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Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.

Otto A, Bernhardt J, Meyer H, Schaffer M, Herbst FA, Siebourg J, Mäder U, Lalk M, Hecker M, Becher D - Nat Commun (2010)

Bottom Line: In this study, we monitor temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation.Quantitative proteomic and corresponding transcriptomic data were analysed with Voronoi treemaps linking functional classification and relative expression changes of gene products according to their fate in the stationary phase.The obtained data comprise the first comprehensive profiling of changes in the membrane subfraction and allow in-depth analysis of major physiological processes, including monitoring of protein degradation.

View Article: PubMed Central - PubMed

Affiliation: Ernst-Moritz-Arndt-Universität Greifswald, Institute for Microbiology, Greifswald 17487, Germany.

ABSTRACT
Functional genomics of the Gram-positive model organism Bacillus subtilis reveals valuable insights into basic concepts of cell physiology. In this study, we monitor temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation. For proteomic profiling, a combination of in vivo metabolic labelling and shotgun mass spectrometric analysis was carried out for five different proteomic subfractions (cytosolic, integral membrane, membrane, surface and extracellular proteome fraction), leading to the identification of ~52% of the predicted proteome of B. subtilis. Quantitative proteomic and corresponding transcriptomic data were analysed with Voronoi treemaps linking functional classification and relative expression changes of gene products according to their fate in the stationary phase. The obtained data comprise the first comprehensive profiling of changes in the membrane subfraction and allow in-depth analysis of major physiological processes, including monitoring of protein degradation.

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Quantitative changes in proteins of the central carbon metabolism.(a) Graphical representation of the central carbon metabolism. The main metabolic intermediates are italicized. (b) Change of protein amount for glycolytic enzymes. (c) Change of protein amount for gluconeogenic key enzymes. (d) Change of protein amount for TCA enzymes. Error bars indicate s.d. of the biological replicates (n=3).
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f4: Quantitative changes in proteins of the central carbon metabolism.(a) Graphical representation of the central carbon metabolism. The main metabolic intermediates are italicized. (b) Change of protein amount for glycolytic enzymes. (c) Change of protein amount for gluconeogenic key enzymes. (d) Change of protein amount for TCA enzymes. Error bars indicate s.d. of the biological replicates (n=3).

Mentions: As expected7, most obvious changes occurred for proteins of the carbohydrate metabolism: the key enzymes for gluconeogenesis, GapB and PckA, strongly increase in amount, whereas glycolytic enzymes of glycolysis remain relatively unaffected. Enzymes of the tricarboxylic acid cycle (TCA) increase more than twofold in protein amount (Fig. 4).


Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.

Otto A, Bernhardt J, Meyer H, Schaffer M, Herbst FA, Siebourg J, Mäder U, Lalk M, Hecker M, Becher D - Nat Commun (2010)

Quantitative changes in proteins of the central carbon metabolism.(a) Graphical representation of the central carbon metabolism. The main metabolic intermediates are italicized. (b) Change of protein amount for glycolytic enzymes. (c) Change of protein amount for gluconeogenic key enzymes. (d) Change of protein amount for TCA enzymes. Error bars indicate s.d. of the biological replicates (n=3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105300&req=5

f4: Quantitative changes in proteins of the central carbon metabolism.(a) Graphical representation of the central carbon metabolism. The main metabolic intermediates are italicized. (b) Change of protein amount for glycolytic enzymes. (c) Change of protein amount for gluconeogenic key enzymes. (d) Change of protein amount for TCA enzymes. Error bars indicate s.d. of the biological replicates (n=3).
Mentions: As expected7, most obvious changes occurred for proteins of the carbohydrate metabolism: the key enzymes for gluconeogenesis, GapB and PckA, strongly increase in amount, whereas glycolytic enzymes of glycolysis remain relatively unaffected. Enzymes of the tricarboxylic acid cycle (TCA) increase more than twofold in protein amount (Fig. 4).

Bottom Line: In this study, we monitor temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation.Quantitative proteomic and corresponding transcriptomic data were analysed with Voronoi treemaps linking functional classification and relative expression changes of gene products according to their fate in the stationary phase.The obtained data comprise the first comprehensive profiling of changes in the membrane subfraction and allow in-depth analysis of major physiological processes, including monitoring of protein degradation.

View Article: PubMed Central - PubMed

Affiliation: Ernst-Moritz-Arndt-Universität Greifswald, Institute for Microbiology, Greifswald 17487, Germany.

ABSTRACT
Functional genomics of the Gram-positive model organism Bacillus subtilis reveals valuable insights into basic concepts of cell physiology. In this study, we monitor temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation. For proteomic profiling, a combination of in vivo metabolic labelling and shotgun mass spectrometric analysis was carried out for five different proteomic subfractions (cytosolic, integral membrane, membrane, surface and extracellular proteome fraction), leading to the identification of ~52% of the predicted proteome of B. subtilis. Quantitative proteomic and corresponding transcriptomic data were analysed with Voronoi treemaps linking functional classification and relative expression changes of gene products according to their fate in the stationary phase. The obtained data comprise the first comprehensive profiling of changes in the membrane subfraction and allow in-depth analysis of major physiological processes, including monitoring of protein degradation.

Show MeSH