title: Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity.
abstract: Anaerobic reductive dehalogenation by Dehalococcoides spp. is an ideal system for studying functional diversity of closely related strains of bacteria. In Dehalococcoides spp., reductive dehalogenases (RDases) are key respiratory enzymes involved in the anaerobic detoxification of halogenated compounds at contaminated sites globally. Although housekeeping genes sequenced from Dehalococcoides spp. are >85% identical at the amino acid level, different strains are capable of dehalogenating diverse ranges of compounds, depending largely on the suite of RDase genes that each strain harbors and expresses. We identified RDase proteins that corresponded to known functions in four characterized cultures and predicted functions in an uncharacterized Dehalococcoides-containing mixed culture. Homologues within RDase subclusters containing PceA, TceA, and VcrA were among the most frequently identified proteins. Several additional proteins, including a formate dehydrogenase-like protein (Fdh), had high coverage in all strains and under all growth conditions.
authors.affiliation: Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA. rmorris@lifesci.ucsb.edu
authors.forename: R M
authors.initials: RM
authors.lastname: Morris
authors.forename: J M
authors.initials: JM
authors.lastname: Fung
authors.forename: B G
authors.initials: BG
authors.lastname: Rahm
authors.forename: S
authors.initials: S
authors.lastname: Zhang
authors.forename: D L
authors.initials: DL
authors.lastname: Freedman
authors.forename: S H
authors.initials: SH
authors.lastname: Zinder
authors.forename: R E
authors.initials: RE
authors.lastname: Richardson
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism; D041862:Chloroflexi / Q000145:classification* / Q000201:enzymology* / Q000254:growth & development; D002853:Chromatography, Liquid; D003470:Culture Media; D005560:Formate Dehydrogenases / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000737:chemistry / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D010802:Phylogeny; D040901:Proteomics; D013045:Species Specificity; D013329:Structure-Activity Relationship; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D003470:Culture Media; D010455:Peptides; D010088:Oxidoreductases; D005560:Formate Dehydrogenases