Identification of New Dioxygenases Able to Recognize Polycyclic Aromatic Hydrocarbons with High Aromaticity

Apolonia Rodríguez,Agatha Bastida,Sandra G Zárate

doi:10.3390/catal12030279

Abstract

Polycyclic aromatic hydrocarbons (PAHs), products from the incomplete combustion of crude oil, are pollutants present in nature. Ring hydroxylating dioxygenase enzymes are able to catalyze polycyclic aromatic hydrocarbons in the biodegradation process with a high degree of stereo-, regio-, and enantiospecificity. In this work, we present the first approximation of the binding modes of 9 PAHs with high aromaticity in the catalytic sites of biphenyl or naphthalene dioxygenases from four microorganisms usually used in bio-remediation processes: Sphingobium yanoikuyae, Rhodococcus jostii RHA1, Pseudomonas sp. C18, and Paraburkholderia xenovorans. Molecular modeling studies of two biphenyl dioxygenases from Sphingobium yanoikuyae and Paraburkholderia xenovorans showed good binding affinity for PAHs with 2–4 benzene rings (fluoranthene, pyrene, and chrysene), and both enzymes had a similar amount of substrate binding. Molecular docking studies using naphthalene dioxygenase from Pseudomonas sp. C18 showed that the enzyme is able to accommodate PAHs with high aromaticity (benzo(a)pyrene, indeno(1,2,3-cd)pyrene), with good docking scores. This study provides important insight into the utility of naphthalene dioxygenases in the degradation of HAPs with high aromaticity.

Highlights

Polycyclic aromatic hydrocarbons (PAHs), products from the incomplete combustion of crude oil, are pollutants present in nature [1,2]
The concentration of PAHs with 2–3 benzene rings in nature decreases faster than the concentration of PAHs with 4–6 rings, which may be due to a recalcitrant effect or a lack of microorganisms capable of degrading these compounds [15]
Molecular modeling was performed in an attempt to identify novel dioxygenases from microorganisms able to degrade PAHs with high aromaticity

Summary

Introduction

Polycyclic aromatic hydrocarbons (PAHs), products from the incomplete combustion of crude oil, are pollutants present in nature [1,2]. There are more than 100 PAHs; their hydrophobicity increases and solubility decreases with an increased number of benzene rings. These compounds are of environmental concern because of their toxic, mutagenic, and carcinogenic properties [3]. Anthracene is decomposed by Actinobacteria (93%), Sphingobium (28%), Mycobacterium (50–70%), Rhodococcus (90%), Nocardia, and Paracoccus [14]. Fluoranthene, and chrysene are decomposed by Sphingomonas (80–90%), Rhodococcus (90%), Dyadobacter, Mycobacterium (50–70%), Sphingobium (20–60%), Pseudomonas aeroginos (60–70%), and Dyadobacter koreensis (80%) (Table S1) [8]. The concentration of PAHs with 2–3 benzene rings in nature decreases faster than the concentration of PAHs with 4–6 rings, which may be due to a recalcitrant effect or a lack of microorganisms capable of degrading these compounds [15]

Methods

Results

Conclusion