Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae

Abstract

Ribosomes of Bacteroidia fail to recognize Shine–Dalgarno (SD) sequences due to sequestration of the 3′ tail of the 16S rRNA on the 30S platform. Yet in these organisms, theprfBgene typically contains the programmed +1 frameshift site with its characteristic SD sequence. Here, we investigateprfBautoregulation inFlavobacterium johnsoniae, a member of the Bacteroidia. We find that the efficiency ofprfBframeshifting inF. johnsoniaeis low (∼7%) relative to that inEscherichia coli(∼50%). Mutation or truncation of bS21 inF. johnsoniaeincreases frameshifting substantially, suggesting that anti-SD (ASD) sequestration is responsible for the reduced efficiency. The frameshift site of certain Flavobacteriales, such asWinogradskyella psychrotolerans, has no SD. InF. johnsoniae, thisW. psychrotoleranssequence supports frameshifting as well as the native sequence, and mutation of bS21 causes no enhancement. These data suggest thatprfBframeshifting normally occurs without SD–ASD pairing, at least under optimal laboratory growth conditions. Chromosomal mutations that remove the frameshift or ablate the SD confer subtle growth defects in the presence of paraquat or streptomycin, respectively, indicating that both the autoregulatory mechanism and the SD element contribute toF. johnsoniaecell fitness. Analysis ofprfBframeshift sites across 2686 representative bacteria shows loss of the SD sequence in many clades, with no obvious relationship to genome-wide SD usage. These data reveal unexpected variation in the mechanism of frameshifting and identify another group of organisms, the Verrucomicrobiales, that globally lack SD sequences.