title: Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria.
abstract: This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation.
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany.
authors.forename: Dragana
authors.initials: D
authors.lastname: Bozinovski
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Taubert
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, 04318 Leipzig, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Kleinsteuber
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
authors.forename: Hans-Hermann
authors.initials: HH
authors.lastname: Richnow
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; UFZ-Helmholtz Centre for Environmental Research, Department of Metabolomics, 04318 Leipzig, Germany; Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Vogt
authors.affiliation: UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; University of Hohenheim, Institute of Animal Nutrition, 70599 Stuttgart, Germany. Electronic address: jseifert@uni-hohenheim.de.
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
mesh_terms: D002247:Carbon Isotopes / Q000378:metabolism; D002853:Chromatography, Liquid; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D007553:Isotope Labeling; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D054892:Metagenome; D059013:Microbial Consortia; D008969:Molecular Sequence Data; D020560:Proteobacteria / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020543:Proteome; D017422:Sequence Analysis, DNA; D053719:Tandem Mass Spectrometry; D014992:Xylenes / Q000378:metabolism*
chemical_list: D002247:Carbon Isotopes; D004269:DNA, Bacterial; D020543:Proteome; D014992:Xylenes; C031285:3-xylene
keywords: Anaerobic m-xylene degradation; Mass spectrometry; Metaproteomics; Protein-SIP