Comprehensive in silico studies on the microbial enzymes capable of degrading organophosphorus pesticide

Abstract

Phorate, an organophosphorus compound is known to have applications against pests. However, its hazardous nature is a matter of concern. Microbial biodegradation is a potent method that can eliminate pesticides from the environment by enzymatic reactions. As toxicity and binding specificity are inherently correlated to each other, this study was focussed on finding out binding sites for ensuing biodegradation. Brevibacterium frigoritolerans GD44 and Enterobacter cloacae subsp. cloacae ATCC 13047 were included in the study for genomic and structural analyses as alkaline phosphatase from Brevibacterium frigoritolerans GD44 and endonuclease/exonuclease/phosphatase from Enterobacter cloacae subsp. cloacae ATCC 13047 were found to degrade phorate. It was apparent from the present findings that alkaline phosphatase containing homologous bacterial species are AT-rich, while the phosphatase containing bacteria are GC-rich. Bacterial species having phosphatase enzyme contain more aromatic amino acids that stabilize the protein structure than alkaline phosphatase containing bacteria. Variation of relative synonymous codon usage (RSCU) value was found to be very little and natural selection pressure was preferred over mutational pressure in determining codon usage pattern. High level of codon adaptation index (CAI) found in both the bacterial species indicates higher level of codon usage bias and gene expression in them. Furthermore, docking results suggest that alkaline phosphatase has higher binding affinity to phorate than phosphatase that might be considered effective in bioremediation. The results obtained are considered to shed further light in the experimental biodegradation of organophosphorus pesticides by the bacteria.