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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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Related in: MedlinePlus

Comparison of identified proteins depending on the maximum transcript intensities.The transcripts are binned according to their maximum array signal intensity over the whole time course. The number of genes belonging to the respective resembling group of transcript intensity is indicated in the bar chart in blue. Displayed in orange is the proportion of transcripts with accordingly identified translation products (proteins). The proteomic coverage of highly expressed genes is >90%, whereas for lowly expressed genes the coverage is significantly lower, as displayed with the circles on the y axis on the right side.
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f6: Comparison of identified proteins depending on the maximum transcript intensities.The transcripts are binned according to their maximum array signal intensity over the whole time course. The number of genes belonging to the respective resembling group of transcript intensity is indicated in the bar chart in blue. Displayed in orange is the proportion of transcripts with accordingly identified translation products (proteins). The proteomic coverage of highly expressed genes is >90%, whereas for lowly expressed genes the coverage is significantly lower, as displayed with the circles on the y axis on the right side.

Mentions: Consequently, the analysis of 2,142 proteins regarding their dynamic change during a biological important process—the shift from growing to non-growing state—in a single study is a great step forward compared with previous studies of B. subtilis, such as Hahne et al.31, as reviewed by Wolff et al.12 or as comprehensive studies most recently published by Soufi et al.32 However, it has to be considered that gene products of lowly expressed genes are still underrepresented in our study (Fig. 6).


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)

Comparison of identified proteins depending on the maximum transcript intensities.The transcripts are binned according to their maximum array signal intensity over the whole time course. The number of genes belonging to the respective resembling group of transcript intensity is indicated in the bar chart in blue. Displayed in orange is the proportion of transcripts with accordingly identified translation products (proteins). The proteomic coverage of highly expressed genes is >90%, whereas for lowly expressed genes the coverage is significantly lower, as displayed with the circles on the y axis on the right side.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Comparison of identified proteins depending on the maximum transcript intensities.The transcripts are binned according to their maximum array signal intensity over the whole time course. The number of genes belonging to the respective resembling group of transcript intensity is indicated in the bar chart in blue. Displayed in orange is the proportion of transcripts with accordingly identified translation products (proteins). The proteomic coverage of highly expressed genes is >90%, whereas for lowly expressed genes the coverage is significantly lower, as displayed with the circles on the y axis on the right side.
Mentions: Consequently, the analysis of 2,142 proteins regarding their dynamic change during a biological important process—the shift from growing to non-growing state—in a single study is a great step forward compared with previous studies of B. subtilis, such as Hahne et al.31, as reviewed by Wolff et al.12 or as comprehensive studies most recently published by Soufi et al.32 However, it has to be considered that gene products of lowly expressed genes are still underrepresented in our study (Fig. 6).

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