Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli.

ABSTRACT: Despite considerable efforts, no physical mechanism has been shown to explain N-terminal codon bias in prokaryotic genomes. Using a systematic study of synonymous substitutions in two endogenous E. coli genes, we show that interactions between the coding region and the upstream Shine-Dalgarno (SD) sequence modulate the efficiency of translation initiation, affecting both intracellular mRNA and protein levels due to the inherent coupling of transcription and translation in E. coli. We further demonstrate that far-downstream mutations can also modulate mRNA levels by occluding the SD sequence through the formation of non-equilibrium secondary structures. By contrast, a non-endogenous RNA polymerase that decouples transcription and translation largely alleviates the effects of synonymous subs

SUBMITTER: Bhattacharyya S 

PROVIDER: S-EPMC6311106 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature