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TitleStructure of a specialized 70S initiation complex.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 6, Year 2026
Publish dateMar 19, 2026
AuthorsDominic Arpin / Bappaditya Roy / Fawwaz M Naeem / Kurt Fredrick / Joaquin Ortega /
PubMed AbstractBacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes ...Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.
External linksNucleic Acids Res / PubMed:41854077 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 2.9 Å
Structure data

71002

9oy8

EMDB-71002, PDB-9oy8:
Flavobacterium johnsoniae 30S ribosomal subunit.
Method: EM (single particle) / Resolution: 2.7 Å

71035

9oyv

EMDB-71035, PDB-9oyv:
Flavobacterium johnsoniae 30S ribosomal subunit, ZAM64 mutant.
Method: EM (single particle) / Resolution: 2.7 Å

71052

9oz9

EMDB-71052, PDB-9oz9:
Flavobacterium johnsoniae 70S initiation complex with Shine-Dalgarno-less mRNA.
Method: EM (single particle) / Resolution: 2.6 Å

71060

9ozn

EMDB-71060, PDB-9ozn:
Flavobacterium johnsoniae 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence. State 1.
Method: EM (single particle) / Resolution: 2.7 Å

71061

9ozz

EMDB-71061, PDB-9ozz:
Flavobacterium johnsoniae 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence. State 2.
Method: EM (single particle) / Resolution: 2.5 Å

71069

9p0e

EMDB-71069, PDB-9p0e:
Flavobacterium johnsoniae ZAM64 mutant 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence.
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-71567: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-71568: Flavobacterium johnsoniae bS18 M7 mutant 70S ribosome.
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-71569: Flavobacterium johnsoniae bS18 M5 mutant 70S ribosome.
Method: EM (single particle) / Resolution: 2.7 Å

74034

9zcd

EMDB-74034, PDB-9zcd:
Flavobacterium johnsoniae 30S ribosomal subunit.
Method: EM (single particle) / Resolution: 2.7 Å

Source
  • flavobacterium johnsoniae (bacteria)
  • flavobacterium johnsoniae uw101 (bacteria)
KeywordsRIBOSOME / 30S / initiation complex / Flavobacterium johnsoniae / 70S / translation.

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