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Journal of Bacteriology, August 2003, p. 4450-4460, Vol. 185, No. 15
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.15.4450-4460.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

CsrA Regulates Translation of the Escherichia coli Carbon Starvation Gene, cstA, by Blocking Ribosome Access to the cstA Transcript

Ashok K. Dubey,1 Carol S. Baker,1 Kazushi Suzuki,2 A. Daniel Jones,3 Pallavi Pandit,1 Tony Romeo,2 and Paul Babitzke1*

Department of Biochemistry and Molecular Biology,1 Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802,3 Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 303222

Received 29 January 2003/ Accepted 7 May 2003

CsrA is a global regulator that binds to two sites in the glgCAP leader transcript, thereby blocking ribosome access to the glgC Shine-Dalgarno sequence. The upstream CsrA binding site (GCACACGGAU) was used to search the Escherichia coli genomic sequence for other genes that might be regulated by CsrA. cstA contained an exact match that overlapped its Shine-Dalgarno sequence. cstA was previously shown to be induced by carbon starvation and to encode a peptide transporter. Expression of a cstA'-'lacZ translational fusion in wild-type and csrA mutant strains was examined. Expression levels in the csrA mutant were approximately twofold higher when cells were grown in Luria broth (LB) and 5- to 10-fold higher when LB was supplemented with glucose. It was previously shown that cstA is regulated by the cyclic AMP (cAMP)-cAMP receptor protein complex and transcribed by E{sigma}70. We investigated the influence of {sigma}S on cstA expression and found that a {sigma}S deficiency resulted in a threefold increase in cstA expression in wild-type and csrA mutant strains; however, CsrA-dependent regulation was retained. The mechanism of CsrA-mediated cstA regulation was also examined in vitro. Cross-linking studies demonstrated that CsrA is a homodimer. Gel mobility shift results showed that CsrA binds specifically to cstA RNA, while coupled-transcription-translation and toeprint studies demonstrated that CsrA regulates CstA synthesis by inhibiting ribosome binding to cstA transcripts. RNA footprint and boundary analyses revealed three or four CsrA binding sites, one of which overlaps the cstA Shine-Dalgarno sequence, as predicted. These results establish that CsrA regulates translation of cstA by sterically interfering with ribosome binding.

* Corresponding author. Mailing address: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802. Phone: (814) 865-0002. Fax: (814) 863-7024. E-mail: pxb28{at}psu.edu.

Journal of Bacteriology, August 2003, p. 4450-4460, Vol. 185, No. 15
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.15.4450-4460.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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