Journal ArticleDOI
A comprehensive proteome map of growing Bacillus subtilis cells.
Christine Eymann,Annette Dreisbach,Dirk Albrecht,Jörg Bernhardt,Dörte Becher,Sandy Gentner,Le Thi Tam,Knut Büttner,Gerrit Buurman,Christian Scharf,Simone Venz,Uwe Völker,Uwe Völker,Michael Hecker +13 more
TLDR
The proteome of growing cells of Bacillus subtilis was analyzed and a reasonable correlation was found for the majority of protein spots, and the vegetative proteome containing 876 proteins in total is now ready for physiological applications.Abstract:
The proteome of growing cells of Bacillus subtilis was analyzed in order to provide the basis for its application in microbial physiology. DNA arrays were used to calculate the number of genes transcribed in growing cells. From the 4100 B. subtilis genes, 2515 were actively transcribed in cells grown under standard conditions. From these genes 1544 proteins should be covered by our standard gel system pI 4-7. Using this standard gel system and supplementary zoom gels (pI 5.5-6.7, 5-6, 4.5-5.5, and 4-5) 693 proteins which are expressed in growing cells were detected that cover more than 40% of the vegetative proteome predicted for this region. Particularly broad coverage and thus comprehensive monitoring will be possible for central carbohydrate metabolism (glycolysis, pentose phosphate shunt, and citric acid cycle), amino acid synthesis pathways, purine and pyrimidine metabolism, fatty acid metabolism, and main cellular functions like replication, transcription, translation, and cell wall synthesis. Comparing the theoretical pI and Mr values with those experimentally determined a reasonable correlation was found for the majority of protein spots. By a color code outliers with dramatic deviations in charge or mass were visualized that may indicate post-translational modifications. In addition to the cytosolic neutral and alkaline proteins, 130 membrane proteins were found relying on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation in combination with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) techniques. The vegetative proteome containing 876 proteins in total is now ready for physiological applications. Two main proteome fractions (pI 4-7 and zoom gel pI 4.5-5.5) should be sufficient for such high-throughput physiological proteomics.read more
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Journal ArticleDOI
Two-dimensional gel electrophoresis in proteomics: Past, present and future.
TL;DR: A historical perspective is made, starting from the days where two-dimensional gels were used and the word proteomics did not even exist to a description of the now well-known limitations of two- dimensional gels in proteomics.
Journal ArticleDOI
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.
You-Kwan Oh,Berrnhard O. Palsson,Sung M. Park,Christophe H. Schilling,Radhakrishnan Mahadevan +4 more
TL;DR: In this article, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information and high-throughput phenotyping experiments is presented.
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and
You-Kwan Oh,Bernhard O. Palsson,Sung M. Park,Christophe H. Schilling,Radhakrishnan Mahadevan,Fromthe ‡ DepartmentofBioengineering +5 more
TL;DR: The in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes and is found to be consistent with experimental observations in 720 of 766 cases evaluated.
Journal ArticleDOI
The depletion attraction: an underappreciated force driving cellular organization
TL;DR: Evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes, is reviewed.
Journal ArticleDOI
Anaerobic Gene Expression in Staphylococcus aureus
TL;DR: An investigation of gene expression in Staphylococcus aureus after a switch from aerobic to anaerobic growth was initiated by using the proteomic and transcriptomic approaches, and the expression of genes related to nitrate respiration and nitrate reduction was found to be upregulated.
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