RDX as the sole nitrogen source affects the nitrogen metabolism in Rhodococcus sp. LMD

Many microorganisms involved in environmental remediation can effectively degrade hazardous nitrogen-containing heterocyclic compounds. Rhodococcus strains have gained increasing interests due to their efficient degradation abilities towards broader range of organic contaminations, including the explosive compound RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine). However, comprehensive tolerant and metabolic mechanism of the Rhodococcus strains are lacked and deserved further characterization. This study compared the transcriptomic and proteomic differences of Rhodococcus sp. LMD under sole inorganic (KNO₂) or organic (RDX) nitrogen source. Whole-genome sequencing identified 4991 genes, including 337 transporters, which indicated strong uptake ability of xenobiotic compounds. Proteomic results found 139 upregulated and 112 downregulated proteins with RDX as sole nitrogen source. Metabolomic results indicated 51 significantly altered metabolites with RDX as sole nitrogen source, with glutamate increased by 2.7-fold. Multi-omics integration highlighted that the glutamate-centered nitrogen pathway was strongly induced, with significantly increased expression of the following genes (e.g., gltB 5.9-fold, gltD 5.4-fold, glnA-2 6.3-fold, narG 74.6-fold at 37 h after RDX feeding). To search candidate RDX-degrading enzymes in Rhodococcus sp. LMD, this study screened 20 cytochrome P450 (CYP450) and the adjacent electron-transfer partners. Docking analysis indicated that two of the candidates CYP108 (-7.0 kcal/mol binding energy) and CYP142-1 (-6.7 kcal/mol binding energy) present the best binding abilities towards RDX. In summary, these results suggest that RDX as sole nitrogen source can affect the amino acid metabolism in Rhodococcus sp. LMD, and is associated with an upregulated glutamate-centered nitrogen flux, providing a potential selection marker for future screening and engineering of RDX bioremediation strains.