Pasternak Zohar, Ben Sasson Tom, Cohen Yossi, Segev Elad, Jurkevitch Edouard
Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
Department of Applied Mathematics, Holon Institute of Technology, Holon, Israel.
PLoS One. 2015 Nov 16;10(11):e0142933. doi: 10.1371/journal.pone.0142933. eCollection 2015.
Predatory bacteria seek and consume other live bacteria. Although belonging to taxonomically diverse groups, relatively few bacterial predator species are known. Consequently, it is difficult to assess the impact of predation within the bacterial realm. As no genetic signatures distinguishing them from non-predatory bacteria are known, genomic resources cannot be exploited to uncover novel predators. In order to identify genes specific to predatory bacteria, we developed a bioinformatic tool called DiffGene. This tool automatically identifies marker genes that are specific to phenotypic or taxonomic groups, by mapping the complete gene content of all available fully-sequenced genomes for the presence/absence of each gene in each genome. A putative 'predator region' of ~60 amino acids in the tryptophan 2,3-dioxygenase (TDO) protein was found to probably be a predator-specific marker. This region is found in all known obligate predator and a few facultative predator genomes, and is absent from most facultative predators and all non-predatory bacteria. We designed PCR primers that uniquely amplify a ~180bp-long sequence within the predators' TDO gene, and validated them in monocultures as well as in metagenetic analysis of environmental wastewater samples. This marker, in addition to its usage in predator identification and phylogenetics, may finally permit reliable enumeration and cataloguing of predatory bacteria from environmental samples, as well as uncovering novel predators.
掠食性细菌会寻找并消耗其他活细菌。尽管它们属于分类学上不同的群体，但已知的细菌捕食者物种相对较少。因此，很难评估捕食行为在细菌领域内的影响。由于目前还没有已知的将它们与非掠食性细菌区分开来的基因特征，所以无法利用基因组资源来发现新的捕食者。为了识别掠食性细菌特有的基因，我们开发了一种名为DiffGene的生物信息学工具。该工具通过绘制所有可用的全序列基因组的完整基因内容，以确定每个基因组中每个基因的存在/缺失情况，从而自动识别特定于表型或分类群体的标记基因。在色氨酸2,3-双加氧酶（TDO）蛋白中发现了一个约60个氨基酸的假定“捕食者区域”，它可能是捕食者特有的标记。这个区域存在于所有已知的专性捕食者和一些兼性捕食者的基因组中，而在大多数兼性捕食者和所有非掠食性细菌中则不存在。我们设计了PCR引物，可特异性扩增捕食者TDO基因内一段约180bp长的序列，并在单培养物以及环境废水样本的宏基因组分析中对其进行了验证。这个标记除了可用于捕食者鉴定和系统发育研究外，最终可能还能实现对环境样本中掠食性细菌的可靠计数和编目，以及发现新的捕食者。
