ArticleG3 (Bethesda, Md.)2016
Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.bioRxiv : the preprint server for biology · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.Synthetic biology (Oxford, England) · 2024Article
- Initiator AUGs Are Discriminated from Elongator AUGs Predominantly through mRNA Accessibility in C. crescentus.Journal of bacteriology · 2023Article
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts.RNA biology · 2021Article
- Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy.Frontiers in microbiology · 2021Article
- Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.Molecular biology and evolution · 2018Article
- Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands.Molecular biology and evolution · 2018Article
- Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs.PloS one · 2018Article
- A novel framework for evaluating the performance of codon usage bias metrics.Journal of the Royal Society, Interface · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Efficient and accurate protein synthesis is crucial for organismal survival in competitive environments. Translation efficiency (the number of proteins translated from a single mRNA in a given time period) is the combined result of differential translation initiation, elongation, and termination rates. Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation initiation in bacterial genes, while codon usage biases are frequently implicated as a primary determinant of elongation rate variation. Recent studies have suggested that SD sequences within coding sequences may negatively affect translation elongation speed, but this claim remains controversial. Here, we present a metric to quantify the prevalence of SD sequences in coding regions. We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. We further show that depletion of SD sequences within ribosomal protein genes is correlated with organismal growth rates, supporting the hypothesis of strong selection against the presence of these sequences in coding regions and suggesting their association with translation efficiency in bacteria.
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Registered trials
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.