Zheng Clarence, Casjens Sherwood R, Davidson Alan R, Amundsen Susan K, Smith Gerald R
Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA.
Department of Pathology, University of Utah, Salt Lake City, Utah 84112, USA.
Genome Res. 2025 Aug 1;35(8):1767-1780. doi: 10.1101/gr.280248.124.
Many phages encode recombination-mediating enzymes, but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of , the RecBCD enzyme. Although no phages inhibited by RecBCD are identified, growth of a newly isolated phage, named LLS, is enhanced by RecBCD. LLS's genome sequence reveals it is related to bacteriophage λ but encodes no recombination-promoting (Rec) proteins or associated RecBCD inhibitor. However, it contains an unexpectedly high number of Chi sites, activators of RecBCD-dependent recombination. Through analysis of 325 genomes of phages related to λ (lambdoid phages), we have found 71 other phage genomes that encode no Rec proteins but mostly possess large numbers of Chi sites. Conversely, phages encoding Rec proteins and a RecBCD inhibitor (collectively a Rec module) mostly lack Chi sites. Lambdoid phages of both diverse enteric bacteria and a pseudomonad have these properties. For this study, we thoroughly analyze the Rec modules of 246 lambdoid phage genomes. These analyses reveal a remarkable heterogeneity of Rec module protein types, both in sequence and in function, and allow us to identify phages that do not contain Rec modules. We conclude that phages lacking their own recombination systems have compensated by becoming enriched in Chi sites, enabling them to use the host's RecBCD to fulfill the requirement for recombination to efficiently replicate. This study highlights the importance of recombination for phage survival and the diversity of strategies to achieve it.
许多噬菌体编码介导重组的酶，但其在噬菌体生命周期中的作用表征有限，且它们对噬菌体复制的影响存在争议。为了解决这些问题，我们寻找了其生长受大肠杆菌主要的促进重组的解旋酶-核酸酶RecBCD影响的噬菌体。虽然未鉴定出受RecBCD抑制的噬菌体，但一种新分离的名为LLS的噬菌体的生长受到RecBCD的增强。LLS的基因组序列显示它与噬菌体λ相关，但不编码促进重组的（Rec）蛋白或相关的RecBCD抑制剂。然而，它含有数量意外之多的Chi位点，即RecBCD依赖性重组的激活剂。通过分析与λ相关的噬菌体（类λ噬菌体）的325个基因组，我们发现另外71个噬菌体基因组不编码Rec蛋白，但大多拥有大量的Chi位点。相反，编码Rec蛋白和RecBCD抑制剂（统称为Rec模块）的噬菌体大多缺乏Chi位点。多种肠道细菌和一种假单胞菌的类λ噬菌体都有这些特性。在本研究中，我们全面分析了246个类λ噬菌体基因组的Rec模块。这些分析揭示了Rec模块蛋白类型在序列和功能上的显著异质性，并使我们能够鉴定出不含Rec模块的噬菌体。我们得出结论，缺乏自身重组系统的噬菌体通过富含Chi位点来进行补偿，使其能够利用宿主的RecBCD来满足重组需求以高效复制。这项研究突出了重组对噬菌体生存的重要性以及实现重组的策略的多样性。
