Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1

Abstract

Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the xenobiotic compounds dibenzodioxin and dibenzofuran (DBF). A number of genes involved in DBF degradation have been previously characterized, such as the dxn cluster, dbfB, and the electron transfer components fdx1, fdx3, and redA2. Here we use a combination of whole genome transcriptome analysis and transposon library screening to characterize RW1 catabolic and other genes implicated in the reaction to or degradation of DBF. To detect differentially expressed genes upon exposure to DBF, we applied three different growth exposure experiments, using either short DBF exposures to actively growing cells or growing them with DBF as sole carbon and energy source. Genome-wide gene expression was examined using a custom-made microarray. In addition, proportional abundance determination of transposon insertions in RW1 libraries grown on salicylate or DBF by ultra-high throughput sequencing was used to infer genes whose interruption caused a fitness loss for growth on DBF. Expression patterns showed that batch and chemostat growth conditions, and short or long exposure of cells to DBF produced very different responses. Numerous other uncharacterized catabolic gene clusters putatively involved in aromatic compound metabolism increased expression in response to DBF. In addition, only very few transposon insertions completely abolished growth on DBF. Some of those (e.g., in dxnA1) were expected, whereas others (in a gene cluster for phenylacetate degradation) were not. Both transcriptomic data and transposon screening suggest operation of multiple redundant and parallel aromatic pathways, depending on DBF exposure. In addition, increased expression of other non-catabolic genes suggests that during initial exposure, S. wittichii RW1 perceives DBF as a stressor, whereas after longer exposure, the compound is recognized as a carbon source and metabolized using several pathways in parallel.

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).…”

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

“…Therefore, in this study we determined the genome-wide gene expression changes in a bacterial strain relevant for bioaugmentation during a transition from typical laboratory cultivation to nonsterile contaminated sand. We chose to study the transition phase upon inoculation into contaminated sand, because, based on previous experience with other strains [11, 14, 15], we expected that the inoculant would display the highest expression changes and that we would see induction of the key genes involved in sand adaptation and contaminant degradation. It is clear, however, that cellular reactions during the transition phase are not necessarily equivalent to those during an actual bioaugmentation process.…”

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

“…While the original isolate was unable to grow on unsubstituted biphenyl, spontaneous mutants were generated after prolonged low exposure (Wittich et al, 1992). Because of its degradative capacities and other interesting features, this strain was the focus of numerous biochemical and molecular investigations (Armengaud and Timmis, 1997;Armengaud et al, 1999;Seah et al, 2007;Raman et al, 2010;Johnson et al, 2011;Kim et al, 2011;Coronado et al, 2012;Ruzzini et al, 2013). Because of its degradative capacities and other interesting features, this strain was the focus of numerous biochemical and molecular investigations (Armengaud and Timmis, 1997;Armengaud et al, 1999;Seah et al, 2007;Raman et al, 2010;Johnson et al, 2011;Kim et al, 2011;Coronado et al, 2012;Ruzzini et al, 2013).…”