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.
Overall design: 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.).
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