Limits...
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.

Show MeSH
Changes in proteins of the central carbon metabolism.Changes in protein amount for proteins of selected biosynthetic pathways. (a) Members of the purine biosynthetic pathway (PurR; PurB; PurK; PurN; PurH*; PurM;PurD*; PurL*; PurQ*; PurC*; PurF*). (b) Members of the pyrimidine biosynthetic pathway (PyrK; Pyre; PyrC*; PyrF;PyrAA*; PyrD; PyrAB; PyrB). (c) Members of the arginine biosynthetic pathway (ArgC; ArgD; ArgF*; ArgH*;ArgB; CarB; ArgG*; ArgJ*). (d) Members of the leucine/isoleucine biosynthetic pathway (LeuC; LeuD; IlvC; LeuB*;IlvB*; IlvH*; LeuA*). (e) Members of the cysteine biosynthetic pathway (YtiB; YvgQ; CysH; YvgR; CysC; Sat*). (f) Members of the bacillibactin biosynthetic pathway (DhbA*;DhbB*; DhbE*; DhbF*; DhbC*). 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. Orange: centroid of all proteins displayed. Blue: possible protease targets.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3105300&req=5

f5: Changes in proteins of the central carbon metabolism.Changes in protein amount for proteins of selected biosynthetic pathways. (a) Members of the purine biosynthetic pathway (PurR; PurB; PurK; PurN; PurH*; PurM;PurD*; PurL*; PurQ*; PurC*; PurF*). (b) Members of the pyrimidine biosynthetic pathway (PyrK; Pyre; PyrC*; PyrF;PyrAA*; PyrD; PyrAB; PyrB). (c) Members of the arginine biosynthetic pathway (ArgC; ArgD; ArgF*; ArgH*;ArgB; CarB; ArgG*; ArgJ*). (d) Members of the leucine/isoleucine biosynthetic pathway (LeuC; LeuD; IlvC; LeuB*;IlvB*; IlvH*; LeuA*). (e) Members of the cysteine biosynthetic pathway (YtiB; YvgQ; CysH; YvgR; CysC; Sat*). (f) Members of the bacillibactin biosynthetic pathway (DhbA*;DhbB*; DhbE*; DhbF*; DhbC*). 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. Orange: centroid of all proteins displayed. Blue: possible protease targets.

Mentions: The proteomic profiles of several biosynthetic enzymes suggest that they undergo targeted degradation: besides the already known protease substrates30 the data reveal PyrB, PurF, ArgG, ArgJ, LeuA, Sat and DhbC as new substrate candidates, according to the steeper slopes of decrease in protein amount compared with other members of functionally related biosynthetic pathways (Fig. 5). The decrease in protein amount is in agreement with the decrease at the transcript level.


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)

Changes in proteins of the central carbon metabolism.Changes in protein amount for proteins of selected biosynthetic pathways. (a) Members of the purine biosynthetic pathway (PurR; PurB; PurK; PurN; PurH*; PurM;PurD*; PurL*; PurQ*; PurC*; PurF*). (b) Members of the pyrimidine biosynthetic pathway (PyrK; Pyre; PyrC*; PyrF;PyrAA*; PyrD; PyrAB; PyrB). (c) Members of the arginine biosynthetic pathway (ArgC; ArgD; ArgF*; ArgH*;ArgB; CarB; ArgG*; ArgJ*). (d) Members of the leucine/isoleucine biosynthetic pathway (LeuC; LeuD; IlvC; LeuB*;IlvB*; IlvH*; LeuA*). (e) Members of the cysteine biosynthetic pathway (YtiB; YvgQ; CysH; YvgR; CysC; Sat*). (f) Members of the bacillibactin biosynthetic pathway (DhbA*;DhbB*; DhbE*; DhbF*; DhbC*). 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. Orange: centroid of all proteins displayed. Blue: possible protease targets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Changes in proteins of the central carbon metabolism.Changes in protein amount for proteins of selected biosynthetic pathways. (a) Members of the purine biosynthetic pathway (PurR; PurB; PurK; PurN; PurH*; PurM;PurD*; PurL*; PurQ*; PurC*; PurF*). (b) Members of the pyrimidine biosynthetic pathway (PyrK; Pyre; PyrC*; PyrF;PyrAA*; PyrD; PyrAB; PyrB). (c) Members of the arginine biosynthetic pathway (ArgC; ArgD; ArgF*; ArgH*;ArgB; CarB; ArgG*; ArgJ*). (d) Members of the leucine/isoleucine biosynthetic pathway (LeuC; LeuD; IlvC; LeuB*;IlvB*; IlvH*; LeuA*). (e) Members of the cysteine biosynthetic pathway (YtiB; YvgQ; CysH; YvgR; CysC; Sat*). (f) Members of the bacillibactin biosynthetic pathway (DhbA*;DhbB*; DhbE*; DhbF*; DhbC*). 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. Orange: centroid of all proteins displayed. Blue: possible protease targets.
Mentions: The proteomic profiles of several biosynthetic enzymes suggest that they undergo targeted degradation: besides the already known protease substrates30 the data reveal PyrB, PurF, ArgG, ArgJ, LeuA, Sat and DhbC as new substrate candidates, according to the steeper slopes of decrease in protein amount compared with other members of functionally related biosynthetic pathways (Fig. 5). The decrease in protein amount is in agreement with the decrease at the transcript level.

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