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

RNA

Volumn 6, Issue 5, 2000, Pages 668-679

  Benito, Yvonne ^a   Kolb, Fabrice A ^b   Romby, Pascale ^b   Lina, Gerard ^a   Etienne, Jerome ^a   Vandenesch, François ^a  

^a UNIVERSITÉ LYON 1   (France)

^b INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Agr locus; Chemical and enzymatic probing; In vivo probing; Regulation; RNAIII

Indexed keywords

PROTEIN A; RNA;

ARTICLE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE REPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RIBOSOME SUBUNIT; RNA STRUCTURE; STAPHYLOCOCCUS AUREUS;

BASE SEQUENCE; BINDING SITES; DNA PRIMERS; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBOSOMES; RNA, ANTISENSE; RNA, BACTERIAL; STAPHYLOCOCCAL PROTEIN A; STAPHYLOCOCCUS AUREUS;

ESCHERICHIA COLI; PROKARYOTA; STAPHYLOCOCCUS AUREUS;

EID: 0034072868     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200992550     Document Type: Article

References (39)

1. Balaban N, Novick RP. 1995. Translation of RNAIII, the Staphylococcus aureus agr regulatory RNA molecule, can be activated by a 3′-end deletion. FEMS Microbiol Lett 133:155-161.
2. Bechhofer D. 1993. 5′ mRNA stabilizers. In: Belasco JG, Brawerman G, eds. Control of messenger RNA stability. London: Academic Press. pp 31-52.
3. Benito Y, Lina G, Greenland T, Etienne J, Vandenesch F. 1998. Transcomplementation of a Staphylococcus aureus agr mutant by Staphylococcus lugdunensis agr RNAIII. J Bacteriol 180:5780-5783.
4. Brunel C, Romby P, Westhof E, Ehresmann C, Ehresmann B. 1991. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J Mol Biol 221:293-308.
5. Chen X, Woodson SA, Burrows CJ, Rokita SE. 1993. A highly sensitive probe for guanine N7 in folded structures of RNA: Application to tRNA(Phe) and Tetrahymena group I intron. Biochemistry 32:7610-7616.
6. de Smit MH, van Duin J. 1994. Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J Mol Biol 244:144-150.
7. Donis-Keller H, Maxam AM, Gilbert W. 1977. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res 4:2527-2538.
8. Ehresmann C, Baudin F, Mougel M, Romby P, Ebel JP, Ehresmann B. 1987. Probing the structure of RNAs in solution. Nucleic Acids Res 15:53-71.
9. England TE, Uhlenbeck OC. 1978. 3′-terminal labelling of RNA with T4 RNA ligase. Nature 275:560-561.
10. Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. 1997. Antisense RNA-regulated programmed cell death. Annu Rev Genet 31:1-31.
11. Gultyaev AP, van Batenburg FH, Pleij CW. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol 250:37-51.
12. Hartz D, McPheeters DS, Traut R, Gold L. 1988. Extension inhibition analysis of translation initiation complexes. Methods Enzymol 164:419-425.
13. Heus HA, Pardi A. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253:191-194.
14. Horinouchi S, Weisblum B. 1982. Nucleotide sequence and functional map of pE194, a plasmid that specifies inducible resistance to macrolide, lincosamine, and streptogramin type B antibiotics. J Bacteriol 150:804-814.
15. Huttenhofer A, Noller HF. 1994. Footprinting mRNA-ribosome complexes with chemical probes. EMBO J 13:3892-3901.
16. Janzon L, Arvidson S. 1990. The role of the delta lysin gene in the regulation of virulence genes by the accessory gene regulator (agr) in Staphylococcus aureus. EMBO J 9:1391-1399.
17. Ji G, Beavis RC, Novick RP. 1995. Cell density control of staphylococcal virulence mediated by an octapeptide pheromone. Proc Natl Acad Sci USA 92:12055-12059.
18. Kornblum J, Kreiswirth B, Projan SJ, Ross H, Novick R. 1990. Agr: a polycistronic locus regulating exoprotein synthesis in Staphylococcus aureus. In: Novick RP, ed. Molecular biology of the staphylococci. New York: VCH Publishers. pp 373-401.
19. Kreiswirth B, Lofdahl S, Betley M, O'Reilly M, Schlievert P, Bergdoll M, Novick RP. 1983. The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature 305:709-712.
20. Lina G, Jarraud S, Ji G, Greenland T, Pedraza A, Etienne J, Novick RP, Vandenesch F. 1998. Transmembrane topology and histidine protein kinase activity of AgrC, the agr signal receptor in Staphylococcus aureus. Mol Microbiol 28:655-662.
21. Makhno VI, Peshin NN, Semenkov Iu P, Kirillov SV. 1988. A modified method of isolation of "tight" 70S ribosomes from Escherichia coli highly active at different stages of the elongation cycle. Mol Biol (Mosk) 22:670-679.
22. Mayford M, Weisblum B. 1989. Conformational alterations in the ermC transcript in vivo during induction. EMBO J 8:4307-4314.
23. Moine H, Ehresmann B, Romby P, Ebel JP, Grunberg-Manago M, Springer M, Ehresmann C. 1990. The translational regulation of threonyl-tRNA synthetase. Functional relationship between the enzyme, the cognate tRNA and the ribosome. Biochim Biophys Acta 1050:343-350.
24. Morfeldt E, Taylor D, von Gabain A, Arvidson S. 1995. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J 14:4569-4577.
25. Murakawa GJ, Nierlich DP. 1989. Mapping the lacZ ribosome binding site by RNA footprinting. Biochemistry 20:8067-8072.
26. Novick RP. 1963. Analysis by transduction of mutations affecting penicillinase formation in Staphylococcus aureus. J Gen Microbiol 33:121-136.
27. Novick RP, Ross HF, Projan SJ, Kornblum J, Kreiswirth B, Moghazeh S. 1993. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12:3967-3975.
28. Peattie DA, Gilbert W. 1980. Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci USA 77:4679-4682.
29. Peng HC, Novick RP, Kreiswirth B, Kornblum J, Schlievert PM. 1988. Cloning, characterization, and sequencing of an accessory gene regulator agr in Staphylococcus aureus. J Bacteriol 170:4365-4372.
30. Pitulle C, Kleineidam RG, Sproat B, Krupp G. 1992. Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis. Gene 112:101-105.
31. Pley HW, Flaherty KM, McKay DB. 1994. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372:111-113.
32. Retallack DM, Friedman DI. 1995. A role for a small stable RNA in modulating the activity of DNA-binding proteins. Cell 83:227-235.
33. Sambrook J, Fritsch E, Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
34. Serganov A, Rak A, Garber M, Reinbolt J, Ehresmann B, Ehresmann C, Grunberg-Manago M, Portier C. 1997. Ribosomal protein S15 from Thermus thermophilus: Cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein. Eur J Biochem 246:291-300.
35. Shinedling S, Gayle M, Pribnow D, Gold L. 1987. Mutations affecting translation of the bacteriophage T4 rIIB gene cloned in Escherichia coli. Mol Gen Genet 207:224-232.
36. Sledjeski D, Gottesman S. 1995. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci USA 92:2003-2007.
37. Tegmark K, Morfeldt E, Arvidson S. 1998. Regulation of agr-dependent virulence genes in Staphylococcus aureus by RNAIII from coagulase-negative staphylococci. J Bacteriol 180:3181-3186.
38. Vandenesch F, Projan S, Kreiswirth B, Etienne J, Novick R. 1993. Agr-related sequences in Staphylococcus lugdunensis. FEMS Microbiol Lett 111:115-122.
39. Zeiler BN, Simons RW. 1998. Antisense RNA structure and function. In: Simons RW, Grunberg-Manago M, eds. RNA structure and function. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 437-464.