Diversity of translation initiation mechanisms across bacterial species is driven by environmental conditions and growth demands

Abstract

The Shine-Dalgarno (SD) sequence is often found upstream of protein coding genes across the bacterial kingdom, where it enhances start codon recognition via hybridization to the anti-SD (aSD) sequence on the small ribosomal subunit. Despite widespread conservation of the aSD sequence, the proportion of SD-led genes within a genome varies widely across species, and the evolutionary pressures shaping this variation remain largely unknown. Here, we conduct a phylogenetically-informed analysis and show that species capable of rapid growth have a significantly higher proportion of SD-led genes in their genome, suggesting a role for SD sequences in meeting the protein production demands of rapidly growing species. Further, we show that utilization of the SD sequence mechanism co-varies with: i) genomic traits that are indicative of efficient translation, and ii) optimal growth temperatures. In contrast to prior surveys, our results demonstrate that variation in translation initiation mechanisms across genomes is largely predictable, and that SD sequence utilization is part of a larger suite of translation-associated traits whose diversity is driven by the differential growth strategies of individual species.