Pollution by polycyclic aromatic hydrocarbons（PAHs） is widespread due to tmsuitable disposal of industrial waste. They are mostly defined as priority pollutants by environmental protection authorities worldwide. Phe...Pollution by polycyclic aromatic hydrocarbons（PAHs） is widespread due to tmsuitable disposal of industrial waste. They are mostly defined as priority pollutants by environmental protection authorities worldwide. Phenanthrene, a typical PAH, was selected as the target in this paper. The PAH-degrading mixed culture, named ZM, was collected from a petroleum contaminated river bed. This culture was injected into phenanthrene solutions at different concentrations to quantify the biodegradation process. Results show near-complete removal of phenanthrene in three days of biodegradation if the initial phenanthrene concentration is low. When the initial concentration is high, the removal rate is increased but 20%-40% of the phenanthrene remains at the end of the experiment. The biomass shows a peak on the third day due to the combined effects of microbial growth and decay. Another peak is evident for cases with a high initial concentration, possibly due to production of an intermediate metabolite. The pH generally decreased during biodegradation because of the production of organic acid. Two phenomenological models were designed to simulate the phenanthrene biodegradation and biomass growth. A relatively simple model that does not consider the intermediate metabolite and its inhibition of phenanthrene biodegradation cannot fit the observed data. A modified Monod model that considered an intermediate metabolite （organic acid） and its inhibiting reversal effect reasonably depicts the experimental results.展开更多
Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentatio...Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has Dmp R protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon,phenol hydroxylase encoded by dmp N gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from Dmp R protein and of the DNA sequences from the two Upstream Activation Sequences（UAS）present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.展开更多
基金The National Natural Science Foundation of China （No. 50178040） the Royal Society of UK and the Hi-Tech Research and Development Program（863） of China（No. 2003AA601080）
文摘Pollution by polycyclic aromatic hydrocarbons（PAHs） is widespread due to tmsuitable disposal of industrial waste. They are mostly defined as priority pollutants by environmental protection authorities worldwide. Phenanthrene, a typical PAH, was selected as the target in this paper. The PAH-degrading mixed culture, named ZM, was collected from a petroleum contaminated river bed. This culture was injected into phenanthrene solutions at different concentrations to quantify the biodegradation process. Results show near-complete removal of phenanthrene in three days of biodegradation if the initial phenanthrene concentration is low. When the initial concentration is high, the removal rate is increased but 20%-40% of the phenanthrene remains at the end of the experiment. The biomass shows a peak on the third day due to the combined effects of microbial growth and decay. Another peak is evident for cases with a high initial concentration, possibly due to production of an intermediate metabolite. The pH generally decreased during biodegradation because of the production of organic acid. Two phenomenological models were designed to simulate the phenanthrene biodegradation and biomass growth. A relatively simple model that does not consider the intermediate metabolite and its inhibition of phenanthrene biodegradation cannot fit the observed data. A modified Monod model that considered an intermediate metabolite （organic acid） and its inhibiting reversal effect reasonably depicts the experimental results.
基金deeply indebted to DST-PURSE program 2012–2015 going on in Department of Biochemistry and Biophysics, University of Kalyani for providing different equipments and essential infrastructural supportDeep gratitude is extended to DBT sponsored Bioinformatics Infrastructure Facility in the Department of Biochemistry and Biophysics, University of Kalyani for the necessary support
文摘Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has Dmp R protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon,phenol hydroxylase encoded by dmp N gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from Dmp R protein and of the DNA sequences from the two Upstream Activation Sequences（UAS）present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.
