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YcgC represents a new protein deacetylase family in prokaryotes
- Source :
- eLife, eLife, Vol 7 (2018), eLife, Vol 4 (2015)
- Publication Year :
- 2015
- Publisher :
- eLife Sciences Publications, Ltd, 2015.
-
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 Zn2+ 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. DOI: http://dx.doi.org/10.7554/eLife.05322.001<br />eLife digest After proteins have been made, they can be modified in several ways. For example, chemical tags called acetyl groups may be added to (and later removed from) the protein to regulate cell activities such as aging and metabolism. Enzymes are proteins that help catalyze the reactions that add or remove the acetyl tags on certain “substrate” proteins. In the bacteria species Escherichia coli, many enzymes that help to add acetyl groups to proteins have been discovered. However, only a single E. coli “deacetylase” enzyme that removes the acetyl group has been identified. Now, Tu, Guo, Chen et al. have devised a technique to identify new deacetylases, called the “clip-chip” approach. In this method, thousands of proteins that are potential deacetylases are arrayed on a glass slide, and substrate proteins are immobilized on another slide. The two slides are then clipped together face-to-face, allowing the potential enzymes to transfer to the substrate slide and interact with the substrates. Using this approach, Tu, Guo, Chen et al. identified a protein called YcgC as a deacetylase in bacteria. Further characterization experiments revealed that YcgC works in a different way to other known deacetylases, and that it targets different substrates to the previously known E. coli deacetylase. Tu, Guo, Chen et al. found that the equivalents of YcgC in other bacteria species are also deacetylases; these enzymes therefore represent a new deacetylase family. In the future, the clip-chip approach could be used to discover new members of other enzyme families. DOI: http://dx.doi.org/10.7554/eLife.05322.002
- Subjects :
- 0301 basic medicine
Lysine Acetyltransferases
Lysine
Biochemistry
Substrate Specificity
Moiety
Biology (General)
biology
Chemistry
Escherichia coli Proteins
General Neuroscience
Serine hydrolase
Acetylation
General Medicine
deacetylase
Proteome
protein lysine deacetylase
Medicine
proteome microarray
Scientific Correspondence
Research Article
QH301-705.5
Science
Saccharomyces cerevisiae
Chemical biology
complex mixtures
General Biochemistry, Genetics and Molecular Biology
Catalysis
Amidohydrolases
03 medical and health sciences
Biochemistry and Chemical Biology
YcgC
Escherichia coli
Humans
Transcription factor
lysine acetylation
General Immunology and Microbiology
E. coli
biology.organism_classification
030104 developmental biology
Protein deacetylase
bacteria
NAD+ kinase
Protein Processing, Post-Translational
Bacteria
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 2050084X
- Volume :
- 4
- Database :
- OpenAIRE
- Journal :
- eLife
- Accession number :
- edsair.doi.dedup.....23faed8b913dc99bea29d15a277c0739