Conformational heterogeneity in the Salmonella typhimurium pyrC and pyrD leader mRNAs produced in vivo.

In Salmonella typhimurium, different conformations of the pyrC and pyrD leader transcripts are produced as a result of nucleotide sensitive selection of the transcriptional start site. The CTP-initiated transcripts, synthesized at high intracellular CTP/GTP pool ratios (repressing conditions), have the potential of forming a stable secondary structure at the 5' end, thereby sequestering the site for translational initiation. At low CTP/GTP pool ratios (derepressing conditions), transcription starts 2-3 bp further downstream, resulting in transcripts with limited potential for stem-loop formation and therefore open for translational initiation. The conformation of the leader regions of wild type pyrC and pyrD mRNA has been investigated by chemical and enzymatic probing of RNA isolated from cultures grown in repressing and derepressing conditions. As controls and to obtain further information on the relation between the leader RNA conformation and the regulatory mechanism, the probing experiments also included pyrC and pyrD mRNA from mutants that contain a base substitution at a position that destabilizes the putative hairpin. In accordance with predictions based on the nucleotide sequence, the results showed that the 5' end of pyrC and pyrD leader mRNA isolated from repressed cultures is folded into a secondary structure, whereas it is largely unstructured in mRNA isolated from derepressed cultures.