Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes.

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  • Author(s): Accetto T;Accetto T; Avguštin G
  • Source:
    PloS one [PLoS One] 2011; Vol. 6 (8), pp. e22914. Date of Electronic Publication: 2011 Aug 12.
  • Publication Type:
    Journal Article; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
    • Publication Information:
      Original Publication: San Francisco, CA : Public Library of Science
    • Subject Terms:
      Bacteroidetes/*genetics ; Prevotella/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Ribosomes/*metabolism; 5' Untranslated Regions/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacteroidetes/classification ; Bacteroidetes/metabolism ; Base Composition/genetics ; Base Sequence ; Binding Sites/genetics ; Codon, Initiator/genetics ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Prevotella/metabolism ; Protein Biosynthesis/genetics ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity
    • 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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    • Accession Number:
      0 (5' Untranslated Regions)
      0 (Bacterial Proteins)
      0 (Codon, Initiator)
      0 (RNA, Messenger)
      0 (RNA, Ribosomal, 16S)
    • Publication Date:
      Date Created: 20110823 Date Completed: 20120215 Latest Revision: 20211020
    • Publication Date:
      20240829
    • Accession Number:
      PMC3155529
    • Accession Number:
      10.1371/journal.pone.0022914
    • Accession Number:
      21857964