Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage
Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage
复制标题
DOI：
10.1128/jb.185.17.5220-5233.2003
复制
发表时间：
2003-09-01
影响因子：
3.2
通讯作者：
Fraser, CM
中科院分区：
文献类型：
--
作者：
Miller, ES;Heidelberg, JF;Fraser, CM
已经确定了t4样，宽宿主范围的噬菌体K-VP40的完整基因组序列。基因组序列为244,835 bp，总G+C含量为42.6%。它编码386个假定的蛋白质编码开放阅读框（cds）， 30个trna， 33个t4样晚期启动子和57个潜在的rho非依赖性终止子。总体而言，92.1%的K-VP40基因组正在编码，平均CDS大小为587 bp。虽然65%的cds是K-VP40独有的，并且没有已知的功能，但基因组序列和组织显示与噬菌体T4广泛保守的特定区域。至少有99个KVP40 CDSs在T4基因组中具有同源物（Blast比对的氨基酸相似性为45 - 68%）。共享cds占所有T4 cds的36%，但仅占K-VP40 cds的26%。DNA复制、重组和修复酶以及病毒衣壳和尾部结构基因广泛存在。K-VP40缺乏参与宿主DNA降解的几种T4酶，似乎不能合成T-even噬菌体中存在的修饰胞嘧啶（羟甲基葡萄糖），并且缺乏I族内含子。K-VP40可能利用了t4型sigma-55晚期转录装置，但早期或中期模式转录的特征尚未确定。有26个cds没有病毒同源物，其中许多不一定起源于弧菌，这表明KVP40的宿主范围更广。从这些后一种cds中，推断出一种在噬菌体中似乎是独特的NAD挽救途径。介绍了KVP40基因组与T4不同的特征，以及那些基本保守的特征，如复制和病毒粒子基因簇。
The complete genome sequence of the T4-like, broad-host-range vibriophage K-VP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the K-VP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to K-VP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from K-VP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. K-VP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. K-VP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.