1887

Microbiology Society logo

Volume 164, Issue 4

RgsA, an RpoS-dependent sRNA, negatively regulates expression in Free

Abstract

As a master regulator, the alternative sigma factor RpoS coordinates the transcription of genes associated with protection against environmental stresses in bacteria. In , RpoS is also involved in quorum sensing and virulence. The cellular RpoS level is regulated at multiple levels, whereas the post-transcriptional regulation of rpoS in remains unclear. To identify and characterize small regulatory RNAs (sRNAs) regulating RpoS in , an sRNA library expressing a total of 263 sRNAs was constructed to examine their regulatory roles on expression. Our results demonstrate that expression is repressed by the RpoS-dependent sRNA RgsA at the post-transcriptional level. Unlike OxyS, an sRNA previously known to repress expression under oxidative stress in , RgsA represses expression during the exponential phase. This repression requires the RNA chaperone Hfq. Furthermore, the 71–77 conserved region of RgsA is necessary for full repression of expression, and the −25 to +27 region of rpoS mRNA is sufficient for RgsA-mediated repression. Together, our results not only add RgsA to the RpoS regulatory circuits but also highlight the complexity of interplay between sRNAs and transcriptional regulators in bacteria.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Hfq , Pseudomonas aeruginosa , RgsA , RpoS and small RNA
© 2018 The Authors
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000632
2018-04-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/micro/164/4/716.html?itemId=/content/journal/micro/10.1099/mic.0.000632&mimeType=html&fmt=ahah

References

  1. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880–891 [View Article][PubMed]
     [Google Scholar]
  2. Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:a003798 [View Article][PubMed]
     [Google Scholar]
  3. Caldelari I, Chao Y, Romby P, Vogel J. RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med 2013; 3:a010298 [View Article][PubMed]
     [Google Scholar]
  4. Bossi L, Figueroa-Bossi N. Competing endogenous RNAs: a target-centric view of small RNA regulation in bacteria. Nat Rev Microbiol 2016; 14:775–784 [View Article][PubMed]
     [Google Scholar]
  5. Kavita K, de Mets F, Gottesman S. New aspects of RNA-based regulation by Hfq and its partner sRNAs. Curr Opin Microbiol 2017; 42:53–61 [View Article][PubMed]
     [Google Scholar]
  6. Wagner EG, Romby P. Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv Genet 2015; 90:133–208 [View Article][PubMed]
     [Google Scholar]
  7. Vogel J, Luisi BF. Hfq and its constellation of RNA. Nat Rev Microbiol 2011; 9:578–589 [View Article][PubMed]
     [Google Scholar]
  8. Hengge-Aronis R. Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 2002; 66:373–395 [View Article][PubMed]
     [Google Scholar]
  9. Dong T, Schellhorn HE. Role of RpoS in virulence of pathogens. Infect Immun 2010; 78:887–897 [View Article][PubMed]
     [Google Scholar]
  10. Schuster M, Hawkins AC, Harwood CS, Greenberg EP. The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing. Mol Microbiol 2004; 51:973–985 [View Article][PubMed]
     [Google Scholar]
  11. Venturi V. Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different?. Mol Microbiol 2003; 49:1–9 [View Article][PubMed]
     [Google Scholar]
  12. Mika F, Hengge R. Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli. RNA Biol 2014; 11:494–507 [View Article][PubMed]
     [Google Scholar]
  13. Battesti A, Majdalani N, Gottesman S. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol 2011; 65:189–213 [View Article][PubMed]
     [Google Scholar]
  14. Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S. DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci USA 1998; 95:12462–12467 [View Article][PubMed]
     [Google Scholar]
  15. Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J et al. sRNA-mediated control of transcription termination in E. coli. Cell 2016; 167:111.e13–121.e13 [View Article][PubMed]
     [Google Scholar]
  16. Repoila F, Majdalani N, Gottesman S. Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol Microbiol 2003; 48:855–861 [View Article][PubMed]
     [Google Scholar]
  17. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R et al. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. Embo J 1998; 17:6061–6068 [View Article][PubMed]
     [Google Scholar]
  18. Sevo M, Buratti E, Venturi V. Ribosomal protein S1 specifically binds to the 5' untranslated region of the Pseudomonas aeruginosa stationary-phase sigma factor rpoS mRNA in the logarithmic phase of growth. J Bacteriol 2004; 186:4903–4909 [View Article][PubMed]
     [Google Scholar]
  19. Jovcic B, Bertani I, Venturi V, Topisirovic L, Kojic M. 5' Untranslated region of the Pseudomonas putida WCS358 stationary phase sigma factor rpoS mRNA is involved in RpoS translational regulation. J Microbiol 2008; 46:56–61 [View Article][PubMed]
     [Google Scholar]
  20. Sonnleitner E, Hagens S, Rosenau F, Wilhelm S, Habel A et al. Reduced virulence of a hfq mutant of Pseudomonas aeruginosa O1. Microb Pathog 2003; 35:217–228 [View Article][PubMed]
     [Google Scholar]
  21. Gómez-Lozano M, Marvig RL, Molin S, Long KS. Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa. Environ Microbiol 2012; 14:2006–2016 [View Article][PubMed]
     [Google Scholar]
  22. González N, Heeb S, Valverde C, Kay E, Reimmann C et al. Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species. BMC Genomics 2008; 9:167 [View Article][PubMed]
     [Google Scholar]
  23. Huerta JM, Aguilar I, López-Pliego L, Fuentes-Ramírez LE, Castañeda M. The role of the ncRNA RgsA in the oxidative stress response and biofilm formation in Azotobacter vinelandii. Curr Microbiol 2016; 72:671–679 [View Article][PubMed]
     [Google Scholar]
  24. Livny J, Brencic A, Lory S, Waldor MK. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 2006; 34:3484–3493 [View Article][PubMed]
     [Google Scholar]
  25. Lu P, Wang Y, Zhang Y, Hu Y, Thompson KM et al. RpoS-dependent sRNA RgsA regulates Fis and AcpP in Pseudomonas aeruginosa. Mol Microbiol 2016; 102:244–259 [View Article][PubMed]
     [Google Scholar]
  26. Park SH, Butcher BG, Anderson Z, Pellegrini N, Bao Z et al. Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology 2013; 159:296–306 [View Article][PubMed]
     [Google Scholar]
  27. Milton DL, O'Toole R, Horstedt P, Wolf-Watz H. Flagellin A is essential for the virulence of Vibrio anguillarum. J Bacteriol 1996; 178:1310–1319 [View Article][PubMed]
     [Google Scholar]
  28. Miller J. Experiments in Molecular Genetics Cold Spring Harbour: Cold Spring Harbor Press; 1972
     [Google Scholar]
  29. Kojic M, Aguilar C, Venturi V. TetR family member psrA directly binds the Pseudomonas rpoS and psrA promoters. J Bacteriol 2002; 184:2324–2330 [View Article][PubMed]
     [Google Scholar]
  30. Jousselin A, Metzinger L, Felden B. On the facultative requirement of the bacterial RNA chaperone, Hfq. Trends Microbiol 2009; 17:399–405 [View Article][PubMed]
     [Google Scholar]
  31. Sonnleitner E, González N, Haas D. Small RNAs of Pseudomonas spp. In Ramos J, Filloux A. (editors) Pseudomonas—Molecular Microbiology, Infection and Biodiversity vol. 6 Dordrecht: Springer; 2010 pp. 3–28
     [Google Scholar]
  32. Brown L, Elliott T. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol 1997; 179:656–662 [View Article][PubMed]
     [Google Scholar]
  33. Urban JH, Vogel J. Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 2007; 35:1018–1037 [View Article][PubMed]
     [Google Scholar]
  34. Mandin P, Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. Embo J 2010; 29:3094–3107 [View Article][PubMed]
     [Google Scholar]
  35. de Lay N, Gottesman S. A complex network of small non-coding RNAs regulate motility in Escherichia coli. Mol Microbiol 2012; 86:524–538 [View Article][PubMed]
     [Google Scholar]
  36. Coornaert A, Chiaruttini C, Springer M, Guillier M. Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB. PLoS Genet 2013; 9:e1003156 [View Article][PubMed]
     [Google Scholar]
  37. Lee HJ, Gottesman S. sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 2016; 44:6907–6923 [View Article][PubMed]
     [Google Scholar]
  38. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406–3415 [View Article][PubMed]
     [Google Scholar]
  39. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004; 10:1507–1517 [View Article][PubMed]
     [Google Scholar]
  40. Updegrove TB, Wartell RM. The influence of Escherichia coli Hfq mutations on RNA binding and sRNA•mRNA duplex formation in rpoS riboregulation. Biochim Biophys Acta 2011; 1809:532–540 [View Article][PubMed]
     [Google Scholar]
  41. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 2002; 9:11–22 [View Article][PubMed]
     [Google Scholar]
  42. Simon R, Priefer U, Pühler A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Biotechnology 1983; 1:784–791 [View Article]
     [Google Scholar]
  43. Blumer C, Heeb S, Pessi G, Haas D. Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites. Proc Natl Acad Sci USA 1999; 96:14073–14078 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000632
Loading
RgsA, an RpoS-dependent sRNA, negatively regulates rpoS expression in Pseudomonas aeruginosa
Microbiology 164, 716 (2018); https://doi.org/10.1099/mic.0.000632
/content/journal/micro/10.1099/mic.0.000632
/content/journal/micro/10.1099/mic.0.000632
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