PT  - JOURNAL ARTICLE
AU  - Sanchari Bhattacharyya
AU  - William M. Jacobs
AU  - Bharat V. Adkar
AU  - Jin Yan
AU  - Wenli Zhang
AU  - Eugene I. Shakhnovich
TI  - Accessibility of the Shine–Dalgarno sequence dictates N-terminal codon bias in <em>E. coli</em>
AID  - 10.1101/195727
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 195727
4099  - http://biorxiv.org/content/early/2018/03/02/195727.short
4100  - http://biorxiv.org/content/early/2018/03/02/195727.full
AB  - 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 substitutions on mRNA levels. Finally, a complementary statistical analysis of the E. coli genome specifically implicates avoidance of intra-molecular base-pairing with the SD sequence. Our results provide general physical insights into the coding-level features that optimize protein expression in prokaryotes.