National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, India.
Viruses. 2021 Jan 5;13(1):63. doi: 10.3390/v13010063.
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host-virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.
巨型噬菌体凭借其非凡的基因组大小和独特的生物学特征引起了广泛关注。通过对 224 种巨型噬菌体进行比较基因组学分析，我们提出了一个基于基因组大小分布的客观纳入标准，并对它们在主要生物系统中的多种适应性进行了综合概述。通过对保守基因的系统发育模式进行聚类和主成分分析，所有已知的巨型噬菌体可分为三个高级群组，其中包括肌病毒和丝病毒形态，表明它们是从小型前体多次独立起源的。我们的研究揭示了 DNA 复制、重组、转录和病毒粒子成熟系统中几个被低估或未被报道的方面。利用敏感的序列分析方法，我们鉴定了可能有助于劫持宿主机制的新型蛋白修饰酶。我们专注于宿主-病毒冲突，检测到用于对抗细菌免疫系统不同方面的策略，例如环核苷酸和 NAD 依赖性效应物激活，以及在假溶原期间防止超感染。我们重建了巨型噬菌体的 RNA 修复系统，以应对 RNA 靶向宿主效应物的后果。这些发现还表明，几种巨型噬菌体蛋白提供了在前细胞生命最后共同祖先之前的古老复制子中发现的系统的快照。
