Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages
Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages
复制标题
DOI：
10.1006/jmbi.2001.4868
复制
发表时间：
2001-08-24
影响因子：
5.6
通讯作者：
Dhillon, TS
中科院分区：
文献类型：
--
作者：
Clark, AJ;Inwood, W;Dhillon, TS
HK620是一种吸附在宿主大肠杆菌H的O抗原上的温带类噬菌体，其基因组由38,297个核苷酸组成，其中我们识别60个开放阅读框(ORF)。其中18个位于基因组的一个区域，我们称之为病毒粒子结构域。另外42个ORF位于我们所说的代谢区域，HK620的病毒粒子与噬菌体P22的病毒粒子相似。病毒粒子结构开放阅读框编码三种与P22病毒粒子蛋白相关的蛋白：(1)几乎(90%)相同的蛋白；(2)弱相同(约30%)的蛋白；(3)由接近和弱相同的片段组成的蛋白。我们假设这些复合蛋白在另外两类病毒粒子蛋白之间形成了桥梁，其中三个假定的病毒粒子蛋白与P22蛋白只有微弱的同源性，分别与噬菌体APSE-1编码的蛋白71、60%和79%相同，后者的病毒粒子也与P22蛋白相似。由于APSE-1和HK620的宿主之间估计有200My的距离，我们建议利用这些蛋白质中积累的氨基酸差异来估计温和的Lambdoid噬菌体的生物时钟。HK620假定的转录调控基因电路似乎类似于噬菌体Lambda。另一方面，整合与卫星噬菌体P4相似，因为attP序列位于左侧的启动子和int之间，而不是int的下游。比较几个Lambdoid噬菌体基因组的代谢域，发现了7个短的保守序列，大致定义了功能模块的边界。我们认为这些边界序列是基因重组的焦点，用于对模块进行分类，并使代谢区域在基因上高度镶嵌。(C)2001年学术出版社。
HK620 is a temperate lambdoid bacteriophage that adsorbs to the O-antigen of its host, Escherichia coli H. The genome of a temperature-sensitive clear-plaque mutant consists of 38,297 nucleotides in which we recognize 60 open reading frames (orfs). Eighteen of these lie in a region of the genome that we call the virion structure domain. The other 42 orfs lie in what we call the metabolic domain.Virions of HK620 resemble those of phage P22. The virion structural orfs encode three kinds of putative proteins relative to the virion proteins of P22: (1) those that are nearly (about 90%) identical; (2) those that are weakly (about 30%) identical; and (3) those composed of nearly and weakly identical segments. We hypothesize that these composite proteins form bridges between the virion proteins of the other two kinds.Three of the putative virion proteins that are only weakly identical to P22 proteins are 71, 60 and 79% identical to proteins encoded by the phage APSE-1, whose virions also resemble those of P22. Because the hosts of APSE-1 and HK620 have been separated from each other by an estimated 200 My, we propose using the amino acid differences that have accumulated in these proteins to estimate a biological clock for temperate lambdoid phages.The putative transcriptional regulatory gene circuitry of HK620 seems to resemble that of phage lambda. Integration, on the other hand, resembles that of satellite phage P4 in that the attP sequence lies between the leftward promoter and int rather than downstream of int.Comparing the metabolic domains of several lambdoid phage genomes reveals seven short conserved sequences roughly defining boundaries of functional modules. We propose that these boundary sequences are foci of genetic recombination that serve to assort the modules and make the metabolic domain highly mosaic genetically. (C) 2001 Academic Press.