Luque Antoni, Benler Sean, Lee Diana Y, Brown Colin, White Simon
Viral Information Institute, San Diego State University, San Diego, CA 92182, USA.
Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA.
Microorganisms. 2020 Dec 8;8(12):1944. doi: 10.3390/microorganisms8121944.
Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.
有尾噬菌体是地球上数量最多、种类最多样的病毒群体。然而，与其他病毒相比，最小的有尾噬菌体却呈现出相对复杂的衣壳和较大的基因组。缺乏形成常见二十面体衣壳结构T = 1和T = 3的有尾噬菌体令人费解。在这里，我们从高分辨率的有尾噬菌体衣壳重建中提取几何特征，并基于物理原理建立了一个统计模型，以预测缺失的小尾噬菌体衣壳的直径和基因组长度。我们将该模型应用于3348个分离的有尾噬菌体基因组和1496个肠道宏基因组组装的有尾噬菌体基因组。预测有4个分离的有尾噬菌体形成T = 3二十面体衣壳，21个宏基因组组装的有尾噬菌体形成T < 3衣壳。预测的最小衣壳是T = 4/3≈1.33结构。没有预测到有尾噬菌体形成最小的二十面体结构T = 1。我们讨论了缺失的T = 1有尾噬菌体衣壳的可行性，以及分离和鉴定小尾噬菌体对病毒进化和噬菌体治疗的意义。
