1887

Microbiology Society logo

Volume 158, Issue 3

Defining the structure of the general stress regulon of using targeted microarray analysis and random forest classification Free

Abstract

The structure of the SigB-dependent general stress regulon of has previously been characterized by proteomics approaches as well as DNA array-based expression studies. However, comparing the SigB targets published in three previous major transcriptional profiling studies it is obvious that although each of them identified well above 100 target genes, only 67 were identified in all three studies. These substantial differences can likely be attributed to the different strains, growth conditions, microarray platforms and experimental setups used in the studies. In order to gain a better understanding of the structure of this important regulon, a targeted DNA microarray analysis covering most of the known SigB-inducing conditions was performed, and the changes in expression kinetics of 252 potential members of the SigB regulon and appropriate control genes were recorded. Transcriptional data for the wild-type strain 168 and its isogenic mutant BSM29 were analysed using random forest, a machine learning algorithm, by incorporating the knowledge from previous studies. This analysis revealed a strictly SigB-dependent expression pattern for 166 genes following ethanol, butanol, osmotic and oxidative stress, low-temperature growth and heat shock, as well as limitation of oxygen or glucose. Kinetic analysis of the data for the wild-type strain identified 30 additional members of the SigB regulon, which were also subject to control by additional transcriptional regulators, thus displaying atypical SigB-independent induction patterns in the mutant strain under some of the conditions tested. For 19 of these 30 SigB regulon members, published reports support control by secondary regulators along with SigB. Thus, this microarray-based study assigns a total of 196 genes to the SigB-dependent general stress regulon of .

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
© 2012 SGM
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.055434-0
2012-03-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/158/3/696.html?itemId=/content/journal/micro/10.1099/mic.0.055434-0&mimeType=html&fmt=ahah

References

  1. Antelmann H., Engelmann S., Schmid R., Hecker M. ( 1996). General and oxidative stress responses in Bacillus subtilis: cloning, expression, and mutation of the alkyl hydroperoxide reductase operon. J Bacteriol 178:6571–6578[PubMed]
     [Google Scholar]
  2. Au N., Kuester-Schoeck E., Mandava V., Bothwell L. E., Canny S. P., Chachu K., Colavito S. A., Fuller S. N., Groban E. S. & other authors ( 2005). Genetic composition of the Bacillus subtilis SOS system. J Bacteriol 187:7655–7666 [View Article][PubMed]
     [Google Scholar]
  3. Banse A. V., Chastanet A., Rahn-Lee L., Hobbs E. C., Losick R. ( 2008). Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis . Proc Natl Acad Sci U S A 105:15547–15552 [View Article][PubMed]
     [Google Scholar]
  4. Baranova N. N., Danchin A., Neyfakh A. A. ( 1999). Mta, a global MerR-type regulator of the Bacillus subtilis multidrug-efflux transporters. Mol Microbiol 31:1549–1559 [View Article][PubMed]
     [Google Scholar]
  5. Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I. & other authors ( 2009). From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758–1775 [View Article][PubMed]
     [Google Scholar]
  6. Bower S., Perkins J. B., Yocum R. R., Howitt C. L., Rahaim P., Pero J. ( 1996). Cloning, sequencing, and characterization of the Bacillus subtilis biotin biosynthetic operon. J Bacteriol 178:4122–4130[PubMed]
     [Google Scholar]
  7. Boylan S. A., Thomas M. D., Price C. W. ( 1991). Genetic method to identify regulons controlled by nonessential elements: isolation of a gene dependent on alternate transcription factor σB of Bacillus subtilis . J Bacteriol 173:7856–7866[PubMed]
     [Google Scholar]
  8. Boylan S. A., Rutherford A., Thomas S. M., Price C. W. ( 1992). Activation of Bacillus subtilis transcription factor σB by a regulatory pathway responsive to stationary-phase signals. J Bacteriol 174:3695–3706[PubMed]
     [Google Scholar]
  9. Boylan S. A., Redfield A. R., Brody M. S., Price C. W. ( 1993). Stress-induced activation of the σB transcription factor of Bacillus subtilis . J Bacteriol 175:7931–7937[PubMed]
     [Google Scholar]
  10. Breiman L. ( 2001). Random forests. Mach Learn 45:5–32 [View Article]
     [Google Scholar]
  11. Brigulla M., Hoffmann T., Krisp A., Völker A., Bremer E., Völker U. ( 2003). Chill induction of the SigB-dependent general stress response in Bacillus subtilis and its contribution to low-temperature adaptation. J Bacteriol 185:4305–4314 [View Article][PubMed]
     [Google Scholar]
  12. Burkholder P. R., Giles N. H. Jr ( 1947). Induced biochemical mutations in Bacillus subtilis. . Am J Bot 34:345–348 [View Article][PubMed]
     [Google Scholar]
  13. Cao M., Kobel P. A., Morshedi M. M., Wu M. F., Paddon C., Helmann J. D. ( 2002). Defining the Bacillus subtilis σW regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol 316:443–457 [View Article][PubMed]
     [Google Scholar]
  14. Chu F., Kearns D. B., Branda S. S., Kolter R., Losick R. ( 2006). Targets of the master regulator of biofilm formation in Bacillus subtilis . Mol Microbiol 59:1216–1228 [View Article][PubMed]
     [Google Scholar]
  15. Chumsakul O., Takahashi H., Oshima T., Hishimoto T., Kanaya S., Ogasawara N., Ishikawa S. ( 2011). Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. Nucleic Acids Res 39:414–428 [View Article][PubMed]
     [Google Scholar]
  16. Comella N., Grossman A. D. ( 2005). Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis . Mol Microbiol 57:1159–1174 [View Article][PubMed]
     [Google Scholar]
  17. Derré I., Rapoport G., Msadek T. ( 1999). CtsR, a novel regulator of stress and heat shock response, controls clp and molecular chaperone gene expression in Gram-positive bacteria. Mol Microbiol 31:117–131 [View Article][PubMed]
     [Google Scholar]
  18. Drzewiecki K., Eymann C., Mittenhuber G., Hecker M. ( 1998). The yvyD gene of Bacillus subtilis is under dual control of σB and σH . J Bacteriol 180:6674–6680[PubMed]
     [Google Scholar]
  19. Ebbole D. J., Zalkin H. ( 1987). Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J Biol Chem 262:8274–8287[PubMed]
     [Google Scholar]
  20. Efron B. ( 1982). The Jackknife, the Bootstrap, and Other Resampling Plans Philadelphia, PA.: Society for Industrial and Applied Mathematics; [View Article]
     [Google Scholar]
  21. Eiamphungporn W., Helmann J. D. ( 2008). The Bacillus subtilis σM regulon and its contribution to cell envelope stress responses. Mol Microbiol 67:830–848 [View Article][PubMed]
     [Google Scholar]
  22. Erwin K. N., Nakano S., Zuber P. ( 2005). Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J Bacteriol 187:4042–4049 [View Article][PubMed]
     [Google Scholar]
  23. Flórez L. A., Roppel S. F., Schmeisky A. G., Lammers C. R., Stülke J. ( 2009). A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database (Oxford) 2009:bap012[PubMed] [CrossRef]
     [Google Scholar]
  24. Gaidenko T. A., Price C. W. ( 1998). General stress transcription factor σB and sporulation transcription factor σH each contribute to survival of Bacillus subtilis under extreme growth conditions. J Bacteriol 180:3730–3733[PubMed]
     [Google Scholar]
  25. Grundy F. J., Henkin T. M. ( 1998). The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol Microbiol 30:737–749 [View Article][PubMed]
     [Google Scholar]
  26. Hecker M., Pané-Farré J., Völker U. ( 2007). SigB-dependent general stress response in Bacillus subtilis and related Gram-positive bacteria. Annu Rev Microbiol 61:215–236 [View Article][PubMed]
     [Google Scholar]
  27. Helmann J. D., Wu M. F., Kobel P. A., Gamo F. J., Wilson M., Morshedi M. M., Navre M., Paddon C. ( 2001). Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183:7318–7328 [View Article][PubMed]
     [Google Scholar]
  28. Helmann J. D., Wu M. F., Gaballa A., Kobel P. A., Morshedi M. M., Fawcett P., Paddon C. ( 2003). The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. J Bacteriol 185:243–253 [View Article][PubMed]
     [Google Scholar]
  29. Höper D., Völker U., Hecker M. ( 2005). Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis . J Bacteriol 187:2810–2826 [View Article][PubMed]
     [Google Scholar]
  30. Jervis A. J., Thackray P. D., Houston C. W., Horsburgh M. J., Moir A. ( 2007). SigM-responsive genes of Bacillus subtilis and their promoters. J Bacteriol 189:4534–4538 [View Article][PubMed]
     [Google Scholar]
  31. Jürgen B., Tobisch S., Wümpelmann M., Gördes D., Koch A., Thurow K., Albrecht D., Hecker M., Schweder T. ( 2005). Global expression profiling of Bacillus subtilis cells during industrial-close fed-batch fermentations with different nitrogen sources. Biotechnol Bioeng 92:277–298 [View Article][PubMed]
     [Google Scholar]
  32. Kearns D. B., Chu F., Branda S. S., Kolter R., Losick R. ( 2005). A master regulator for biofilm formation by Bacillus subtilis . Mol Microbiol 55:739–749 [View Article][PubMed]
     [Google Scholar]
  33. Klein-Seetharaman J., Tastan O., Qi Y. J., Carbonell J. G. ( 2009). Prediction of interactions between HIV-1 and human proteins by information integration. Pac Symp Biocomput 2009:516–527
     [Google Scholar]
  34. Krüger E., Msadek T., Hecker M. ( 1996). Alternate promoters direct stress-induced transcription of the Bacillus subtilis clpC operon. Mol Microbiol 20:713–723 [View Article][PubMed]
     [Google Scholar]
  35. Kumaraswami M., Newberry K. J., Brennan R. G. ( 2010). Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. J Mol Biol 398:264–275 [View Article][PubMed]
     [Google Scholar]
  36. Kunst F., Ogasawara N., Moszer I., Albertini A. M., Alloni G., Azevedo V., Bertero M. G., Bessières P., Bolotin A. & other authors ( 1997). The complete genome sequence of the Gram-positive bacterium Bacillus subtilis . Nature 390:249–256 [View Article][PubMed]
     [Google Scholar]
  37. Leelakriangsak M., Kobayashi K., Zuber P. ( 2007). Dual negative control of spx transcription initiation from the P3 promoter by repressors PerR and YodB in Bacillus subtilis . J Bacteriol 189:1736–1744 [View Article][PubMed]
     [Google Scholar]
  38. Lei J., Zhou Y. F., Li L. F., Su X. D. ( 2009). Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis . Protein Sci 18:1792–1800 [View Article][PubMed]
     [Google Scholar]
  39. Marvasi M., Visscher P. T., Casillas Martinez L. ( 2010). Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis. FEMS Microbiol Lett 313:1–9 [View Article][PubMed]
     [Google Scholar]
  40. Méndez M. B., Orsaria L. M., Philippe V., Pedrido M. E., Grau R. R. ( 2004). Novel roles of the master transcription factors Spo0A and σB for survival and sporulation of Bacillus subtilis at low growth temperature. J Bacteriol 186:989–1000 [View Article][PubMed]
     [Google Scholar]
  41. Mostertz J., Scharf C., Hecker M., Homuth G. ( 2004). Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology 150:497–512 [View Article][PubMed]
     [Google Scholar]
  42. Nakano S., Küster-Schöck E., Grossman A. D., Zuber P. ( 2003). Spx-dependent global transcriptional control is induced by thiol-specific oxidative stress in Bacillus subtilis . Proc Natl Acad Sci U S A 100:13603–13608 [View Article][PubMed]
     [Google Scholar]
  43. Nguyen T. T., Eiamphungporn W., Mäder U., Liebeke M., Lalk M., Hecker M., Helmann J. D., Antelmann H. ( 2009). Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR). Mol Microbiol 71:876–894 [View Article][PubMed]
     [Google Scholar]
  44. Perkins J. B., Bower S., Howitt C. L., Yocum R. R., Pero J. ( 1996). Identification and characterization of transcripts from the biotin biosynthetic operon of Bacillus subtilis . J Bacteriol 178:6361–6365[PubMed]
     [Google Scholar]
  45. Petersohn A., Antelmann H., Gerth U., Hecker M. ( 1999a). Identification and transcriptional analysis of new members of the σB regulon in Bacillus subtilis . Microbiology 145:869–880 [View Article][PubMed]
     [Google Scholar]
  46. Petersohn A., Bernhardt J., Gerth U., Höper D., Koburger T., Völker U., Hecker M. ( 1999b). Identification of σB-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J Bacteriol 181:5718–5724[PubMed]
     [Google Scholar]
  47. Petersohn A., Engelmann S., Setlow P., Hecker M. ( 1999c). The katX gene of Bacillus subtilis is under dual control of σB and σF . Mol Gen Genet 262:173–179 [View Article][PubMed]
     [Google Scholar]
  48. Petersohn A., Brigulla M., Haas S., Hoheisel J. D., Völker U., Hecker M. ( 2001). Global analysis of the general stress response of Bacillus subtilis . J Bacteriol 183:5617–5631 [View Article][PubMed]
     [Google Scholar]
  49. Price C. W. ( 2000). Protective function and regulation of the general stress response in Bacillus subtilis and related Gram-positive bacteria. Bacterial Stress Responses179–197 Storz G., Hengge-Aronis R. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  50. Price C. W. ( 2002). General stress response. Bacillus subtilis and its Closest Relatives: from Genes to Cells369–384 Sonenshein A. L., Hoch J. A., Losick R. Washington, DC: American Society for Microbiology; [CrossRef]
     [Google Scholar]
  51. Price C. W. 2011; General stress response in Bacillus subtilis and related Gram-positive bacteria. Bacterial Stress Responses301–318 Storz G., Hengge R. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  52. Price C. W., Fawcett P., Cérémonie H., Su N., Murphy C. K., Youngman P. ( 2001). Genome-wide analysis of the general stress response in Bacillus subtilis . Mol Microbiol 41:757–774 [View Article][PubMed]
     [Google Scholar]
  53. Scharf C., Riethdorf S., Ernst H., Engelmann S., Völker U., Hecker M. ( 1998). Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis . J Bacteriol 180:1869–1877[PubMed]
     [Google Scholar]
  54. Sekowska A., Danchin A. ( 2002). The methionine salvage pathway in Bacillus subtilis . BMC Microbiol 2:8 [View Article][PubMed]
     [Google Scholar]
  55. Sierro N., Makita Y., de Hoon M., Nakai K. ( 2008). DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36:Database issueD93–D96 [View Article][PubMed]
     [Google Scholar]
  56. Staden R. ( 1984). Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res 12:505–519 [View Article][PubMed]
     [Google Scholar]
  57. Strobl C., Boulesteix A. L., Zeileis A., Hothorn T. ( 2007). Bias in random forest variable importance measures: illustrations, sources and a solution. BMC Bioinformatics 8:25 [View Article][PubMed]
     [Google Scholar]
  58. Stülke J., Hanschke R., Hecker M. ( 1993). Temporal activation of β-glucanase synthesis in Bacillus subtilis is mediated by the GTP pool. J Gen Microbiol 139:2041–2045[PubMed] [CrossRef]
     [Google Scholar]
  59. van Hijum S. A., García de la Nava J., Trelles O., Kok J., Kuipers O. P. ( 2003). MicroPreP: a cDNA microarray data pre-processing framework. Appl Bioinformatics 2:241–244[PubMed]
     [Google Scholar]
  60. Varón D., Brody M. S., Price C. W. ( 1996). Bacillus subtilis operon under the dual control of the general stress transcription factor σB and the sporulation transcription factor σH . Mol Microbiol 20:339–350 [View Article][PubMed]
     [Google Scholar]
  61. Völker U., Engelmann S., Maul B., Riethdorf S., Völker A., Schmid R., Mach H., Hecker M. ( 1994). Analysis of the induction of general stress proteins of Bacillus subtilis . Microbiology 140:741–752 [View Article][PubMed]
     [Google Scholar]
  62. Völker U., Voelker A., Maul B., Hecker M., Dufour A., Haldenwang W. G. ( 1995). Separate mechanisms activate σB of Bacillus subtilis in response to environmental and metabolic stresses. J Bacteriol 177:3771–3780[PubMed]
     [Google Scholar]
  63. Völker U., Maul B., Hecker M. ( 1999). Expression of the σB-dependent general stress regulon confers multiple stress resistance in Bacillus subtilis . J Bacteriol 181:3942–3948[PubMed]
     [Google Scholar]
  64. Waldmüller S., Freund P., Mauch S., Toder R., Vosberg H. P. ( 2002). Low-density DNA microarrays are versatile tools to screen for known mutations in hypertrophic cardiomyopathy. Hum Mutat 19:560–569 [View Article][PubMed]
     [Google Scholar]
  65. Wang S. T., Setlow B., Conlon E. M., Lyon J. L., Imamura D., Sato T., Setlow P., Losick R., Eichenberger P. ( 2006). The forespore line of gene expression in Bacillus subtilis . J Mol Biol 358:16–37 [View Article][PubMed]
     [Google Scholar]
  66. Weng M., Nagy P. L., Zalkin H. ( 1995). Identification of the Bacillus subtilis pur operon repressor. Proc Natl Acad Sci U S A 92:7455–7459 [View Article][PubMed]
     [Google Scholar]
  67. You C., Sekowska A., Francetic O., Martin-Verstraete I., Wang Y., Danchin A. ( 2008). Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis . BMC Microbiol 8:128 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.055434-0
Loading
Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification
Microbiology 158, 696 (2012); https://doi.org/10.1099/mic.0.055434-0
/content/journal/micro/10.1099/mic.0.055434-0
/content/journal/micro/10.1099/mic.0.055434-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error