Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review.

Shweta Jaiswal,Dileep Kumar Singh,Pratyoosh Shukla

doi:10.3389/fmicb.2019.00087

Shweta Jaiswal, Dileep Kumar Singh + Show 1 more

Open Access

https://doi.org/10.3389/fmicb.2019.00087

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Abstract

Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

Highlights

Due to ever-increasing world population and their corresponding food commodities need to be enhanced (Cazalis et al, 2018; Drangert et al, 2018)
Pesticidal compounds have ill effects on health affecting the function of organs and damage the DNA at molecular level leading to neurological diseases and cancer, i.e., azoxystrobin and atrazine
Study (Table 4) data make us to understand the genotype and phenotype of particular biodegrading microbes. This prediction aids in determining genome scale model (GEM). This model would give the best microorganisms for bioremediation of pesticides and other xenobiotics

Summary

INTRODUCTION

Due to ever-increasing world population and their corresponding food commodities need to be enhanced (Cazalis et al, 2018; Drangert et al, 2018). This gene mining from a diversity of microbial strains would be done for integration in a particular and specific microbial GEM (Genome Scale Model) is possible by OptStrain. Fang et al, 2014 studied biodegradation pathways of persistent pesticides present in ecosystems of marine and freshwater sediments They did analysis of metagenomic DNA for determining the BDGs involved in degradation of three pesticides namely DDT (dichlorodiphenyltrichloroethane), HCH (hexachlorocyclohexane), and ATZ (atrazine) and created data of 3 giga base pairs. The genome annotation allowed the identification of functional genes involved in bioremediation and biodegradation It enhances the description of existing metabolic pathways for consumption of pesticidal compounds as substrate or metabolites. Fenner et al, 2013; Ahad et al, 2018; Lin et al, 2018; Subashchandrabose et al, 2018

Method

CONCLUSION AND FUTURE