Carbon Allocation in Rhodococcus jostii RHA1 in Response to Disruption and Overexpression of nlpR Regulatory Gene, Based on 13C-labeling Analysis

Nitrogen lipid regulator (NlpR) is a pleiotropic regulator that positively controls genes associated with both nitrogen and lipid metabolism in the oleaginous bacterium Rhodococcus jostii RHA1. In this study, we investigated the effect of nlpR disruption and overexpression on the assimilation of ¹³C-labeled glucose as carbon source, during cultivation of cells under nitrogen-limiting and nitrogen-rich conditions, respectively. Label incorporation into the total lipid extract (TLE) fraction was about 30% lower in the mutant strain in comparison with the wild type strain under low-nitrogen conditions. Moreover, a higher ¹³C abundance (∼60%) into the extracellular polymeric substance fraction was observed in the mutant strain. nlpR disruption also promoted a decrease in the label incorporation into several TLE-derivative fractions including neutral lipids (NL), glycolipids (GL), phospholipids (PL), triacylglycerols (TAG), diacylglycerols (DAG), and free fatty acids (FFA), with the DAG being the most affected. In contrast, the nlpR overexpression in RHA1 cells under nitrogen-rich conditions produced an increase of the label incorporation into the TLE and its derivative NL and PL fractions, the last one being the highest ¹³C enriched. In addition, a higher ¹³C enrichment occurred in the TAG, DAG, and FFA fractions after nlpR induction, with the FFA fraction being the most affected within the TLE. Isotopic-labeling experiments demonstrated that NlpR regulator is contributing in oleaginous phenotype of R. jostii RHA1 to the allocation of carbon into the different lipid fractions in response to nitrogen levels, increasing the rate of carbon flux into lipid metabolism.

Identification of novel extracellular protein for PCB/biphenyl metabolism in Rhodococcus jostii RHA1

Rhodococcus jostii RHA1 (RHA1) degrades polychlorinated biphenyl (PCB) via co-metabolism with biphenyl. To identify the novel open reading frames (ORFs) that contribute to PCB/biphenyl metabolism in RHA1, we compared chromatin immunoprecipitation chip and transcriptomic data. Six novel ORFs involved in PCB/biphenyl metabolism were identified. Gene deletion mutants of these 6 ORFs were made and were tested for their ability to grow on biphenyl. Interestingly, only the ro10225 deletion mutant showed deficient growth on biphenyl. Analysis of Ro10225 protein function showed that growth of the ro10225 deletion mutant on biphenyl was recovered when exogenous recombinant Ro10225 protein was added to the culture medium. Although Ro10225 protein has no putative secretion signal sequence, partially degraded Ro10225 protein was detected in conditioned medium from wild-type RHA1 grown on biphenyl. This Ro10225 fragment appeared to form a complex with another PCB/biphenyl oxidation enzyme. These results indicated that Ro10225 protein is essential for the formation of the PCB/biphenyl dioxygenase complex in RHA1.