Dataset Information

Protein Deacetylase CobB Interplays with c-di-GMP

ABSTRACT: As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes like bacterial motility and transcription regulation. We found that c-di-GMP had impact on lysine acetylation level. To further investigate the regulation role, we performed a quantitative analysis of E. coli acetylome. In addition, we found that CobB is an effective deacetylase of YdeH, a major diguanylate cyclase (DGC) of E.coli that is endogenously acetylated. Mass spectrometry analysis identified YdeH K4 as the major site of acetylation, and it could be deacetylated by CobB.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Zhaowei Xu

LAB HEAD: Zhaowei Xu

PROVIDER: PXD010558 | Pride | 2019-06-17

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20171125_QLL_YdeH_CobB.raw	Raw
	20171125_QLL_YdeH_CobB.xml	Xml
	20171125_QLL_YdeH_WT.raw	Raw
	20171125_QLL_YdeH_WT.xml	Xml
	20171210_YdeH_AQUA_R1.msf	Msf

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Publications

Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP.

Xu Zhaowei Z Zhang Hainan H Zhang Xingrun X Jiang Hewei H Liu Chengxi C Wu Fanlin F Qian Lili L Hao Bingbing B Czajkowsky Daniel M DM Guo Shujuan S Xu Zhijing Z Bi Lijun L Wang Shihua S Li Haitao H Tan Minjia M Yan Wei W Feng Lei L Hou Jingli J Tao Sheng-Ce SC

The EMBO journal 20190816 18

As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis ...[more]

PMID: 31418899

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Project description:Acetylation of lysine residues is conserved in all three kingdoms; however, its role in prokaryotes is unknown. Here we demonstrate that acetylation enables the reference bacterium Escherichia coli to withstand environmental stress. Specifically, the bacterium reaches higher cell densities and becomes more resistant to heat and oxidative stress when its proteins are acetylated, as shown by deletion of the gene encoding acetyltransferase YfiQ and the gene encoding deacetylase CobB, as well as by overproducing YfiQ and CobB. Furthermore, we show that the increase in oxidative stress resistance with acetylation is due to the induction of catalase activity through enhanced katG expression. We also found that two-component system proteins CpxA, PhoP, UvrY, and BasR are associated with cell catalase activity and may be responsible as the connection between bacterial acetylation and the stress response. This is the first demonstration of a specific environmental role of acetylation in prokaryotes. Overnight cultures of cobB/pCA24N-cobB and cobB/pCA24N were cultured to a turbidity of 0.05 at 600 nm and grown 2 h. Then, 0.1 mM IPTG was added for another 4 h to induce cobB expression, and then the cells were exposed to 20 mM H2O2 for 10 min. Cell pellets were collected and resuspended in RNAlater (Ambion Inc., Austin, TX), and total RNA was isolated using the RNeasy Mini Kit (Qiagen Inc., Valencia, CA). The E. coli GeneChip Genome 2.0 array (Affymetrix, P/N 900551) was used, and cDNA synthesis, fragmentation, and hybridizations were performed as described previously. If the gene with the larger transcription rate did not have a consistent transcription rate based on the 11-15 probe pairs (P-value less than 0.05), these genes were discarded. A gene was considered differentially expressed when the P-value for comparing two chips was lower than 0.05 (to assure that the change in gene expression was statistically significant and that false positives arise less than 5%) and if their fold change is higher than the standard deviation for the whole genome.