ArticleMolecular cell2018
Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli.
Article in Molecular cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 82 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- Approaches for Studying Context Specificity of Translation Inhibitor Action.International journal of molecular sciences · 2026Review
- Evaluation of synthetic post-transcription regulatory sequences reveals design principle to enhance mRNA stability and translation efficiency.Synthetic and systems biotechnology · 2026Article
- Elucidating the regulatory role of the Shine-Dalgarno sequence in structural gene expression of the malolactic enzyme operon using a GFP/mCherry model.World journal of microbiology & biotechnology · 2026Article
- Highly mutagenic continuous evolution in E. coli using a Φ29-based orthogonal replication system.Nature biotechnology · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli.Nucleic acids research · 2025Article
- OPT: Codon optimize gene sequences for E. coli protein overexpression.Journal of molecular biology · 2025Article
- Why AGG is associated with high transgene output: passenger effects and their implications for transgene design.NAR genomics and bioinformatics · 2025Article
- Deciphering Transcription-Translation-Folding (TX-TL-FD) for Enhancing Cutinase Production in T7 System and Genetic Chaperone-EquippedACS synthetic biology · 2025Article
- Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Effects of Codon Usage on Protein Structure and Folding.Annual review of biophysics · 2024Review
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene.BMC genomics · 2023Article
- Article
- Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.PLoS computational biology · 2023Article
- Efficient recombinant production of mouse-derived cryptdin family peptides by a novel facilitation strategy for inclusion body formation.Microbial cell factories · 2023Article
- Heterologous Gene Regulation in Clostridia: Rationally Designed Gene Regulation for Industrial and Medical Applications.ACS synthetic biology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
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 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.