Supplemental Material

Techniques

Papers and supplemental material

(In reverse chronological order. Last update: April 2009)


17. W. Eiamphungporn and J. D. Helmann. The Bacillus subtilis sigmaM 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
    1. 294 genes.txt
    2. 294 genes.gtr
    3. 294 genes.cdt
    4. All genes.txt
    5. All genes.gtr
    6. 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 sigmaM-ROMA experiment)

16. W. Eiamphungporn and J. D. Helmann. 2008. The Bacillus subtilis sigmaM 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.


15. M. Cao, C. Moore, J. Helmann. 2005. Bacillus subtilis paraquat resistance is directed by sigma M, an extracytoplasmic function sigma factor, and is confirmed 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.

Long-Flanking Homology PCR

Original Microarray Data Sets


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.

Note that all ratios are expressed in log2 format. Access all primary data and arrays at the Stanford Microarray Database (SMD)


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.

  • fur vs. WT (DP): Genes derepressed in a fur mutant vs. wild-type; both treated with dipyridul.
  • fur vs. WT (Fe): Genes derepressed in a fur mutant vs. wild-type; both treated with iron.
  • DP vs. Fe (WT): Genes derepressed in wild-type by iron starvation.
  • Interactive Fig. 1. Excel spread sheet used for the generation of Figure 1 (868 kb) and Figure 1.
  • Fig 1 data. data used for Fig. 1 as tab-delimited text (196 kb).
  • Table S1. Additional genes regulated by iron and/or by mutation of fur.

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.

  • Vancomycin Read Me: explanation of the vancomycin datasets
  • Van3: explanation 3 min. treatment with vancomycin (2 micrograms per ml)
  • Van10: explanation 10 min. treatment with vancomycin (2 micrograms per ml)

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.

  1. PDF of the scanned paper (warning: this is a 7 Mb file)
  2. Figures 1 - 7 (PowerPoint)
  3. Fig. 8: ECF sigma factor family tree
  4. Tables 1-8
  5. Table 12
  6. Table 9
  7. Table 10
  8. Table 11
  9. MS Word document of Text and Figure legends (as submitted)

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.

  • S1: Explanation and proof of normalization method
  • Table S2: Complete dataset of fold induction vs. time (caution: this is a 4800 Kb Excel file)
  • Table S3: Additional members of the Heat Shock stimulon
  • Heat shock Induction vs. Peroxide stress: Fold induction data vs. time is also available integrated into a larger dataset containing peroxide stress data and from the Stanford Microarray Database (SMD).

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.

  • Table 1. Compilation of SigA-dependent promoter sites