Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression
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ABSTRACT:
PROVIDER: PRJNA475689 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7293890.fastq.gz | Fastqsanger.gz | |||
| SRR7293900.fastq.gz | Fastqsanger.gz | |||
| SRR7293891.fastq.gz | Fastqsanger.gz | |||
| SRR7293901.fastq.gz | Fastqsanger.gz | |||
| SRR7293882.fastq.gz | Fastqsanger.gz |
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Project description:Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemcially-related pollutants categorically known as dioxins. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. Strain RW1 grew on and completely degraded dioxin intercalated in smectite clay. To characterize the effects of sorption and bioavailability of dioxin on RW1, transcriptomes of RW1 either grown with dioxin intercalated to clay (DDSAP) or with free crystalline dioxin (DD) were sequenced using RNA-Seq. While either condition caused RW1 large-scale shifts in gene expression compared to succinate control (SUC), differences in gene expression between these two conditions were marked by a small number (86) of differentially expressed genes. The differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated in the clay.
2019-06-30 | GSE115658 | GEO
Project description:Sphingomonas wittichii strain RW1 (RW1) is one of few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite (SAP), an important geosorbent of toxicants in soil, with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition and transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated by both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB dependent receptor proteins, but the patterns of changes differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay (SAP) caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as geosorbent for toxic pollutants. Similar to clay, DD and DF also affect motility and chemotaxis.
2015-11-13 | GSE74831 | GEO
Project description:Whole transcriptome shotgun sequencing of Sphingomonas wittichii strain RW1
| PRJNA312499 | ENA
Project description:Genome-wide gene expression to dibenzofuran in Sphingomonas wittichii RW1
| PRJNA159767 | ENA
Project description: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.
2013-10-22 | PXD000403 | Pride
Project description:Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the toxic polyaromatic hydrocarbon dibenzofuran (dbf) and its polychlorinated derivatives. Its genome consists of a chromosome and two plasmids, encoding for more than 5300 genes. We studied genome-wide expression of strain RW1 to dbf in three different experimental setups, including both batch cultures and chemostats, comparing in all cases to the transcriptome of cells grown on phenylalanine as carbon source. A short exposure to DBF in chemostat or in batch, provoked the up-regulation of the ECF sigma 24, catalases, peroxiredoxins, chaperones, an aquaporin, several OmpA domain-containing proteins and the down-regulation of genes involved in TCA cycle, oxidative phosphorylation, amino acid metabolism and ribosomal proteins. When growing strain RW1 on DBF, genes known to be involved in DBF degradation were induced 2 to 4 fold. Additionally, two cluster of genes, putatively participating in the gentisate and meta-cleavage branches of the DBF degradation pathway, were induced from 12 to 19 fold.
2012-04-18 | GSE37328 | GEO
Project description:Global transcriptome profiling after exposure to solute, matric, and sand desiccation stress in S. wittichii RW1
| PRJNA136163 | ENA
Project description:Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand [experment 2]
| PRJNA237753 | ENA
Project description:Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand [experiment 1]
| PRJNA237750 | ENA
Project description:Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the toxic polyaromatic hydrocarbon dibenzofuran (dbf) and its polychlorinated derivatives. Its genome consists of a chromosome and two plasmids, encoding for more than 5300 genes. We studied genome-wide expression of strain RW1 to dbf in three different experimental setups, including both batch cultures and chemostats, comparing in all cases to the transcriptome of cells grown on phenylalanine as carbon source. A short exposure to DBF in chemostat or in batch, provoked the up-regulation of the ECF sigma 24, catalases, peroxiredoxins, chaperones, an aquaporin, several OmpA domain-containing proteins and the down-regulation of genes involved in TCA cycle, oxidative phosphorylation, amino acid metabolism and ribosomal proteins. When growing strain RW1 on DBF, genes known to be involved in DBF degradation were induced 2 to 4 fold. Additionally, two cluster of genes, putatively participating in the gentisate and meta-cleavage branches of the DBF degradation pathway, were induced from 12 to 19 fold. Three experiments are summarized here. 1. Compares the response of exponentially growing S.wittichii RW1 cells on phenylalanine (Phe), washed and resuspended in Phe for 30 min, with that of cells resuspended in DBF medium for 30 min (Phe1_shock, DBF1_schock, etc.). 2. Compares response of RW1 cells grown in batch medium with Phe or DBF as sole carbon and energy source, and harvested in exponential phase (Phe1_long, DBF1_long, etc. triplicates). 3. Comparison of transcriptome of RW1 cells grown continuously in chemostat on phenylalanine as carbon-limited substrate, with cells that have experienced instant exposure to phenylalanine plus DBF. This is done by pulsing DBF to maximum solubility and a simultaneous change in feed medium to Phe+ DBF. Samples before transition (Phe ctrl1-chem, etc. quadruplates), after 30 min (DBF 30m1-chem, etc), 1 h, 2 h and 6 h (DBF6h1-chem, etc.).
2012-04-17 | E-GEOD-37328 | biostudies-arrayexpress