Maturation of 23S rRNA includes removal of helix H1 in many bacteria

In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms <i>Escherichia coli</i> and <i>Bacillus subtilis</i>, rRNA processing results in similar mature rRNAs, despite substantial differences in the cohort of RNAses involved. A recent study of <i>Flavobacterium johnsoniae</i>, a member of the phylum Bacteroidota (formerly Bacteroidetes), revealed that helix H1 of 23S rRNA is absent from ribosomes, apparently a consequence of rRNA maturation. In this work, we mined RNA-seq data from 19 individual organisms and ocean metatranscriptomic samples to compare rRNA processing across diverse bacterial lineages. We found that mature ribosomes from multiple clades lack H1, and typically these ribosomes also lack an encoded H98. For all groups analysed, H1 is predicted to form in precursor rRNA as part of a longer leader-trailer helix. Hence, we infer that evolutionary loss of H98 sets the stage for H1 removal during 50S subunit maturation.

在多数细菌中，3种核糖体RNA（ribosomal RNA，rRNA）会在数个近乎一致的操纵子（operon）中共同被编码。新生的前体rRNA一旦从RNA聚合酶（RNA polymerase）中合成并释放，核糖体组装过程便会启动。该过程涵盖核糖体蛋白结合、rRNA折叠、rRNA修饰与rRNA加工。在模式生物大肠杆菌（Escherichia coli）与枯草芽孢杆菌（Bacillus subtilis）中，尽管所涉及的核糖核酸酶（ribonuclease，RNase）类群存在显著差异，但经rRNA加工后产生的成熟rRNA却高度相似。近期一项针对拟杆菌门（Bacteroidota，旧称Bacteroidetes）成员约氏黄杆菌（Flavobacterium johnsoniae）的研究显示，其核糖体中缺失23S核糖体RNA（23S rRNA）的螺旋H1（helix H1），这一现象显然是rRNA成熟过程的产物。本研究通过挖掘19个独立生物体及海洋宏转录组（metatranscriptome）样本的RNA测序（RNA-seq）数据，对不同细菌谱系的rRNA加工过程开展了比较分析。结果发现，多个演化支的成熟核糖体均缺失H1螺旋，且这类核糖体通常也不含有编码序列对应的H98螺旋。针对所有分析的类群，研究预测H1螺旋会在前体rRNA中形成，作为更长的前导-尾随螺旋（leader-trailer helix）的一部分。据此我们推断：H98螺旋的演化缺失为50S核糖体亚基（50S subunit）成熟过程中H1螺旋的移除创造了条件。