Koonin Eugene V, Lee Benjamin D
Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Nucleic Acids Res. 2025 Jan 24;53(3). doi: 10.1093/nar/gkae1278.
Viroids, the agents of several plant diseases, are the smallest and simplest known replicators that consist of covalently closed circular (ccc) RNA molecules between 200 and 400 nucleotides in size. Viroids encode no proteins and rely on host RNA polymerases for replication, but some contain ribozymes involved in replication intermediate processing. Although other viroid-like agents with cccRNAs genomes, such as satellite RNAs, ribozyviruses and retrozymes, have been discovered, until recently, the spread of these agents in the biosphere appeared narrow, and their actual diversity and evolution remained poorly understood. Extensive, targeted metatranscriptome mining dramatically expanded the known diversity of cccRNAs genomes. These searches identified numerous, diverse viroid-like cccRNAs, many found in environments devoid of plant and animal material, suggesting replication in unicellular eukaryotic and/or prokaryotic hosts. Several cccRNAs are targeted by CRISPR systems, supporting their association with bacteria. In addition to small cccRNAs in the viroid size range, a broad variety of ribozyviruses and novel viruses with cccRNAs genomes, with genomes reaching nearly 5 kilobases, were discovered. Thus, metatranscriptome mining shows that the diversity of viroid-like cccRNAs genomes is far greater than previously suspected, prompting reassessment of the relevance of these replicators for understanding the primordial RNA world.
类病毒是几种植物疾病的病原体，是已知最小且最简单的复制因子，由大小在200至400个核苷酸之间的共价闭合环状（ccc）RNA分子组成。类病毒不编码蛋白质，依靠宿主RNA聚合酶进行复制，但有些类病毒含有参与复制中间体加工的核酶。尽管已经发现了其他具有cccRNA基因组的类病毒样因子，如卫星RNA、核酶病毒和逆转录酶，但直到最近，这些因子在生物圈中的传播范围似乎很窄，它们的实际多样性和进化仍知之甚少。广泛的、有针对性的宏转录组挖掘极大地扩展了已知的cccRNA基因组的多样性。这些搜索鉴定出了许多不同的类病毒样cccRNA，其中许多是在没有动植物材料的环境中发现的，这表明它们在单细胞真核生物和/或原核宿主中进行复制。几种cccRNA被CRISPR系统靶向，这支持了它们与细菌的关联。除了类病毒大小范围内的小cccRNA外，还发现了各种各样的核酶病毒和具有cccRNA基因组的新型病毒，其基因组大小接近5千碱基。因此，宏转录组挖掘表明，类病毒样cccRNA基因组的多样性远比之前怀疑的要大得多，这促使人们重新评估这些复制因子对于理解原始RNA世界的相关性。
