In silico analysis for prediction of degradative capacity of Pseudomonas putida SF1.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida strain SF-1 for different aromatic compounds.
Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI Nehru Marg, Nagpur 440020, India.
Hitesh
H
Tikariha
Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI Nehru Marg, Nagpur 440020, India.
Rajesh Ramavadh
RR
Pal
Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI Nehru Marg, Nagpur 440020, India.
Asifa
A
Qureshi
Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI Nehru Marg, Nagpur 440020, India.
Atya
A
Kapley
Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI Nehru Marg, Nagpur 440020, India. Electronic address: hemantdrd@hotmail.com.
Hemant J
HJ
Purohit
D001673:Biodegradation, Environmental; D003198:Computer Simulation; D016384:Consensus Sequence; D016680:Genome, Bacterial; D005810:Multigene Family; D009596:Nitrophenols / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D016958:Pseudomonas putida / Q000378:metabolism*
D009596:Nitrophenols; C024836:4-nitrophenol
Catabolic gene annotation; Genome sequencing; Pseudomonas putida SF1; p-nitrophenol degradation