State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
Appl Environ Microbiol. 2010 Jan;76(2):589-95. doi: 10.1128/AEM.01450-09. Epub 2009 Nov 30.
Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this "hidden" prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.
噬菌体普遍存在于许多细菌基因组中。区分有潜在活性的噬菌体和无活性的序列可能具有挑战性，因为一些噬菌体是曾经功能正常的噬菌体的残余物，这些噬菌体由于突变而失去了活性。在某些情况下，由于缺乏可识别的噬菌体基因座，可能会错过一个假定的噬菌体。最近对海洋玫瑰杆菌 Roseovarius nubinhibens ISM（以下简称 ISM）的基因组进行了测序，并根据常规生物信息学分析报告称该基因组中没有完整的噬菌体。然而，对该生物体进行的噬菌体诱导实验得出了不同的结论。在实验室中，用丝裂霉素 C 诱导 ISM 培养物后，病毒样颗粒的数量增加了超过 3 个数量级。在仔细检查 ISM 基因组序列后，鉴定出一个假定的噬菌体（ISM-pro1）。尽管这个噬菌体只含有最小的噬菌体样基因，但我们证明了这个“隐藏”的噬菌体是可诱导的。基因组分析和重新注释表明，ISM-pro1 的大多数开放阅读框（ORF）与红杆菌目细菌基因具有最高的序列相似性，一些 ORF 与其他已知噬菌体或原噬菌体的基因只有较远的关系。比较基因组分析表明，其他红杆菌目基因组中也存在 ISM-pro1 样噬菌体或噬菌体残余物。此外，这种以前未被识别的噬菌体对 ISM 的裂解似乎增加了基因转移剂（GTA）的产生。我们的研究表明，需要结合计算机基因组分析和实验实验室工作来充分了解给定细菌的溶原特性。
