TreeBASE Search-Trees for study 18113

@ARTICLE{TreeBASE2Ref24972, author = {Fernando Hayashi Sant'Anna and Alexander V Lebedinsky and Tatyana G Sokolova and Frank T Robb and Juan M Gonzalez}, title = {Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity}, year = {2015}, keywords = {Caldanaerobacter subterraneus; genome; horizontal gene transfer; hydrogenase; carbon monoxide dehydrogenase; glycosidase; protease, esterase; phylogeny; thermophile}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, abstract = {Background The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms. Results The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from fourteen families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around one hundred proteases from fifty subfamilies, as well about ten different esterases. Conclusions Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.} }

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Trees for Study 18113

Citation title: "Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity".

Study name: "Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity".

This study is part of submission 18113 (Status: Published).

Trees

ID	Tree Label	Tree Title	Tree Type	Tree Kind	Taxa
Tr89916	HypE ML	Tr89916	Single	Species Tree	View Taxa
Tr89857	MbxH ML	Tr89857	Single	Gene Tree	View Taxa
Tr89892	EchE ML	Tr89892	Single	Gene Tree	View Taxa
Tr89840	HyfB ML	Tr89840	Single	Species Tree	View Taxa
Tr89899	HypB ML	Tr89899	Single	Gene Tree	View Taxa
Tr89855	MbxF ML	Tr89855	Single	Species Tree	View Taxa
Tr89844	HyfF ML	Tr89844	Single	Species Tree	View Taxa
Tr89897	HydD ML	Tr89897	Single	Gene Tree	View Taxa
Tr89918	HypF ML	Tr89918	Single	Gene Tree	View Taxa
Tr89827	CooS tree	Tr89827	Single	Gene Tree	View Taxa
Tr89885	11495	Tr89885	Single	Species Tree	View Taxa
Tr89847	HyfI ML	Tr89847	Single	Species Tree	View Taxa
Tr89880	MbxJ ML	Tr89880	Single	Species Tree	View Taxa
Tr89896	HydC ML	Tr89896	Single	Gene Tree	View Taxa
Tr89900	HypC ML	Tr89900	Single	Gene Tree	View Taxa
Tr89895	HydB ML	Tr89895	Single	Gene Tree	View Taxa
Tr89887	HyfE ML	Tr89843	Single	Gene Tree	View Taxa
Tr89881	MbxK ML	Tr89881	Single	Species Tree	View Taxa
Tr89882	HyfI ML	Tr89847	Single	Gene Tree	View Taxa
Tr89891	EchD ML	Tr89891	Single	Gene Tree	View Taxa
Tr89862	MbxH' ML	Tr89862	Single	Species Tree	View Taxa
Tr89841	HyfC ML	Tr89841	Single	Species Tree	View Taxa
Tr89886	11565 ML	Tr89886	Single	Species Tree	View Taxa
Tr89890	EchC ML	Tr89890	Single	Gene Tree	View Taxa
Tr89854	MbxD ML	Tr89854	Single	Species Tree	View Taxa
Tr89883	MbxM ML	Tr89883	Single	Species Tree	View Taxa
Tr89837	CooF	Tr89837	Single	Gene Tree	View Taxa
Tr89845	HyfG ML	Tr89845	Single	Species Tree	View Taxa
Tr89846	HyfH ML	Tr89846	Single	Species Tree	View Taxa
Tr89889	EchB ML	Tr89889	Single	Gene Tree	View Taxa
Tr89842	HyfD ML	Tr89842	Single	Species Tree	View Taxa
Tr89838	HycH ML	Tr89838	Single	Species Tree	View Taxa
Tr89915	HypD ML	Tr89915	Single	Gene Tree	View Taxa
Tr89826	16S_ML	Tr89826	Single	Species Tree	View Taxa
Tr89839	HycI ML	Tr89839	Single	Gene Tree	View Taxa
Tr89856	MbxG ML	Tr89856	Single	Species Tree	View Taxa
Tr89898	HypA ML	Tr89898	Single	Gene Tree	View Taxa
Tr89851	MbxG ML	Tr89856	Single	Gene Tree	View Taxa
Tr89828	CooC tree	Tr89828	Single	Species Tree	View Taxa
Tr89852	MbxB ML	Tr89852	Single	Species Tree	View Taxa
Tr89888	EchA ML	Tr89888	Single	Gene Tree	View Taxa
Tr89884	MbxN ML	Tr89884	Single	Species Tree	View Taxa
Tr89894	HydA ML	Tr89894	Single	Gene Tree	View Taxa
Tr89843	HyfE ML	Tr89843	Single	Species Tree	View Taxa
Tr89893	EchF ML	Tr89893	Single	Gene Tree	View Taxa
Tr89853	MbxC ML	Tr89853	Single	Species Tree	View Taxa