Helmann Laboratory Supplemental Material (last update: April 2009)

Techniques:

1. long-flanking homology PCR (LFH-PCR)

 

Supplementary Material for:

W. Eiamphungporn and J. D. Helmann. The Bacillus subtilis sigma^M Regulon and its contribution to cell envelope stress responses. Mol. Microbiol, 2008 Jan 2; [Epub ahead of print]

 

1. Excel spreadsheet of the vancomycin stimulon with regulon assignments (Fig. 1).

 

2. Files Related to Hierarchical Clustering (Fig. 3)

                        Files ending with .txt are formatted for use with Gene Cluster 3.0

                        Files ending with .cdt can be viewed with TreeView (version 1.6) by Michael Eisen

 

                        A. 294 genes.txt                     D. All genes.txt

                        B. 294 genes.gtr                   E.  All genes.gtr

                        C. 294 genes.cdt                  F. All genes.cdt

 

3. Supplemental PDF as posted to the Mol. Microbiol. Web site (contains Table S1. Plasmids used in this work; Table S2. Strains used in this work; Table S3. Oligonucleotides used in this work; and Table S4. Pixel intensities for sigma^M-ROMA experiment)

 

 

Papers (In reverse chronological order):

16. W. Eiamphungporn and J. D. Helmann. 2008. The Bacillus subtilis sigma^M Regulon and its contribution to cell envelope stress responses. Mol. Microbiol. 67:830-848.

15. M. Cao, C. Moore, J. Helmann. 2005. Bacillus subtilis paraquat resistance is directed by sigma M, an extracytoplasmic function sigma factor, and is conferred by YqjL and BcrC. J. Bacteriol. 187:2948-2956.

14. C. M. Moore, A. Gaballa, M. Hui, R. W. Ye, and J. D. Helmann. 2005. Genetic and physiological responses of Bacillus subtilis to metal ion stress. Mol Microbiool. 57:27-40.

13. C. M. Moore, M. M. Nakano, T. Wang, R. W. Ye, J.D. Helmann. 2004. The response of Bacillus subtilis to nitric oxide and the nitrosating agent sodium nitroprusside. J. Bacteriol. 186: 4655-4664.

12. T. Mascher, N. G. Margulis, T. Wang, R. W. Ye, J.D. Helmann. 2003. Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon. Mol. Microbiol. 50: 1591-1604.

11. E. Guedon, C.M. Moore, Q. Que, T. Wang, R.W. Ye, and J. D. Helmann. 2003. The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA, and sigma-B Regulons. Mol. Microbiol. 49:1477-1491.

10. M. Cao, L. Salzberg, C.S. Tsai, T. Mascher, C. Bonilla, T. Wang, R.W. Ye , L. Marquez-Magana, J.D. Helmann. 2003. Regulation of the Bacillus subtilis extracytoplasmic function protein sigma(Y) and its target promoters. J. Bacteriol. 185:4883-4890.

9. Guedon and J.D. Helmann. 2003. Origins of metal ion selectivity in the DtxR/MntR family of metalloregulators. Mol. Microbiol. 48:495-506.

8. J.D. Helmann, M.F.W. Wu, A. Gaballa, P.A. Kobel, M.M. Morshedi, P. Fawcett, and C. Paddon. 2003. The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. J Bacteriol. 185:243-253.

7. A. Gaballa, T. Wang, R. Ye, and J.D. Helmann. 2002. Functional Analysis of the Bacillus subtilis Zur regulon. J. Bacteriol. 184:6508-6514.

6. N. Baichoo, T. Wang, R. Ye, and J.D. Helmann. 2002 Global analysis of the Bacillus subtilis Fur Regulon and the Iron Starvation Stimulon. Mol. Microl. 45:1613-1619.

5. M. Cao, T. Wang, R. Ye, and J. D. Helmann. 2002. Antibiotics That Inhibit Cell Wall Biosynthesis Induce Expression of the Bacillus subtilis SigW and SigM Regulons. Mol. Microbiol. 45:1267-1276.

4. M. Cao, M.M. Morshedi, P.A. Kobel, M.F.W. Wu, C. Paddon, and J.D. Helmann. 2002. Defining the Bacillus subtilis sigma(W) regulon: A comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J. Mol. Biol. 316:443-457.

3. J.D. Helmann. 2002. ECF sigma factors in gram positive bacteria. In Advances in Microbial Physiology, Vol. 46:47-110.

2. J.D. Helmann, M.F.W. Wu, P.A. Kobel, F-J. Gamo, M. Wilson, M.M. Morshedi, M. Navre, and C. Paddon. 2001. The global transcriptional response of Bacillus subtilis to heat-shock. J. Bacteriol. 183:7318-738.

1. J.D. Helmann. 1995. Compilation and Analysis of Bacillus subtilis sigma-A-Dependent Promoter Sequences: Evidence for Extended Contact Between RNA Polymerase and Upstream Promoter DNA. Nucleic Acids Research. 23:2351-2360.