title: Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source.
abstract: Lysine residues can be post-translationally modified by various acyl modifications in bacteria and eukarya. Here, we showed that two major acyl modifications, acetylation and succinylation, were changed in response to the carbon source in the Gram-positive model bacterium Bacillus subtilis. Acetylation was more common when the cells were grown on glucose, glycerol, or pyruvate, whereas succinylation was upregulated when the cells were grown on citrate, reflecting the metabolic states that preferentially produce acetyl-CoA and succinyl-CoA, respectively. To identify and quantify changes in acetylation and succinylation in response to the carbon source, we performed a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate. We identified 629 acetylated proteins with 1355 unique acetylation sites and 204 succinylated proteins with 327 unique succinylation sites. Acetylation targeted different metabolic pathways under the two growth conditions: branched-chain amino acid biosynthesis and purine metabolism in glucose and the citrate cycle in citrate. Succinylation preferentially targeted the citrate cycle in citrate. Acetylation and succinylation mostly targeted different lysine residues and showed a preference for different residues surrounding the modification sites, suggesting that the two modifications may depend on different factors such as characteristics of acyl-group donors, molecular environment of the lysine substrate, and/or the modifying enzymes. Changes in acetylation and succinylation were observed in proteins involved in central carbon metabolism and in components of the transcription and translation machineries, such as RNA polymerase and the ribosome. Mutations that modulate protein acylation affected B. subtilis growth. A mutation in acetate kinase (ackA) increased the global acetylation level, suggesting that acetyl phosphate-dependent acetylation is common in B. subtilis, just as it is in Escherichia coli. Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.
authors.affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan; RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
authors.forename: Saori
authors.initials: S
authors.lastname: Kosono
authors.affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tamura
authors.affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Shota
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
authors.forename: Yumi
authors.initials: Y
authors.lastname: Kawamura
authors.affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Yoshida
authors.affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Nishiyama
authors.affiliation: RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Yoshida
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism; D000107:Acetylation; D000214:Acyl Coenzyme A / Q000378:metabolism; D000597:Amino Acids, Branched-Chain / Q000378:metabolism; D001412:Bacillus subtilis / Q000378:metabolism* / Q000502:physiology; D015153:Blotting, Western; D002244:Carbon / Q000378:metabolism; D019343:Citric Acid / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D008239:Lysine / Q000378:metabolism; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways / Q000502:physiology; D040901:Proteomics; D011687:Purines / Q000378:metabolism; D019802:Succinic Acid / Q000378:metabolism
chemical_list: D000214:Acyl Coenzyme A; D000597:Amino Acids, Branched-Chain; D011687:Purines; D019343:Citric Acid; D000105:Acetyl Coenzyme A; D002244:Carbon; D019802:Succinic Acid; C012046:succinyl-coenzyme A; D008239:Lysine; C030985:purine