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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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Change of protein amount for ribosomal proteins from the cytosolic fraction.Relative quantitative changes for proteins belonging to the ribosome (YpfD; RpsL; RpsO; RpsJ*; RpmB; RpsP;*RpsD; RpsI; RpsH; RplD; RpsM*; RplB*; RpsE*; RpsF*; RpsR; RpsS; RpsG*; RpsT*; RplC*; RpmA; RplU*; RplR*; RplQ*; RpsQ*; RplE*; RplK; RpsB; RpmI; RplS*; RplF; RplI; RplX; RplW*; RpsK*; RplA*; RplP*; RplO*; RpsC; RplV*; RplT*; RplJ*; RplN*; RplL*; RplM*). Log2 ratios are corrected for the first time point. Asterisks indicate proteins that are significantly altered as determined by analysis of variance (P-value<0.01). Error bars indicate s.d. of the biological replicates (n=3). Grey shading: area of maximal s.d.s. Orange: centroid of all proteins displayed.
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f7: Change of protein amount for ribosomal proteins from the cytosolic fraction.Relative quantitative changes for proteins belonging to the ribosome (YpfD; RpsL; RpsO; RpsJ*; RpmB; RpsP;*RpsD; RpsI; RpsH; RplD; RpsM*; RplB*; RpsE*; RpsF*; RpsR; RpsS; RpsG*; RpsT*; RplC*; RpmA; RplU*; RplR*; RplQ*; RpsQ*; RplE*; RplK; RpsB; RpmI; RplS*; RplF; RplI; RplX; RplW*; RpsK*; RplA*; RplP*; RplO*; RpsC; RplV*; RplT*; RplJ*; RplN*; RplL*; RplM*). Log2 ratios are corrected for the first time point. Asterisks indicate proteins that are significantly altered as determined by analysis of variance (P-value<0.01). Error bars indicate s.d. of the biological replicates (n=3). Grey shading: area of maximal s.d.s. Orange: centroid of all proteins displayed.

Mentions: Upon transition to the stationary phase, extensive reprogramming of gene expression takes place3, shutting down gene expression needed for exponential growth, including amino-acid biosynthesis, purine and pyrimidine synthesis and the translational machinery (Supplementary Movie S3). Confirming the findings of Eymann et al.38 and as displayed in Supplementary Movie S4, genes of the stringent response are immediately downregulated by nutrient starvation. Ribosomal proteins as part of the negative stringent response regulon decrease markedly in protein amount (Fig. 7), leading to a reduction <70% of the original amount of the ribosomal machinery inside the cell 2 h after nutrient depletion. The ribosomes contain a substantial fraction of intracellular protein content39, and consequently the degradation and recycling of amino acids represent a source of nutrients in times of starvation.


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)

Change of protein amount for ribosomal proteins from the cytosolic fraction.Relative quantitative changes for proteins belonging to the ribosome (YpfD; RpsL; RpsO; RpsJ*; RpmB; RpsP;*RpsD; RpsI; RpsH; RplD; RpsM*; RplB*; RpsE*; RpsF*; RpsR; RpsS; RpsG*; RpsT*; RplC*; RpmA; RplU*; RplR*; RplQ*; RpsQ*; RplE*; RplK; RpsB; RpmI; RplS*; RplF; RplI; RplX; RplW*; RpsK*; RplA*; RplP*; RplO*; RpsC; RplV*; RplT*; RplJ*; RplN*; RplL*; RplM*). Log2 ratios are corrected for the first time point. Asterisks indicate proteins that are significantly altered as determined by analysis of variance (P-value<0.01). Error bars indicate s.d. of the biological replicates (n=3). Grey shading: area of maximal s.d.s. Orange: centroid of all proteins displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: Change of protein amount for ribosomal proteins from the cytosolic fraction.Relative quantitative changes for proteins belonging to the ribosome (YpfD; RpsL; RpsO; RpsJ*; RpmB; RpsP;*RpsD; RpsI; RpsH; RplD; RpsM*; RplB*; RpsE*; RpsF*; RpsR; RpsS; RpsG*; RpsT*; RplC*; RpmA; RplU*; RplR*; RplQ*; RpsQ*; RplE*; RplK; RpsB; RpmI; RplS*; RplF; RplI; RplX; RplW*; RpsK*; RplA*; RplP*; RplO*; RpsC; RplV*; RplT*; RplJ*; RplN*; RplL*; RplM*). Log2 ratios are corrected for the first time point. Asterisks indicate proteins that are significantly altered as determined by analysis of variance (P-value<0.01). Error bars indicate s.d. of the biological replicates (n=3). Grey shading: area of maximal s.d.s. Orange: centroid of all proteins displayed.
Mentions: Upon transition to the stationary phase, extensive reprogramming of gene expression takes place3, shutting down gene expression needed for exponential growth, including amino-acid biosynthesis, purine and pyrimidine synthesis and the translational machinery (Supplementary Movie S3). Confirming the findings of Eymann et al.38 and as displayed in Supplementary Movie S4, genes of the stringent response are immediately downregulated by nutrient starvation. Ribosomal proteins as part of the negative stringent response regulon decrease markedly in protein amount (Fig. 7), leading to a reduction <70% of the original amount of the ribosomal machinery inside the cell 2 h after nutrient depletion. The ribosomes contain a substantial fraction of intracellular protein content39, and consequently the degradation and recycling of amino acids represent a source of nutrients in times of starvation.

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
Related in: MedlinePlus