IlMytFerr1
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ABSTRACT:
PROVIDER: PRJEB45327 | ENA |
REPOSITORIES: ENA
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Project description:Mythimna ferrago (the clay) genome assembly, ilMytFerr1, alternate haplotype
| PRJEB45326 | ENA
Project description:Mythimna ferrago (the clay), genomic and transcriptomic data
| PRJEB45141 | ENA
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: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