The E. coli sirtuin CobB shows no preference for enzymatic and nonenzymatic lysine acetylation substrate sites

Alaa Abouelfetouh, Misty L. Kuhn, Linda I. Hu, Michael D. Scholle, Dylan J. Sorensen, Alexandria K. Sahu, Dörte Becher, Haike Antelmann, Milan Mrksich, Wayne F. Anderson, Bradford W. Gibson, Birgit Schilling, Alan J. Wolfe*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

47 Scopus citations

Abstract

Nε-lysine acetylation is an abundant posttranslational modification of thousands of proteins involved in diverse cellular processes. In the model bacterium Escherichia coli, the ε-amino group of a lysine residue can be acetylated either catalytically by acetyl-coenzyme A (acCoA) and lysine acetyltransferases, or nonenzymatically by acetyl phosphate (acP). It is well known that catalytic acCoA-dependent Nε-lysine acetylation can be reversed by deacetylases. Here, we provide genetic, mass spectrometric, structural and immunological evidence that CobB, a deacetylase of the sirtuin family of NAD+-dependent deacetylases, can reverse acetylation regardless of acetyl donor or acetylation mechanism. We analyzed 69 lysines on 51 proteins that we had previously detected as robustly, reproducibly, and significantly more acetylated in a cobB mutant than in its wild-type parent. Functional and pathway enrichment analyses supported the hypothesis that CobB regulates protein function in diverse and often essential cellular processes, most notably translation. Combined mass spectrometry, bioinformatics, and protein structural data provided evidence that the accessibility and three-dimensional microenvironment of the target acetyllysine help determine CobB specificity. Finally, we provide evidence that CobB is the predominate deacetylase in E. coli. We provide genetic, mass spectrometric, structural, and immunological evidence that CobB, a member of the sirtuin family of protein deacetylases, can reverse acetylation regardless of acetyl donor or acetylation mechanism. We also provide evidence that CobB is the predominant or perhaps the sole deacetylase in E. coli. Finally, we present evidence that three-dimensional structure should be used to predict CobB substrates.

Original languageEnglish (US)
Pages (from-to)66-83
Number of pages18
JournalMicrobiologyOpen
Volume4
Issue number1
DOIs
StatePublished - Feb 1 2015

Keywords

  • Acetyl phosphate
  • Bacteria
  • Crystallography
  • Deacetylase
  • Mass spectrometry
  • Posttranslational modification

ASJC Scopus subject areas

  • Microbiology

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