State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China.
Environ Microbiol. 2021 Jul;23(7):3743-3757. doi: 10.1111/1462-2920.15412. Epub 2021 Feb 17.
Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG)， most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.
海洋噬菌体经常拥有辅助代谢基因 (AMGs)，这些基因在噬菌体感染宿主时加速宿主代谢。然而，这些 AMGs 在感染生态重要的玫瑰杆菌群（主要存在于海洋环境中）中的意义仍有待确定。在这里，我们分析了 50 个玫瑰噬菌体基因组中 180 个 AMG 的分布和基因组上下文，这些 AMG 被注释为 20 种类型。玫瑰噬菌体共享七种高频 AMGs（trx、grx、RNR、thyX、DCD、phoH 和 mazG），它们大多参与核苷酸生物合成途径，代表保守的种内和种间操作分类单元 (OTUs)，并且共享≥97%全长 DNA 序列相似性。零星 AMGs（dUTPase、lexA、degS、Que、NAPRT、AHL、pcnB、ctrA、RTX、RNR-nrdA、RNR-nrdE、wclP 和 flgJ）仅存在于一个或两个 OTUs 中，表现出高度的功能多样性。玫瑰噬菌体 AMG 谱与环境因素弱相关，而宿主范围部分解释了零星 AMG 的分布。局部共线性块分布指数 (LDI) 分析表明，高频玫瑰杆噬菌体 AMGs 局限于特定的基因组岛，可能源自有限的历史获取事件。低频玫瑰杆噬菌体 AMGs 和所有玫瑰噬菌体 AMGs 的 LDI 值较高，表明存在多次历史获取事件。总之，玫瑰噬菌体通过水平基因转移获得了一系列 AMGs，并且描述了塑造玫瑰噬菌体进化的力量。
