本期文章：《细胞》：Online/在线发表

美国国立卫生研究院Eugene V. Koonin团队通过对元转录组的挖掘揭示一个巨大的类病毒环状RNA世界。相关论文于2023年1月24日在线发表在《细胞》杂志上。

研究人员开发了一种用于识别类病毒共价闭合环（ccc）RNA的计算方案，并将其应用于5131个元转录组和1344个植物转录组。该研究获得了11378个类病毒cccRNA，涵盖4409个物种水平的类病毒元件，与之前确定的类病毒元件相比增加了5倍。在这个多样化的集合中，研究人员发现了许多假定的类病毒、卫星RNA、逆转录酶和核酶样病毒。研究人员在ccRNA中鉴定出不同的核酶组合和独特的核酶。自切割核酶在ambiviruse、一些线粒体样病毒和衣壳编码卫星病毒样cccRNA中被鉴定出来。类病毒cccRNA在不同的转录组和生态系统中广泛存在，这意味着它们的宿主范围比目前已知的要广泛得多，并且与CRISPR间隔序列的匹配表明一些cccRNA在原核生物中复制。

研究人员表示，类病毒和类病毒cccRNA是最小复制因子，通常不编码蛋白质并劫持细胞酶进行复制。类病毒的范围和多样性尚不清楚。

附：英文原文

Title: Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Author: Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin

Issue&Volume: 2023-01-24

Abstract: Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.

DOI: 10.1016/j.cell.2022.12.039