title: Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans.
abstract: Desulfitobacterium dehalogenans is able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components, and shotgun proteomics to study elements of the organohalide respiratory electron transport chain. The genome of Desulfitobacterium dehalogenans JW/IU-DC1(T) consists of a single circular chromosome of 4,321,753 bp with a GC content of 44.97%. The genome contains 4,252 genes, including six rRNA operons and six predicted reductive dehalogenases. One of the reductive dehalogenases, CprA, is encoded by a well-characterized cprTKZEBACD gene cluster. Redox active components were identified in concentrated suspensions of cells grown on formate and Cl-OHPA or formate and fumarate, using electron paramagnetic resonance (EPR), visible spectroscopy, and high-performance liquid chromatography (HPLC) analysis of membrane extracts. In cell suspensions, these components were reduced upon addition of formate and oxidized after addition of Cl-OHPA, indicating involvement in organohalide respiration. Genome analysis revealed genes that likely encode the identified components of the electron transport chain from formate to fumarate or Cl-OHPA. Data presented here suggest that the first part of the electron transport chain from formate to fumarate or Cl-OHPA is shared. Electrons are channeled from an outward-facing formate dehydrogenase via menaquinones to a fumarate reductase located at the cytoplasmic face of the membrane. When Cl-OHPA is the terminal electron acceptor, electrons are transferred from menaquinones to outward-facing CprA, via an as-yet-unidentified membrane complex, and potentially an extracellular flavoprotein acting as an electron shuttle between the quinol dehydrogenase membrane complex and CprA.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Thomas
authors.identifier: http://orcid.org/0000-0002-7551-1505
authors.initials: T
authors.lastname: Kruse
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Bram A
authors.initials: BA
authors.lastname: van de Pas
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands Unité de Bioénergétique et Ingénierie des Protéines-UMR 7281, CNRS-Aix-Marseille Univ, Marseille, France.
authors.forename: Ariane
authors.initials: A
authors.lastname: Atteia
authors.affiliation: BCA/IMBW Section Microbiology, Free University, Amsterdam, The Netherlands.
authors.forename: Klaas
authors.initials: K
authors.lastname: Krab
authors.affiliation: Kluyver Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
authors.forename: Wilfred R
authors.initials: WR
authors.lastname: Hagen
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.affiliation: Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Chain
authors.affiliation: Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
authors.forename: Sjef
authors.initials: S
authors.lastname: Boeren
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Farai
authors.initials: F
authors.lastname: Maphosa
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Gosse
authors.initials: G
authors.lastname: Schraa
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Hauke
authors.initials: H
authors.lastname: Smidt
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands Fons.stams@wur.nl.
authors.forename: Alfons J M
authors.initials: AJ
authors.lastname: Stams
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D045858:Desulfitobacterium / Q000737:chemistry / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D004579:Electron Transport; D005561:Formates / Q000378:metabolism; D005650:Fumarates / Q000378:metabolism; D016680:Genome, Bacterial; D023281:Genomics; D006219:Halogens / Q000378:metabolism*; D008969:Molecular Sequence Data; D009876:Operon; D040901:Proteomics
chemical_list: D001426:Bacterial Proteins; D005561:Formates; D005650:Fumarates; D006219:Halogens; C030544:formic acid