ArticleOpen biology2017
Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.
Article in Open biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
- Initiator AUGs Are Discriminated from Elongator AUGs Predominantly through mRNA Accessibility in C. crescentus.Journal of bacteriology · 2023Article
- Ribosome profiling enhances understanding of mycobacterial translation.Frontiers in microbiology · 2022Review
- Generating dynamic gene expression patterns without the need for regulatory circuits.PloS one · 2022Article
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- Comparative Analysis of anti-Shine- Dalgarno Function inFrontiers in molecular biosciences · 2021Article
- Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria.Nucleic acids research · 2019Article
- Unique Shine-Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation.Genome biology and evolution · 2019Article
- Ribosome Profiling: Global Views of Translation.Cold Spring Harbor perspectives in biology · 2019Review
- RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3' Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species.G3 (Bethesda, Md.) · 2018Article
- 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
- Re-annotation of 12,495 prokaryotic 16S rRNA 3' ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences.PloS one · 2018Article
- Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.Scientific reports · 2017Article
- Noncanonical Translation Initiation Comes of Age.Journal of bacteriology · 2017Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Studies dating back to the 1970s established that sequence complementarity between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic ribosomes and the 5' untranslated region of mRNAs helps to facilitate translation initiation. The optimal location of aSD sequence binding relative to the start codon, the full extents of the aSD sequence and the functional form of the relationship between aSD sequence complementarity and translation efficiency have not been fully resolved. Here, we investigate these relationships by leveraging the sequence diversity of endogenous genes and recently available genome-wide estimates of translation efficiency. We show that-after accounting for predicted mRNA structure-aSD sequence complementarity increases the translation of endogenous mRNAs by roughly 50%. Further, we observe that this relationship is nonlinear, with translation efficiency maximized for mRNAs with intermediate levels of aSD sequence complementarity. The mechanistic insights that we observe are highly robust: we find nearly identical results in multiple datasets spanning three distantly related bacteria. Further, we verify our main conclusions by re-analysing a controlled experimental dataset.
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