title: Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome.
abstract: 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.
authors.affiliation: Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China.
authors.forename: Peizhen
authors.initials: P
authors.lastname: Li
authors.forename: Biaobang
authors.initials: B
authors.lastname: Chen
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Song
authors.forename: Yulong
authors.initials: Y
authors.lastname: Song
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Yang
authors.forename: Ping
authors.initials: P
authors.lastname: Ma
authors.forename: Huifeng
authors.initials: H
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Ying
authors.forename: Ping
authors.initials: P
authors.lastname: Ren
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.forename: Guohui
authors.initials: G
authors.lastname: Gao
authors.forename: Shouguang
authors.initials: S
authors.lastname: Jin
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Bao
authors.forename: Hongjiang
authors.initials: H
authors.lastname: Yang
mesh_terms: D040981:Acinetobacter baumannii / Q000472:pathogenicity / Q000821:virology*; D001435:Bacteriophages / Q000235:genetics* / Q000502:physiology; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics; D019295:Computational Biology; D015254:DNA Modification Methylases / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D045522:Recombinases / Q000235:genetics; D017376:Viral Tail Proteins / Q000235:genetics; D019065:Virus Assembly / Q000235:genetics; D014779:Virus Replication / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D004279:DNA, Viral; D012367:RNA, Viral; D045522:Recombinases; D017376:Viral Tail Proteins; D012343:RNA, Transfer; D015254:DNA Modification Methylases; D012321:DNA-Directed RNA Polymerases