Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India.
Department of Veterinary Pathology, Madras Veterinary College, Veterinary and Animal Sciences University (TANUVAS), Vepery, Chennai, Tamil Nadu, India.
Microbiol Spectr. 2022 Dec 21;10(6):e0105722. doi: 10.1128/spectrum.01057-22. Epub 2022 Nov 8.
The CRESS-DNA viruses are the ubiquitous virus detected in almost all eukaryotic life trees and play an essential role in the maintaining ecosystem of the globe. Still, their genetic diversity is not fully understood. Here, we bring to light the genetic diversity of replication (Rep) and capsid (Cap) proteins of CRESS-DNA viruses. We divided the Rep protein of the CRESS-DNA virus into 10 clusters using CLANS and phylogenetic analyses. Also, most of the Rep protein in Rep cluster 1 (R1) and R2 (, , , and CRESSV1-5) contain the Viral_Rep superfamily and P-loop_NTPase superfamily domains, while the Rep protein of viruses in other clusters has no such characterized functional domain. The , , and CRESSV1-3 viruses contain two domains, such as Viral_Rep and P-loop_NTPase; the CRESSV4 and CRESSV5 viruses have only the Viral_Rep domain; most of the sequences in the pCRESS-related group have only P-loop_NTPase; and do not have these two domains. Further, we divided the Cap protein of the CRESS-DNA virus into 20 clusters using CLANS and phylogenetic analyses. The Rep and Cap proteins of and are grouped into a specific cluster. Cap protein of CRESS-DNA viruses grouped with one cluster and Rep protein with another cluster. Further, our study reveals that selection pressure plays a significant role in the evolution of CRESS-DNA viruses' Rep and Cap genes rather than mutational pressure. We hope this study will help determine the genetic diversity of CRESS-DNA viruses as more sequences are discovered in the future. The genetic diversity of CRESS-DNA viruses is not fully understood. CRESS-DNA viruses are classified as CRESSV1 to CRESSV6 using only Rep protein. This study revealed that the Rep protein of the CRESS-DNA viruses is classified as CRESSV1 to CRESSV6 groups and the new Smacoviridae-related, CRESSV2-related, pCRESS-related, Circoviridae-related, and 1 to 4 outgroups, according to the Viral_Rep and P-loop_NTPase domain organization, CLANS, and phylogenetic analysis. Furthermore, for the first time in this study, the Cap protein of CRESS-DNA viruses was classified into 20 distinct clusters by CLANS and phylogenetic analysis. Through this classification, the genetic diversity of CRESS-DNA viruses clarifies the possibility of recombinations in Cap and Rep proteins. Finally, it has been shown that selection pressure plays a significant role in the evolution and genetic diversity of Cap and Rep proteins. This study explains the genetic diversity of CRESS-DNA viruses and hopes that it will help classify future detected viruses.
类质体 DNA 病毒是在几乎所有真核生物中都能检测到的普遍存在的病毒，在维持全球生态系统中起着至关重要的作用。然而，它们的遗传多样性尚未完全了解。在这里，我们揭示了类质体 DNA 病毒的复制（Rep）和衣壳（Cap）蛋白的遗传多样性。我们使用 CLANS 和系统发育分析将类质体 DNA 病毒的 Rep 蛋白分为 10 个簇。此外，Rep 簇 1（R1）和 R2（、、和 CRESSV1-5）中的大多数 Rep 蛋白都包含病毒 Rep 超家族和 P 环 NTPase 超家族结构域，而其他簇中的 Rep 蛋白则没有这种特征性功能域。、和 CRESSV1-3 病毒含有两个结构域，如病毒 Rep 和 P 环 NTPase；CRSSV4 和 CRESSV5 病毒只有病毒 Rep 结构域；pCRESS 相关群的大多数序列只有 P 环 NTPase；而没有这两个结构域。此外，我们使用 CLANS 和系统发育分析将类质体 DNA 病毒的 Cap 蛋白分为 20 个簇。和 的 Rep 和 Cap 蛋白被归为一个特定的簇。类质体 DNA 病毒的 Cap 蛋白与一个簇分组，Rep 蛋白与另一个簇分组。此外，我们的研究表明，选择压力而不是突变压力在类质体 DNA 病毒的 Rep 和 Cap 基因进化中起着重要作用。我们希望这项研究将有助于确定类质体 DNA 病毒的遗传多样性，因为未来会发现更多的序列。类质体 DNA 病毒的遗传多样性尚未完全了解。仅使用 Rep 蛋白将类质体 DNA 病毒分类为 CRESSV1 至 CRESSV6。本研究表明，根据病毒 Rep 和 P 环 NTPase 结构域组织、CLANS 和系统发育分析，类质体 DNA 病毒的 Rep 蛋白被分类为 CRESSV1 至 CRESSV6 组以及新的 Smacoviridae 相关、CRESSV2 相关、pCRESS 相关、Circoviridae 相关和 1 至 4 个外群。此外，在本研究中，类质体 DNA 病毒的 Cap 蛋白首次通过 CLANS 和系统发育分析分为 20 个不同的簇。通过这种分类，类质体 DNA 病毒的遗传多样性阐明了 Cap 和 Rep 蛋白中重组的可能性。最后，结果表明选择压力在 Cap 和 Rep 蛋白的进化和遗传多样性中起着重要作用。本研究解释了类质体 DNA 病毒的遗传多样性，并希望有助于对未来检测到的病毒进行分类。
