Whole-cell physiology and gene expression patterns in the co-metabolism of and tolerance to PCBs by Burkholderia xenovorans LB400

Aerobic biodegradation of polychlorinated biphenyls (PCBs) occurs gratuitously via the biphenyl (bph) pathway. Although many PCB-degrading bacteria exhibit similar degradation profiles, I have found a wide range of sensitivity to PCBs and hypothesize involvement of genes outside the bph pathway in efficient degradation. To date, little information is available on mechanisms beyond the bph pathway that bestow PCB tolerance to microorganisms or increase degradation efficiency. This work combines physiological information on the response of Burkholderia xenovorans LB400 (LB400) with microarray techniques to investigate the transcriptomic response to growth substrate and growth phase on the degradation of PCBs. I report the induction of the bph and (chloro)catechol pathways during PCB degradation, however during growth on simple carbon sources, such as succinate, PCBs inhibit the bph pathway. Importantly, among the putative genes induced on degradation of PCBs, a putative chloroacetaldehyde dehydrogenase exhibited 83% (amino acid) identity to a homolog responsible for rapid conversion of the highly toxic chloroacetaldehyde intermediate in dichloroethane (DCE) degraders. The statistical analysis of genome-wide expression patterns of 11 different treatments reveals a close relationship in expression of the acetaldehyde dehydrogenase in the lower biphenyl pathway (BphJ) and chloroacetaldehyde dehydrogenase, suggesting a similar role. In addition, transcriptional profiling indicates very limited expression response to PCB degradation compared with changes in growth rate and substrate and identifies several candidate genes, such as transporters and regulators that may be involved in the degradation of biphenyl. Resting-cell assays of LB400 show a dynamic change in degradation profiles as a result of culture conditions (carbon source and growth phase). Microarray analyses indicate several pathways associate with PCB degradation are influenced by sigma-54 (sigma54). Subsequent Q-RT-PCR analysis of both sigma54 factors in the LB400 genome indicate the involvement of only one (located on the mini chromosome) associated with the degradation of biphenyl. Further Q-RT-PCR analyses of the response of the biphenyl pathway to carbon source competition and growth phase reveals inhibition of the biphenyl pathway by PCBs. Metabolic footprinting of knockout mutants of the C1 pathway (LB400DeltaxoxF and LB400DeltaflhAfdhAmtdB) in LB400 indicates the involvement of this pathway in detoxification of formaldehyde that accumulates during growth on biphenyl and degradation of PCBs that has not been reported previously. Although I show that the affect of PCBs on gene expression profiles is minimal, several auxiliary mechanisms involved in PCB degradation have been identified. This work has outlined several factors, such as biotoxicity (detoxification), carbon source competition, and regulation and transport that are essential to the degradation of PCBs in an environmental context.