title: [Transcriptomic and benzoate metabolic pathways of Rhodococcus sp. R04 cultured in biphenyl].
abstract: OBJECTIVE
  Studying transcriptional characteristics of Rhodococcus sp. R04 is to find the genes that participate in the transportation, metabolism and regulation of polychlorinated biphenyls (PCBs), and disclose the molecular mechanism of biodegradation of PCBs.
  
  
  METHODS
  Strain R04 was separately cultivated on ethanol, glucose and biphenyl. The total RNA of the above different cultures was extracted, and the cDNA was obtained by reverse transcription and determined by high-throughput sequencing. The data obtained by sequencing were analyzed to find the correlation among the PCBs metabolic network, gene transcription regulation and metabolic response.
  
  
  RESULTS
  The sequencing results showed that 375 genes were up-regulated during grown on biphenyl, relative to growth on glucose, and 332 genes were up-regulated, relative to growth on ethanol. Those genes were found to participate in multiple biological processes of biphenyl metabolite. Among the genes relative to biphenyl/PCBs degradation, the genes located on the gene cluster in the upper biphenyl pathway were significantly up-regulated, while bphC4 and bphD2 were up-regulated slightly. By contrast, the other genes encoding BphC and BphD isozymes in the biphenyl pathway were down-regulated even if growth on biphenyl.
  
  
  CONCLUSIONS
  Transcriptomic analysis suggested that benzoate was degraded via ortho cleavage pathway, meta cleavage pathway or protocatechuic acid pathway, which provide more valuable data for us to reveal the characteristics and regulation of downstream metabolic pathways of biphenyl and PCBs.
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Yang
authors.forename: Jingwen
authors.initials: J
authors.lastname: Xi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001565:Benzoates / Q000737:chemistry / Q000378:metabolism*; D001673:Biodegradation, Environmental; D015964:Gene Expression Regulation, Bacterial; D053858:Metabolic Networks and Pathways; D015394:Molecular Structure; D011078:Polychlorinated Biphenyls / Q000737:chemistry / Q000378:metabolism*; D012240:Rhodococcus / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D001565:Benzoates; D011078:Polychlorinated Biphenyls