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

Area of Science:

• Environmental Microbiology
• Bioremediation
• Molecular Biology

Background:

• Microorganisms are crucial for degrading hazardous nitrogen-containing heterocyclic compounds.
• Rhodococcus strains show promise in degrading organic contaminants like the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine).
• Understanding the metabolic mechanisms and tolerance of Rhodococcus strains in RDX degradation is essential.

Purpose of the Study:

• To investigate the transcriptomic and proteomic responses of Rhodococcus sp. LMD when using RDX as a sole nitrogen source.
• To elucidate the metabolic pathways and identify key enzymes involved in RDX utilization and degradation.
• To discover potential biomarkers for screening and engineering RDX-degrading strains.

Main Methods:

• Whole-genome sequencing of Rhodococcus sp. LMD.
• Comparative transcriptomic and proteomic analyses under RDX or KNO₂ nitrogen sources.
• Metabolomic profiling to identify altered metabolic pathways.
• Bioinformatic analysis, including gene expression analysis and molecular docking of candidate enzymes.

Main Results:

• Whole-genome sequencing revealed 4991 genes, including 337 transporters, indicating strong xenobiotic uptake capabilities.
• Proteomic analysis identified 139 upregulated and 112 downregulated proteins when RDX was the sole nitrogen source.
• Metabolomic analysis showed 51 significantly altered metabolites, with a 2.7-fold increase in glutamate.
• Multi-omics integration highlighted an induced glutamate-centered nitrogen pathway with significantly increased gene expression (e.g., gltB, gltD, glnA-2, narG).
• Molecular docking identified CYP108 and CYP142-1 as potential RDX-degrading enzymes with favorable binding energies.

Conclusions:

• RDX as a sole nitrogen source significantly impacts amino acid metabolism in Rhodococcus sp. LMD.
• The study demonstrates an upregulated glutamate-centered nitrogen flux in response to RDX.
• The identified metabolic pathways and candidate enzymes provide a basis for future screening and engineering of RDX bioremediation strains.