Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.

在T4噬菌体（bacteriophage T4）中，可区分出两类依赖重组的DNA复制（recombination-dependent DNA replication）主要途径：即‘连接-复制’（join-copy）与‘连接-切割-复制’（join-cut-copy）。连接-复制途径仅需早期与中期基因（early and middle genes）参与，而连接-切割-复制途径则独有两个晚期蛋白（late proteins）——核酸内切酶VII（endonuclease VII）与末端酶（terminase）发挥关键作用。在野生型T4噬菌体（wild-type T4）中，这两类途径的时序调控与噬菌体发育程序（developmental program）相整合，并与DNA的转录及包装（transcription and packaging of DNA）过程密切相关。对于引物酶突变体（primase mutants）——这类突变体的依赖复制起点的后随链DNA合成（origin-dependent lagging-strand DNA synthesis）功能存在缺陷——晚期途径可弥补后随链DNA合成引物（primers for lagging-strand DNA synthesis）的缺失。核酸内切酶VII及其编码基因所表达的两种蛋白的精细调控合成，解释了引物酶（以及拓扑异构酶（topoisomerase））突变体中重组依赖型DNA复制的延迟现象，以及该延迟的温度依赖性（temperature-dependence）。其他蛋白，例如单链DNA结合蛋白（single-stranded DNA binding protein）以及46、47号基因的编码产物，在所有重组途径中均发挥重要作用，但它们在不同途径中与其他蛋白的互作模式存在差异。这些同源重组途径（homologous recombination pathways）可推动进化进程：其能够在水平基因转移（horizontal gene transfer）过程中，帮助噬菌体获取序列同源性有限的外源DNA，且无需依赖转座或位点特异性重组功能（transposition or site-specific recombination functions）。部分异源双链修复（partial heteroduplex repair）可从单一重组中间体（recombinational intermediate）产生看似多重突变的结果。由此产生的序列分歧（sequence divergence）会对有活力重组体（viable recombinants）的形成形成阻碍。这些多重序列改变还可能导致系统发育分析（phylogenetic analyses）中出现错误的评估结果。