Decewicz Przemyslaw, Radlinska Monika, Dziewit Lukasz
Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
Viruses. 2017 Jun 26;9(7):161. doi: 10.3390/v9070161.
The genus mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes. In addition to the previously identified temperate phage, ΦLM21, and the phage-plasmid, pLM21S1, the analysis revealed the presence of three prophage regions. Moreover, four novel phage-encoded DNA methyltransferase (MTase) genes were identified and the enzymes were characterized. It was shown that two of the identified viral MTases methylated the same target sequence (GANTC) as cell cycle-regulated methyltransferase (CcrM) of the bacterial host strain, LM21. This discovery was recognized as an example of the evolutionary convergence between enzymes of sinorhizobial viruses and their host, which may play an important role in virus cycle. In the last part of the study, thorough comparative analyses of 31 sinorhizobial (pro)phages (including active sinorhizobial phages and novel putative prophages retrieved and manually re-annotated from spp. genomes) were performed. The networking analysis revealed the presence of highly conserved proteins (e.g., holins and endolysins) and a high diversity of viral integrases. The analysis also revealed a large number of viral DNA MTases, whose genes were frequently located within the predicted replication modules of analyzed prophages, which may suggest their important regulatory role. Summarizing, complex analysis of the phage protein similarity network enabled a new insight into overall sinorhizobial virome diversity.
该属主要包含固氮细菌，这些细菌在豆科植物的根或茎上形成根瘤，并将大气中的氮转化为氨，从而提高植物的生产力。尽管这些具有重要生物技术意义的细菌在各种土壤环境中普遍存在，但人们对其噬菌体却知之甚少。在本研究中，对从波兰一个重金属污染的铜矿中分离出的sp. LM21的基因组进行了研究，以检测原噬菌体和DNA甲基转移酶编码基因的存在。除了先前鉴定出的温和噬菌体ΦLM21和噬菌体质粒pLM21S1外，分析还揭示了三个原噬菌体区域的存在。此外，还鉴定出四个新的噬菌体编码DNA甲基转移酶（MTase）基因，并对这些酶进行了表征。结果表明，所鉴定的两种病毒MTase与细菌宿主菌株LM21的细胞周期调节甲基转移酶（CcrM）甲基化相同的靶序列（GANTC）。这一发现被认为是中华根瘤菌病毒及其宿主酶之间进化趋同的一个例子，这可能在病毒周期中发挥重要作用。在研究的最后部分，对31种中华根瘤菌（原）噬菌体（包括活性中华根瘤菌噬菌体以及从spp.基因组中检索并手动重新注释的新推定原噬菌体）进行了全面的比较分析。网络分析揭示了高度保守的蛋白质（如孔蛋白和内溶素）的存在以及病毒整合酶的高度多样性。分析还揭示了大量的病毒DNA MTase，其基因经常位于所分析原噬菌体的预测复制模块内，这可能表明它们具有重要的调节作用。总之，对噬菌体蛋白质相似性网络的复杂分析为深入了解中华根瘤菌病毒群落的整体多样性提供了新的视角。
