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Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source.

Kosono S, Tamura M, Suzuki S, Kawamura Y, Yoshida A, Nishiyama M, Yoshida M - PLoS ONE (2015)

Bottom Line: 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.Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan; RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.

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.

No MeSH data available.


Related in: MedlinePlus

The acetylome and succinylome of B. subtilis profiled in this study.(A) Functional classification of the identified acetylated proteins (629) and succinylated proteins (204) based on the KEGG pathway database. Red and blue bars represent the number of acetylated and succinylated proteins, respectively. (B) Overlap between acetylation (1355) and succinylation (327) sites. Red and blue circles enclose the number of acetylation and succinylation sites, respectively.
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pone.0131169.g003: The acetylome and succinylome of B. subtilis profiled in this study.(A) Functional classification of the identified acetylated proteins (629) and succinylated proteins (204) based on the KEGG pathway database. Red and blue bars represent the number of acetylated and succinylated proteins, respectively. (B) Overlap between acetylation (1355) and succinylation (327) sites. Red and blue circles enclose the number of acetylation and succinylation sites, respectively.

Mentions: A total of 1355 unique acetyllysine sites were identified on 629 acetylated proteins (Table 2). We performed a functional classification analysis of acetylated proteins based on the KEGG pathway database (Fig 3A). The largest groups contained proteins involved in amino acid metabolism (70 proteins, 11% of the total), followed by proteins involved in translation (62 proteins, 10%) and carbohydrate metabolism (49 proteins, 8%). This profile is similar to a profile previously reported for the B. subtilis acetylome [7]. The most heavily acetylated proteins included SrfAA (21 sites), SrfAB (21 sites), Tuf (12 sites), PurB (10 sites), and RplB (10 sites).


Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source.

Kosono S, Tamura M, Suzuki S, Kawamura Y, Yoshida A, Nishiyama M, Yoshida M - PLoS ONE (2015)

The acetylome and succinylome of B. subtilis profiled in this study.(A) Functional classification of the identified acetylated proteins (629) and succinylated proteins (204) based on the KEGG pathway database. Red and blue bars represent the number of acetylated and succinylated proteins, respectively. (B) Overlap between acetylation (1355) and succinylation (327) sites. Red and blue circles enclose the number of acetylation and succinylation sites, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476798&req=5

pone.0131169.g003: The acetylome and succinylome of B. subtilis profiled in this study.(A) Functional classification of the identified acetylated proteins (629) and succinylated proteins (204) based on the KEGG pathway database. Red and blue bars represent the number of acetylated and succinylated proteins, respectively. (B) Overlap between acetylation (1355) and succinylation (327) sites. Red and blue circles enclose the number of acetylation and succinylation sites, respectively.
Mentions: A total of 1355 unique acetyllysine sites were identified on 629 acetylated proteins (Table 2). We performed a functional classification analysis of acetylated proteins based on the KEGG pathway database (Fig 3A). The largest groups contained proteins involved in amino acid metabolism (70 proteins, 11% of the total), followed by proteins involved in translation (62 proteins, 10%) and carbohydrate metabolism (49 proteins, 8%). This profile is similar to a profile previously reported for the B. subtilis acetylome [7]. The most heavily acetylated proteins included SrfAA (21 sites), SrfAB (21 sites), Tuf (12 sites), PurB (10 sites), and RplB (10 sites).

Bottom Line: 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.Our results suggest that acyl modifications play a role in the physiological adaptations to changes in carbon nutrient availability of B. subtilis.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Center, the University of Tokyo, Bunkyo-ku, Tokyo, Japan; RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.

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.

No MeSH data available.


Related in: MedlinePlus