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. 2000 May;6(5):668–679. doi: 10.1017/s1355838200992550

Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.

Y Benito 1, F A Kolb 1, P Romby 1, G Lina 1, J Etienne 1, F Vandenesch 1
PMCID: PMC1369947  PMID: 10836788

Abstract

RNAIII, a 514-nt RNA molecule, regulates the expression of many Staphylococcus aureus genes encoding exoproteins and cell-wall-associated proteins. We have studied the structure of RNAIII in solution, using a combination of chemical and enzymatic probes. A model of the secondary structure was derived from experimental data with the help of computer simulation of RNA folding. The model contains 14 hairpin structures connected by unpaired nucleotides. The data also point to three helices formed by distant nucleotides that close off structural domains. This model was generally compatible with the results of in vivo probing experiments with dimethylsulfate in late exponential-phase cultures. Toe-printing experiments revealed that the ribosome binding site of hld, which is encoded by RNAIII, was accessible to the Escherichia coli 30S ribosomal subunit, suggesting that the in vitro structure represented a translatable form of RNAIII. We also found that, within the 3' end of RNAIII, the conserved hairpin 13 and the terminator form an intrinsic structural domain that exerts specific regulatory activity on protein A gene expression.

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Selected References

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  1. Balaban N., Novick R. P. Translation of RNAIII, the Staphylococcus aureus agr regulatory RNA molecule, can be activated by a 3'-end deletion. FEMS Microbiol Lett. 1995 Nov 1;133(1-2):155–161. doi: 10.1111/j.1574-6968.1995.tb07877.x. [DOI] [PubMed] [Google Scholar]
  2. Benito Y., Lina G., Greenland T., Etienne J., Vandenesch F. trans-complementation of a Staphylococcus aureus agr mutant by Staphylococcus lugdunensis agr RNAIII. J Bacteriol. 1998 Nov;180(21):5780–5783. doi: 10.1128/jb.180.21.5780-5783.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brunel C., Romby P., Westhof E., Ehresmann C., Ehresmann B. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J Mol Biol. 1991 Sep 5;221(1):293–308. doi: 10.1016/0022-2836(91)80220-o. [DOI] [PubMed] [Google Scholar]
  4. Chen X., Woodson S. A., Burrows C. J., Rokita S. E. A highly sensitive probe for guanine N7 in folded structures of RNA: application to tRNA(Phe) and Tetrahymena group I intron. Biochemistry. 1993 Aug 3;32(30):7610–7616. doi: 10.1021/bi00081a002. [DOI] [PubMed] [Google Scholar]
  5. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. England T. E., Uhlenbeck O. C. 3'-terminal labelling of RNA with T4 RNA ligase. Nature. 1978 Oct 12;275(5680):560–561. doi: 10.1038/275560a0. [DOI] [PubMed] [Google Scholar]
  7. Gerdes K., Gultyaev A. P., Franch T., Pedersen K., Mikkelsen N. D. Antisense RNA-regulated programmed cell death. Annu Rev Genet. 1997;31:1–31. doi: 10.1146/annurev.genet.31.1.1. [DOI] [PubMed] [Google Scholar]
  8. Gultyaev A. P., van Batenburg F. H., Pleij C. W. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol. 1995 Jun 30;250(1):37–51. doi: 10.1006/jmbi.1995.0356. [DOI] [PubMed] [Google Scholar]
  9. Hartz D., McPheeters D. S., Traut R., Gold L. Extension inhibition analysis of translation initiation complexes. Methods Enzymol. 1988;164:419–425. doi: 10.1016/s0076-6879(88)64058-4. [DOI] [PubMed] [Google Scholar]
  10. Heus H. A., Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 1991 Jul 12;253(5016):191–194. doi: 10.1126/science.1712983. [DOI] [PubMed] [Google Scholar]
  11. Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pE194, a plasmid that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibodies. J Bacteriol. 1982 May;150(2):804–814. doi: 10.1128/jb.150.2.804-814.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hüttenhofer A., Noller H. F. Footprinting mRNA-ribosome complexes with chemical probes. EMBO J. 1994 Aug 15;13(16):3892–3901. doi: 10.1002/j.1460-2075.1994.tb06700.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Janzon L., Arvidson S. The role of the delta-lysin gene (hld) in the regulation of virulence genes by the accessory gene regulator (agr) in Staphylococcus aureus. EMBO J. 1990 May;9(5):1391–1399. doi: 10.1002/j.1460-2075.1990.tb08254.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ji G., Beavis R. C., Novick R. P. Cell density control of staphylococcal virulence mediated by an octapeptide pheromone. Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12055–12059. doi: 10.1073/pnas.92.26.12055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kreiswirth B. N., Löfdahl S., Betley M. J., O'Reilly M., Schlievert P. M., Bergdoll M. S., Novick R. P. The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature. 1983 Oct 20;305(5936):709–712. doi: 10.1038/305709a0. [DOI] [PubMed] [Google Scholar]
  16. Lina G., Jarraud S., Ji G., Greenland T., Pedraza A., Etienne J., Novick R. P., Vandenesch F. Transmembrane topology and histidine protein kinase activity of AgrC, the agr signal receptor in Staphylococcus aureus. Mol Microbiol. 1998 May;28(3):655–662. doi: 10.1046/j.1365-2958.1998.00830.x. [DOI] [PubMed] [Google Scholar]
  17. Makhno V. I., Peshin N. N., Semenkov Iu P., Kirillov S. V. Modifitsirovannyi sposob polucheniia "tight" 70S ribosom iz Escherichia coli, vysokoaktivnykh v otdel'nykh stadiiakh tsikla élongatsii. Mol Biol (Mosk) 1988 May-Jun;22(3):670–679. [PubMed] [Google Scholar]
  18. Mayford M., Weisblum B. Conformational alterations in the ermC transcript in vivo during induction. EMBO J. 1989 Dec 20;8(13):4307–4314. doi: 10.1002/j.1460-2075.1989.tb08617.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moine H., Ehresmann B., Romby P., Ebel J. P., Grunberg-Manago M., Springer M., Ehresmann C. The translational regulation of threonyl-tRNA synthetase. Functional relationship between the enzyme, the cognate tRNA and the ribosome. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):343–350. doi: 10.1016/0167-4781(90)90192-5. [DOI] [PubMed] [Google Scholar]
  20. Morfeldt E., Taylor D., von Gabain A., Arvidson S. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J. 1995 Sep 15;14(18):4569–4577. doi: 10.1002/j.1460-2075.1995.tb00136.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Murakawa G. J., Nierlich D. P. Mapping the lacZ ribosome binding site by RNA footprinting. Biochemistry. 1989 Oct 3;28(20):8067–8072. doi: 10.1021/bi00446a015. [DOI] [PubMed] [Google Scholar]
  22. NOVICK R. P. ANALYSIS BY TRANSDUCTION OF MUTATIONS AFFECTING PENICILLINASE FORMATION IN STAPHYLOCOCCUS AUREUS. J Gen Microbiol. 1963 Oct;33:121–136. doi: 10.1099/00221287-33-1-121. [DOI] [PubMed] [Google Scholar]
  23. Novick R. P., Ross H. F., Projan S. J., Kornblum J., Kreiswirth B., Moghazeh S. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J. 1993 Oct;12(10):3967–3975. doi: 10.1002/j.1460-2075.1993.tb06074.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Peattie D. A., Gilbert W. Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679–4682. doi: 10.1073/pnas.77.8.4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Peng H. L., Novick R. P., Kreiswirth B., Kornblum J., Schlievert P. Cloning, characterization, and sequencing of an accessory gene regulator (agr) in Staphylococcus aureus. J Bacteriol. 1988 Sep;170(9):4365–4372. doi: 10.1128/jb.170.9.4365-4372.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pitulle C., Kleineidam R. G., Sproat B., Krupp G. Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis. Gene. 1992 Mar 1;112(1):101–105. doi: 10.1016/0378-1119(92)90309-d. [DOI] [PubMed] [Google Scholar]
  27. Pley H. W., Flaherty K. M., McKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 1994 Nov 3;372(6501):111–113. doi: 10.1038/372111a0. [DOI] [PubMed] [Google Scholar]
  28. Retallack D. M., Friedman D. I. A role for a small stable RNA in modulating the activity of DNA-binding proteins. Cell. 1995 Oct 20;83(2):227–235. doi: 10.1016/0092-8674(95)90164-7. [DOI] [PubMed] [Google Scholar]
  29. Serganov A., Rak A., Garber M., Reinbolt J., Ehresmann B., Ehresmann C., Grunberg-Manago M., Portier C. Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein. Eur J Biochem. 1997 Jun 1;246(2):291–300. doi: 10.1111/j.1432-1033.1997.00291.x. [DOI] [PubMed] [Google Scholar]
  30. Shinedling S., Gayle M., Pribnow D., Gold L. Mutations affecting translation of the bacteriophage T4 rIIB gene cloned in Escherichia coli. Mol Gen Genet. 1987 May;207(2-3):224–232. doi: 10.1007/BF00331582. [DOI] [PubMed] [Google Scholar]
  31. Sledjeski D., Gottesman S. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2003–2007. doi: 10.1073/pnas.92.6.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Tegmark K., Morfeldt E., Arvidson S. Regulation of agr-dependent virulence genes in Staphylococcus aureus by RNAIII from coagulase-negative staphylococci. J Bacteriol. 1998 Jun;180(12):3181–3186. doi: 10.1128/jb.180.12.3181-3186.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Vandenesch F., Projan S. J., Kreiswirth B., Etienne J., Novick R. P. Agr-related sequences in Staphylococcus lugdunensis. FEMS Microbiol Lett. 1993 Jul 15;111(1):115–122. doi: 10.1111/j.1574-6968.1993.tb06370.x. [DOI] [PubMed] [Google Scholar]
  34. de Smit M. H., van Duin J. Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J Mol Biol. 1994 Nov 25;244(2):144–150. doi: 10.1006/jmbi.1994.1714. [DOI] [PubMed] [Google Scholar]

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