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Wang W, Fan Q, Gong T, Zhang M, Li C, Zhang Y, Li H. Superb green cycling strategies for microbe-Fe 0 neural network-type interaction: Harnessing eight key genes encoding enzymes and mineral transformations to efficiently treat PFOA. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134143. [PMID: 38554507 DOI: 10.1016/j.jhazmat.2024.134143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/02/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024]
Abstract
To address time-consuming and efficiency-limited challenges in conventional zero-valent iron (ZVI, Fe0) reduction or biotransformation for perfluorooctanoic acid (PFOA) treatment, two calcium alginate-embedded amendments (biochar-immobilized PFOA-degrading bacteria (CB) and ZVI (CZ)) were developed to construct microbe-Fe0 high-rate interaction systems. Interaction mechanisms and key metabolic pathways were systematically explored using metagenomics and a multi-process coupling model for PFOA under microbe-Fe0 interaction. Compared to Fe0 (0.0076 day-1) or microbe (0.0172 day-1) systems, the PFOA removal rate (0.0426 day-1) increased by 1.5 to 4.6 folds in the batch microbe-Fe0 interaction system. Moreover, Pseudomonas accelerated the transformation of Fe0 into Fe3+, which profoundly impacted PFOA transport and fate. Model results demonstrated microbe-Fe0 interaction improved retardation effect for PFOA in columns, with decreased dispersivity a (0.48 to 0.20 cm), increased reaction rate λ (0.15 to 0.22 h-1), distribution coefficient Kd (0.22 to 0.46 cm3∙g-1), and fraction f´(52 % to 60 %) of first-order kinetic sorption of PFOA in microbe-Fe0 interaction column system. Moreover, intermediates analysis showed that microbe-Fe0 interaction diversified PFOA reaction pathways. Three key metabolic pathways (ko00362, ko00626, ko00361), eight functional genes, and corresponding enzymes for PFOA degradation were identified. These findings provide insights into microbe-Fe0 "neural network-type" interaction by unveiling biotransformation and mineral transformation mechanisms for efficient PFOA treatment.
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Affiliation(s)
- Wenbing Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China.
| | - Qifeng Fan
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Tiantian Gong
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Meng Zhang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Chunyang Li
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Yunhui Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Hui Li
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China.
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Xiao J, Huang J, Wang Y, Qian X. The fate and behavior of perfluorooctanoic acid (PFOA) in constructed wetlands: Insights into potential removal and transformation pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160309. [PMID: 36403847 DOI: 10.1016/j.scitotenv.2022.160309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Although constructed wetland (CW) technology is widely used to eliminate emerging organic pollutants, the removal pathway of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in CW system have not been fully understood yet. This study aims to deeply probe into the fate and behavior of perfluorooctanoic acid (PFOA) in CW system. Findings indicated that the removal efficiency of PFOA by CW system was 49.69-73.63 % with initial concentrations at 100-1000 μg/L. Substrate was the main "sink" of PFOA into the CWs (46.22-50.83 %), and the plant uptake (1.99-2.48 %) accounted for a small proportion. Transformation products in the effluent of CW systems included a series of short-chain perfluorinated carboxylic acids (PFCAs), hydrogen-containing perfluoroalkanes and other organic fluorides. Activated pathways of xenobiotics biodegradation suggested that enzyme-mediated biochemical reactions might be responsible for the PFOA transformation. The transformation pathway included enzymatic decarboxylation, hydroxylation, hydrolysis, dehydrogenation and dehalogenation, as well as non-enzymatic reactions. These discoveries provide new insights into the in-depth understanding environmental behavior of PFOA in ecosystem and lay the foundation for further ecological remediation.
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Affiliation(s)
- Jun Xiao
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Juan Huang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China.
| | - Ying Wang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Xiuwen Qian
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
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The Operon Encoding Hydrolytic Dehalogenation of 4-Chlorobenzoate Is Transcriptionally Regulated by the TetR-Type Repressor FcbR and Its Ligand 4-Chlorobenzoyl Coenzyme A. Appl Environ Microbiol 2021; 87:AEM.02652-20. [PMID: 33397703 DOI: 10.1128/aem.02652-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022] Open
Abstract
The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a coenzyme A (CoA)-activation-type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and inducibly expressed in response to 4CBA. However, the associated molecular mechanism remains unknown. In this study, a gene (fcbR) adjacent to the fcb operon was predicted to encode a TetR-type transcriptional regulator in Comamonas sediminis strain CD-2. The fcbR knockout strain exhibited constitutive expression of the fcb cluster. In the host Escherichia coli, the expression of the Pfcb -fused green fluorescent protein (gfp) reporter was repressed by the introduction of the fcbR gene, and genetic studies combining various catabolic genes suggest that the ligand for FcbR may be an intermediate metabolite. Purified FcbR could bind to the Pfcb DNA probe in vitro, and the metabolite 4-chlorobenzyl-CoA (4CBA-CoA) prevented FcbR binding to the P fcb DNA probe. Isothermal titration calorimetry (ITC) measurements showed that 4CBA-CoA could bind to FcbR at a 1:1 molar ratio. DNase I footprinting showed that FcbR protected a 42-bp DNA motif (5'-GGAAATCAATAGGTCCATAGAAAATCTATTGACTAATCGAAT-3') that consists of two sequence repeats containing four pseudopalindromic sequences (5'-TCNATNGA-3'). This binding motif overlaps with the -35 box of Pfcb and was proposed to prevent the binding of RNA polymerase. This study characterizes a transcriptional repressor of the fcb operon, together with its ligand, thus identifying halogenated benzoyl-CoA as belonging to the class of ligands of transcriptional regulators.IMPORTANCE The bacterial hydrolytic dehalogenation of 4CBA is a special CoA-activation-type catabolic pathway that plays an important role in the biodegradation of polychlorinated biphenyls and some herbicides. With genetic and biochemical approaches, the present study identified the transcriptional repressor and its cognate effector of a 4CBA hydrolytic dehalogenation operon. This work extends halogenated benzoyl-CoA as a new member of CoA-derived effector compounds that mediate allosteric regulation of transcriptional regulators.
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Pimviriyakul P, Wongnate T, Tinikul R, Chaiyen P. Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microb Biotechnol 2020; 13:67-86. [PMID: 31565852 PMCID: PMC6922536 DOI: 10.1111/1751-7915.13488] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.
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Affiliation(s)
- Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn UniversityNakhon Pathom73000Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol UniversityBangkok10400Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
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Tiedt O, Fuchs J, Eisenreich W, Boll M. A catalytically versatile benzoyl-CoA reductase, key enzyme in the degradation of methyl- and halobenzoates in denitrifying bacteria. J Biol Chem 2018; 293:10264-10274. [PMID: 29769313 DOI: 10.1074/jbc.ra118.003329] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
Class I benzoyl-CoA (BzCoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds. They catalyze the ATP-dependent reduction of the central BzCoA intermediate and analogues of it to conjugated cyclic 1,5-dienoyl-CoAs probably by a radical-based, Birch-like reduction mechanism. Discovered in 1995, the enzyme from the denitrifying bacterium Thauera aromatica (BCRTar) has so far remained the only isolated and biochemically accessible BCR, mainly because BCRs are extremely labile, and their heterologous production has largely failed so far. Here, we describe a platform for the heterologous expression of the four structural genes encoding a designated 3-methylbenzoyl-CoA reductase from the related denitrifying species Thauera chlorobenzoica (MBRTcl) in Escherichia coli This reductase represents the prototype of a distinct subclass of ATP-dependent BCRs that were proposed to be involved in the degradation of methyl-substituted BzCoA analogues. The recombinant MBRTcl had an αβγδ-subunit architecture, contained three low-potential [4Fe-4S] clusters, and was highly oxygen-labile. It catalyzed the ATP-dependent reductive dearomatization of BzCoA with 2.3-2.8 ATPs hydrolyzed per two electrons transferred and preferentially dearomatized methyl- and chloro-substituted analogues in meta- and para-positions. NMR analyses revealed that 3-methylbenzoyl-CoA is regioselectively reduced to 3-methyl-1,5-dienoyl-CoA. The unprecedented reductive dechlorination of 4-chloro-BzCoA to BzCoA probably via HCl elimination from a reduced intermediate allowed for the previously unreported growth of T. chlorobenzoica on 4-chlorobenzoate. The heterologous expression platform established in this work enables the production, isolation, and characterization of bacterial and archaeal BCR and BCR-like radical enzymes, for many of which the function has remained unknown.
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Affiliation(s)
- Oliver Tiedt
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
| | - Jonathan Fuchs
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Technische Universität München, 85747 Garching, Germany
| | - Matthias Boll
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
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Lohans CT, Wang DY, Wang J, Hamed RB, Schofield CJ. Crotonases: Nature’s Exceedingly Convertible Catalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Christopher T. Lohans
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - David Y. Wang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Jimmy Wang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Refaat B. Hamed
- Department
of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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Satpathy R, Konkimalla VB, Ratha J. Microbial dehalogenation: 3-chloropropanoic acid (3-CPA) degradation as a case study. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261716060175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Parachin NS, Gorwa-Grauslund MF. Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:9. [PMID: 21545702 PMCID: PMC3113934 DOI: 10.1186/1754-6834-4-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 05/05/2011] [Indexed: 05/15/2023]
Abstract
BACKGROUND Xylose isomerase (XI) catalyses the isomerisation of xylose to xylulose in bacteria and some fungi. Currently, only a limited number of XI genes have been functionally expressed in Saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. The objective of the present study was to search for novel XI genes in the vastly diverse microbial habitat present in soil. As the exploitation of microbial diversity is impaired by the ability to cultivate soil microorganisms under standard laboratory conditions, a metagenomic approach, consisting of total DNA extraction from a given environment followed by cloning of DNA into suitable vectors, was undertaken. RESULTS A soil metagenomic library was constructed and two screening methods based on protein sequence similarity and enzyme activity were investigated to isolate novel XI encoding genes. These two screening approaches identified the xym1 and xym2 genes, respectively. Sequence and phylogenetic analyses revealed that the genes shared 67% similarity and belonged to different bacterial groups. When xym1 and xym2 were overexpressed in a xylA-deficient Escherichia coli strain, similar growth rates to those in which the Piromyces XI gene was expressed were obtained. However, expression in S. cerevisiae resulted in only one-fourth the growth rate of that obtained for the strain expressing the Piromyces XI gene. CONCLUSIONS For the first time, the screening of a soil metagenomic library in E. coli resulted in the successful isolation of two active XIs. However, the discrepancy between XI enzyme performance in E. coli and S. cerevisiae suggests that future screening for XI activity from soil should be pursued directly using yeast as a host.
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Affiliation(s)
- Nádia Skorupa Parachin
- Department of Applied Microbiology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- Present affiliation - Laboratório de Biologia Molecular, Universidade de Brasília, 70910-900 Brasília (DF), Brazil
| | - Marie F Gorwa-Grauslund
- Department of Applied Microbiology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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Wang Q, Wu H, Wang A, Du P, Pei X, Li H, Yin X, Huang L, Xiong X. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J Biol Chem 2010; 285:41509-16. [PMID: 20962349 DOI: 10.1074/jbc.m110.139659] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA family shuffling is a powerful method for enzyme engineering, which utilizes recombination of naturally occurring functional diversity to accelerate laboratory-directed evolution. However, the use of this technique has been hindered by the scarcity of family genes with the required level of sequence identity in the genome database. We describe here a strategy for collecting metagenomic homologous genes for DNA shuffling from environmental samples by truncated metagenomic gene-specific PCR (TMGS-PCR). Using identified metagenomic gene-specific primers, twenty-three 921-bp truncated lipase gene fragments, which shared 64-99% identity with each other and formed a distinct subfamily of lipases, were retrieved from 60 metagenomic samples. These lipase genes were shuffled, and selected active clones were characterized. The chimeric clones show extensive functional and genetic diversity, as demonstrated by functional characterization and sequence analysis. Our results indicate that homologous sequences of genes captured by TMGS-PCR can be used as suitable genetic material for DNA family shuffling with broad applications in enzyme engineering.
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Affiliation(s)
- Qiuyan Wang
- Center for Biomedicine and Health, Hangzhou Normal University, Hangzhou 310012, China
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Tuffin M, Anderson D, Heath C, Cowan DA. Metagenomic gene discovery: how far have we moved into novel sequence space? Biotechnol J 2010; 4:1671-83. [PMID: 19946882 DOI: 10.1002/biot.200900235] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.
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Affiliation(s)
- Marla Tuffin
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of Western Cape, Cape town, South Africa
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11
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Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 2009; 20:616-22. [DOI: 10.1016/j.copbio.2009.09.010] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/18/2009] [Accepted: 09/25/2009] [Indexed: 11/17/2022]
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