title: A New Comparative-Genomics Approach for Defining Phenotype-Specific Indicators Reveals Specific Genetic Markers in Predatory Bacteria.
abstract: 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.
authors.affiliation: Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Zohar
authors.initials: Z
authors.lastname: Pasternak
authors.affiliation: Department of Applied Mathematics, Holon Institute of Technology, Holon, Israel.
authors.forename: Tom
authors.initials: T
authors.lastname: Ben Sasson
authors.affiliation: Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Yossi
authors.initials: Y
authors.lastname: Cohen
authors.affiliation: Department of Applied Mathematics, Holon Institute of Technology, Holon, Israel.
authors.forename: Elad
authors.initials: E
authors.lastname: Segev
authors.affiliation: Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Edouard
authors.initials: E
authors.lastname: Jurkevitch
mesh_terms: D001419:Bacteria / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D001483:Base Sequence; D005798:Genes, Bacterial; D005819:Genetic Markers; D023281:Genomics / Q000379:methods*; D016013:Likelihood Functions; D058885:Multilocus Sequence Typing; D010641:Phenotype; D010802:Phylogeny; D015203:Reproducibility of Results; D014366:Tryptophan Oxygenase
chemical_list: D005819:Genetic Markers; D014366:Tryptophan Oxygenase