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Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques
Author(s) -
Dreisbach Annette,
Otto Andreas,
Becher Dörte,
Hammer Elke,
Teumer Alexander,
Gouw Joost W.,
Hecker Michael,
Völker Uwe
Publication year - 2008
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200701081
Subject(s) - stable isotope labeling by amino acids in cell culture , proteome , bacillus subtilis , amino acid , proteomics , biochemistry , biology , quantitative proteomics , membrane protein , chemistry , membrane , bacteria , gene , genetics
Bacillus subtilis has been developed as a model system for physiological proteomics. However, thus far these studies have mainly been limited to cytoplasmic, extracellular, and cell‐wall attached proteins. Although being certainly important for cell physiology, the membrane protein fraction has not been studied in comparable depth due to inaccessibility by traditional 2‐DE‐based workflows and limitations in reliable quantification. In this study, we now compare the potential of stable isotope labeling with amino acids (SILAC) and 14 N/ 15 N‐labeling for the analysis of bacterial membrane fractions in physiology‐driven proteomic studies. Using adaptation of B. subtilis to amino acid (lysine) and glucose starvation as proof of principle scenarios, we show that both approaches provide similarly valuable data for the quantification of bacterial membrane proteins. Even if labeling with stable amino acids allows a more straightforward analysis of data, the 14 N/ 15 N‐labeling has some advantages in general such as labeling of all amino acids and thereby increasing the number of peptides for quantification. Both, SILAC as well as 14 N/ 15 N‐labeling are compatible with 2‐DE, 2‐D LC‐MS/MS, and GeLC‐MS/MS and thus will allow comprehensive simultaneous interrogation of cytoplasmic and enriched membrane proteomes.