Rare codons play a positive role in the expression of the stationary phase sigma factor RpoS (σS) in Escherichia coli

Rare codons can influence the stability of messenger RNAs, promote regular spacing of ribosomes on a transcript, or modulate stability and proper folding of nascent proteins. The mRNA specifying the stationary phase master regulator RpoS, which belongs to the RpoD family of sigma factors, contains a high number of rare codons, including many codons at positions corresponding to more frequent codons encoding the same amino acids in the homologous RpoD sequence. Substituting these rare codons in rpoS by the more frequent synonymous rpoD codons resulted in decreased transcript and protein levels compared to the natural rare-codon wildtype version of rpoS. The frequent-codon mutant rpoS transcript exhibited faster turnover than the rare-codon wildtype mRNA. Studies with endoribonuclease-deficient strains revealed RNase E to be crucial for this accelerated mRNA degradation. Thus, in the case of RpoS expression, "less is obviously more," as our data suggest a model, in which slowing down translational speed by ribosomal pausing at many rare codons along a transcript could reduce ribosome spacing and thereby protect the transcript against ribonucleolytic attack by RNase E. Such a mechanism may be especially important for translationally controlled genes like rpoS where the formation of secondary structure in the translational initiation region competes with (therefore relatively inefficient) ribosome loading. Moreover, strong codon differences in genes encoding isoenzymes expressed in exponential and stationary phase suggest that transcript protection by repetitive ribosome pausing at multiple rare codons in stationary phase-expressed transcripts may be a general principle to save resources under nutrient-limited conditions.