Dataset Information

Sphingomonas wittichii RW1 shotgun proteomics

ABSTRACT: Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichii RW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S. wittichii RW1 have been biochemically and genetically characterized, but its genome sequence has indicated the existence of a tremendous potential for aromatic compound transformation, with 56 ring-hydroxylating dioxygenase subunits, 34 extradiol dioxygenases, and 40 hydrolases. To further characterize this enzymatic arsenal, new methodological approaches should be employed. Here, a large shotgun proteomic survey has been performed on cells grown on dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin, and compared to growth on acetate. Changes in the proteome were monitored over time. Peak lists were generated with the Mascot Daemon software (version 2.3.2; Matrix Science, London, UK) using the extract_msn.exe data import filter (Thermo Fisher Scientific) from the Xcalibur FT package (version 2.0.7; Thermo Fisher Scientific). Data import filter options were set to 400 (minimum mass), 5000 (maximum mass), 0 (grouping tolerance), 0 (intermediate scans) and 1000 (threshold). The mgf files from technical triplicates were merged, and MS/MS spectra were assigned using the Mascot Daemon 2.3.2 (Matrix Science) and a database containing the nonredundant RefSeq protein entries for S. wittichii RW1 (NCBI Taxonomy ID: 392499), comprising 5345 protein sequences totalling 1 800 684 amino acids. The search was performed using the following criteria: tryptic peptides with a maximum of two miscleavages, mass tolerances of 5 ppm on the parent ion and 0.5 Da on the MS/MS, fixed modification for carbamidomethylated cysteine, and variable modification for methionine oxidation. Mascot results were parsed using the IRMa 1.28.0 software. Peptides were identified with a P-value threshold below 0.05. Proteins were considered validated when at least two distinct peptides were detected. Using a selection of 11 result files and the appropriate decoy database, the false discovery rate for protein identification was estimated to be 0.33% with these parameters.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Sphingomonas Wittichii

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean ARMENGAUD

PROVIDER: PXD000403 | Pride | 2013-10-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20121203_50ml_dibenzofuran_t72_0394-02.RAW	Raw
	20121203_50ml_dibenzofuran_t72_0394-03.RAW	Raw
	20121203_50ml_dibenzofuran_t72_0394.RAW	Raw
	20121210_50ml_dibenzofuran_t72_0235-02.RAW	Raw
	20121210_50ml_dibenzofuran_t72_0235-03.RAW	Raw

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Publications

Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1.

Hartmann Erica M EM Armengaud Jean J

Environmental microbiology 20130930 1

Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichii RW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S. wittichii RW1 have been biochemically and genetically characterized, but its genome sequence indicated the existence of a tremendous potential for aromatic compound transformation, with 5 ...[more]

PMID: 24118890

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