RNA



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


YVONNE  BENITO a1, FABRICE A.  KOLB a2, PASCALE  ROMBY a2, GERARD  LINA a1, JEROME  ETIENNE a1 and FRANÇOIS  VANDENESCH a1c1
a1 EA1655, Faculté de Médecine Laennec, 69372 Lyon Cedex 08, France
a2 UPR 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France

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.

(Received December 10 1999)
(Revised February 3 2000)
(Accepted February 28 2000)


Key Words: agr locus; chemical and enzymatic probing; in vivo probing; regulation; RNAIII.

Correspondence:
c1 Reprint requests to: Francois Vandenesch, EA1655, Faculté de Médecine Laennec, Rue Guillaume Paradin, 69372 Lyon Cedex 08, France; e-mail: denesch@univ-lyon1.fr.