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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

Changes in the acyl modification of central carbon metabolism proteins under glucose or citrate conditions.Red, blue, and green circles represent acetylated, succinylated, and overlapping sites, respectively. The number of circles represents the number of modification sites in each condition. Left, glucose condition; right, citrate condition.
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pone.0131169.g004: Changes in the acyl modification of central carbon metabolism proteins under glucose or citrate conditions.Red, blue, and green circles represent acetylated, succinylated, and overlapping sites, respectively. The number of circles represents the number of modification sites in each condition. Left, glucose condition; right, citrate condition.

Mentions: Lysine acetylation frequently occurs in enzymes involved in central carbon metabolism in bacteria and eukarya [5,7,8,11,12,56,57]. Our acetylome analysis confirmed these findings (Fig 4). Acetylation of enzymes involved in glycolysis (GapA, TpiA, Pgk, and Eno) and the pentose phosphate pathway (Zwf and GndA) was more common in the glucose condition than in the citrate condition. In contrast, in the citrate condition, succinylation occurred at more sites and/or was upregulated, especially in proteins associated with the citrate cycle (CitZ, CitB, Icd, OdhB, SucC, SdhA, and FumC) and pyruvate metabolism (PdhA, PdhD, PycA, PckA, and Acs). This observation indicated that acetylation and succinylation of central carbon metabolism proteins changed substantially in response to the carbon source. The correlations between enzyme expression and flux in glycolysis, the pentose phosphate pathway, and pyruvate metabolism are weak [41]. It would be interesting to determine if the acyl modifications found in these pathways have a role in the control of enzymatic activity and/or flux.


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)

Changes in the acyl modification of central carbon metabolism proteins under glucose or citrate conditions.Red, blue, and green circles represent acetylated, succinylated, and overlapping sites, respectively. The number of circles represents the number of modification sites in each condition. Left, glucose condition; right, citrate condition.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131169.g004: Changes in the acyl modification of central carbon metabolism proteins under glucose or citrate conditions.Red, blue, and green circles represent acetylated, succinylated, and overlapping sites, respectively. The number of circles represents the number of modification sites in each condition. Left, glucose condition; right, citrate condition.
Mentions: Lysine acetylation frequently occurs in enzymes involved in central carbon metabolism in bacteria and eukarya [5,7,8,11,12,56,57]. Our acetylome analysis confirmed these findings (Fig 4). Acetylation of enzymes involved in glycolysis (GapA, TpiA, Pgk, and Eno) and the pentose phosphate pathway (Zwf and GndA) was more common in the glucose condition than in the citrate condition. In contrast, in the citrate condition, succinylation occurred at more sites and/or was upregulated, especially in proteins associated with the citrate cycle (CitZ, CitB, Icd, OdhB, SucC, SdhA, and FumC) and pyruvate metabolism (PdhA, PdhD, PycA, PckA, and Acs). This observation indicated that acetylation and succinylation of central carbon metabolism proteins changed substantially in response to the carbon source. The correlations between enzyme expression and flux in glycolysis, the pentose phosphate pathway, and pyruvate metabolism are weak [41]. It would be interesting to determine if the acyl modifications found in these pathways have a role in the control of enzymatic activity and/or flux.

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