1887

Microbiology Society logo

Volume 162, Issue 10

Characterization of a protein–protein interaction within the SigO–RsoA two-subunit σ factor: the σ region 2.3-like segment of RsoA mediates interaction with SigO Free

Abstract

σ factors are single subunit general transcription factors that reversibly bind core RNA polymerase and mediate gene-specific transcription in bacteria. Previously, an atypical two-subunit σ factor was identified that activates transcription from a group of related promoters in . Both of the subunits, named SigO and RsoA, share primary sequence similarity with the canonical σ family of σ factors and interact with each other and with RNA polymerase subunits. Here we show that the σ region 2.3-like segment of RsoA is unexpectedly sufficient for interaction with the amino-terminus of SigO and the β′ subunit. A mutational analysis of RsoA identified aromatic residues conserved amongst all RsoA homologues, and often amongst canonical σ factors, that are particularly important for the SigO–RsoA interaction. In a canonical σ factor, region 2.3 amino acids bind non-template strand DNA, trapping the promoter in a single-stranded state required for initiation of transcription. Accordingly, we speculate that RsoA region 2.3 protein-binding activity likely arose from a motif that, at least in its ancestral protein, participated in DNA-binding interactions.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacillus subtilis , protein–protein interaction , RNA polymerase , sigma factor and transcription
© 2016 The Authors
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000358
2016-10-01
2023-11-30
Loading full text...

Full text loading...

/deliver/fulltext/micro/162/10/1857.html?itemId=/content/journal/micro/10.1099/mic.0.000358&mimeType=html&fmt=ahah

References

  1. Arthur T. M., Burgess R. R. 1998; Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta' subunit. J Biol Chem 273:31381–31387 [View Article][PubMed]
     [Google Scholar]
  2. Banta A. B., Chumanov R. S., Yuan A. H., Lin H., Campbell E. A., Burgess R. R., Gourse R. L. 2013; Key features of σS required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme. Proc Natl Acad Sci U S A 110:15955–15960 [View Article][PubMed]
     [Google Scholar]
  3. Bao X., Nickels B. E., Fan H. 2012; Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66. Proc Natl Acad Sci U S A 109:16870–16875 [View Article][PubMed]
     [Google Scholar]
  4. Battesti A., Bouveret E. 2012; The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli . Methods 58:325–334 [View Article][PubMed]
     [Google Scholar]
  5. Bhandari V., Ahmod N. Z., Shah H. N., Gupta R. S. 2013; Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus . Int J Syst Evol Microbiol 63:2712–2726 [View Article][PubMed]
     [Google Scholar]
  6. Burgess R. R., Travers A. A., Dunn J. J., Bautz E. K. 1969; Factor stimulating transcription by RNA polymerase. Nature 221:43–46 [View Article][PubMed]
     [Google Scholar]
  7. Campagne S., Marsh M. E., Capitani G., Vorholt J. A., Allain F. H. 2014; Structural basis for −10 promoter element melting by environmentally induced sigma factors. Nat Struct Mol Biol 21:269–276 [View Article][PubMed]
     [Google Scholar]
  8. Cole C., Barber J. D., Barton G. J. 2008; The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36:W197–W201 [View Article][PubMed]
     [Google Scholar]
  9. Davey N. E., Van Roey K., Weatheritt R. J., Toedt G., Uyar B., Altenberg B., Budd A., Diella F., Dinkel H., Gibson T. J. 2012; Attributes of short linear motifs. Mol Biosyst 8:268–281 [View Article][PubMed]
     [Google Scholar]
  10. deHaseth P. L., Helmann J. D. 1995; Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol Microbiol 16:817–824 [View Article][PubMed]
     [Google Scholar]
  11. Dove S. L., Hochschild A. 2004; A bacterial two-hybrid system based on transcription activation. Methods Mol Biol 261:231–246 [View Article][PubMed]
     [Google Scholar]
  12. Feklistov A., Darst S. A. 2011; Structural basis for promoter −10 element recognition by the bacterial RNA polymerase σ subunit. Cell 147:1257–1269 [View Article][PubMed]
     [Google Scholar]
  13. Geszvain K., Gruber T. M., Mooney R. A., Gross C. A., Landick R. 2004; A hydrophobic patch on the flap-tip helix of E.coli RNA polymerase mediates sigma(70) region 4 function. J Mol Biol 343:569–587 [View Article][PubMed]
     [Google Scholar]
  14. Gribskov M., Burgess R. R. 1986; Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res 14:6745–6763 [View Article][PubMed]
     [Google Scholar]
  15. Gundlach J., Rath H., Herzberg C., Mäder U., Stülke J. 2016; Second messenger signaling in Bacillus subtilis: Accumulation of cyclic di-AMP inhibits biofilm formation. Front Microbiol 7:804 [View Article][PubMed]
     [Google Scholar]
  16. Hachmann A. B., Angert E. R., Helmann J. D. 2009; Genetic analysis of factors affecting susceptibility of Bacillus subtilis to daptomycin. Antimicrob Agents Chemother 53:1598–1609 [View Article][PubMed]
     [Google Scholar]
  17. Helmann J. D. 2002; The extracytoplasmic function (ECF) sigma factors. Adv Microb Physiol 46:47–110[PubMed] [CrossRef]
     [Google Scholar]
  18. Helmann J. D., Chamberlin M. J. 1988; Structure and function of bacterial sigma factors. Annu Rev Biochem 57:839–872 [View Article][PubMed]
     [Google Scholar]
  19. Johnston E. B., Lewis P. J., Griffith R. 2009; The interaction of Bacillus subtilis sigmaA with RNA polymerase. Protein Sci 18:2287–2297 [View Article][PubMed]
     [Google Scholar]
  20. Juang Y. L., Helmann J. D. 1994; A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J Mol Biol 235:1470–1488 [View Article][PubMed]
     [Google Scholar]
  21. Karimova G., Pidoux J., Ullmann A., Ladant D. 1998; A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc Natl Acad Sci U S A 95:5752–5756 [View Article][PubMed]
     [Google Scholar]
  22. Kuznedelov K., Minakhin L., Niedziela-Majka A., Dove S. L., Rogulja D., Nickels B. E., Hochschild A., Heyduk T., Severinov K. 2002; A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295:855–857 [View Article][PubMed]
     [Google Scholar]
  23. Liu B., Zuo Y., Steitz T. A. 2016; Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 113:4051–4056 [CrossRef]
     [Google Scholar]
  24. Lonetto M., Gribskov M., Gross C. A. 1992; The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol 174:3843–3849[PubMed]
     [Google Scholar]
  25. Ma C., Yang X., Kandemir H., Mielczarek M., Johnston E. B., Griffith R., Kumar N., Lewis P. J. 2013; Inhibitors of bacterial transcription initiation complex formation. ACS Chem Biol 8:1972–1980 [View Article][PubMed]
     [Google Scholar]
  26. MacLellan S. R., Wecke T., Helmann J. D. 2008; A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis . Mol Microbiol 69:954–967 [View Article][PubMed]
     [Google Scholar]
  27. MacLellan S. R., Helmann J. D., Antelmann H. 2009a; The YvrI alternative σ factor Is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis . J Bacteriol 191:931–939 [View Article][PubMed]
     [Google Scholar]
  28. MacLellan S. R., Guariglia-Oropeza V., Gaballa A., Helmann J. D. 2009b; A two-subunit bacterial σ-factor activates transcription in Bacillus subtilis . Proc Natl Acad Sci 106:21323–21328 [View Article]
     [Google Scholar]
  29. Malhotra A., Severinova E., Darst S. A. 1996; Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87:127–136 [View Article][PubMed]
     [Google Scholar]
  30. Missiakas D., Raina S. 1998; The extracytoplasmic function sigma factors: role and regulation. Mol Microbiol 28:1059–1066 [View Article][PubMed]
     [Google Scholar]
  31. Monteil V., Kolb A., Mayer C., Hoos S., England P., Norel F. 2010; Crl binds to domain 2 of σ(S) and confers a competitive advantage on a natural rpoS mutant of Salmonella enterica serovar Typhi. J Bacteriol 192:6401–6410 [View Article][PubMed]
     [Google Scholar]
  32. Murakami K. S. 2013; X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme. J Biol Chem 288:9126–9134 [View Article][PubMed]
     [Google Scholar]
  33. Murakami K. S. 2015; Structural biology of bacterial RNA polymerase. Biomolecules 5:848–864 [View Article][PubMed]
     [Google Scholar]
  34. Murakami K. S., Darst S. A. 2003; Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 13:31–39 [View Article][PubMed]
     [Google Scholar]
  35. Neduva V., Russell R. B. 2005; Linear motifs: evolutionary interaction switches. FEBS Lett 579:3342–3345 [View Article][PubMed]
     [Google Scholar]
  36. Paget M. S. B., Helmann J. D. 2003; The sigma70 family of sigma factors. Genome Biol 4:203[PubMed] [CrossRef]
     [Google Scholar]
  37. Panaghie G., Aiyar S. E., Bobb K. L., Hayward R. S., de Haseth P. L. 2000; Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex. J Mol Biol 299:1217–1230 [View Article][PubMed]
     [Google Scholar]
  38. Rong J. C., Helmann J. D. 1994; Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting. J Bacteriol 176:5218–5224[PubMed]
     [Google Scholar]
  39. Sengupta S., Prajapati R. K., Mukhopadhyay J. 2015; Promoter escape with bacterial two-component σ factor suggests retention of σ region two in the elongation complex. J Biol Chem 290:28575–28583 [View Article][PubMed]
     [Google Scholar]
  40. Sievers F., Wilm A., Dineen D., Gibson T. J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M. et al. 2011; Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539 [View Article][PubMed]
     [Google Scholar]
  41. Tabib-Salazar A., Liu B., Doughty P., Lewis R. A., Ghosh S., Parsy M. L., Simpson P. J., O'Dwyer K., Matthews S. J., Paget M. S. 2013; The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase. Nucleic Acids Res 41:5679–5691 [View Article][PubMed]
     [Google Scholar]
  42. Tanaka K., Takayanagi Y., Fujita N., Ishihama A., Takahashi H. 1993; Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A 90:3511–3515 [View Article][PubMed]
     [Google Scholar]
  43. Van Roey K., Uyar B., Weatheritt R. J., Dinkel H., Seiler M., Budd A., Gibson T. J., Davey N. E. 2014; Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chem Rev 114:6733–6778 [View Article][PubMed]
     [Google Scholar]
  44. Wagner G. P., Lynch V. J. 2008; The gene regulatory logic of transcription factor evolution. Trends Ecol Evol 23:377–385 [View Article]
     [Google Scholar]
  45. Zuo Y., Steitz T. A. 2015; Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 58:534–540 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000358
Loading
Characterization of a protein–protein interaction within the SigO–RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO
Microbiology 162, 1857 (2016); https://doi.org/10.1099/mic.0.000358
/content/journal/micro/10.1099/mic.0.000358
/content/journal/micro/10.1099/mic.0.000358
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

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