Gemler Bryan T, Warner Benjamin R, Bundschuh Ralf, Fredrick Kurt
Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.
Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
RNA. 2024 Sep 16;30(10):1264-1276. doi: 10.1261/rna.080091.124.
Ribosomal RNAs are transcribed as part of larger precursor molecules. In , complementary RNA segments flank each rRNA and form long leader-trailer (LT) helices, which are crucial for subunit biogenesis in the cell. A previous study of 15 representative species suggested that most but not all prokaryotes contain LT helices. Here, we use a combination of in silico folding and covariation methods to identify and characterize LT helices in 4464 bacterial and 260 archaeal organisms. Our results suggest that LT helices are present in all phyla, including Deinococcota, which had previously been suspected to lack LT helices. In very few organisms, our pipeline failed to detect LT helices for both 16S and 23S rRNA. However, a closer case-by-case look revealed that LT helices are indeed present but escaped initial detection. Over 3600 secondary structure models, many well supported by nucleotide covariation, were generated. These structures show a high degree of diversity. Yet, all exhibit extensive base-pairing between the leader and trailer strands, in line with a common and essential function.
核糖体RNA作为较大前体分子的一部分被转录。在原核生物中，互补RNA片段位于每个rRNA两侧，形成长的前导-尾随（LT）螺旋，这对细胞中的亚基生物合成至关重要。先前对15个代表性物种的研究表明，大多数但并非所有原核生物都含有LT螺旋。在这里，我们结合计算机折叠和共变方法，对4464种细菌和260种古生菌中的LT螺旋进行识别和表征。我们的结果表明，LT螺旋存在于所有门中，包括以前被怀疑缺乏LT螺旋的异常球菌门。在极少数生物中，我们的流程未能检测到16S和23S rRNA的LT螺旋。然而，逐个案例仔细观察发现，LT螺旋确实存在，但最初未被检测到。我们生成了3600多个二级结构模型，其中许多得到了核苷酸共变的有力支持。这些结构显示出高度的多样性。然而，所有结构在前导链和尾随链之间都表现出广泛的碱基配对，这与一个共同且重要的功能一致。
