Merk Liana N, Jones Thomas A, Eddy Sean R
Department of Molecular and Cellular Biology, Harvard University, 02138, Cambridge, USA.
Howard Hughes Medical Institute, Harvard University, 02138, Cambridge, USA.
bioRxiv. 2025 May 23:2025.05.22.655115. doi: 10.1101/2025.05.22.655115.
Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce host burden by autocatalytically splicing out of RNA before translation. While widely known in bacterial, archaeal, and eukaryotic organellar genomes, group II introns have been considered absent in phage. Identifying group II introns in genome sequences has previously been challenging because of their lack of primary sequence similarity. Advances in RNA structure-based homology searches using covariance models has provided the ability to identify the conserved secondary structures of group II introns. Here, we discover that group II introns are widely prevalent in phages from diverse phylogenetic backgrounds, from endosymbiont phage to jumbophage.
尽管噬菌体基因组在高编码密度方面面临强大的选择压力，但它们仍频繁受到移动遗传元件（MGEs）的侵袭。II类内含子是一种MGEs，可通过在翻译前自动催化从RNA中剪接出来来减轻宿主负担。虽然II类内含子在细菌、古菌和真核细胞器基因组中广为人知，但以前认为噬菌体中不存在。由于缺乏一级序列相似性，以前在基因组序列中识别II类内含子具有挑战性。使用协方差模型进行基于RNA结构的同源性搜索的进展提供了识别II类内含子保守二级结构的能力。在这里，我们发现II类内含子在来自不同系统发育背景的噬菌体中广泛存在，从内共生体噬菌体到巨型噬菌体。
