title: Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor.
abstract: Dehalococcoides mccartyi strain CBDB1 is an obligate organohalide-respiring anaerobic bacterium that is able to transform a wide range of highly relevant halogenated organic contaminants and has been detected in natural and engineered environments. In order to understand the molecular principles, we generated a protein profile of CBDB1 cultivated in a synthetic anaerobic medium with hexachlorobenzene as the sole electron acceptor. The proteome characterization through two different proteomic techniques resulted in 8491 distinct peptides corresponding to 1023 proteins that covered 70% of the annotated 1458 protein-coding sequences. From the 32 annotated reductive dehalogenases homologous genes (rdhA) we were able to detect 16 RdhA proteins. High-quality MS spectra were further used to build a spectra library to provide a platform for precise and fast proteomic searches. In addition, the derived proteome data set was used to apply a proteogenomic approach that led to a refinement of genome annotation of CBDB1. This was mostly due to protein prolongation (13 cases) and detection of translated sequences without an obvious link to existing annotations (5 cases). These data go beyond the current knowledge of the bacterial proteome and provide an expanded platform for a better understanding of the functional cellular.
  
  
  CONCLUSIONS
  Anaerobic reductive dehalogenation of chlorinated organic molecules is a key process for the recycling of halogenated organic substances in natural habitats and highly relevant for groundwater bioremediation. The ability to couple reductive dehalogenation of halogenated compounds to ATP-generation via a respiratory chain is one remarkable capability prevalent in the model organism D. mccartyi strain CBDB1. Therefore, a reference proteome map was generated by comprehensive LC-MS analysis and converted into a SpectraST library to provide a platform for precise and fast shotgun proteomic searches. A proteogenomics approach led to a refinement of gene annotation of CBDB1 and will extend the current knowledge of the bacterial proteome. The approach provides an expanded platform for a better understanding of the functional cellular metabolism and thereby constitutes a tool for comparative studies of protein expression as well as further research on organohalide respiration.
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany. Electronic address: christian.schiffmann@ufz.de.
authors.forename: Christian L
authors.initials: CL
authors.lastname: Schiffmann
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany. Electronic address: nico.jehmlich@ufz.de.
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany. Electronic address: wolfgang.otto@ufz.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Otto
authors.affiliation: Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark. Electronic address: rh@bio.aau.dk.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Hansen
authors.affiliation: Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark. Electronic address: phn@bio.aau.dk.
authors.forename: Per Halkjær
authors.initials: PH
authors.lastname: Nielsen
authors.affiliation: Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany. Electronic address: lorenz.adrian@ufz.de.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Adrian
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; Institute of Animal Nutrition, Hohenheim University, 70593 Stuttgart, Germany. Electronic address: seifert.jana@uni-hohenheim.de.
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark; Department of Metabolomics, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany. Electronic address: martin.vonbergen@ufz.de.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D041862:Chloroflexi / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D001556:Hexachlorocyclohexane / Q000494:pharmacology*; D007306:Insecticides / Q000494:pharmacology*; D020543:Proteome / Q000096:biosynthesis / Q000235:genetics; D040901:Proteomics
chemical_list: D001426:Bacterial Proteins; D007306:Insecticides; D020543:Proteome; D001556:Hexachlorocyclohexane
keywords: Dehalococcoides mccartyi strain CBDB1; Proteogenomics; Proteomic reference profile; Shotgun proteomics