title: Global identification of CobB interactors by an Escherichia coli proteome microarray.
abstract: Protein acetylation is one of the most abundant post-translational modifications and plays critical roles in many important biological processes. Based on the recent advances in mass spectrometry technology, in bacteria, such as Escherichia coli, tremendous acetylated proteins and acetylation sites have been identified. However, only one protein deacetylase, i.e. CobB, has been identified in E. coli so far. How CobB is regulated is still elusive. One right strategy to study the regulation of CobB is to globally identify its interacting proteins. In this study, we used a proteome microarray containing ∼4000 affinity-purified E. coli proteins to globally identify CobB interactors, and finally identified 183 binding proteins of high stringency. Bioinformatics analysis showed that these interacting proteins play a variety of roles in a wide range of cellular functions and are highly enriched in carboxylic acid metabolic process and hexose catabolic process, and also enriched in transferase and hydrolase. We further used bio-layer interferometry to analyze the interaction and quantify the kinetic parameters of putative CobB interactors, and clearly showed that CobB could strongly interact with TopA and AccC. The novel CobB interactors that we identified could serve as a start point for further functional analysis.
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Cheng-xi
authors.initials: CX
authors.lastname: Liu
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Fan-lin
authors.initials: FL
authors.lastname: Wu
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: He-wei
authors.initials: HW
authors.lastname: Jiang
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: He
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Shu-juan
authors.initials: SJ
authors.lastname: Guo
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China taosc@sjtu.edu.cn.
authors.forename: Sheng-ce
authors.initials: SC
authors.lastname: Tao
mesh_terms: D029968:Escherichia coli Proteins / Q000378:metabolism*; D040081:Protein Array Analysis; D011485:Protein Binding; D020543:Proteome
chemical_list: D029968:Escherichia coli Proteins; D020543:Proteome
keywords: CobB; E. coli; acetylation; protein–protein interaction; proteome microarray