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, the prfB gene typically contains the programmed +1 frameshift site with its characteristic SD sequence. Here, we investigate prfB autoregulation in Flavobacterium johnsoniae, a member of the Bacteroidia. We find that the efficiency of prfB frameshifting in F. johnsoniae is low (∼7%) relative to that in Escherichia coli (∼50%). Mutation or truncation of bS21 in F. johnsoniae increases frameshifting substantially, suggesting that anti-SD (ASD) sequestration is responsible for the reduced efficiency. The frameshift site of certain Flavobacteriales, such as Winogradskyella psychrotolerans, has no SD. In F. johnsoniae, this W. psychrotolerans sequence supports frameshifting as well as the native sequence, and mutation of bS21 causes no enhancement. These data suggest that prfB frameshifting 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 to F. johnsoniae cell fitness. Analysis of prfB frameshift 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.

中文翻译：

---

约氏黄杆菌prfB翻译过程中程序性移码分析

由于 16S rRNA 的 3' 尾部被隔离在 30S 平台上，拟杆菌属的核糖体无法识别 Shine-Dalgarno (SD) 序列。然而在这些生物体中，prfB基因通常包含编程的 +1 移码位点及其特征性 SD 序列。在这里，我们研究了拟杆菌属成员约氏黄杆菌中prfB 的自动调节。我们发现，与大肠杆菌中的prfB移码效率 (∼50 %) 相比，约氏杆菌中的 prfB 移码效率较低 (∼7%) 。约氏杆菌中 bS21 的突变或截短会显着增加移码，表明抗 SD (ASD) 隔离是效率降低的原因。某些黄杆菌目（例如Winogradskyella psychrotolerans）的移码位点没有 SD。在约氏杆菌中，该W. psychrotolerans序列支持移码以及天然序列，并且 bS21 的突变不会导致增强。这些数据表明，prfB移码通常在没有 SD-ASD 配对的情况下发生，至少在最佳实验室生长条件下是这样。消除移码或消除 SD 的染色体突变分别在百草枯或链霉素存在的情况下产生细微的生长缺陷，表明自动调节机制和 SD 元件都有助于约氏杆菌细胞的适应性。对 2686 个代表性细菌的prfB移码位点的分析表明，许多进化枝中 SD 序列丢失，与全基因组 SD 使用没有明显关系。这些数据揭示了移码机制中意想不到的变化，并确定了另一类生物体，即疣微生物目，它们在全球范围内缺乏 SD 序列。