Vladimirova Maria E, Roumiantseva Marina L, Saksaganskaia Alla S, Kozlova Alexandra P, Muntyan Victoria S, Gaponov Sergey P
Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia.
Novikov Labs, 420033 Kazan, Russia.
Int J Mol Sci. 2025 Sep 6;26(17):8704. doi: 10.3390/ijms26178704.
A comprehensive comparative analysis was conducted on the nucleotide and amino acid sequences of intact phiLM21-like prophages (phiLM21-LPhs), which currently represent the most prevalent prophages in -a symbiotic partner of plants. Remarkably, the nucleotide sequences of 25 phiLM21-LPhs, identified across 36 geographically dispersed strains, covered no more than 34% of the phiLM21 phage genome. All prophages were integrated into specific isoacceptor tRNA genes and carried a tyrosine-type integrase gene; however, this integration did not exhibit features of tRNA-dependent lysogeny. Only one-fifth of phiLM21-LPhs encoded the minimal set of regulators for lysogenic/lytic cycle transitions, while the remainder contained either uncharacterized regulatory elements or appeared to be undergoing genomic "anchoring" within the host bacterium. The phiLM21-LPhs harbored open reading frames (ORFs) of diverse origins (phage-derived, bacterial, and unknown), yet over half of these ORFs had undeterminable functions, representing genetic "dark matter". The observed diversification of intact phiLM21-like prophages likely stems from recombination events involving both virulent/temperate phages and phylogenetically remote bacterial taxa. The evolutionary and biological significance of the substantial genetic "dark matter" within these prophages in soil saprophytic bacteria remains an unresolved question.
对完整的类phiLM21前噬菌体（phiLM21-LPhs）的核苷酸和氨基酸序列进行了全面的比较分析，phiLM21-LPhs是植物共生伙伴中目前最普遍的前噬菌体。值得注意的是，在36个地理分布菌株中鉴定出的25个phiLM21-LPhs的核苷酸序列，覆盖的phiLM21噬菌体基因组不超过34%。所有前噬菌体都整合到特定的同功受体tRNA基因中，并携带一个酪氨酸型整合酶基因；然而，这种整合并未表现出tRNA依赖性溶原性的特征。只有五分之一的phiLM21-LPhs编码了溶原/裂解周期转换的最小调控因子集，而其余的则包含未表征的调控元件，或者似乎正在宿主细菌内进行基因组“锚定”。phiLM21-LPhs含有多种来源（噬菌体衍生、细菌和未知）的开放阅读框（ORF），但这些ORF中有一半以上功能无法确定，代表了遗传“暗物质”。观察到的完整类phiLM21前噬菌体的多样化可能源于涉及烈性/温和噬菌体和系统发育上遥远的细菌类群的重组事件。这些土壤腐生细菌前噬菌体中大量遗传“暗物质”的进化和生物学意义仍然是一个未解决的问题。
