The gel spots were then dehydrated in acetonitrile for 30′ and dried in a speed vac for 10′. Thirty microliters of 50 mM ammonium bicarbonate containing 0.3 μg of trypsin (Sigma-Aldrich, St Louis, MO) were added to each sample, and samples were incubated at 37°C for 16 hours. Digested Alvocidib supplier peptides were extracted from gel spots by two washes of 50% acetonitrile/0.1% trifluoroacetic acid, and purified with Ziptips

(Millipore, Billerica, MA). Purified peptides were eluted from Ziptips with 50% acetonitrile/0.05% trifluoroacetic acid with 10 mg/ml alpha-cyano-4-hydroxycinnamic acid, and spotted on a sample plate to obtain mass spectra using an Axima CFR Plus MALDI-ToF mass spectrometer (Shimadzu Biotech, Columbia, MD). Each spectrum was calibrated externally using the ProteoMass peptide MALDI-MS calibration kit INCB018424 mouse (Sigma-Aldrich, St Louis, MO). Peptide fingerprints obtained for each sample

were used to search the databases at NCBI and SWISS-PROT using MASCOT search engine http://​www.​Matrixscience.​com. Search parameters used were variable carbamidomethyl and propionamide modifications of cysteines and oxidation of methionines. A peptide tolerance window of 0.5 daltons was used for all searches. Once an identification was made with a statistically significant score, data were accepted when the peptide coverage of the protein was at least 20%, and the molecular weight and isoelectric point of the protein matched those observed on the 2D gel electrophoresis. Acknowledgements We thank Drs. Stuart Linn and Hiroshi Nikaido for insightful this website discussions. This work was supported by USDA CALR-2005-01892 (to S. L.). References 1. Hoch JA: Two-Component Signal Transduction Washington, DC: American Society for Microbiology Press 1995. 2. Nixon BT, Ronson CW, Ausubel FM: Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation Celastrol regulatory genes ntrB and ntrC. Proc Natl Acad Sci USA 1986, 83:7850–7854.CrossRefPubMed 3. Iuchi S, Weiner L: Cellular and molecular physiology of Escherichia coli in the adaptation to aerobic environments. J Biochem (Tokyo) 1996, 120:1055–1063. 4. Bauer

CE, Elsen S, Bird TH: Mechanisms for redox control of gene expression. Annual Review of Microbiology 1999, 53:495–523.CrossRefPubMed 5. Hidalgo E, Ding H, Demple B: Redox signal transduction via iron-sulfur clusters in the SoxR transcription activator. Trends Biochem Sci 1997, 22:207–210.CrossRefPubMed 6. Demple B: Study of redox-regulated transcription factors in prokaryotes. Methods 1997, 11:267–278.CrossRefPubMed 7. Ding H, Demple B: Glutathione-mediated destabilization in vitro of [2Fe-2S] centers in the SoxR regulatory protein. Proc Natl Acad Sci USA 1996, 93:9449–9453.CrossRefPubMed 8. Nunoshiba T, Hidalgo E, Amabile Cuevas CF, Demple B: Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene.