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Updated: Nov 7, 2025
Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR
Published on: June 11, 2016
Genome and transcriptome sequencing of a newly isolated 2,4-dinitrophenol-degrading strain Rhodococcus imtechensis
Fan Hu1, Longhe Yang1, Zhaokai Wang2
1Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China.
Background:
2,4-Dinitrophenol (2,4-DNP) is an important organic environmental pollutant that is highly toxic to all forms of living organisms. A gram-positive strain (designated XM24D) was isolated from 2,4-DNP-contaminated soil by an enrichment technique.
Objective:
The study was designed to analyze the ability of XM24D to degrade 2,4-DNP and its analogs and to reveal the degradation pathways of these aromatic compounds.
Methods:
The degradation ability of XM24D was tested by a growth experiment. 2,4-DNP and its analog degradation pathways were predicted by genome and comparative transcriptome sequencing.
Results:
Growth profiles showed that XM24D was able to utilize 2,4-DNP as the sole source of carbon, nitrogen and energy. Analogs of 2,4-DNP, including 4-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP), can also be degraded by XM24D. Genome analysis showed that the XM24D genome contains two chromosomes with a combined size of 9.08 Mb and an average GC content of 67.07 %. Average nucleotide identity analysis indicated that Rhodococcus imtechensis RKJ300 is the most closely related strain to XM24D. Comparative transcriptome analysis revealed that the 2,4-DNP/PNP/2C4NP degradation pathway in XM24D is highly similar in sequence and organization to the 2,4-DNP degradation pathway in Rhodococcus opacus HL PM-1, the PNP degradation pathway in Rhodococcus opacus SAO101 and the 2C4NP degradation pathway in Rhodococcus imtechensis RKJ300. These results suggested that 2,4-DNP/PNP/2C4NP was degraded via the 2,4-dinitrocyclohexanone/4-nitrocatechol/hydroxyquinol pathway in XM24D.
Conclusions:
Genomic and transcriptomic information on XM24D provides a valuable reference for further investigating the evolutionary characteristics of nitrophenol degradation pathways in microorganisms.
