CsrA Represses Translation ofsdiA, Which Encodes theN-Acylhomoserine-l-Lactone Receptor of Escherichia coli, by Binding Exclusively within the Coding Region ofsdiAmRNA

The RNA binding protein CsrA is the central component of a conserved global regulatory system that activates or represses gene expression posttranscriptionally. In every known example of CsrA-mediated translational control, CsrA binds to the 5′ untranslated region of target transcripts, thereby repressing translation initiation and/or altering the stability of the RNA. Furthermore, with few exceptions, repression by CsrA involves binding directly to the Shine-Dalgarno sequence and blocking ribosome binding.sdiA encodes the quorum-sensing receptor forN -acyl-l -homoserine lactone inEscherichia coli . BecausesdiA indirectly stimulates transcription ofcsrB , which encodes a small RNA (sRNA) antagonist of CsrA, we further explored the relationship betweensdiA and the Csr system. Primer extension analysis revealed four putative transcription start sites within 85 nucleotides of thesdiA initiation codon. Potential σ70 -dependent promoters were identified for each of these primer extension products. In addition, two CsrA binding sites were predicted in the initially translated region ofsdiA . Expression of chromosomally integratedsdiA ′-′lacZ translational fusions containing the entire promoter and CsrA binding site regions indicates that CsrA repressessdiA expression. The results from gel shift and footprint studies demonstrate that tight binding of CsrA requires both of these sites. Furthermore, the results from toeprint andin vitro translation experiments indicate that CsrA represses translation ofsdiA by directly competing with 30S ribosomal subunit binding. Thus, this represents the first example of CsrA preventing translation by interacting solely within the coding region of an mRNA target.