Structural analysis of lactococcal ceduovirus phages c2 and bIL67

Bacteriophages, or phages, are sophisticated nanomachines that efficiently infect bacteria. Their infection of lactic acid bacteria (LAB) used in fermentation can lead to significant industrial losses. Among phages that infect monoderm bacteria, those with siphovirion morphology characterized by a long, non-contractile, tail are predominant. The initial stage of phage infection involves precise host recognition and binding. To achieve this, phages feature host adhesion devices (HAD) located at the distal end of their tails, that have evolved to recognize specific proteinaceous or saccharidic receptors on the host cell wall. Ceduovirus represents a group of unique lytic siphophages that specifically infect the LAB Lactococcus lactis by targeting proteinaceous receptors. Despite having compact ge- nomes, most of their structural genes are poorly annotated and the architecture and func- tion of their HADs remain unknown. Here we used AlphaFold3 to explore the Ceduovirus HADs and their interaction with the host. We show that Ceduovirus HADs exhibit unprecedented features among bacteriophages infecting Gram+, share structural similarities with bacterial secretion systems VI and combine both saccharide and protein binding modules. Moreover, we could annotate the majority of Ceduovirus genes encoding structural proteins by leveraging their predicted structures, highlighting AlphaFold's sig- nificant contribution to phage genome annotation.噬菌体（Bacteriophages，常简称phages）是一类结构精密的纳米机器，能够高效侵染细菌。其侵染发酵工业中常用的乳酸菌（lactic acid bacteria, LAB），可引发显著的工业损失。在侵染单膜细菌（monoderm bacteria）的噬菌体中，具有长非收缩性尾部特征的长尾噬菌体（siphovirion）类群占据绝对优势。噬菌体侵染的初始阶段涉及精准的宿主识别与结合过程：为达成这一过程，噬菌体在尾部远端进化出宿主黏附装置（host adhesion devices, HAD），该装置可识别宿主细胞壁上特定的蛋白类或多糖类受体。赛杜噬菌体属（Ceduovirus）是一类独特的裂解性长尾噬菌体（siphophages），可通过识别蛋白类受体专一性侵染乳酸菌中的乳酸乳球菌（Lactococcus lactis）。尽管该类噬菌体基因组十分紧凑，但绝大多数结构基因的注释质量较低，其宿主黏附装置的结构组成与功能仍未明确。本研究利用阿尔法折叠3（AlphaFold3）对赛杜噬菌体属的宿主黏附装置及其与宿主的相互作用展开探究。研究发现，赛杜噬菌体属的宿主黏附装置在侵染革兰氏阳性菌（Gram+）的噬菌体中展现出前所未有的特征：其结构与细菌Ⅵ型分泌系统具有相似性，同时兼具糖类结合模块与蛋白质结合模块。此外，本研究通过利用预测得到的蛋白质结构，完成了赛杜噬菌体属绝大多数结构蛋白编码基因的注释，凸显了阿尔法折叠在噬菌体基因组注释领域的重要价值。