Laanto Elina, Ravantti Janne J, Sundberg Lotta-Riina
Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland.
Microorganisms. 2020 Dec 2;8(12):1919. doi: 10.3390/microorganisms8121919.
The role of prophages in the evolution, diversification, or virulence of the fish pathogen has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between strains and the fF4 phage, and another putative prophage in the strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese strains. Second, CRISPR analysis revealed four strains that contain unique spacers targeting different regions of the putative prophage p49512 in the strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the prophages and different host strains.
到目前为止，原噬菌体在鱼类病原体的进化、多样化或毒力方面的作用尚未得到研究。在此，我们描述了一种来自模式菌株ATCC 23463的功能性自发诱导原噬菌体fF4，常用的原噬菌体搜索方法无法检测到它。我们表明，这种原噬菌体类型具有全球分布，存在于从芬兰、泰国、日本和北美分离的菌株中。fF4的病毒粒子是具有收缩尾的肌尾噬菌体，仅感染源自芬兰北部的细菌菌株。fF4通过相似的基因组组织和几个基因直系同源物类似于转座噬菌体。额外的生物信息学分析揭示了拟杆菌门中的几个物种，它们宿主类似类型的假定原噬菌体，包括重要的动物和人类病原体细菌。此外，对成簇规律间隔短回文重复序列（CRISPR）间隔序列的调查表明，菌株与fF4噬菌体以及菌株ATCC 49512中另一种假定原噬菌体p49512之间存在共同的进化历史。首先，fF4溶原菌ATCC 23463的两个CRISPR位点（II - C型和VI - B型）的CRISPR间隔序列内容显示，VI - B位点存在一个与噬菌体末端酶蛋白匹配的间隔序列。该间隔序列也存在于两个中国菌株中。其次，CRISPR分析揭示了四个菌株，尽管不同菌株的地理距离或基因组变种不同，但它们含有靶向菌株ATCC 49512中假定原噬菌体p49512不同区域的独特间隔序列。这表明原噬菌体和不同宿主菌株有共同的祖先。
