title: A comprehensive proteome map of growing Bacillus subtilis cells.
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.
authors.affiliation: Institute for Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany.
authors.forename: Christine
authors.initials: C
authors.lastname: Eymann
authors.forename: Annette
authors.initials: A
authors.lastname: Dreisbach
authors.forename: Dirk
authors.initials: D
authors.lastname: Albrecht
authors.forename: Jörg
authors.initials: J
authors.lastname: Bernhardt
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
authors.forename: Sandy
authors.initials: S
authors.lastname: Gentner
authors.forename: Le Thi
authors.initials: le T
authors.lastname: Tam
authors.forename: Knut
authors.initials: K
authors.lastname: Büttner
authors.forename: Gerrit
authors.initials: G
authors.lastname: Buurman
authors.forename: Christian
authors.initials: C
authors.lastname: Scharf
authors.forename: Simone
authors.initials: S
authors.lastname: Venz
authors.forename: Uwe
authors.initials: U
authors.lastname: Völker
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D015153:Blotting, Western; D050260:Carbohydrate Metabolism; D019295:Computational Biology; D015180:Electrophoresis, Gel, Two-Dimensional; D004591:Electrophoresis, Polyacrylamide Gel; D005798:Genes, Bacterial; D006863:Hydrogen-Ion Concentration; D007525:Isoelectric Focusing; D013058:Mass Spectrometry; D020411:Oligonucleotide Array Sequence Analysis; D010449:Peptide Mapping; D011499:Protein Processing, Post-Translational; D020543:Proteome; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D020543:Proteome