In silico modeling, docking of ThPON1-like protein, and in vitro validation of pesticide tolerance in Trichoderma harzianum

Abstract

Overuse of pesticides in agriculture has extremely detrimental effects on the environment and various life forms. Agricultural soils containing residual pesticides can be decontaminated economically and effectively using microbes that produce pesticide degrading enzymes. Before onsite bioremediation, in silico studies can identify the potential microbes that can degrade pesticides. This study aims to identify the organophosphate (OP) pesticide degrading potential of beneficial fungi Trichoderma harzianum using in silico tools. Among various types of OP hydrolyzing enzymes (PTE/PON1/SsoPox), only a Trichoderma atroviride paraoxonase 1 like (TaPON1-like) enzyme was found in T. harzianum. Pfam domain searches revealed an arylesterase domain that has a role in OP degradation. Phylogenetic analyses and multiple alignments of the sequences of various OP hydrolyzing enzymes revealed their diversity. Homology modeling of TaPON1-like protein in T. harzianum was done using MODELER 10. Model evaluation and validation led to the choice of the best model with the lowest DOPE score. Modeled T. harzianum paraoxonase 1 like protein was docked with six selected hazardous OP pesticides/intermediate. This study helped to identify the OP pesticide degrading enzyme in T. harzianum. In vitro and in silico studies showed similarities, suggesting that in silico screening for pesticide degrading microbes might be feasible before cumbersome onsite remediation.