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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

Positions of acyl modification sites in RNA polymerase subunits.Location of acetylation (red line) and succinylation (blue line) sites with amino acid residue numbers are shown. K638, at which succinylation was reproducibly upregulated in the citrate condition, is underlined. Functional and structural regions are shown with black bars; the positions were estimated using amino acid sequence alignment and structural modeling based on information from E. coli RNAP [60,61].
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pone.0131169.g005: Positions of acyl modification sites in RNA polymerase subunits.Location of acetylation (red line) and succinylation (blue line) sites with amino acid residue numbers are shown. K638, at which succinylation was reproducibly upregulated in the citrate condition, is underlined. Functional and structural regions are shown with black bars; the positions were estimated using amino acid sequence alignment and structural modeling based on information from E. coli RNAP [60,61].

Mentions: Acetylation of RNA polymerase (RNAP) has been reported in E. coli [12,58,59]. In this study, we detected acetylation and succinylation in various B. subtilis RNAP subunits, including RpoA (α), RpoB (β), RpoC (βʹ), and RpoZ (ω), and sigma factors, including SigA, SigF, and SigH (Fig 5, S2 and S3 Tables). RpoB (β) contained nine acylation sites (eight acetylation sites and one succinylation site). K837, K891, and K916 were located in and close to the G flap region, which undergoes a structural change during holoenzyme formation [60]. RpoC (βʹ) contained 12 acylation sites (nine acetylation sites and three succinylation sites), which were scattered around the structural regions critical for RNAP function (Fig 5). Succinylation at K638 of RpoC was reproducibly upregulated in the citrate condition (Table 6). RpoA (α) and RpoZ (ω) contained two and one acetylation sites, respectively.


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)

Positions of acyl modification sites in RNA polymerase subunits.Location of acetylation (red line) and succinylation (blue line) sites with amino acid residue numbers are shown. K638, at which succinylation was reproducibly upregulated in the citrate condition, is underlined. Functional and structural regions are shown with black bars; the positions were estimated using amino acid sequence alignment and structural modeling based on information from E. coli RNAP [60,61].
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131169.g005: Positions of acyl modification sites in RNA polymerase subunits.Location of acetylation (red line) and succinylation (blue line) sites with amino acid residue numbers are shown. K638, at which succinylation was reproducibly upregulated in the citrate condition, is underlined. Functional and structural regions are shown with black bars; the positions were estimated using amino acid sequence alignment and structural modeling based on information from E. coli RNAP [60,61].
Mentions: Acetylation of RNA polymerase (RNAP) has been reported in E. coli [12,58,59]. In this study, we detected acetylation and succinylation in various B. subtilis RNAP subunits, including RpoA (α), RpoB (β), RpoC (βʹ), and RpoZ (ω), and sigma factors, including SigA, SigF, and SigH (Fig 5, S2 and S3 Tables). RpoB (β) contained nine acylation sites (eight acetylation sites and one succinylation site). K837, K891, and K916 were located in and close to the G flap region, which undergoes a structural change during holoenzyme formation [60]. RpoC (βʹ) contained 12 acylation sites (nine acetylation sites and three succinylation sites), which were scattered around the structural regions critical for RNAP function (Fig 5). Succinylation at K638 of RpoC was reproducibly upregulated in the citrate condition (Table 6). RpoA (α) and RpoZ (ω) contained two and one acetylation sites, respectively.

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