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. 2024 Sep 27;25(19):10421. doi: 10.3390/ijms251910421.
The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as , were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to 88.98 kb, were identified in the genomes of 27 strains. The amount of genetic information foreign to accumulated in all identified PRSs was 6.30 Mb. However, more than 53% of this information was contained in prophages (Phs) and genomic islands (GIs) integrated into genes encoding tRNAs (tRNA genes) located on the chromosomes of the rhizobial strains studied. It was found that phiLM21-like Phs were predominantly abundant in the genomes of strains of distant geographical origin, whereas RR1-A- and 16-3-like Phs were much less common. In addition, GIs predominantly contained fragments of phages infecting bacteria of distant taxa, while rhizobiophage-like sequences were unique. A site-specific integration analysis revealed that not all tRNA genes in are integration sites, but among those in which integration occurred, there were "hot spots" of integration into which either Phs or GIs were predominantly inserted. For the first time, it is shown that at these integration "hot spots", not only is the homology of and strictly preserved, but integrases in PRSs similar to those of phages infecting the Proteobacteria genera or are also present. The data presented greatly expand the understanding of the fate of phage-related sequences in host bacterial genomes and also raise new questions about the role of phages in bacterial-phage coevolution.
本研究评估了噬菌体相关序列 (PRSs) 的多样性及其在非致病性、具有农业价值、固氮根瘤细菌（如 ）基因组中的特异性整合。在 27 株菌的基因组中鉴定出了 314 个 PRSs，大小从 3.24 kb 到 88.98 kb 不等。在所有鉴定的 PRSs 中，外源遗传信息量为 6.30 Mb。然而，超过 53%的信息包含在整合到位于根瘤菌菌株染色体上的 tRNA 基因（tRNA 基因）的噬菌体 (Phs) 和基因组岛 (GI) 中。研究发现，phiLM21 样 Phs 在来自遥远地理起源的 菌株的基因组中占主导地位，而 RR1-A-和 16-3 样 Phs 则较少见。此外，GI 主要包含感染远缘细菌的噬菌体片段，而根瘤噬菌体样序列是独特的。特异性整合分析表明，并非所有的 tRNA 基因都是 整合的靶点，但在发生整合的基因中，存在整合的“热点”，主要插入 Phs 或 GI。首次表明，在这些整合“热点”处，不仅 与 的同源性严格保守，而且 PRSs 中的整合酶也类似于感染变形菌属 或 属噬菌体的整合酶。所提供的数据极大地扩展了对噬菌体相关序列在宿主细菌基因组中命运的理解，也提出了关于噬菌体在细菌-噬菌体共同进化中的作用的新问题。
