Jin Jing, Li Zhen-Jiang, Wang Shu-Wei, Wang Shan-Mei, Chen Song-Jian, Huang De-Hai, Zhang Gai, Li Ya-Hui, Wang Xiao-Ting, Wang Jin, Zhao Guo-Qiang
Department of Pathogen Biology and Immunology, Henan Medical College, Shuanghu Road #8, Zhengzhou 451191, P, R, China.
BMC Genomics. 2014 Sep 14;15(1):793. doi: 10.1186/1471-2164-15-793.
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.
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.
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.
噬菌体ZZ1能有效感染致病性鲍曼不动杆菌菌株，是迄今为止第五个完成全序列测定的类T4不动杆菌噬菌体。为了更好地了解ZZ1的遗传特征，对T4噬菌体进行了生物信息学和比较基因组分析。
ZZ1的双链DNA基因组大小为166,687 bp，在已测序的类T4不动杆菌噬菌体中GC含量最低（34.4%）。共预测到256个蛋白质编码基因和8个tRNA基因。预测的ZZ1蛋白中有43%与T4蛋白的氨基酸序列一致性高达73%，同源基因通常保持相同的顺序和转录方向。除了保守的结构和DNA复制模块外，T4和ZZ1通过获取和缺失大量不相关基因而发生了显著分化，尤其是在它们基因组的前半部分。此外，ZZ1与其他四个类T4不动杆菌噬菌体基因组（Acj9、Acj61、133和Ac42）共享一个组织良好且高度保守的核心基因组，特别是在编码DNA复制和病毒粒子结构蛋白的区域。ZZ1蛋白中，分别有70%、64%、61%和56%与Acj9、Acj61、133和Ac42蛋白的氨基酸序列一致性高达86%、85%、81%和83%。ZZ1的tRNA数量和类型与其他4种不动杆菌噬菌体不同，尽管ZZ1编码的一些tRNA与这些噬菌体的tRNA具有高度的序列相似性。超过一半的ZZ1编码tRNA（8个中的5个）与ZZ1蛋白的最佳密码子使用相关。然而，其他4种不动杆菌噬菌体中均不存在这种相关性。
这些噬菌体的比较基因组分析为不动杆菌噬菌体的进化和多样性提供了一些新见解，这可能有助于阐明这些噬菌体的进化起源和宿主特异性适应性。
