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A Gene Expression Study of the Activities of Aromatic Ring-Cleavage Dioxygenases in Mycobacterium gilvum PYR-GCK to Changes in Salinity and pH during Pyrene Degradation

Title
A Gene Expression Study of the Activities of Aromatic Ring-Cleavage Dioxygenases in Mycobacterium gilvum PYR-GCK to Changes in Salinity and pH during Pyrene Degradation
Other Titles
Mycobacterium gilvum PYR-GCK에서 Omics 기술을 이용한 피렌 분해에 대한 분자적 고찰
Author
채영규
Keywords
QUANTITATIVE PCR; DEGRADING BACTERIA; VANBAALENII PYR-1; CRUDE-OIL; CANCER; QUANTIFICATION; HYDROCARBONS; PHENANTHRENE; SMEGMATIS; CLUSTER
Issue Date
2013-02
Publisher
PUBLIC LIBRARY SCIENCE
Citation
PLOS ONE, 8권, 2호
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents. The rate of PAH biodegradation is affected by environmental conditions of pH, salinity and temperature. Adaptation of the pyrene degrading bacteria, Mycobacterium gilvum PYR-GCK, to fluctuating environmental conditions during pyrene biodegrading activity was studied using the quantitative real time - Polymerase Chain Reaction (qRT-PCR) technique. Four aromatic ring-cleavage dioxygenase genes: phdF, phdI, pcaG and pcaH; critical to pyrene biodegradation, were studied in pH states of 5.5, 6.5, 7.5 and NaCl concentrations 0 M, 0.17 M, 0.5 M, 0.6 M, 1 M. First, we conducted a residual pyrene study using gas chromatography and flame ionization technologies. Central to a gene expression study is the use of a valid endogenous reference gene, making its determination our next approach, using the geNorm/NormFinder algorithms. Armed with a valid control gene, rpoB, we applied it to a gene expression study, using the comparative critical threshold (2(Delta Delta CT)) quantification method. The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (similar to 70% degraded after 48 hours of cultivation). The transcripts quantification of three genes backed this observation with high expression levels. The gene expression levels also revealed pH 6.5 as optimal for pyrene degradation and weak degradation activity at pH of 5.5, corroborating the residual pyrene analysis. The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.
URI
http://hdl.handle.net/20.500.11754/42841
ISSN
1932-6203
DOI
10.1371/journal.pone.0058066
Appears in Collections:
GRADUATE SCHOOL[S](대학원) > BIONANOTECHNOLOGY(바이오나노학과) > Articles
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