-binding protein of the Ras superfamily regulating fundamental cellular processes: nucleo-cytoplasmic transport, nuclear envelope formation and mitotic spindle assembly. An intracellular Ran•GTP/Ran•GDP gradient created by the distinct subcellular localization of its regulators RCC1 and RanGAP mediates many of its cellular effects. Recent proteomic screens identified five Ran lysine acetylation sites in human and eleven sites in mouse/rat tissues. Some of these sites are located in functionally highly important regions such as switch I and switch II. Here, we show that lysine acetylation interferes with essential aspects of Ran function: nucleotide exchange and hydrolysis, subcellular Ran localization, GTP hydrolysis, and the interaction with import and export receptors. Deacetylation activity of certain sirtuins was detected for two Ran acetylation sites in vitro. Moreover, Ran was acetylated by CBP/p300 and Tip60 in vitro and on transferase overexpression in vivo. Overall, this study addresses many important challenges of the acetylome field, which will be discussed.
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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Rauh D, Fischer F, Gertz M, Lakshminarasimhan M, Bergbrede T, Aladini F, Kambach C, Becker CFW, Zerweck J, Schutkowski M, Steegborn C. An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms. Nat Commun 2014; 4:2327. [PMID: 23995836 DOI: 10.1038/ncomms3327] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 07/19/2013] [Indexed: 12/22/2022] Open
Abstract
Sirtuin enzymes regulate metabolism and aging processes through deacetylation of acetyl-lysines in target proteins. More than 6,800 mammalian acetylation sites are known, but few targets have been assigned to most sirtuin isoforms, hampering our understanding of sirtuin function. Here we describe a peptide microarray system displaying 6,802 human acetylation sites for the parallel characterisation of their modification by deacetylases. Deacetylation data for all seven human sirtuins obtained with this system reveal isoform-specific substrate preferences and deacetylation substrate candidates for all sirtuin isoforms, including Sirt4. We confirm malate dehydrogenase protein as a Sirt3 substrate and show that peroxiredoxin 1 and high-mobility group B1 protein are deacetylated by Sirt5 and Sirt1, respectively, at the identified sites, rendering them likely new in vivo substrates. Our microarray platform enables parallel studies on physiological acetylation sites and the deacetylation data presented provide an exciting resource for the identification of novel substrates for all human sirtuins.
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Affiliation(s)
- David Rauh
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University, Kurt-Mothes-Staße 3, 06120 Halle (Saale), Germany
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Schutkowski M, Fischer F, Roessler C, Steegborn C. New assays and approaches for discovery and design of Sirtuin modulators. Expert Opin Drug Discov 2014; 9:183-99. [DOI: 10.1517/17460441.2014.875526] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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Tinti M, Nardozza AP, Ferrari E, Sacco F, Corallino S, Castagnoli L, Cesareni G. The 4G10, pY20 and p-TYR-100 antibody specificity: profiling by peptide microarrays. N Biotechnol 2011; 29:571-7. [PMID: 22178400 DOI: 10.1016/j.nbt.2011.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/26/2011] [Accepted: 12/03/2011] [Indexed: 10/14/2022]
Abstract
The reversible phosphorylation of tyrosine residues is one of the most frequent post-translational modifications regulating enzymatic activities and protein-protein interactions in eukaryotic cells. Cells responding to internal or external regulatory inputs modify their phosphorylation status and diseased cells can often be diagnosed by observing alterations in their qualitative or quantitative phosphorylation profile. As a consequence the ability to describe the phosphorylation profile of a cell is central to many approaches aiming at the characterisation of signalling pathways. Anti-phosphotyrosine (pY) antibodies are widely used as experimental tools to monitor the phosphorylation status of a cell. By using peptide microarray technology we have characterised the substrate specificity of three widely used pY antibodies. We report that they are more sensitive to sequence context than is generally assumed and that their sequence preferences differ.
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Affiliation(s)
- Michele Tinti
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy
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Thiele A, Weiwad M, Zerweck J, Fischer G, Schutkowski M. High density peptide microarrays for proteome-wide fingerprinting of kinase activities in cell lysates. Methods Mol Biol 2011; 669:173-81. [PMID: 20857366 DOI: 10.1007/978-1-60761-845-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Protein function is highly regulated in pathways that are responsible for complex biochemical mechanisms such as growth, metabolism, and signal transduction. One of the most important mechanisms is posttranslational modification (PTM) changing protein surfaces by phosphorylation, sulfation, acetylation, methylation, glycosylation, and sumoylation resulting in a more than 100-fold higher complexity (Geiss-Friedlander and Melchior, Nat Rev Mol Cell Biol 8, 947-956, 2007; Hunter, Mol Cell 28, 730-738, 2007). This chapter presents a very efficient way to detect potential phosphorylation sites in protein families using overlapping peptides covering the complete primary structures (peptide scans) immobilized on glass slides. Results of kinase activity fingerprinting of cell lysates using peptide microarrays displaying peptide scans through all human peptidyl-prolyl-cis/trans-isomerases are shown.
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Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
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