title: The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics.
abstract: Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter, which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood-Ljungdahl (WL) pathway for CO2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA, has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases.
authors.affiliation: Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, 1015 Lausanne, Switzerland.
authors.forename: Aamani
authors.initials: A
authors.lastname: Rupakula
authors.forename: Thomas
authors.initials: T
authors.lastname: Kruse
authors.forename: Sjef
authors.initials: S
authors.lastname: Boeren
authors.forename: Christof
authors.initials: C
authors.lastname: Holliger
authors.forename: Hauke
authors.initials: H
authors.lastname: Smidt
authors.forename: Julien
authors.initials: J
authors.lastname: Maillard
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D003001:Cloning, Molecular; D045728:Corrinoids / Q000096:biosynthesis / Q000235:genetics; D004579:Electron Transport; D004734:Energy Metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D006859:Hydrogen / Q000378:metabolism; D006864:Hydrogenase / Q000235:genetics / Q000378:metabolism; D006865:Hydrogenation; D005810:Multigene Family; D010459:Peptococcaceae / Q000201:enzymology / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D020543:Proteome / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D045728:Corrinoids; D020543:Proteome; D006859:Hydrogen; D006864:Hydrogenase