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Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype

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Abstract

The emerging interest in RNA research is due to the discovery that bacterial non-protein-coding RNAs (npcRNAs; often referred to as “non-coding RNAs”) are central regulatory molecules. While single npcRNAs have been described in Staphylococcus aureus, mostly based on computational-based approaches, experimental data on npcRNAs and their impact on the formation of different phenotypes of S. aureus are missing. Consequently, two specialized cDNA libraries were constructed from total RNA collected from different growth phases of an isogenic clinical strain pair of S. aureus displaying both the normal and the small-colony variant phenotype. Overall, 142 candidates for novel npcRNAs were identified and their expression analyzed by Northern blot assays. Of these, the presence of 18 novel npcRNAs in S. aureus was experimentally confirmed. In fact, growth phase-specific regulation was detected for almost all of the novel npcRNAs, with different npcRNA expression patterns detectable for both phenotypes. Of particular interest, S. aureus phenotype-specific expression of four novel npcRNAs was documented. Thus, the presence of differentially expressed npcRNAs in S. aureus may help to understand the phenotypic variation and its associated pathogenicity.

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References

  1. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM, Pollock DA, Fridkin SK (2008) NHSN annual update: antimicrobial-resistant pathogens associated with healthcare-associated infections: annual summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007. Infect Control Hosp Epidemiol 29:996–1011

    Article  PubMed  Google Scholar 

  2. Proctor RA, von Eiff C, Kahl BC, Becker K, McNamara P, Herrmann M, Peters G (2006) Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections. Nat Rev Microbiol 4:295–305

    Article  PubMed  CAS  Google Scholar 

  3. von Eiff C, Becker K, Metze D, Lubritz G, Hockmann J, Schwarz T, Peters G (2001) Intracellular persistence of Staphylococcus aureus small-colony variants within keratinocytes: a cause for antibiotic treatment failure in a patient with Darier’s disease. Clin Infect Dis 32:1643–1647

    Article  Google Scholar 

  4. Vaudaux P, Kelley WL, Lew DP (2006) Staphylococcus aureus small colony variants: difficult to diagnose and difficult to treat. Clin Infect Dis 43:968–970

    Article  PubMed  Google Scholar 

  5. Lånnergard J, von Eiff C, Sander G, Cordes T, Seggewiß J, Peters G, Proctor RA, Becker K, Hughes D (2008) Identification of the genetic basis for clinical menadione-auxotrophic small-colony variant isolates of Staphylococcus aureus. Antimicrob Agents Chemother 52:4017–4022

    Article  PubMed  CAS  Google Scholar 

  6. Chatterjee I, Kriegeskorte A, Fischer A, Deiwick S, Theimann N, Proctor RA, Peters G, Herrmann M, Kahl BC (2008) In vivo mutations of thymidylate synthase (encoded by thyA) are responsible for thymidine dependency in clinical small-colony variants of Staphylococcus aureus. J Bacteriol 190:834–842

    Article  PubMed  CAS  Google Scholar 

  7. Brosius J (2005) Waste not, want not—transcript excess in multicellular eukaryotes. Trends Genet 21:287–288

    Article  PubMed  CAS  Google Scholar 

  8. Brosius J (2005) Echoes from the past—are we still in an RNP world? Cytogenet Genome Res 110:8–24

    Article  PubMed  CAS  Google Scholar 

  9. Majdalani N, Vanderpool CK, Gottesman S (2005) Bacterial small RNA regulators. Crit Rev Biochem Mol Biol 40:93–113

    Article  PubMed  CAS  Google Scholar 

  10. Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P (2007) Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21:1353–1366

    Article  PubMed  CAS  Google Scholar 

  11. Hershberg R, Altuvia S, Margalit H (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 31:1813–1820

    Article  PubMed  CAS  Google Scholar 

  12. Livny J, Fogel MA, Davis BM, Waldor MK (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 33:4096–4105

    Article  PubMed  CAS  Google Scholar 

  13. Hüttenhofer A, Vogel J (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 34:635–646

    Article  PubMed  CAS  Google Scholar 

  14. Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG (2003) RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 31:6435–6443

    Article  PubMed  CAS  Google Scholar 

  15. Hüttenhofer A, Cavaille J, Bachellerie JP (2004) Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms. Methods Mol Biol 265:409–428

    PubMed  Google Scholar 

  16. Halfmann A, Kovács M, Hakenbeck R, Brückner R (2007) Identification of the genes directly controlled by the response regulator CiaR in Streptococcus pneumoniae: five out of 15 promoters drive expression of small non-coding RNAs. Mol Microbiol 66:110–126

    Article  PubMed  CAS  Google Scholar 

  17. Preis H, Eckart RA, Gudipati RK, Heidrich N, Brantl S (2009) CodY activates transcription of a small RNA in Bacillus subtilis. J Bacteriol 191:5446–5457

    Article  PubMed  CAS  Google Scholar 

  18. 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 U S A 102:14249–14254

    Article  PubMed  CAS  Google Scholar 

  19. Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM (2006) Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188:6739–6756

    Article  PubMed  CAS  Google Scholar 

  20. Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D (2009) Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 19:1084–1092

    Article  PubMed  CAS  Google Scholar 

  21. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37:7239–7257

    Article  PubMed  CAS  Google Scholar 

  22. von Eiff C, Bettin D, Proctor RA, Rolauffs B, Lindner N, Winkelmann W, Peters G (1997) Recovery of small colony variants of Staphylococcus aureus following gentamicin bead placement for osteomyelitis. Clin Infect Dis 25:1250–1251

    Article  Google Scholar 

  23. Rolauffs B, Bernhardt TM, von Eiff C, Hart ML, Bettin D (2002) Osteopetrosis, femoral fracture, and chronic osteomyelitis caused by Staphylococcus aureus small colony variants (SCV) treated by girdlestone resection—6-year follow-up. Arch Orthop Trauma Surg 122:547–550

    PubMed  CAS  Google Scholar 

  24. Becker K, Harmsen D, Mellmann A, Meier C, Schumann P, Peters G, von Eiff C (2004) Development and evaluation of a quality-controlled ribosomal sequence database for 16 S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol 42:4988–4995

    Article  PubMed  CAS  Google Scholar 

  25. von Eiff C, Becker K, Machka K, Stammer H, Peters G (2001) Nasal carriage as a source of Staphylococcus aureus bacteremia. Study Group. N Engl J Med 344:11–16

    Article  Google Scholar 

  26. Seggewiß J, Becker K, Kotte O, Eisenacher M, Khoschkhoi Yazdi MR, Fischer A, McNamara P, Al Laham N, Proctor R, Peters G, Heinemann M, von Eiff C (2006) Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype. J Bacteriol 188:7765–7777

    Article  PubMed  CAS  Google Scholar 

  27. Chen XS, Rozhdestvensky TS, Collins LJ, Schmitz J, Penny D (2007) Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res 35:4619–4628

    Article  PubMed  CAS  Google Scholar 

  28. Kahl BC, Belling G, Becker P, Chatterjee I, Wardecki K, Hilgert K, Cheung AL, Peters G, Herrmann M (2005) Thymidine-dependent Staphylococcus aureus small-colony variants are associated with extensive alterations in regulator and virulence gene expression profiles. Infect Immun 73:4119–4126

    Article  PubMed  CAS  Google Scholar 

  29. von Eiff C, McNamara P, Becker K, Bates D, Lei XH, Ziman M, Bochner BR, Peters G, Proctor RA (2006) Phenotype microarray profiling of Staphylococcus aureus menD and hemB mutants with the small-colony-variant phenotype. J Bacteriol 188:687–693

    Article  CAS  Google Scholar 

  30. Hüttenhofer A, Brosius J, Bachellerie JP (2002) RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 6:835–843

    Article  PubMed  Google Scholar 

  31. Wang Z, Luo X, Lu Y, Yang B (2008) miRNAs at the heart of the matter. J Mol Med 86:771–783

    Article  PubMed  CAS  Google Scholar 

  32. Mocellin S, Costa R, Nitti D (2006) RNA interference: ready to silence cancer? J Mol Med 84:4–15

    Article  PubMed  CAS  Google Scholar 

  33. Vogel J, Sharma CM (2005) How to find small non-coding RNAs in bacteria. Biol Chem 386:1219–1238

    Article  PubMed  CAS  Google Scholar 

  34. Dahary D, Elroy-Stein O, Sorek R (2005) Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res 15:364–368

    Article  PubMed  CAS  Google Scholar 

  35. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941–950

    Article  PubMed  CAS  Google Scholar 

  36. Johansson J, Cossart P (2003) RNA-mediated control of virulence gene expression in bacterial pathogens. Trends Microbiol 11:280–285

    Article  PubMed  CAS  Google Scholar 

  37. Bronner S, Monteil H, Prevost G (2004) Regulation of virulence determinants in Staphylococcus aureus: complexity and applications. FEMS Microbiol Rev 28:183–200

    Article  PubMed  CAS  Google Scholar 

  38. Novick RP, Geisinger E (2008) Quorum sensing in staphylococci. Annu Rev Genet 42:541–564

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by grants to CvE and KB from the Bundesministerium für Bildung und Forschung (BMBF), Germany (01KI07100 “Skin Staph” [Susceptibility and Resistance towards Infections] and PTJ-BIO/0313801B [Pathogenomic Plus Network]), by grants to KB (BE2546/1-1) and CvE (EI247/7-1) from the Deutsche Forschungsgemeinschaft as well as by grants to JB and TSR from the Nationales Genomforschungsnetz (NGFNII-EP 0313358A and NGFNIII 016S0808). LFA received a scholarship by the DAAD (A/05/55152).

The authors sincerely thank C. A. Raabe for support in computational analyses and helpful discussion. The authors are grateful to D. Kuhn for excellent technical assistance.

Conflict of interest statement

The authors declare no conflict of interest.

Author information

Author notes

  1. Jochen Seggewiß

    Present address: Integrated Functional Genomics (IFG) of the Interdisciplinary Center for Clinical Research (IZKF) of the University of Münster, Münster, Germany

  2. Christof von Eiff

    Present address: Wyeth Pharma GmbH, Münster, Germany

Authors and Affiliations

  1. University Hospital of Münster, Institute of Medical Microbiology, Domagkstr. 10, 48149, Münster, Germany

    Luay F. Abu-Qatouseh, Jochen Seggewiß, Georg Peters, Christof von Eiff & Karsten Becker

  2. University of Münster, Institute of Experimental Pathology, 48149, Münster, Germany

    Suresh V. Chinni, Jürgen Brosius & Timofey S. Rozhdestvensky

  3. Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA

    Richard A. Proctor

  4. Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA

    Richard A. Proctor

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  1. Luay F. Abu-Qatouseh
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Corresponding author

Correspondence to Karsten Becker.

Additional information

L. F. Abu-Qatouseh and S. V. Chinni as well as C. von Eiff and K. Becker contributed equally to this work.

Electronic supplementary materials

Below is the link to the electronic supplementary material.

Supplementary data file 1

Three tables listing the 142 candidates for novel npcRNAs with their genomic origin and orientation, statistical analysis of the distribution of cDNA clones in the library and the expression patterns of the npcRNAs as provided by Northern blot analysis. (PDF 37 kb)

Supplementary data file 2

Previously described npcRNAs recovered in the libraries of this study. (PDF 13 kb)

Supplementary data file 3

Two tables listing the sequences of oligonucleotides used in Northern blot assays for the detection of previously described npcRNAs and novel S. aureus npcRNAs. (PDF 23 kb)

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Abu-Qatouseh, L.F., Chinni, S.V., Seggewiß, J. et al. Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med 88, 565–575 (2010). https://doi.org/10.1007/s00109-010-0597-2

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  • DOI: https://doi.org/10.1007/s00109-010-0597-2

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