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TitleStructural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.
Journal, issue, pagesNucleic Acids Res, Vol. 49, Issue 1, Page 547-567, Year 2021
Publish dateJan 11, 2021
AuthorsVikash Jha / Bappaditya Roy / Dushyant Jahagirdar / Zakkary A McNutt / Elan A Shatoff / Bethany L Boleratz / Dean E Watkins / Ralf Bundschuh / Kaustuv Basu / Joaquin Ortega / Kurt Fredrick /
PubMed AbstractGenomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the ...Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein-bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
External linksNucleic Acids Res / PubMed:33330920 / PubMed Central
MethodsEM (single particle)
Resolution2.8 Å
Structure data

22345

7jil

EMDB-22345, PDB-7jil:
70S ribosome Flavobacterium johnsoniae
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • flavobacterium johnsoniae (bacteria)
  • flavobacterium sp. root186 (bacteria)
KeywordsRIBOSOME / Translation Initiation / Protein synthesis / bS21

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