Genome organisation of the Acinetobacter lytic phage ZZ1 and comparison with other T4-like Acinetobacter phages

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• 作者：Jing Jin (1) (2)
  Zhen-Jiang Li (1)
  Shu-Wei Wang (1)
  Shan-Mei Wang (3)
  Song-Jian Chen (1)
  De-Hai Huang (1)
  Gai Zhang (1)
  Ya-Hui Li (1)
  Xiao-Ting Wang (1)
  Jin Wang (1)
  Guo-Qiang Zhao (2)
  
  1. Department of Pathogen Biology and Immunology ; Henan Medical College ; Shuanghu Road #8 ; Zhengzhou ; 451191 ; P. R. China
  2. Department of Pathogen Biology ; Basic Medical College of Zhengzhou University ; Kexue Road #100 ; Zhengzhou ; 450001 ; P. R. China
  3. Clinical Laboratory ; Henan Provincial People鈥檚 Hospital ; Zhengzhou ; 450003 ; P. R. China
  
• 关键词：Phage genome annotation ; Phage genome organisation ; Comparative genomic analyses ; T4 ; like phage
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：3,615 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Phage ZZ1, which efficiently infects pathogenic Acinetobacter baumannii strains, is the fifth completely sequenced T4-like Acinetobacter phage to date. To gain a better understanding of the genetic characteristics of ZZ1, bioinformatics and comparative genomic analyses of the T4 phages were performed. Results The 166,687-bp double-stranded DNA genome of ZZ1 has the lowest GC content (34.4%) of the sequenced T4-like Acinetobacter phages. A total of 256 protein-coding genes and 8 tRNA genes were predicted. Forty-three percent of the predicted ZZ1 proteins share up to 73% amino acid identity with T4 proteins, and the homologous genes generally retained the same order and transcriptional direction. Beyond the conserved structural and DNA replication modules, T4 and ZZ1 have diverged substantially by the acquisition and deletion of large blocks of unrelated genes, especially in the first halves of their genomes. In addition, ZZ1 and the four other T4-like Acinetobacter phage genomes (Acj9, Acj61, 133, and Ac42) share a well-organised and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. Of the ZZ1 proteins, 70, 64, 61, and 56% share up to 86, 85, 81, and 83% amino acid identity with Acj9, Acj61, 133, and Ac42 proteins, respectively. ZZ1 has a different number and types of tRNAs than the other 4 Acinetobacter phages, although some of the ZZ1-encoded tRNAs share high sequence similarity with the tRNAs from these phages. Over half of ZZ1-encoded tRNAs (5 out of 8) are related to optimal codon usage for ZZ1 proteins. However, this correlation was not present in any of the other 4 Acinetobacter phages. Conclusions The comparative genomic analysis of these phages provided some new insights into the evolution and diversity of Acinetobacter phages, which might elucidate the evolutionary origin and host-specific adaptation of these phages.