Limits...
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.

Badejo AC, Badejo AO, Shin KH, Chai YG - PLoS ONE (2013)

Bottom Line: Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents.The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation).The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Life Sciences, Hanyang University, Ansan, Korea.

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(ΔΔCT)) 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 (∼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.

Show MeSH

Related in: MedlinePlus

Pyrene degradation profiles showing the residual pyrene (%) in the various cultures.Graph of culture induced with pH states of 5.5, 6.5 and 7.5 (A) and NaCl concentrations of 0 M, 0.17 M, 0.5, 0.6 and 1 M (B). pH states correspond to acidic nature of the oceans and polluted terrestrial environments while the NaCl concentrations correspond to the saline nature of the ocean and some industrial waste effluents. Data and standard error are means from two replicates.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3585252&req=5

pone-0058066-g001: Pyrene degradation profiles showing the residual pyrene (%) in the various cultures.Graph of culture induced with pH states of 5.5, 6.5 and 7.5 (A) and NaCl concentrations of 0 M, 0.17 M, 0.5, 0.6 and 1 M (B). pH states correspond to acidic nature of the oceans and polluted terrestrial environments while the NaCl concentrations correspond to the saline nature of the ocean and some industrial waste effluents. Data and standard error are means from two replicates.

Mentions: At various times during bacterial growth/induction, 10 ml samples were extracted for residual pyrene determination. Fig. 1A of the residual pyrene profile shows reduced pyrene degradation activity at pH 5.5 with 30% of total pyrene degraded after 48 hours of cultivation. Extreme degradation activities were observed at the 48th hour of cultivation in the pH 6.5 and 7.5 cultures. The highest degradation activity was recorded in the pH 6.5 culture with zero residual pyrene after 58 hours. This makes a slightly acidic condition, probably, the best condition for pyrene degradation in our experimental strain.


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.

Badejo AC, Badejo AO, Shin KH, Chai YG - PLoS ONE (2013)

Pyrene degradation profiles showing the residual pyrene (%) in the various cultures.Graph of culture induced with pH states of 5.5, 6.5 and 7.5 (A) and NaCl concentrations of 0 M, 0.17 M, 0.5, 0.6 and 1 M (B). pH states correspond to acidic nature of the oceans and polluted terrestrial environments while the NaCl concentrations correspond to the saline nature of the ocean and some industrial waste effluents. Data and standard error are means from two replicates.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585252&req=5

pone-0058066-g001: Pyrene degradation profiles showing the residual pyrene (%) in the various cultures.Graph of culture induced with pH states of 5.5, 6.5 and 7.5 (A) and NaCl concentrations of 0 M, 0.17 M, 0.5, 0.6 and 1 M (B). pH states correspond to acidic nature of the oceans and polluted terrestrial environments while the NaCl concentrations correspond to the saline nature of the ocean and some industrial waste effluents. Data and standard error are means from two replicates.
Mentions: At various times during bacterial growth/induction, 10 ml samples were extracted for residual pyrene determination. Fig. 1A of the residual pyrene profile shows reduced pyrene degradation activity at pH 5.5 with 30% of total pyrene degraded after 48 hours of cultivation. Extreme degradation activities were observed at the 48th hour of cultivation in the pH 6.5 and 7.5 cultures. The highest degradation activity was recorded in the pH 6.5 culture with zero residual pyrene after 58 hours. This makes a slightly acidic condition, probably, the best condition for pyrene degradation in our experimental strain.

Bottom Line: Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents.The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation).The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Life Sciences, Hanyang University, Ansan, Korea.

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(ΔΔCT)) 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 (∼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.

Show MeSH
Related in: MedlinePlus