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Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications

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Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications molecules Review Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications Anming Xu 1, Xiaoxiao Zhang 1, Shilei Wu 1, Ning Xu 1, Yan Huang 2, Xin Yan 2, Jie Zhou 1, Zhongli Cui 2,* and Weiliang Dong 1,* 1 State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; [email protected] (A.X.); [email protected] (X.Z.); [email protected] (S.W.); [email protected] (N.X.); [email protected] (J.Z.) 2 Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; [email protected] (Y.H.); [email protected] (X.Y.) * Correspondence: [email protected] (Z.C.); [email protected] (W.D.) Abstract: The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, Citation: Xu, A.; Zhang, X.; Wu, S.; which strictly limited the enhancement of the degradation efficiency. Accordingly, this review Xu, N.; Huang, Y.; Yan, X.; Zhou, J.; will comprehensively summarize the function of various degrading enzymes with an emphasis Cui, Z.; Dong, W. Pollutant on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading Degrading Enzyme: Catalytic Mechanisms and Their Expanded enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes Applications. Molecules 2021, 26, 4751. will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate https://doi.org/10.3390/ concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants molecules26164751 with the help of gene-editing technology and synthetic biology. Academic Editors: Liangcai Peng, Keywords: microbial enzyme; catalytic mechanism; biodegradation; application; environmental Feng Peng, Wanbin Zhu, pollutants Łukasz Chrzanowski and M. Gilles Mailhot Received: 2 June 2021 1. Introduction Accepted: 30 July 2021 Published: 6 August 2021 The burden of disease and death attributable to environmental contaminants is be- coming a public health challenge worldwide [1]. In the last few decades, the environment Publisher’s Note: MDPI stays neutral is being continuously polluted by a large array of pollutants with different structures and with regard to jurisdictional claims in ecotoxicities. These pollutants are released from several anthropogenic sources and pose a published maps and institutional affil- major threat to ecosystem security and public health, including cancer, type 2 diabetes, and iations. damage to the immune system [2]. Environmental pollutants are commonly divided into organic pollutants and inorganic pollutants. Organic pollutants are widely distributed in the environment, including pesticides, polycyclic aromatic hydrocarbons (PAHs), polychlo- rinated biphenyls (PCBs), etc. Of particular concern are the persistent organic pollutants (POPs), such as aldrin, DDT, chlordane, and hexachlorobenzene. These POPs are ex- Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. tremely harmful to public health due to their intrinsic chemical stability, recalcitrance, This article is an open access article acute toxicity, and mutagenicity or carcinogenicity [3]. Due to the acceleration of global distributed under the terms and urbanization, modern industries synthesize a huge amount of POPs that are released into conditions of the Creative Commons the environment [4]. Attribution (CC BY) license (https:// Despite the threat caused by POPs, agricultural activities remain one of the main creativecommons.org/licenses/by/ sources of environmental pollutants. During the traditional agricultural process, exces- 4.0/). sive use of pesticides has led to continuous contamination of the environment. These Molecules 2021, 26, 4751. https://doi.org/10.3390/molecules26164751 https://www.mdpi.com/journal/molecules Molecules 2021, 26, x FOR PEER REVIEW 2 of 15 Molecules 2021, 26, 4751 Despite the threat caused by POPs, agricultural activities remain one of the 2main of 14 sources of environmental pollutants. During the traditional agricultural process, excessive use of pesticides has led to continuous contamination of the environment. These pollu- pollutantstants are poorly are poorly degraded degraded through through natural natural microbes microbes and plants, and plants, and hence, and hence, persist persist in the inenvironment the environment for decades for decades [5]. Moreover, [5]. Moreover, they can they spread can spread to great to great distances distances by wind by wind and andocean ocean current, current, including including the polar the polar regions regions and the and open the openoceans oceans [6]. There [6]. Thereis concern is concern about aboutthe presence the presence of pollutants of pollutants in the inenvironmen the environmentt because because of their of long-term their long-term residual, residual, bioac- bioaccumulative,cumulative, and toxic and nature. toxic nature. Therefore, Therefore, the study the studyof new of and new effective and effective degradation degradation mech- mechanismsanisms for pollutants for pollutants has become has become an international an international focal focalpoint. point. Bioremediation was viewed as the safest and eco-friendly procedure to combat an- thropogenic compounds compounds in in ecosystems. ecosystems. Many Many microbes microbes and and microbial microbial enzymes enzymes with with po- potentialtential bioremediation bioremediation abilities abilities have have been been isolated isolated and and characterized characterized [7,8]. [7, 8However,]. However, in insome some cases, cases, they they are areunable unable to degrade to degrade the ta thergeted targeted pollutant pollutant completely completely or are or ineffective are inef- fectivein the real in the natural real natural environment. environment. Nevertheless, Nevertheless, with the with enhanced the enhanced understanding understanding of the ofcatalysis the catalysis mechanisms mechanisms involved involved in the indegradation the degradation of pollutants, of pollutants, the application the application of these of thesedegradation degradation enzymes enzymes has aroused has aroused extensive extensive attention. attention. Many Many pollu pollutantstants degrading degrading en- enzymeszymes have have been been applied applied in in industry industry and and mo moderndern agriculture, agriculture, such such as biosensors andand drug synthesis [[9,10]9,10] (Figure1 1).). ThisThis studystudy willwill presentpresent aa comprehensivecomprehensive overview overview of of the the latest research progressprogress inin thethe fieldfield ofof pollutantpollutant treatmenttreatment andand degradationdegradation andand mainlymainly focus on pollutant-degrading enzymesenzymes andand theirtheir industrialindustrial applications.applications. Figure 1. Schematic illustration of the microbial bioremediationbioremediation of environmental pollutantspollutants andand itsits “expanded”“expanded ” applications. applications. EmergingEmerging contaminantscontaminants areare oftenoften releasedreleased intointo thethe environment,environment, causingcausing harmful impactsimpacts andand health health problems. problems. Researches Researches on on the the mechanism mechanism of theof the pollutants pollutants bioremediation bioremedia- microbestion microbes and enzymesand enzymes will helpwill help the application the applicatio of bioremediationn of bioremediation to environmental to environmental clean-ups, clean-ups, and and the characterize enzymes will also contribute to industrial processes such as pharmaceutical the characterize enzymes will also contribute to industrial processes such as pharmaceutical and and chemical compounds. chemical compounds. 2. Enzymes Involved in Organic Pollutant Degradation and Transformation 2.1. Oxygenases in Degradation of Aromatic Compounds Monooxygenases andand dioxygenasesdioxygenases areare thethe twotwo main subgroups ofof oxygenases. They are involved in in the the process process of of desulfurization, desulfurization, dehalogenation, dehalogenation, the the oxidative oxidative release release of the of thenitro nitro group, group, and hydroxylation and hydroxylation of various of various aromatic aromatic and aliphatic and aliphatic compounds compounds [11]. Alkane [11]. Alkanemonooxygenases monooxygenases are one are of onethe ofbest-studied the best-studied monooxygenases, monooxygenases, which which catalyze catalyze the first the firststep stepof alkane of alkane degradation. degradation. Two Two common common alkane alkane monooxygenases monooxygenases are AlkB-relatedAlkB-related monooxygenases and and the the cytochrome cytochrome P450 P450 family family proteins proteins [12]. [12]. These These two two categories categories of ofenzymes enzymes can can utilize utilize short-chain short-chain alkanes alkanes for for growth. growth.
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