College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany.
J Virol. 2020 May 18;94(11). doi: 10.1128/JVI.00149-20.
Virophages are small parasitic double-stranded DNA (dsDNA) viruses of giant dsDNA viruses infecting unicellular eukaryotes. Except for a few isolated virophages characterized by parasitization mechanisms, features of virophages discovered in metagenomic data sets remain largely unknown. Here, the complete genomes of seven virophages (26.6 to 31.5 kbp) and four large DNA viruses (190.4 to 392.5 kbp) that coexist in the freshwater lake Dishui Lake, Shanghai, China, have been identified based on environmental metagenomic investigation. Both genomic and phylogenetic analyses indicate that Dishui Lake virophages (DSLVs) are closely related to each other and to other lake virophages, and Dishui Lake large DNA viruses are affiliated with the micro-green alga-infecting of the (named Dishui Lake phycodnaviruses [DSLPVs]) and protist (protozoan and alga)-infecting (named Dishui Lake large alga virus [DSLLAV]). The DSLVs possess more genes with closer homology to that of large alga viruses than to that of giant protozoan viruses. Furthermore, the DSLVs are strongly associated with large green alga viruses, including DSLPV4 and DSLLAV1, based on codon usage as well as oligonucleotide frequency and correlation analyses. Surprisingly, a nonhomologous CRISPR-Cas like system is found in DSLLAV1, which appears to protect DSLLAV1 from the parasitization of DSLV5 and DSLV8. These results suggest that novel cell-virus-virophage (CVv) tripartite infection systems of green algae, large green alga virus (- and -related), and virophage exist in Dishui Lake, which will contribute to further deep investigations of the evolutionary interaction of virophages and large alga viruses as well as of the essential roles that the CVv plays in the ecology of algae. Virophages are small parasitizing viruses of large/giant viruses. To our knowledge, the few isolated virophages all parasitize giant protozoan viruses () for propagation and form a tripartite infection system with hosts, here named the cell-virus-virophage (CVv) system. However, the CVv system remains largely unknown in environmental metagenomic data sets. In this study, we systematically investigated the metagenomic data set from the freshwater lake Dishui Lake, Shanghai, China. Consequently, four novel large alga viruses and seven virophages were discovered to coexist in Dishui Lake. Surprisingly, a novel CVv tripartite infection system comprising green algae, large green alga viruses (- and -related), and virophages was identified based on genetic link, genomic signature, and CRISPR system analyses. Meanwhile, a nonhomologous CRISPR-like system was found in Dishui Lake large alga viruses, which appears to protect the virus host from the infection of Dishui Lake virophages (DSLVs). These findings are critical to give insight into the potential significance of CVv in global evolution and ecology.
噬病毒体是感染单细胞真核生物的巨型双链 DNA (dsDNA) 病毒的小型寄生双链 DNA (dsDNA) 病毒。除了少数已被表征的寄生机制的孤立噬病毒体外，从宏基因组数据集发现的噬病毒体的特征在很大程度上仍然未知。在这里，根据环境宏基因组调查，已从中国上海淡水湖滇池湖中鉴定出七种噬病毒体（26.6 至 31.5 kbp）和四种大型 DNA 病毒（190.4 至 392.5 kbp）的完整基因组。基因组和系统发育分析均表明，滇池噬病毒体（DSLVs）彼此之间以及与其他湖泊噬病毒体密切相关，而滇池大型 DNA 病毒与感染微绿藻的 （命名为滇池噬藻体 [DSLPVs]）和感染原生动物（原生动物和藻类）的 （命名为滇池大型藻类病毒 [DSLLAV]）有关。DSLVs 具有更多与大型藻类病毒而不是巨型原生动物病毒具有更密切同源性的基因。此外，基于密码子使用、寡核苷酸频率和相关性分析，DSLVs 与包括 DSLPV4 和 DSLLAV1 在内的大型绿色藻类病毒强烈相关。令人惊讶的是，在 DSLLAV1 中发现了一种非同源的 CRISPR-Cas 样系统，该系统似乎可以防止 DSLLAV1 被 DSLLAV1 寄生。这些结果表明，新型的绿藻、大型绿藻病毒（-和-相关）和噬病毒体的 CVv 三分体感染系统存在于滇池，这将有助于进一步深入研究噬病毒体和大型藻类病毒的进化相互作用，以及 CVv 在藻类生态学中的重要作用。噬病毒体是大型/巨型病毒的小型寄生病毒。据我们所知，少数已分离的噬病毒体均寄生巨型原生动物病毒（）以进行繁殖，并与宿主形成一种三分体感染系统，这里称为细胞-病毒-噬病毒体（CVv）系统。然而，在环境宏基因组数据集中，CVv 系统在很大程度上仍然未知。在本研究中，我们系统地研究了来自中国上海淡水湖滇池的宏基因组数据集。结果发现，四种新型大型藻类病毒和七种噬病毒体在滇池中共存。令人惊讶的是，基于遗传联系、基因组特征和 CRISPR 系统分析，发现了一种由绿藻、大型绿藻病毒（-和-相关）和噬病毒体组成的新型 CVv 三分体感染系统。同时，在滇池大型藻类病毒中发现了一种非同源的 CRISPR 样系统，该系统似乎可以保护病毒宿主免受滇池噬病毒体（DSLVs）的感染。这些发现对于深入了解 CVv 在全球进化和生态学中的潜在意义至关重要。
