title: YcgC represents a new protein deacetylase family in prokaryotes.
abstract: Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a 'clip-chip' strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD(+) or Zn(2+) like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC's bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs.
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: Shun
authors.initials: S
authors.lastname: Tu
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: Shu-Juan
authors.initials: SJ
authors.lastname: Guo
authors.affiliation: Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.
authors.forename: Chien-Sheng
authors.initials: CS
authors.lastname: Chen
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: Cheng-Xi
authors.initials: CX
authors.lastname: Liu
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: He-Wei
authors.initials: HW
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Jiao-Yu
authors.initials: JY
authors.lastname: Deng
authors.affiliation: National Engineering Research Center for Beijing Biochip Technology, Beijing, China.
authors.forename: Yi-Ming
authors.initials: YM
authors.lastname: Zhou
authors.affiliation: Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Czajkowsky
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
authors.forename: Bang-Ruo
authors.initials: BR
authors.lastname: Qi
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Young-Hoon
authors.initials: YH
authors.lastname: Ahn
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Philip A
authors.initials: PA
authors.lastname: Cole
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.|The High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Heng
authors.initials: H
authors.lastname: Zhu
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.|Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Sheng-Ce
authors.initials: SC
authors.lastname: Tao
mesh_terms: D000581:Amidohydrolases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism*; D008239:Lysine / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D013379:Substrate Specificity; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; C530619:RutR protein, E coli; D014157:Transcription Factors; C000611411:YcgC protein, E coli; D000581:Amidohydrolases; D008239:Lysine
keywords: E. coli; biochemistry; protein lysine deacetylase; proteome microarray