Dehalobacterium formicoaceticum
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ABSTRACT:
PROVIDER: PRJNA1105196 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dehalobacterium formicoaceticum Genome sequencing and assembly
| PRJNA390963 | ENA
Project description:Dehalobacterium formicoaceticum overview
| PRJNA549991 | ENA
Project description:Dehalobacterium formicoaceticum isolate:X Genome sequencing
| PRJNA1091430 | ENA
Project description:Dehalobacterium formicoaceticum strain:strain DMC Genome sequencing
| PRJNA391200 | ENA
Project description:Dehalobacterium formicoaceticum strain:J2 | isolate:J2 Genome sequencing
| PRJNA1418954 | ENA
Project description:Dehalobacterium formicoaceticum strain:J2 | isolate:J2 Genome sequencing
| PRJNA1455893 | ENA
Project description:Dehalobacterium formicoaceticum is recognised for its unusual ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic culture representative of its class, the Dehalobacteriia, however much diversity has been revealed in this lineage through recent culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation is a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as sole carbon sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes, and S-layers. The ability of D. formicoaceticum to grow on serine alone was subsequently confirmed experimentally and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We conclude that members of the Dehalobacteriia are low abundance fermentative scavengers in anoxic habitats.
2023-04-13 | PXD038410 | Pride
Project description:Dichloromethane (DCM, methylene chloride) is a toxic chemical with substantial ozone-depleting capacity that is released by anthropogenic activities and natural processes. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of three known anaerobic DCM-degrading bacteria, including the bacterial isolate, Dehalobacterium formicoaceticum strain DMC (Defo), revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising eight to ten genes with predicted 79.6-99.7% amino acid identity. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system. To support these observations at the functional level, global proteome analysis of Defo cultures growing with DCM as the sole energy source was performed.
Briefly, axenic cultures (n = 3 biological replicates) of Defo were grown in 100 mL of anoxic mineral basal salt medium with 0.2 mM sodium sulfide, 0.2 mM L-cysteine and 30 mM bicarbonate (pH 7.3) under a headspace of N2/CO2 (80:20, vol/vol) with 156 umol (10 uL) of DCM. Cultures were initiated with a 5% (vol/vol) inoculum, incubated at 30C in the dark without agitation, and provided one additional feeding of DCM once the initial amendment was consumed. Biomass for proteomic analyses was collected after 2 weeks of incubation when approximately 95% of the second DCM feedings were consumed. After protein extraction and digestion, global proteomics analyses of 2 ug peptide solutions were performed with an Orbitrap Q Exactive Plus mass spectrometer (Thermo Fisher Scientific, Waltham, MA, US) equipped with a nano-electrospray source (ESI) interfaced with a Proxeon EASY-nLC 1200 system. Tandem mass spectrometry data (MS/MS) were searched against protein databases from the IMG Defo annotated genome (ID. 2757320304) to which common laboratory contaminant proteins were appended. For standard database searching, the peptide MS/MS data was searched using Proteome Discoverer v2.4. The MS/MS data were searched using the SEQUEST HT algorithm. Peptide spectrum match (PSM) confidence was evaluated with Percolator. PSM and peptides were considered identified at a q value of < 0.01.
The shotgun proteomics analysis reported here revealed high expression of proteins encoded on the mec gene cluster during Defo anaerobic growth with DCM.
2021-04-19 | MSV000087235 | MassIVE
Project description: Not available
| S-EPMC5597755 | biostudies-literature