Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome
Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome
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DOI：
10.1016/j.gene.2012.07.029
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发表时间：
2012-10-10
期刊：
影响因子：
3.5
通讯作者：
Yang, Hongjiang
中科院分区：
文献类型：
--
作者：
Li, Peizhen;Chen, Biaobang;Yang, Hongjiang
鲍曼不动杆菌作为医院感染的病原菌之一，给公众健康带来巨大挑战。鲍曼不动杆菌噬菌体可能是对抗多重耐药鲍曼不动杆菌的有效方法。在这里，我们完成了鲍曼不动杆菌噬菌体AB1全基因组的全基因组测序，该噬菌体由45,159 bp组成，是一个双链DNA分子，平均GC含量为37.7%。该基因组编码1个tRNA基因和85个开放阅读框（ORF），ORF的平均长度为531 bp。在85个ORF中，仅鉴定出14个与已知功能的基因具有显着的序列相似性，而28个与数据库中功能未知的基因在序列上相似，并且43个ORF独特地存在于噬菌体AB1基因组中。 14个具有假定功能的功能指定基因包括5个噬菌体结构蛋白、1个RNA聚合酶、终止酶的大亚基和小亚基、甲基化酶和重组酶以及参与DNA复制的蛋白质等。对这些同源蛋白进行多重序列比对，并重建系统发育树，以分析这些必需基因的进化过程。比较基因组学分析清楚地表明，噬菌体基因组框架主要由来自黄单胞菌噬菌体、伯克霍尔德氏菌噬菌体和肠杆菌噬菌体的基因组成，而仅零星地包含其宿主鲍曼不动杆菌的基因。噬菌体基因组的镶嵌特征表明水平基因转移发生在噬菌体基因组之间以及噬菌体与宿主细菌基因组之间。分析噬菌体的基因组序列将为研究噬菌体如何适应环境并感染宿主奠定良好的基础，甚至有助于促进针对病原菌的生物制剂的开发。 (c) 2012 Elsevier B.V. 保留所有权利。
As one of the pathogens of hospital-acquired infections, Acinetobacter baumannii poses great challenges to the public health. A. baumannii phage could be an effective way to fight multi-resistant A. baumannii. Here, we completed the whole genome sequencing of the complete genome of A. baumannii phage AB1, which consists of 45,159 bp and is a double-stranded DNA molecule with an average GC content of 37.7%. The genome encodes one tRNA gene and 85 open reading frames (ORFs) and the average size of the ORF is 531 bp in length. Among 85 ORFs, only 14 have been identified to share significant sequence similarities to the genes with known functions, while 28 are similar in sequence to the genes with function-unknown genes in the database and 43 ORFs are uniquely present in the phage AB1 genome. Fourteen function-assigned genes with putative functions include five phage structure proteins, an RNA polymerase, a big sub-unit and a small sub-unit of a terminase, a methylase and a recombinase and the proteins involved in DNA replication and so on. Multiple sequence alignment was conducted among those homologous proteins and the phylogenetic trees were reconstructed to analyze the evolutionary courses of these essential genes. From comparative genomics analysis, it turned out clearly that the frame of the phage genome mainly consisted of genes from Xanthomonas phages, Burkholderia ambifaria phages and Enterobacteria phages and while it comprises genes of its host A. baumannii only sporadically. The mosaic feature of the phage genome suggested that the horizontal gene transfer occurred among the phage genomes and between the phages and the host bacterium genomes. Analyzing the genome sequences of the phages should lay sound foundation to investigate how phages adapt to the environment and infect their hosts, and even help to facilitate the development of biological agents to deal with pathogenic bacteria. (c) 2012 Elsevier B.V. All rights reserved.