1
|
Bozinovski D, Taubert M, Kleinsteuber S, Richnow HH, von Bergen M, Vogt C, Seifert J. 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. Syst Appl Microbiol 2014; 37:488-501. [PMID: 25156802 DOI: 10.1016/j.syapm.2014.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/02/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022]
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.
Collapse
Affiliation(s)
- Dragana Bozinovski
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany
| | - Martin Taubert
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Sabine Kleinsteuber
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, 04318 Leipzig, Germany
| | - Hans-Hermann Richnow
- UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Martin von Bergen
- 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
| | - Carsten Vogt
- UFZ-Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Jana Seifert
- UFZ-Helmholtz Centre for Environmental Research, Department of Proteomics, 04318 Leipzig, Germany; University of Hohenheim, Institute of Animal Nutrition, 70599 Stuttgart, Germany.
| |
Collapse
|