title: Energy metabolism in Mycobacterium gilvum PYR-GCK: insights from transcript expression analyses following two states of induction.
abstract: Mycobacterium gilvum PYR-GCK, a pyrene degrading bacterium, has been the subject of functional studies aimed at elucidating mechanisms related to its outstanding pollutant bioremediation/biodegradation activities. Several studies have investigated energy production and conservation in Mycobacterium, however, they all focused on the pathogenic strains using their various hosts as induction sources. To gain greater insight into Mycobacterium energy metabolism, mRNA expression studies focused on respiratory functions were performed under two different conditions using the toxic pollutant pyrene as a test substrate and glucose as a control substrate. This was done using two transcriptomic techniques: global transcriptomic RNA-sequencing and quantitative Real-Time PCR. Growth in the presence of pyrene resulted in upregulated expression of genes associated with limited oxygen or anaerobiosis in M. gilvum PYR-GCK. Upregulated genes included succinate dehydrogenases, nitrite reductase and various electron donors including formate dehydrogenases, fumarate reductases and NADH dehydrogenases. Oxidative phosphorylation genes (with respiratory chain complexes I, III -V) were expressed at low levels compared to the genes coding for the second molecular complex in the bacterial respiratory chain (fumarate reductase); which is highly functional during microaerophilic or anaerobic bacterial growth. This study reveals a molecular adaptation to a hypoxic mode of respiration during aerobic pyrene degradation. This is likely the result of a cellular oxygen shortage resulting from exhaustion of the oxygenase enzymes required for these degradation activities in M. gilvum PYR-GCK.
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea.
authors.forename: Abimbola Comfort
authors.initials: AC
authors.lastname: Badejo
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
authors.forename: Won Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
authors.forename: Nam Shin
authors.initials: NS
authors.lastname: Kim
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea.
authors.forename: Jin Choul
authors.initials: JC
authors.lastname: Chai
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea.
authors.forename: Young Seek
authors.initials: YS
authors.lastname: Lee
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea.
authors.forename: Kyoung Hwa
authors.initials: KH
authors.lastname: Jung
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea.
authors.forename: Hyo Joon
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Department of Molecular and Life Science, Hanyang University, Ansan, Korea; Department of Nanobiotechnology, Hanyang University, Seoul, Korea.
authors.forename: Young Gyu
authors.initials: YG
authors.lastname: Chai
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004734:Energy Metabolism / Q000187:drug effects; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005947:Glucose / Q000494:pharmacology; D009170:Nontuberculous Mycobacteria / Q000201:enzymology* / Q000235:genetics; D011721:Pyrenes / Q000494:pharmacology; D017423:Sequence Analysis, RNA
chemical_list: D001426:Bacterial Proteins; D011721:Pyrenes; C030984:pyrene; D005947:Glucose