Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

Abstract

Sphingomonas wittichii strain RW1 (RW1) is one of the 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 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, 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 in response to 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 change 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 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 an environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.

Novel Three-Component Phenazine-1-Carboxylic Acid 1,2-Dioxygenase in Sphingomonas wittichii DP58

“…Moreover, culturing strain DP58 with phenazine-1-carboxylic acid resulted in the upregulation of genes in the catechol ortho-pathway, and the taurine dioxygenase-and gentisate 1,2-dioxygenase-coding genes were also found to be upregulated (supplemental material). Thus, the central pathway appeared to be a dynamic network that the strain can adjust according to the substrate(s) present (23,24).…”

Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico

“…In particular, we have evidence that classifies the 16S rRNA gene (470 bp) fragment as Sphingomonas wittichii. The S. wittichii RW1 is known for their metabolic diversity and is capable of degrading dioxins (dibenzo-p-dioxin) chlorinated contaminants and aromatic compounds from decaying plants, some of the most abundant genes in S. wittichii RW1 genome are TonB-dependent receptors (TBDR), general dehydrogenases, and ring-related phenylpropionate dioxygenases (Miller et al, 2010;Moreno-Forero and Van Der Meer, 2015;Chai et al, 2016). TBDR is part of a carbohydrate scavenging response of plant carbohydrates (Blanvillain et al, 2007).…”

Microbial Ecology: Where are we now?

“…For example, RNA-seq was recently used to examine the differential expression of genes from Sphingomonas wittichii RW1 [debatably the only organism in isolation that is able to utilize the toxin dibenzo- p -dioxin (DD) as its sole carbon and energy source] in the presence of either DD, dibenzofuran (DF; a similar molecule with lower toxicity), or succinate (SUC; negative control carbon source) with and without clay particles (a prominent soil component) (Chai et al 2016). Such investigations can assist in understanding why dibenzo- p -dioxin is so resistant to biodegradation, whereas dibenzofuran biodegradation is relatively common (toxicity, molecular structure, or something else entirely?…”