ArticlePloS one2011
Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 50 citations in OpenAlex.
- Role of the anti-Shine-Dalgarno sequence of 16S rRNA in Flavobacterium johnsoniae.Nucleic acids research · 2026Article
- The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.Microbiology spectrum · 2025Article
- Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.Nucleic acids research · 2025Article
- Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity.Nature communications · 2024Article
- Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Nature communications · 2024Article
- Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements.Nature communications · 2024Article
- Analysis of programmed frameshifting during translation ofRNA (New York, N.Y.) · 2024Article
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria.Nature communications · 2023Article
- Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae.Nucleic acids research · 2023Article
- Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus.Applied microbiology and biotechnology · 2022Article
- Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas.Nucleic acids research · 2021Article
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.Nucleic acids research · 2021Article
- Elucidation of the Translation Initiation Factor Interaction Network ofFrontiers in microbiology · 2021Article
- Comparative Analysis of anti-Shine- Dalgarno Function inFrontiers in molecular biosciences · 2021Article
- How Many Messenger RNAs Can Be Translated by the START Mechanism?International journal of molecular sciences · 2020Article
- Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria.Nucleic acids research · 2019Article
- Translational coupling via termination-reinitiation in archaea and bacteria.Nature communications · 2019Article
- Genes within Genes in Bacterial Genomes.Microbiology spectrum · 2018Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5' untranslated mRNA regions (5'-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5'-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5'-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5'-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished.
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