The anti-Shine-Dalgarno element of 16S rRNA is needed for translation of one gene, rpsU, in Flavobacterium johnsoniae

ABSTRACT: Bacteroidia ribosomes are “blind” to SD sequences, even though they contain the conserved anti-SD (ASD) element of 16S rRNA. A structure of the Flavobacterium johnsoniae ribosome shows that the 3’ tail of 16S rRNA is sequestered in a pocket formed by bS21, bS18, and bS6 on the 30S platform, explaining the basis of ASD inhibition. Interestingly, there is one gene of F. johnsoniae with a strong SD sequence—rpsU, which encodes bS21. F. johnsoniae ribosomes lacking bS21 exhibit a liberated ASD and translate rpsU at a higher rate, which sets up an autoregulatory cycle. Here, we targeted the ASD of each 16S rRNA gene in F. johnsoniae, ablating the core element (CCUCC to GAAGC). Consecutive replacement of each 16S gene with this quadruple-substituted (QS) allele had little effect on cell growth until the last gene was changed. The final strain, containing QS ribosomes only, grows very slowly. This growth defect can be largely rescued by replacing the native translation initiation region (TIR) with the SD-less TIR of tuf. Purified QS ribosomes are unable to translate native rpsU mRNA but are active on other mRNAs. We also selected suppressors of the ASD-ablated strain, many of which carried a single mutation in the SD of rpsU. Interestingly, wild-type ribosomes fail to initiate on these variant rpsU mRNAs, demonstrating that an extended SD-ASD duplex is normally needed for initiation on this message. These findings indicate that the main purpose of the ASD in F. johnsoniae is to facilitate translation of one gene, rpsU.

INSTRUMENT(S):

ORGANISM(S): Flavobacterium Johnsoniae

SUBMITTER: Jenny Moon  

LAB HEAD: Leonard Foster

PROVIDER: PXD067211 | Pride | 2026-03-05

REPOSITORIES: Pride