弗氏柠檬酸杆菌噬菌体NM4.3生物学特性及全基因组分析

Isolation and whole genome analysis of a Citrobacter freundii phage NM4.3

  • 摘要: 弗氏柠檬酸杆菌 (Citrobacter freundii) 是近年来牛蛙 (Rana catesbeiana) 养殖中新出现的高致病性病原菌,其多重耐药性增加了防控难度。从牛蛙养殖尾水中分离出1株裂解弗氏柠檬酸杆菌的噬菌体NM4.3,通过全基因组测序、生物学特性和系统发育分析,评估其潜在应用价值。结果显示,NM4.3为圆环dsDNA噬菌体,基因组大小为174 351 bp ,GC含量为38.74%,编码310个开放阅读框 (ORF),包含病毒粒子结构、宿主裂解及DNA代谢相关功能基因,还额外编码13个tRNA。生物学特性结果表明,NM4.3潜伏期短 (10 min),裂解效率高 (爆发量76 PFU·细胞−1),在60 ℃和pH 3~12处理1 h后仍可维持一定活性。基于基因组的核酸序列和保守基因末端酶大亚基 (Ter-L) 的氨基酸序列分析,鉴定NM4.3属于StraboviridaeTevenvirinaeMoonvirus,与已知成员的平均核苷酸一致性 (ANI) 低于95%,定义为该属下的一个新种。基因组注释发现其长尾纤维蛋白存在变异,这可能是影响宿主特异性的因素。

     

    Abstract: Citrobacter freundii has been a highly pathogenic pathogen in the breeding of Rana catesbeiana in recent years. Its multi-drug resistance makes the prevention and control of disease difficult. Thus, by isolating a lytic phage NM4.3 specific to C. freundii from bullfrog culture tailwater, we conducted the comprehensive analyses of its whole genome, biological characteristics, and phylogenetic relationships in order to evaluate its potential therapeutic applications. The results indicate that NM4.3 was a circular dsDNA phage with a genome size of 174 351 bp and a GC content of 38.74%. It encoded 310 open reading frames (ORFs), including genes related to virion structure, host lysis, and DNA metabolism, as well as 13 tRNAs. The biological characteristics demonstrate that NM4.3 had a short incubation period (10 min) and a high lytic efficiency (Burst size of 76 PFU·cell−1). NM4.3 retained some activity after being treated at 60 °C and at pH levels ranging from 3 to 12 for 1 hour. Based on the nucleic acid and amino acid sequence analysis of the conserved terminase large subunit (Ter-L) of the genome, NM4.3 was classified as a member of the Straboviridae, Tevenvirinae, Moonvirus, with an average nucleotide identity (ANI) of less than 95% compared to known members, thus defining it as a new species within this family. Genome annotation reveals variations in its long tail fibrin, which may serve as a host-specific factor.

     

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