ArticlePloS one2018
Re-annotation of 12,495 prokaryotic 16S rRNA 3' ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 26 citations in OpenAlex.
- Structure of a specialized 70S initiation complex.Nucleic acids research · 2026Article
- Role of the anti-Shine-Dalgarno sequence of 16S rRNA in Flavobacterium johnsoniae.Nucleic acids research · 2026Article
- Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.Nucleic acids research · 2025Article
- Isolation and Characterization of a NovelMicroorganisms · 2024Article
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- Contrasting Genetic Diversity ofApplied and environmental microbiology · 2023Article
- Three Phages One Host: Isolation and Characterization ofInternational journal of molecular sciences · 2023Article
- Article
- Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis.RNA (New York, N.Y.) · 2022Article
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- Genome Characterization of Nocturne116, NovelMicroorganisms · 2021Article
- Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.Nucleic acids research · 2021Article
- Simplification of Ribosomes in Bacteria with Tiny Genomes.Molecular biology and evolution · 2021Article
- Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.The Journal of biological chemistry · 2020Article
- The Effect of Translation Promoting Site (TPS) on Protein Expression in E. coli Cells.Molecular biotechnology · 2020Article
- Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?RNA biology · 2020Article
- Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria.Nucleic acids research · 2019Article
- Dengue and Zika Virus 5' Untranslated Regions Harbor Internal Ribosomal Entry Site Functions.mBio · 2019Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
We examined 20,648 prokaryotic unique taxids with respect to the annotation of the 3' end of the 16S rRNA, which contains the anti-Shine-Dalgarno sequence. We used the sequence of highly conserved helix 45 of the 16S rRNA as a guide. By this criterion, 8,153 annotated 3' ends correctly included the anti-Shine-Dalgarno sequence, but 12,495 were foreshortened or otherwise mis-annotated, missing part or all of the anti-Shine-Dalgarno sequence, which immediately follows helix 45. We re-annotated, giving a total of 20,648 16S rRNA 3' ends. The vast majority indeed contained a consensus anti-Shine-Dalgarno sequence, embedded in a highly conserved 13 base "tail". However, 128 exceptional organisms had either a variant anti-Shine-Dalgarno, or no recognizable anti-Shine-Dalgarno, in their 16S rRNA(s). For organisms both with and without an anti-Shine-Dalgarno, we identified the Shine-Dalgarno motifs actually enriched in front of each organism's open reading frames. This showed to what extent the Shine-Dalgarno motifs correlated with anti-Shine Dalgarno motifs. In general, organisms whose rRNAs lacked a perfect anti-Shine-Dalgarno motif also lacked a recognizable Shine-Dalgarno. For organisms whose 16S rRNAs contained a perfect anti-Shine-Dalgarno motif, a variety of results were obtained. We found one genus, Alteromonas, where several taxids apparently maintain two different types of 16S rRNA genes, with different, but conserved, antiSDs. The fact that some organisms do not seem to have or use Shine-Dalgarno motifs supports the idea that prokaryotes have other robust mechanisms for recognizing start codons for translation.
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