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Global Discovery of Small Noncoding RNAs in Pathogenic Yersinia Species

  • Jovanka T. Koo
  • Wyndham W. Lathem
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 954)

Abstract

Small noncoding RNAs (sRNAs) function as regulatory elements in both eukaryotes and bacteria. Trans-acting bacterial sRNAs posttranscriptionally regulate gene expression by base pairing with target mRNAs, which often leads to changes in translation efficiency and/or stability of the transcript. Bioinformatic search algorithms along with a variety of experimental approaches have become increasingly useful for the discovery of sRNAs and their mRNA targets. Our laboratory and others recently demonstrated that Hfq, a protein chaperone of sRNAs in bacteria, is required for the full virulence of both Yersinia pestis, the bacterium that causes the disease plague, and the genetically related gastrointestinal pathogen Yersinia pseudotuberculosis. This led us to pursue the first global identification and analysis of sRNAs in pathogenic Yersinia species. We have identified 150 previously unannotated sRNAs expressed by Y. pseudotuberculosis when cultured in vitro at either 26°C or 37°C, the majority of which are Yersinia-specific. The deletion of multiple Yersinia-specific sRNAs from either Y. pseudotuberculosis or Y. pestis leads to the attenuation of these pathogens in mouse models of infection. In addition, we have identified the mRNA targets controlled by one of these virulence-associated sRNAs, suggesting potential new virulence determinants in Y. pseudotuberculosis.

Notes

Acknowledgements

We thank Trevis Alleyne for assistance with bioinformatics analysis of the deep sequencing data, Chelsea Schiano for contributing reagents, and Lauren Bellows for technical assistance. This work was sponsored by the Northwestern University Feinberg School of Medicine and the NIH/NIAID Regional Center of Excellence for Bio-defense and Emerging Infectious Diseases Research (RCE) Program. We also acknowledge membership within and support from the Region V “Great Lakes” RCE (NIH award U54 AI057153).

References

  1. Akama T, Suzuki K, Tanigawa K et al (2009) Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions. J Bacteriol 191:3321–3327PubMedCrossRefGoogle Scholar
  2. Allocati N, Federici L, Masulli M et al (2009) Glutathione transferases in bacteria. FEBS J 276:58–75PubMedCrossRefGoogle Scholar
  3. Arnvig KB, Young DB (2009) Identification of small RNAs in Mycobacterium tuberculosis. Mol Microbiol 73:397–408PubMedCrossRefGoogle Scholar
  4. Busch A, Richter AS, Backofen R (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24:2849–2856PubMedCrossRefGoogle Scholar
  5. Christiansen JK, Larsen MH, Ingmer H et al (2004) The RNA-binding protein Hfq of Listeria monocytogenes: role in stress tolerance and virulence. J Bacteriol 186:3355–3362PubMedCrossRefGoogle Scholar
  6. Coornaert A, Lu A, Mandin P et al (2010) MicA sRNA links the PhoP regulon to cell envelope stress. Mol Microbiol 76:467–479PubMedCrossRefGoogle Scholar
  7. Delihas N (2003) Annotation and evolutionary relationships of a small regulatory RNA gene micF and its target ompF in Yersinia species. BMC Microbiol 3:13PubMedCrossRefGoogle Scholar
  8. Fantappie L, Metruccio MM, Seib KL et al (2009) The RNA chaperone Hfq is involved in stress response and virulence in Neisseria meningitidis and is a pleiotropic regulator of protein expression. Infect Immun 77:1842–1853PubMedCrossRefGoogle Scholar
  9. Faucher SP, Friedlander G, Livny J et al (2010) Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci USA 107:7533–7538PubMedCrossRefGoogle Scholar
  10. Geisinger E, Adhikari RP, Jin R et al (2006) Inhibition of rot translation by RNAIII, a key feature of agr function. Mol Microbiol 61:1038–1048PubMedCrossRefGoogle Scholar
  11. Geng J, Song Y, Yang L et al (2009) Involvement of the post-transcriptional regulator Hfq in Yersinia pestis virulence. PLoS One 4:e6213PubMedCrossRefGoogle Scholar
  12. Gopel Y, Luttmann D, Heroven AK et al (2011) Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae. Nucleic Acids Res 39:1294–1309PubMedCrossRefGoogle Scholar
  13. Gottesman S, Storz G (2010) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol. doi: doi:10.1101/cshperspect.a003798
  14. Guillier M, Gottesman S (2006) Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs. Mol Microbiol 59:231–247PubMedCrossRefGoogle Scholar
  15. Heroven AK, Bohme K, Rohde M et al (2008) A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM. Mol Microbiol 68:1179–1195PubMedCrossRefGoogle Scholar
  16. Horler RS, Vanderpool CK (2009) Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res 37:5465–5476PubMedCrossRefGoogle Scholar
  17. Huntzinger E, Boisset S, Saveanu C et al (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J 24:824–835PubMedCrossRefGoogle Scholar
  18. Karzai AW, Roche ED, Sauer RT (2000) The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol 7:449–455PubMedCrossRefGoogle Scholar
  19. Koo JT, Alleyne TM, Schiano CA et al (2011) Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific sRNAs required for virulence. Proc Natl Acad Sci USA 108:E709–17Google Scholar
  20. Kulesus RR, Diaz-Perez K, Slechta ES et al (2008) Impact of the RNA chaperone Hfq on the fitness and virulence potential of uropathogenic Escherichia coli. Infect Immun 76:3019–3026PubMedCrossRefGoogle Scholar
  21. Kumar R, Shah P, Swiatlo E et al (2010) Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics 11:350PubMedCrossRefGoogle Scholar
  22. Landt SG, Abeliuk E, McGrath PT et al (2008) Small non-coding RNAs in Caulobacter crescentus. Mol Microbiol 68:600–614PubMedCrossRefGoogle Scholar
  23. Liu JM, Livny J, Lawrence MS et al (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37:e46PubMedCrossRefGoogle Scholar
  24. Livny J, Waldor MK (2007) Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 10:96–101PubMedCrossRefGoogle Scholar
  25. Livny J, Brencic A, Lory S et al (2006) Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34:3484–3493PubMedCrossRefGoogle Scholar
  26. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296PubMedGoogle Scholar
  27. Mandin P, Gottesman S (2009) A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol Microbiol 72:551–565PubMedCrossRefGoogle Scholar
  28. Masse E, Vanderpool CK, Gottesman S (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187:6962–6971PubMedCrossRefGoogle Scholar
  29. McCullen CA, Benhammou JN, Majdalani N et al (2010) Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J Bacteriol 192:5559–5571PubMedCrossRefGoogle Scholar
  30. Meibom KL, Forslund AL, Kuoppa K et al (2009) Hfq, a novel pleiotropic regulator of virulence-associated genes in Francisella tularensis. Infect Immun 77:1866–1880PubMedCrossRefGoogle Scholar
  31. Moller T, Franch T, Udesen C et al (2002) Spot 42 RNA mediates discoordinate expression of the Escherichia coli galactose operon. Genes Dev 16:1696–1706PubMedCrossRefGoogle Scholar
  32. Morfeldt E, Taylor D, von Gabain A et al (1995) Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J 14:4569–4577PubMedGoogle Scholar
  33. Murphy ER, Payne SM (2007) RyhB, an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence. Infect Immun 75:3470–3477PubMedCrossRefGoogle Scholar
  34. Nakao H, Watanabe H, Nakayama S et al (1995) yst gene expression in Yersinia enterocolitica is positively regulated by a chromosomal region that is highly homologous to Escherichia coli host factor 1 gene (hfq). Mol Microbiol 18:859–865PubMedCrossRefGoogle Scholar
  35. Okan NA, Bliska JB, Karzai AW (2006) A role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis. PLoS Pathog 2:e6PubMedCrossRefGoogle Scholar
  36. Okan NA, Mena P, Benach JL et al (2010) The smpB-ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection. Infect Immun 78:1284–1293PubMedCrossRefGoogle Scholar
  37. Padalon-Brauch G, Hershberg R, Elgrably-Weiss M et al (2008) Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 36:1913–1927PubMedCrossRefGoogle Scholar
  38. Papenfort K, Pfeiffer V, Mika F et al (2006) SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 62:1674–1688PubMedCrossRefGoogle Scholar
  39. Passalacqua KD, Varadarajan A, Ondov BD et al (2009) Structure and complexity of a bacterial transcriptome. J Bacteriol 191:3203–3211PubMedCrossRefGoogle Scholar
  40. Pichon C, Felden B (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102:14249–14254PubMedCrossRefGoogle Scholar
  41. Ramirez-Pena E, Trevino J, Liu Z et al (2010) The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript. Mol Microbiol 78:1332–1347PubMedCrossRefGoogle Scholar
  42. Rasmussen AA, Johansen J, Nielsen JS et al (2009) A conserved small RNA promotes silencing of the outer membrane protein YbfM. Mol Microbiol 72:566–577PubMedCrossRefGoogle Scholar
  43. Rowley G, Spector M, Kormanec J et al (2006) Pushing the envelope: extracytoplasmic stress responses in bacterial pathogens. Nat Rev Microbiol 4:383–394PubMedCrossRefGoogle Scholar
  44. Schiano CA, Bellows LE, Lathem WW (2010) The small RNA chaperone Hfq is required for the virulence of Yersinia pseudotuberculosis. Infect Immun 78:2034–2044PubMedCrossRefGoogle Scholar
  45. Sharma CM, Vogel J (2009) Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 12:536–546PubMedCrossRefGoogle Scholar
  46. Sharma CM, Darfeuille F, Plantinga TH et al (2007) A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21:2804–2817PubMedCrossRefGoogle Scholar
  47. Sharma CM, Hoffmann S, Darfeuille F et al (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255PubMedCrossRefGoogle Scholar
  48. Silvaggi JM, Perkins JB, Losick R (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol 188:532–541PubMedCrossRefGoogle Scholar
  49. Sittka A, Lucchini S, Papenfort K et al (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator Hfq. PLoS Genet 4:e1000163CrossRefGoogle Scholar
  50. Sonnleitner E, Sorger-Domenigg T, Madej MJ et al (2008) Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology 154:3175–3187PubMedCrossRefGoogle Scholar
  51. Srivatsan A, Han Y, Peng J et al (2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet 4:e1000139PubMedCrossRefGoogle Scholar
  52. Tjaden B (2008) TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 36:W109–W113PubMedCrossRefGoogle Scholar
  53. Toledo-Arana A, Dussurget O, Nikitas G et al (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459:950–956PubMedCrossRefGoogle Scholar
  54. Tramonti A, De Canio M, De Biase D (2008) GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Mol Microbiol 70:965–982PubMedGoogle Scholar
  55. Urban JH, Vogel J (2007) Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 35:1018–1037PubMedCrossRefGoogle Scholar
  56. Urbanowski ML, Stauffer LT, Stauffer GV (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol Microbiol 37:856–868PubMedCrossRefGoogle Scholar
  57. Vockenhuber MP, Sharma CM, Statt MG et al (2011) Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 8:3CrossRefGoogle Scholar
  58. Vogel J, Papenfort K (2006) Small non-coding RNAs and the bacterial outer membrane. Curr Opin Microbiol 9:605–611PubMedCrossRefGoogle Scholar
  59. Vogel J, Sharma CM (2005) How to find small non-coding RNAs in bacteria. Biol Chem 386:1219–1238PubMedGoogle Scholar
  60. Wadler CS, Vanderpool CK (2009) Characterization of homologs of the small RNA SgrS reveals diversity in function. Nucleic Acids Res 37:5477–5485PubMedCrossRefGoogle Scholar
  61. Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615–628PubMedCrossRefGoogle Scholar
  62. Yoder-Himes DR, Chain PS, Zhu Y et al (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci USA 106:3976–3981PubMedCrossRefGoogle Scholar
  63. Zhang A, Wassarman KM, Rosenow C et al (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Department of Microbiology-ImmunologyNorthwestern University, Feinberg School of MedicineChicagoUSA

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