A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes
A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes
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DOI：
10.1093/molbev/msl036
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发表时间：
2006-09-01
影响因子：
10.7
通讯作者：
Krisch, H. M.
中科院分区：
文献类型：
--
作者：
Filee, Jonathan;Bapteste, Eric;Krisch, H. M.
噬菌体的基因组分析经常揭示出由来自不同来源的模块组成的镶嵌结构。这一事实导致了普遍接受的概念，猖獗和混杂的横向基因转移（LGT）在噬菌体进化中起着至关重要的作用。然而，最近对一系列T4型病毒的测序显示，这些大而复杂的基因组都共享编码复制和病毒体结构基因的2个实质性同线性基因块。为了分析这种核心T4基因组的遗传模式，我们比较了16个T4型猪的全基因组序列。我们确定了所有这些T4型基因组中存在的一组24个基因。有些令人惊讶的是，这些基因中只有一个编码核糖核苷酸还原酶（NrdA）的基因显示出与细菌宿主LGT的证据。我们使用热图分析和比较的参考拓扑结构与23个单独的基因同源性测试的一致性的其他23个标记的遗传。这些核心基因中的绝大多数都有着共同的进化历史。相反，对位于基因组增生区域的16个基因组中的所有非核心基因的分析显示了大量频繁LGT的证据。T4型噬菌体基因组中核心复制和病毒体结构基因的类似进化表明，与许多其他噬菌体组中的情况不同，T4型基因组的这些部分作为一个块遗传，没有显著的LGT，来自遥远的共同祖先。核心T4基因组的同线性的保存可能是由协同作用的几个因素引起的，例如转录的复杂调控所施加的限制。此外，在病毒体形态发生过程中，许多复杂的蛋白质-蛋白质相互作用也可以对LGT施加补充屏障。最后，保持大范围的保守序列可能具有某些真实的进化优势。这些片段可能是一种遗传胶水，通过最保守序列内的重组来维持T4型噬菌体的遗传凝聚力。这可以介导它们侧翼的非保守序列的交换。
Genomic analysis of bacteriophages frequently reveals a mosaic structure made up from modules that come from disparate sources. This fact has led to the general acceptance of the notion that rampant and promiscuous lateral gene transfer (LGT) plays a critical role in phage evolution. However, recent sequencing of a series of the T4-type phages has revealed that these large and complex genomes all share 2 substantial syntenous blocks of genes encoding the replication and virion structural genes. To analyze the pattern of inheritance of this core T4 genome, we compared the complete genome sequences of 16 T4-type phages. We identified a set of 24 genes present in all these T4-type genomes. Somewhat surprisingly, only one of these genes, that encodes for ribonucleotide reductase (NrdA), displayed evidence of LGT with the bacterial host. We test the congruence of the inheritance of the other 23 markers using heat map analyses and comparison of a reference topology with the 23 individual gene phylogenies. The vast majority of these core genes share a common evolutionary history. In contrast, analyses of all the noncore genes present in the same 16 genomes, located in the hyperplastic regions of the genome, show considerable evidence of frequent LGT. The similar evolution of the core replication and virion structural genes in the T4-type phage genomes suggests that, unlike the situation in many other phage groups, such portions of T4-type genome have been inherited as a block, without significant LGT, from a distant common ancestor. The preservation of the synteny of the core T4 genome could result from several factors acting in synergy, such as the constraints imposed by the sophisticated regulation of the transcription. Moreover, numerous and complex protein-protein interactions during virion morphogenesis could also impose a supplementary barrier against LGT. Finally, there may be some real evolutionary advantage to maintaining large regions of conserved sequence. Such segments could be a sort of genetic glue that maintains the genetic cohesion of the T4-type phages via recombination within the most conserved sequences. This could mediate the swapping of nonconserved sequences that they flank.