Dehalococcoides Biology and Genomics
Dechlorinating Chloroflexi are uniquely adapted to use organochlorine compounds as catabolic electron acceptors and hydrogen as electron donor. All dechlorinating Chloroflexi are strictly anaerobic, small (0.5 mm diameter) microbes with a genome of ~1.5 Mbp in size, which is among the smallest of any free-living microbe. Physiological experiments and comparative genome analysis revealed that the known Dehalococcoides strains are highly adapted to this dehalogenating process, and do not contain any catabolic alternative to organohalogen respiration. Reflective of the specialized organohalogen-respiring lifestyle are high numbers (up to 36 in strain VS) of putative reductive dehalogenase (rdh) genes on the genomes of dechlorinating Chloroflexi. We conducted a comprehensive comparative genomic analysis of our VS isolate and other Dhcs. The sequenced Dhc genomes share a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the replication origin (Ori) of chromosome, which contain the majority of the rdh genes. Despite highly similar 16S rRNA genes, the sequenced genomes share only three core rdh genes, contrasted with the high rdh gene numbers per genome. rdh genes show signatures of horizontal transfer, suggesting that niche adaptation to respire specific organohalogen compounds via gene acquisition is a fundamental ecological strategy in dechlorinating Chloroflexi. This adaptation has been exacted through multiple recombination mechanisms that are mainly confined within HPRs in an otherwise remarkably syntenic, streamlined genome. Our recent analysis showed that this localized diversity in rdh genes is primarily due to an ssrA-dependent site-specific mechanism for acquisition and integration of non-Dehalococcoides rdh genes, rather than to gene duplication. Moreover, we have designed cloning strategies by making use of these unique genome features surrounding rdh genes, to retrieve these regions and analyze Dehalococcoides biodiversity in environmental samples without the need for cultivation. We are exploring this tool for characterizing rdh gene diversity in pristine and engineered environments to develop a fundamental understanding of the evolution of rdh genes in natural environments and under varying selective pressures.
Most recent publications:
Site Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides.
McMurdie PJ, Hug LA, Edwards EA, Holmes S, and Spormann AM.
BMC Genomics 2011, 12:287
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
Paul J McMurdie, Sebastian F Behrens, Jochen A Müller, Jonathan Göke, Kirsti M Ritalahti, Ryan Wagner, Eugene Goltsman, Alla Lapidus, Susan Holmes, Frank E Löffler, Alfred M Spormann.
PLoS Genet (2009) vol. 5 (11) pp. e1000714