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Lu Q, Liang Q, Wang S. Burning question: Rethinking organohalide degradation strategy for bioremediation applications. Microb Biotechnol 2024; 17:e14539. [PMID: 39075849 PMCID: PMC11286677 DOI: 10.1111/1751-7915.14539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024] Open
Abstract
Organohalides are widespread pollutants that pose significant environmental hazards due to their high degree of halogenation and elevated redox potentials, making them resistant to natural attenuation. Traditional bioremediation approaches, primarily relying on bioaugmentation and biostimulation, often fall short of achieving complete detoxification. Furthermore, the emergence of complex halogenated pollutants, such as per- and polyfluoroalkyl substances (PFASs), further complicates remediation efforts. Therefore, there is a pressing need to reconsider novel approaches for more efficient remediation of these recalcitrant pollutants. This review proposes novel redox-potential-mediated hybrid bioprocesses, tailored to the physicochemical properties of pollutants and their environmental contexts, to achieve complete detoxification of organohalides. The possible scenarios for the proposed bioremediation approaches are further discussed. In anaerobic environments, such as sediment and groundwater, microbial reductive dehalogenation coupled with fermentation and methanogenesis can convert organohalides into carbon dioxide and methane. In environments with anaerobic-aerobic alternation, such as paddy soil and wetlands, a synergistic process involving reduction and oxidation can facilitate the complete mineralization of highly halogenated organic compounds. Future research should focus on in-depth exploration of microbial consortia, the application of ecological principles-guided strategies, and the development of bioinspired-designed techniques. This paper contributes to the academic discourse by proposing innovative remediation strategies tailored to the complexities of organohalide pollution.
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Affiliation(s)
- Qihong Lu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐Sen UniversityGuangzhouChina
| | - Qi Liang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐Sen UniversityGuangzhouChina
| | - Shanquan Wang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐Sen UniversityGuangzhouChina
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2
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Lu Y, Lu F, Zhang J, Tang Q, Yang D, Liu Y. Understanding the sources, function, and irreplaceable role of cobamides in organohalide-respiring bacteria. Front Microbiol 2024; 15:1435674. [PMID: 39139376 PMCID: PMC11321594 DOI: 10.3389/fmicb.2024.1435674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 08/15/2024] Open
Abstract
Halogenated organic compounds are persistent pollutants that pose a serious threat to human health and the safety of ecosystems. Cobamides are essential cofactors for reductive dehalogenases (RDase) in organohalide-respiring bacteria (OHRB), which catalyze the dehalogenation process. This review systematically summarizes the impact of cobamides on organohalide respiration. The catalytic processes of cobamide in dehalogenation processes are also discussed. Additionally, we examine OHRB, which cannot synthesize cobamide and must obtain it from the environment through a salvage pathway; the co-culture with cobamide producer is more beneficial and possible. This review aims to help readers better understand the importance and function of cobamides in reductive dehalogenation. The presented information can aid in the development of bioremediation strategies.
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Affiliation(s)
- Yongfeng Lu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Fancheng Lu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Jian Zhang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Qianwei Tang
- College & Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Dan Yang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
- Guangxi Yuhuacheng Environmental Protection Technology Co., Nanning, China
| | - Yaqing Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
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3
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Yu Y, Xu F, Zhao W, Thoma C, Che S, Richman JE, Jin B, Zhu Y, Xing Y, Wackett L, Men Y. Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by Acetobacterium spp. SCIENCE ADVANCES 2024; 10:eado2957. [PMID: 39018407 PMCID: PMC466959 DOI: 10.1126/sciadv.ado2957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Enzymatic cleavage of C─F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. The microbial defluorination products were structurally confirmed and showed regiospecificity and stereospecificity, consistent with their formation by enzymatic reactions. A comparison of defluorination activities among several Acetobacterium species indicated that a functional fluoride exporter was required for the detoxification of the released fluoride. Results from both in vivo inhibition tests and in silico enzyme modeling suggested the involvement of enzymes of the flavin-based electron-bifurcating caffeate reduction pathway [caffeoyl-CoA reductase (CarABCDE)] in the reductive defluorination. This is a report on specific microorganisms carrying out enzymatic reductive defluorination of PFAS, which could be linked to electron-bifurcating reductases that are environmentally widespread.
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Affiliation(s)
- Yaochun Yu
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Fengjun Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Weiyang Zhao
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Calvin Thoma
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, MN 55108, USA
| | - Shun Che
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Jack E. Richman
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, MN 55108, USA
| | - Bosen Jin
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Yiwen Zhu
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Yue Xing
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Lawrence Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, MN 55108, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
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4
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Zhao S, Rogers MJ, Ding C, Xu G, He J. Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4214-4225. [PMID: 38373236 DOI: 10.1021/acs.est.3c09171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.
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Affiliation(s)
- Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Chang Ding
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research─UFZ, Permoserstraße, 15, Leipzig 04318, Germany
| | - Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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5
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Rahmatullah R, Marquis CP. Evaluation of alternate hosts for recombinant expression of a reductive dehalogenase. Enzyme Microb Technol 2024; 174:110390. [PMID: 38147780 DOI: 10.1016/j.enzmictec.2023.110390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Abstract
Organohalides are recalcitrant, toxic environmental pollutants. Reductive dehalogenase enzymes (RDases) found in organohalide respiring bacteria (OHRB) utilise organohalides as electron acceptors for cellular energy and growth, producing lesser-halogenated compounds. Consequently, microbial reductive dehalogenation via organohalide respiration represents a promising solution for clean-up of organohalide pollutants. Dehalobacter sp. UNSWDHB is an OHRB capable of respiring highly toxic chloroform (CF) and converting it to dichloromethane (DCM). TmrA has been identified as an RDase responsible for this conversion and different strategies for generation of functional recombinant TmrA is the focus of this article. In this study, TmrA was recovered from inclusion bodies expressed in E. coli and refolded in the presence of FeCl3, Na2S and cobalamin to yield functional enzyme. TmrA has been previously expressed in a soluble and functional form in the corrinoid-producing Bacillus megaterium. Using a fractional experimental design for cultivation and induction combined with purification under anaerobic conditions resulted in substantially higher activity of recombinant and native TmrA than previously reported. TmrA was then expressed in a soluble and active form in Shimwellia blattae. Co-expression with two different putative chaperone proteins from the original host did not increase the level of soluble expression in S. blattae, however activity assays showed that removing the TAT signal from TmrA increases the dechlorination activity compared to when the TAT signal is present. Finally, TmrA was successfully expressed in a soluble and active form in the H2-oxidizing C. necator H16, a novel host for the expression of RDases.
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Affiliation(s)
- Rabeya Rahmatullah
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Sydney, NSW 2052 Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Sydney, NSW 2052 Australia.
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6
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Iyer A, Soto Martín EC, Cameron GA, Louis P, Duncan SH, Bestwick CS, Russell WR. Gorse (Ulex europeaus) wastes with 5,6-dimethyl benzimidazole supplementation can support growth of vitamin B12 producing commensal gut microbes. PLoS One 2024; 19:e0290052. [PMID: 38422016 PMCID: PMC10903898 DOI: 10.1371/journal.pone.0290052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024] Open
Abstract
Many commensal gut microbes are recognized for their potential to synthesize vitamin B12, offering a promising avenue to address deficiencies through probiotic supplementation. While bioinformatics tools aid in predicting B12 biosynthetic potential, empirical validation remains crucial to confirm production, identify cobalamin vitamers, and establish biosynthetic yields. This study investigates vitamin B12 production in three human colonic bacterial species: Anaerobutyricum hallii DSM 3353, Roseburia faecis DSM 16840, and Anaerostipes caccae DSM 14662, along with Propionibacterium freudenreichii DSM 4902 as a positive control. These strains were selected for their potential use as probiotics, based on speculated B12 production from prior bioinformatic analyses. Cultures were grown in M2GSC, chemically defined media (CDM), and Gorse extract medium (GEM). The composition of GEM was similar to CDM, except that the carbon and nitrogen sources were replaced with the protein-depleted liquid waste obtained after subjecting Gorse to a leaf protein extraction process. B12 yields were quantified using liquid chromatography with tandem mass spectrometry. The results suggested that the three butyrate-producing strains could indeed produce B12, although the yields were notably low and were detected only in the cell lysates. Furthermore, B12 production was higher in GEM compared to M2GSC medium. The positive control, P. freudenreichii DSM 4902 produced B12 at concentrations ranging from 7 ng mL-1 to 12 ng mL-1. Univariate-scaled Principal Component Analysis (PCA) of data from previous publications investigating B12 production in P. freudenreichii revealed that B12 yields diminished when the carbon source concentration was ≤30 g L-1. In conclusion, the protein-depleted wastes from the leaf protein extraction process from Gorse can be valorised as a viable substrate for culturing B12-producing colonic gut microbes. Furthermore, this is the first report attesting to the ability of A. hallii, R. faecis, and A. caccae to produce B12. However, these microbes seem unsuitable for industrial applications owing to low B12 yields.
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Affiliation(s)
- Ajay Iyer
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Eva C Soto Martín
- Institue of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gary A Cameron
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Petra Louis
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | | | - Wendy R Russell
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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7
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Ng TL, Silver PA. Sustainable B 12-Dependent Dehalogenation of Organohalides in E. coli. ACS Chem Biol 2024; 19:380-391. [PMID: 38254247 DOI: 10.1021/acschembio.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial bioremediation can provide an environmentally friendly and scalable solution to treat contaminated soil and water. However, microbes have yet to optimize pathways for degrading persistent anthropogenic pollutants, in particular organohalides. In this work, we first expand our repertoire of enzymes useful for bioremediation. By screening a panel of cobalamin (B12)-dependent reductive dehalogenases, we identified previously unreported enzymes that dechlorinate perchloroethene and regioselectively deiodinate the thyroidal disruptor 2,4,6-triiodophenol. One deiodinase, encoded by the animal-associated anaerobe Clostridioides difficile, was demonstrated to dehalogenate the naturally occurring metabolites L-halotyrosines. In cells, several combinations of ferredoxin oxidoreductase and flavodoxin extract and transfer low-potential electrons from pyruvate to drive reductive dehalogenation without artificial reductants and mediators. This work provides new insights into a relatively understudied family of B12-dependent enzymes and sets the stage for engineering synthetic pathways for degrading unnatural small molecule pollutants.
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Affiliation(s)
- Tai L Ng
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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8
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Chen JJ. Interfacial Electron Transfer in Chemical and Biological Transformation of Pollutants in Environmental Catalysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21540-21549. [PMID: 38086095 DOI: 10.1021/acs.est.3c05608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Interfacial electron transfer (IET) is essential for chemical and biological transformation of pollutants, operative across diverse lengths and time scales. This Perspective presents an array of multiscale molecular simulation methodologies, supplemented by in situ monitoring and imaging techniques, serving as robust tools to decode IET enhancement mechanisms such as interface molecular modification, catalyst coordination mode, and atomic composition regulation. In addition, three IET-based pollutant transformation systems, an electrocatalytic oxidation system, a bioelectrochemical spatial coupling system, and an enzyme-inspired electrocatalytic system, were developed, demonstrating a high effect in transforming and degrading pollutants. To improve the effectiveness and scalability of IET-based strategies, the refinement of these systems is necessitated through rigorous research and theoretical exploration, particularly in the context of practical wastewater treatment scenarios. Future endeavors aim to elucidate the synergy between biological and chemical modules, edit the environmental functional microorganisms, and harness machine learning for designing advanced environmental catalysts to boost efficiency. This Perspective highlights the powerful potential of IET-focused environmental remediation strategies, emphasizing the critical role of interdisciplinary research in addressing the urgent global challenge of water pollution.
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Affiliation(s)
- Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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9
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Li J, Kumar A, Lewis JC. Non-native Intramolecular Radical Cyclization Catalyzed by a B 12 -Dependent Enzyme. Angew Chem Int Ed Engl 2023; 62:e202312893. [PMID: 37874184 DOI: 10.1002/anie.202312893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Despite the unique reactivity of vitamin B12 and its derivatives, B12 -dependent enzymes remain underutilized in biocatalysis. In this study, we repurposed the B12 -dependent transcription factor CarH to enable non-native radical cyclization reactions. An engineered variant of this enzyme, CarH*, catalyzes the formation γ- and δ-lactams through either redox-neutral or reductive ring closure with marked enhancement of reactivity and selectivity relative to the free B12 cofactor. CarH* also catalyzes an unusual spirocyclization by dearomatization of pendant arenes to produce bicyclic 1,3-diene products instead of 1,4-dienes provided by existing methods. These results and associated mechanistic studies highlight the importance of protein scaffolds for controlling the reactivity of B12 and expanding the synthetic utility of B12 -dependent enzymes.
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Affiliation(s)
- Jianbin Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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10
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Yu Y, Xu F, Zhao W, Thoma C, Che S, Richman JE, Jin B, Zhu Y, Xing Y, Wackett L, Men Y. Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.568471. [PMID: 38168399 PMCID: PMC10760045 DOI: 10.1101/2023.12.13.568471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo ; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by 19 F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.
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11
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Marciesky M, Aga DS, Bradley IM, Aich N, Ng C. Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS). J Chem Inf Model 2023; 63:7299-7319. [PMID: 37981739 PMCID: PMC10716909 DOI: 10.1021/acs.jcim.3c01303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023]
Abstract
Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.
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Affiliation(s)
- Melissa Marciesky
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Diana S Aga
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Ian M Bradley
- Department of Civil, Structural, and Environmental Engineering, State University of New York at Buffalo, Buffalo, New York 14228, United States
- Research and Education in Energy, Environmental and Water (RENEW) Institute, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Nirupam Aich
- Department of Civil and Environmental Engineering, University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0531, United States
| | - Carla Ng
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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12
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Wu R, Shen R, Liang Z, Zheng S, Yang Y, Lu Q, Adrian L, Wang S. Improve Niche Colonization and Microbial Interactions for Organohalide-Respiring-Bacteria-Mediated Remediation of Chloroethene-Contaminated Sites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17338-17352. [PMID: 37902991 DOI: 10.1021/acs.est.3c05932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation is promising in in situ bioremediation of chloroethene-contaminated sites. The bioremediation efficiency of this approach is largely determined by the successful colonization of fastidious OHRB, which is highly dependent on the presence of proper growth niches and microbial interactions. In this study, based on two ecological principles (i.e., Priority Effects and Coexistence Theory), three strategies were developed to enhance niche colonization of OHRB, which were tested both in laboratory experiments and field applications: (i) preinoculation of a niche-preparing culture (NPC, being mainly constituted of fermenting bacteria and methanogens); (ii) staggered fermentation; and (iii) increased inoculation of CE40 (a Dehalococcoides-containing tetrachloroethene-to-ethene dechlorinating enrichment culture). Batch experimental results show significantly higher dechlorination efficiencies, as well as lower concentrations of volatile fatty acids (VFAs) and methane, in experimental sets with staggered fermentation and niche-preconditioning with NPC for 4 days (CE40_NPC-4) relative to control sets. Accordingly, a comparatively higher abundance of Dehalococcoides as major OHRB, together with a lower abundance of fermenting bacteria and methanogens, was observed in CE40_NPC-4 with staggered fermentation, which indicated the balanced syntrophic and competitive interactions between OHRB and other populations for the efficient dechlorination. Further experiments with microbial source tracking analyses suggested enhanced colonization of OHRB by increasing the inoculation ratio of CE40. The optimized conditions for enhanced colonization of OHRB were successfully employed for field bioremediation of trichloroethene (TCE, 0.3-1.4 mM)- and vinyl chloride (VC, ∼0.04 mM)-contaminated sites, resulting in 96.6% TCE and 99.7% VC dechlorination to ethene within 5 and 3 months, respectively. This study provides ecological principles-guided strategies for efficient bioremediation of chloroethene-contaminated sites, which may be also employed for removal of other emerging organohalide pollutants.
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Affiliation(s)
- Rifeng Wu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Rui Shen
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhiwei Liang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shengzhi Zheng
- China State Science Dingshi Environmental Engineering Co., Ltd., Beijing 100102, China
| | - Yong Yang
- China State Science Dingshi Environmental Engineering Co., Ltd., Beijing 100102, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Shanquan Wang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
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13
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Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J. Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun 2023; 14:7038. [PMID: 37923808 PMCID: PMC10624902 DOI: 10.1038/s41467-023-42927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Babatunde E Ekundayo
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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14
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Mendoza J, Purchal M, Yamada K, Koutmos M. Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Nat Commun 2023; 14:6365. [PMID: 37821448 PMCID: PMC10567725 DOI: 10.1038/s41467-023-42037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MS) is a key enzyme in methionine and folate one-carbon metabolism. MS is a large multi-domain protein capable of binding and activating three substrates: homocysteine, folate, and S-adenosylmethionine for methylation. Achieving three chemically distinct methylations necessitates significant domain rearrangements to facilitate substrate access to the cobalamin cofactor at the right time. The distinct conformations required for each reaction have eluded structural characterization as its inherently dynamic nature renders structural studies difficult. Here, we use a thermophilic MS homolog (tMS) as a functional MS model. Its exceptional stability enabled characterization of MS in the absence of cobalamin, marking the only studies of a cobalamin-binding protein in its apoenzyme state. More importantly, we report the high-resolution full-length MS structure, ending a multi-decade quest. We also capture cobalamin loading in crystallo, providing structural insights into holoenzyme formation. Our work paves the way for unraveling how MS orchestrates large-scale domain rearrangements crucial for achieving challenging chemistries.
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Affiliation(s)
- Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meredith Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- New England Biolabs, Inc., Ipswich, MA, 01938, England
| | - Kazuhiro Yamada
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
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15
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Song G, Wu H, Jing J, Zhang X, Wang X, Li S, Zhou M. Insights into Electrochemical Dehalogenation by Non-Noble Metal Single-Atom Cobalt with High Efficiency and Low Energy Consumption. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:14482-14492. [PMID: 37699122 DOI: 10.1021/acs.est.3c06021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
It is critical to discover a non-noble metal catalyst with high catalytic activity capable of replacing palladium in electrochemical reduction. In this work, a highly efficient single-atom Co-N/C catalyst was synthesized with metal-organic frameworks (MOFs) as a precursor for electrochemical dehalogenation. X-ray absorption spectroscopy (XAS) revealed that Co-N/C exhibited a Co-N4 configuration, which had more active sites and a faster charge-transfer rate and thus enabled the efficient removal of florfenicol (FLO) at a wide pH, achieving a rate constant 3.5 and 2.1 times that of N/C and commercial Pd/C, respectively. The defluorination and dechlorination efficiencies were 67.6 and 95.6%, respectively, with extremely low Co leaching (6 μg L-1), low energy consumption (22.7 kWh kg-1), and high turnover frequency (TOF) (0.0350 min-1), demonstrating excellent dehalogenation performance. Spiking experiments and density functional theory (DFT) verified that Co-N4 was the active site and had the lowest energy barrier for forming atomic hydrogen (H*) (ΔGH*). Capture experiments, electron paramagnetic resonance (EPR), electrochemical tests, and in situ Fourier transform infrared (FTIR) proved that H* and direct electron transfer were responsible for dehalogenation. Toxicity assessment indicated that FLO toxicity decreased significantly after dehalogenation. This work develops a non-noble metal catalyst with broad application prospects in electrocatalytic dehalogenation.
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Affiliation(s)
- Ge Song
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Huizhong Wu
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jiana Jing
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xuyang Zhang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xuechun Wang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shuaishuai Li
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Minghua Zhou
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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16
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Fisher K, Halliwell T, Payne KAP, Ragala G, Hay S, Rigby SEJ, Leys D. Efficient NADPH-dependent dehalogenation afforded by a self-sufficient reductive dehalogenase. J Biol Chem 2023; 299:105086. [PMID: 37495113 PMCID: PMC10463259 DOI: 10.1016/j.jbc.2023.105086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Reductive dehalogenases are corrinoid and iron-sulfur cluster-containing enzymes that catalyze the reductive removal of a halogen atom. The oxygen-sensitive and membrane-associated nature of the respiratory reductive dehalogenases has hindered their detailed kinetic study. In contrast, the evolutionarily related catabolic reductive dehalogenases are oxygen tolerant, with those that are naturally fused to a reductase domain with similarity to phthalate dioxygenase presenting attractive targets for further study. We present efficient heterologous expression of a self-sufficient catabolic reductive dehalogenase from Jhaorihella thermophila in Escherichia coli. Combining the use of maltose-binding protein as a solubility-enhancing tag with the btuCEDFB cobalamin uptake system affords up to 40% cobalamin occupancy and a full complement of iron-sulfur clusters. The enzyme is able to efficiently perform NADPH-dependent dehalogenation of brominated and iodinated phenolic compounds, including the flame retardant tetrabromobisphenol, under both anaerobic and aerobic conditions. NADPH consumption is tightly coupled to product formation. Surprisingly, corresponding chlorinated compounds only act as competitive inhibitors. Electron paramagnetic resonance spectroscopy reveals loss of the Co(II) signal observed in the resting state of the enzyme under steady-state conditions, suggesting accumulation of Co(I)/(III) species prior to the rate-limiting step. In vivo reductive debromination activity is readily observed, and when the enzyme is expressed in E. coli strain W, supports growth on 3-bromo-4-hydroxyphenylacetic as a sole carbon source. This demonstrates the potential for catabolic reductive dehalogenases for future application in bioremediation.
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Affiliation(s)
- Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Tom Halliwell
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel Ragala
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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17
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Min Y, Mei SC, Pan XQ, Chen JJ, Yu HQ, Xiong Y. Mimicking reductive dehalogenases for efficient electrocatalytic water dechlorination. Nat Commun 2023; 14:5134. [PMID: 37612275 PMCID: PMC10447495 DOI: 10.1038/s41467-023-40906-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Electrochemical technology is a robust approach to removing toxic and persistent chlorinated organic pollutants from water; however, it remains a challenge to design electrocatalysts with high activity and selectivity as elaborately as natural reductive dehalogenases. Here we report the design of high-performance electrocatalysts toward water dechlorination by mimicking the binding pocket configuration and catalytic center of reductive dehalogenases. Specifically, our designed electrocatalyst is an assembled heterostructure by sandwiching a molecular catalyst into the interlayers of two-dimensional graphene oxide. The electrocatalyst exhibits excellent dechlorination performance, which enhances reduction of intermediate dichloroacetic acid by 7.8 folds against that without sandwich configuration and can selectively generate monochloro-groups from trichloro-groups. Molecular simulations suggest that the sandwiched inner space plays an essential role in tuning solvation shell, altering protonation state and facilitating carbon-chlorine bond cleavage. This work demonstrates the concept of mimicking natural reductive dehalogenases toward the sustainable treatment of organohalogen-contaminated water and wastewater.
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Affiliation(s)
- Yuan Min
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shu-Chuan Mei
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiao-Qiang Pan
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie-Jie Chen
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.
| | - Yujie Xiong
- Hefei National Research Center for Physical Sciences at the Microscale, Collaborative Innovative Center of Chemistry for Energy Materials (iChEM), School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China.
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18
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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19
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Zhang S, Wen W, Xia X, Ouyang W, Mai BX, Adrian L, Schüürmann G. Insight into the Mechanism Underlying Dehalococcoides mccartyi Strain CBDB1-Mediated B 12-Dependent Aromatic Reductive Dehalogenation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37428517 DOI: 10.1021/acs.est.3c00364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Anaerobic bacteria transform aromatic halides through reductive dehalogenation. This dehalorespiration is catalyzed by the supernucleophilic coenzyme vitamin B12, cob(I)alamin, in reductive dehalogenases. So far, the underlying inner-sphere electron transfer (ET) mechanism has been discussed controversially. In the present study, all 36 chloro-, bromo-, and fluorobenzenes and full-size cobalamin are analyzed at the quantum chemical density functional theory level with respect to a wide range of theoretically possible inner-sphere ET mechanisms. The calculated reaction free energies within the framework of CoI···X (X = F, Cl, and Br) attack rule out most of the inner-sphere pathways. The only route with feasible energetics is a proton-coupled two-ET mechanism that involves a B12 side-chain tyrosine (modeled by phenol) as a proton donor. For 12 chlorobenzenes and 9 bromobenzenes with experimental data from Dehalococcoides mccartyi strain CBDB1, the newly proposed PC-TET mechanism successfully discriminates 16 of 17 active from 4 inactive substrates and correctly predicts the observed regiospecificity to 100%. Moreover, fluorobenzenes are predicted to be recalcitrant in agreement with experimental findings. Conceptually, based on the Bell-Evans-Polanyi principle, the computational approach provides novel mechanistic insights and may serve as a tool for predicting the energetic feasibility of reductive aromatic dehalogenation.
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Affiliation(s)
- Shangwei Zhang
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wu Wen
- Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai 519087, China
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Bi-Xian Mai
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lorenz Adrian
- UFZ Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, Berlin 13355, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany
- Institute of Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Straße 29, Freiberg 09596, Germany
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20
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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21
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Fu Y, Liu X, Xia Y, Guo X, Guo J, Zhang J, Zhao W, Wu Y, Wang J, Zhong F. Whole-cell-catalyzed hydrogenation/deuteration of aryl halides with a genetically repurposed photodehalogenase. Chem 2023. [DOI: 10.1016/j.chempr.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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22
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Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation. Sci Rep 2023; 13:4082. [PMID: 36906658 PMCID: PMC10008544 DOI: 10.1038/s41598-023-30310-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two Fe4S4 iron-sulfur clusters for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility in complex with the ligands, i.e., in their native states. Therefore, an apo-protein predicted by AF2 is actually a holo-protein awaiting ligands.
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23
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Ghosh R, Thomas DS, Arcot J. Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies. Foods 2023; 12:foods12030575. [PMID: 36766105 PMCID: PMC9914923 DOI: 10.3390/foods12030575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Ligand-receptor molecular recognition is the basis of biological processes. The Saturation Transfer Difference-NMR (STD-NMR) technique has been recently used to gain qualitative and quantitative information about physiological interactions at an atomic resolution. The molecular recognition patterns between the cyanocobalamin (CNBL)/aqua cobalamin (OHBL) and different plant and animal proteins were investigated via STD-NMR supplemented by molecular docking. This study demonstrates that myoglobin has the highest binding affinity and that gluten has the lowest affinity. Casein also shows a higher binding affinity for cyanocobalamin when compared with that of plant-based proteins. STD-NMR results showed the moderate binding capability of casein with both CNBL and OHBL. Computer simulation confirmed the recognition mode in theory and was compared with the experiments. This work is beneficial for understanding the binding affinity and biological action of cyanocobalamin and will attract researchers to use NMR technology to link the chemical and physiological properties of nutrients.
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Affiliation(s)
- Ruchira Ghosh
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Jayashree Arcot
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: ; Tel.: +61-293855360
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24
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Zhang X, Wang Z, Li Z, Shaik S, Wang B. [4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Zhen Li
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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Wang S, He J, Shen C, Manefield MJ. Editorial: Organohalide respiration: New findings in metabolic mechanisms and bioremediation applications, Volume II. Front Microbiol 2022; 13:1112309. [PMID: 36590394 PMCID: PMC9800048 DOI: 10.3389/fmicb.2022.1112309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Affiliation(s)
- Shanquan Wang
- Environmental Microbiome Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China,*Correspondence: Shanquan Wang ✉
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Michael J. Manefield
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
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Koide T, Ono T, Shimakoshi H, Hisaeda Y. Functions of bioinspired pyrrole cobalt complexes–recently developed catalytic systems of vitamin B12 related complexes and porphycene complexes–. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Cobalamin Riboswitches Are Broadly Sensitive to Corrinoid Cofactors to Enable an Efficient Gene Regulatory Strategy. mBio 2022; 13:e0112122. [PMID: 35993747 PMCID: PMC9600662 DOI: 10.1128/mbio.01121-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In bacteria, many essential metabolic processes are controlled by riboswitches, gene regulatory RNAs that directly bind and detect metabolites. Highly specific effector binding enables riboswitches to respond to a single biologically relevant metabolite. Cobalamin riboswitches are a potential exception because over a dozen chemically similar but functionally distinct cobalamin variants (corrinoid cofactors) exist in nature. Here, we measured cobalamin riboswitch activity in vivo using a Bacillus subtilis fluorescent reporter system and found, among 38 tested riboswitches, a subset responded to corrinoids promiscuously, while others were semiselective. Analyses of chimeric riboswitches and structural models indicate, unlike other riboswitch classes, cobalamin riboswitches indirectly differentiate among corrinoids by sensing differences in their structural conformation. This regulatory strategy aligns riboswitch-corrinoid specificity with cellular corrinoid requirements in a B. subtilis model. Thus, bacteria can employ broadly sensitive riboswitches to cope with the chemical diversity of essential metabolites. IMPORTANCE Some bacterial mRNAs contain a region called a riboswitch which controls gene expression by binding to a metabolite in the cell. Typically, riboswitches sense and respond to a limited range of cellular metabolites, often just one type. In this work, we found the cobalamin (vitamin B12) riboswitch class is an exception, capable of sensing and responding to multiple variants of B12-collectively called corrinoids. We found cobalamin riboswitches vary in corrinoid specificity with some riboswitches responding to each of the corrinoids we tested, while others responding only to a subset of corrinoids. Our results suggest the latter class of riboswitches sense intrinsic conformational differences among corrinoids in order to support the corrinoid-specific needs of the cell. These findings provide insight into how bacteria sense and respond to an exceptionally diverse, often essential set of enzyme cofactors.
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Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux. Appl Environ Microbiol 2022; 88:e0118222. [PMID: 36036586 PMCID: PMC9499029 DOI: 10.1128/aem.01182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N11-ATG), compared to those of odcA/orf419 (CAT-N11-ATG) and odcC (CAT-N11-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.
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Yu F, Luo W, Xie W, Li Y, Meng S, Kan J, Ye X, Peng T, Wang H, Huang T, Hu Z. Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129159. [PMID: 35643009 DOI: 10.1016/j.jhazmat.2022.129159] [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: 03/25/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Shanshan Meng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Jie Kan
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, PR China.
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Chen K, Xu X, Yang M, Liu T, Liu B, Zhu J, Wang B, Jiang J. Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats. Environ Microbiol 2022; 24:5123-5138. [PMID: 35876302 DOI: 10.1111/1462-2920.16141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Muji Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tairong Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Bin Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jianchun Zhu
- Laboratory Centre of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
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Vasileiadis S, Perruchon C, Scheer B, Adrian L, Steinbach N, Trevisan M, Plaza-Bolaños P, Agüera A, Chatzinotas A, Karpouzas DG. Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole. Environ Microbiol 2022; 24:5105-5122. [PMID: 35799498 DOI: 10.1111/1462-2920.16116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13 C-labelled versus 12 C-TBZ showed that 66% of the 13 C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.
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Affiliation(s)
- Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Benjamin Scheer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nicole Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Marco Trevisan
- Department of Sustainable Food Process, Universitá Cattolica del Sacro Cuore, Piacenza, Italy
| | - Patricia Plaza-Bolaños
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
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Yin Y, Shi L, Zhang S, Duan X, Zhang J, Sun H, Wang S. Two−dimensional nanomaterials confined single atoms: New opportunities for environmental remediation. NANO MATERIALS SCIENCE 2022. [DOI: 10.1016/j.nanoms.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Phillips E, Bulka O, Picott K, Kümmel S, Edwards E, Nijenhuis I, Gehre M, Dworatzek S, Webb J, Lollar BS. Investigation of Active Site Amino Acid Influence on Carbon and Chlorine Isotope Fractionation during Reductive Dechlorination. FEMS Microbiol Ecol 2022; 98:6608266. [PMID: 35700008 DOI: 10.1093/femsec/fiac072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically-catalyzed reactions to reference experiments with abiotic corrinoid-catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzyme mechanisms and kinetics, including RDases. Here, we report isotopic fractionation (ε) during biotransformation of chloroform (CF) for carbon (εC = -1.52 ± 0.34‰) and chlorine (εCl = -1.84 ± 0.19‰), corresponding to a ΛC/Cl value of 1.13 ± 0.35. These results are highly suppressed compared to isotope effects observed both during CF biotransformation by another organism with a highly similar RDase (> 95% sequence identity) at the amino acid level, and to those observed during abiotic dehalogenation of CF. Amino acid differences occur at four locations within the two different RDases' active sites, and this study examines whether these differences potentially affect the observed εC, εCl, and ΛC/Cl. Structural protein models approximating the locations of the residues elucidate possible controls on reaction mechanisms and/or substrate binding efficiency. These four locations are not conserved among other chloroalkane reducing RDases with high amino acid similarity (> 90%), suggesting that these locations may be important in determining isotope fractionation within this homologous group of RDases.
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Affiliation(s)
- Elizabeth Phillips
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
| | - Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Matthias Gehre
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | | | | | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
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Chlorination of arenes via the degradation of toxic chlorophenols. Proc Natl Acad Sci U S A 2022; 119:e2122425119. [PMID: 35588450 PMCID: PMC9173806 DOI: 10.1073/pnas.2122425119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceChlorination reactions are widely applied in organic synthesis, with aryl chlorides being key intermediates in the synthesis of many pharmaceutical products. Here, we demonstrate that waste materials such as chlorophenol pollutants can be valorized as chlorination reagents via catalytic transfer of the chloro group during their mineralization for the generation of valuable aryl chlorides. This process adds value to the destruction of chlorophenol pollutants, and the concept could potentially be extended to the valorization of other classes of stockpiles awaiting mineralization.
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Halliwell T, Fisher K, Rigby SEJ, Leys D. Heterologous production and biophysical characterization of catabolic Nitratireductor pacificus pht-3B reductive dehalogenase. Methods Enzymol 2022; 668:327-347. [PMID: 35589200 DOI: 10.1016/bs.mie.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Reductive dehalogenases provide a possible route to the biotechnological remediation of widespread anthropogenic environmental organohalide contamination. These bacterial enzymes employ cobalamin and an internal electron transfer chain of two [4Fe-4S] clusters to remove halide ions from organohalides, leaving an organic molecule more amenable to further transformations. Detailed protocols for the cloning, heterologous expression, purification, crystallization and characterization of the catabolic dehalogenase from Nitratireductor pacificus pht-3B (NpRdhA) are presented, together with insight into enzyme turnover, substrate selectivity and the use of electron paramagnetic resonance (EPR) spectroscopy as an active site probe.
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Affiliation(s)
- Tom Halliwell
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl Fisher
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Stephen E J Rigby
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- School of Chemistry, University of Manchester, Manchester, United Kingdom.
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Heckel B, Elsner M. Exploring Mechanisms of Biotic Chlorinated Alkane Reduction: Evidence of Nucleophilic Substitution (S N2) with Vitamin B 12. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6325-6336. [PMID: 35467338 DOI: 10.1021/acs.est.1c06066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chlorinated alkanes are notorious groundwater contaminants. Their natural reductive dechlorination by microorganisms involves reductive dehalogenases (RDases) containing cobamide as a cofactor. However, underlying mechanisms of reductive dehalogenation have remained uncertain. Here, observed products, radical trap experiments, UV-vis, and mass spectra demonstrate that (i) reduction by cobalamin (vitamin B12) involved chloroalkyl-cobalamin complexes (ii) whose formation involved a second-order nucleophilic substitution (SN2). Dual element isotope analysis subsequently linked insights from our model system to microbial reductive dehalogenation. Identical observed isotope effects in reduction of trichloromethane by Dehalobacter CF and cobalamin (Dehalobacter CF, εC = -27.9 ± 1.7‰; εCl = -4.2 ± 0.‰; λ = 6.6 ± 0.1; cobalamin, εC = -26.0 ± 0.9‰; εCl = -4.0 ± 0.2‰; λ = 6.5 ± 0.2) indicated the same underlying mechanism, as did identical isotope effects in the reduction of 1,2-dichloroethane by Dehalococcoides and cobalamin (Dehalococcoides, εC = -33.0 ± 0.4‰; εCl = -5.1 ± 0.1‰; λ = 6.5 ± 0.2; cobalamin, εC = -32.8 ± 1.7‰; εCl = -5.1 ± 0.2‰; λ = 6.4 ± 0.2). In contrast, a different, non-SN2 reaction was evidenced by different isotope effects in reaction of 1,2-dichloroethane with Dehalogenimonas (εC = -23.0 ± 2.0‰; εCl = -12.0 ± 0.8‰; λ = 1.9 ± 0.02) illustrating a diversity of biochemical reaction mechanisms manifested even within the same class of enzymes (RDases). This study resolves open questions in our understanding of bacterial reductive dehalogenation and, thereby, provides important information on the biochemistry of bioremediation.
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Affiliation(s)
- Benjamin Heckel
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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Genomic Evidence for the Recycling of Complex Organic Carbon by Novel
Thermoplasmatota
Clades in Deep-Sea Sediments. mSystems 2022; 7:e0007722. [PMID: 35430893 PMCID: PMC9239135 DOI: 10.1128/msystems.00077-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Thermoplasmatota have been widely reported in a variety of ecosystems, but their distribution and ecological role in marine sediments are still elusive. Here, we obtained four draft genomes affiliated with the former RBG-16-68-12 clade, which is now considered a new order, “Candidatus Yaplasmales,” of the Thermoplasmatota phylum in sediments from the South China Sea. The phylogenetic trees based on the 16S rRNA genes and draft genomes showed that “Ca. Yaplasmales” archaea are composed of three clades: A, B, and C. Among them, clades A and B are abundantly distributed (up to 10.86%) in the marine anoxic sediment layers (>10-cm depth) of six of eight cores from 1,200- to 3,400-m depths. Metabolic pathway reconstructions indicated that all clades of “Ca. Yaplasmales” have the capacity for alkane degradation by predicted alkyl-succinate synthase. Clade A of “Ca. Yaplasmales” might be mixotrophic microorganisms for the identification of the complete Wood-Ljungdahl pathway and putative genes involved in the degradation of aromatic and halogenated organic compounds. Clades B and C were likely heterotrophic, especially with the potential capacity of the spermidine/putrescine and aromatic compound degradation, as suggested by a significant negative correlation between the concentrations of aromatic compounds and the relative abundances of clade B. The sulfide-quinone oxidoreductase and pyrophosphate-energized membrane proton pump were encoded by all genomes of “Ca. Yaplasmales,” serving as adaptive strategies for energy production. These findings suggest that “Ca. Yaplasmales” might synergistically transform benthic pollutant and detrital organic matter, possibly playing a vital role in the marine and terrestrial sedimentary carbon cycle. IMPORTANCE Deep oceans receive large amounts of complex organic carbon and anthropogenic pollutants. The deep-sea sediments of the continental slopes serve as the biggest carbon sink on Earth. Particulate organic carbons and detrital proteins accumulate in the sediment. The microbially mediated recycling of complex organic carbon is still largely unknown, which is an important question for carbon budget in global oceans and maintenance of the deep-sea ecosystem. In this study, we report the prevalence (up to 10.86% of the microbial community) of archaea from a novel order of Thermoplasmatota, “Ca. Yaplasmales,” in six of eight cores from 1,200- to 3,400-m depths in the South China Sea. We provide genomic evidence of “Ca. Yaplasmales” in the anaerobic microbial degradation of alkanes, aliphatic and monoaromatic hydrocarbons, and halogenated organic compounds. Our study identifies the key archaeal players in anoxic marine sediments, which are probably critical in recycling the complex organic carbon in global oceans.
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Zhang S, Li Y, Wang S. Microbial reductive dechlorination of polychlorinated dibenzo-p-dioxins: Pathways and features unravelled via electron density. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127673. [PMID: 34776298 DOI: 10.1016/j.jhazmat.2021.127673] [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: 09/12/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Microbial reductive dechlorination provides a promising approach for remediating sites contaminated with polychlorinated dibenzo-p-dioxins (PCDDs). Nonetheless, the overall dechlorination pathways and features remain elusive. Herein, we address these issues by quantum chemical calculations, considering the calibrations of reductive dechlorination of 15 PCDDs mediated by three Dehalococcoides strains. Chlorine substituents with lower electron density are prone to be microbially abstracted, which differentiates 72 microbe-active PCDDs from 3 nonactive analogues with a success rate of 100%. For all 256 transformation routes of 75 PCDDs, electron density differences of chlorines pinpoint 105 viable and 125 unviable pathways, corresponding a success rate of 90%. The feasibility of 26 reductive dechlorination pathways are uncertain because of the limited available experimental data. 98% (251/256) of microbial chlorine abstraction follows an order of ClO,Cl>ClCl,Cl>ClH,O>ClH,Cl>ClH,H=0. PCDDs solely containing chlorines at C1, C4, C6, and/or C9 can be completely dechlorinated to non-chlorinated dioxin; while PCDDs housing chlorines at C2, C3, C7, and/or C8 can be dechlorinated to 2-MCDD or 2,7/8-DCDD as final products. These findings also support reductive dechlorination of PCDDs in mixed cultures and sediments (> 98% and 83%). These findings would promote the application of dechlorinating bacteria in targeted remediation and facilitate the respective studies on other POPs.
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Affiliation(s)
- Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Yiyang Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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Greenhalgh ED, Kincannon W, Bandarian V, Brunold TC. Spectroscopic and Computational Investigation of the Epoxyqueuosine Reductase QueG Reveals Intriguing Similarities with the Reductive Dehalogenase PceA. Biochemistry 2022; 61:195-205. [PMID: 35061353 PMCID: PMC8935625 DOI: 10.1021/acs.biochem.1c00644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Queuosine (Q) is a highly modified nucleoside of transfer RNA that is formed from guanosine triphosphate over the course of eight steps. The final step in this process, involving the conversion of epoxyqueuosine (oQ) to Q, is catalyzed by the enzyme QueG. A recent X-ray crystallographic study revealed that QueG possesses the same cofactors as reductive dehalogenases, including a base-off Co(II)cobalamin (Co(II)Cbl) species and two [4Fe-4S] clusters. While the initial step in the catalytic cycle of QueG likely involves the formation of a reduced Co(I)Cbl species, the mechanisms employed by this enzyme to accomplish the thermodynamically challenging reduction of base-off Co(II)Cbl to Co(I)Cbl and to convert oQ to Q remain unknown. In this study, we have used electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) spectroscopies in conjunction with whole-protein quantum mechanics/molecular mechanics (QM/MM) computations to further characterize wild-type QueG and select variants. Our data indicate that the Co(II)Cbl cofactor remains five-coordinate upon substrate binding to QueG. Notably, during a QM/MM optimization of a putative QueG reaction intermediate featuring an alkyl-Co(III) species, the distance between the Co ion and coordinating C atom of oQ increased to >3.3 Å and the C-O bond of the epoxide reformed to regenerate the oQ-bound Co(I)Cbl reactant state of QueG. Thus, our computations indicate that the QueG mechanism likely involves single-electron transfer from the transient Co(I)Cbl species to oQ rather than direct Co-C bond formation, similar to the mechanism that has recently been proposed for the tetrachloroethylene reductive dehalogenase PceA.
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Affiliation(s)
- Elizabeth D. Greenhalgh
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - William Kincannon
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States,Corresponding Author:. Phone: (608) 265-9056
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Yang X, Gerroll BHR, Jiang Y, Kumar A, Zubi YS, Baker LA, Lewis JC. Controlling Non-Native Cobalamin Reactivity and Catalysis in the Transcription Factor CarH. ACS Catal 2022; 12:935-942. [PMID: 35340760 DOI: 10.1021/acscatal.1c04748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Vitamin B12 derivatives catalyze a wide range of organic transformations, but B12-dependent enzymes are underutilized in biocatalysis relative to other metalloenzymes. In this study, we engineered a variant of the transcription factor CarH, called CarH*, that catalyzes styrene C-H alkylation with improved yields (2-6.5-fold) and selectivity relative to cobalamin. While the native function of CarH involves transcription regulation via adenosylcobalamin (AdoCbl) Co(III)-carbon bond cleavage and β-hydride elimination to generate 4',5'-didehydroadenosine, CarH*-catalyzed styrene alkylation proceeds via non-native oxidative addition and olefin addition coupled with a native-like β-hydride elimination. Mechanistic studies on this reaction echo findings from earlier studies on AdoCbl homolysis to suggest that CarH* selectivity results from its ability to impart a cage effect on radical intermediates. These findings lay the groundwork for the development of B12-dependent enzymes as catalysts for non-native transformations.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | | | - Yuhua Jiang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yasmine S. Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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41
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Wang G, Liu Y, Wang X, Dong X, Jiang N, Wang H. Application of dual carbon-bromine stable isotope analysis to characterize anaerobic micro-degradation mechanisms of PBDEs in wetland bottom-water. WATER RESEARCH 2022; 208:117854. [PMID: 34800854 DOI: 10.1016/j.watres.2021.117854] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs), one kind of persistent organic pollutants, were widely detected in coastal wetlands. Microbial reductive debromination is one of the most important attenuation processes for PBDEs in anaerobic environment, whereas the underlying reaction mechanisms remain elusive. Dual-element stable isotope analysis was recently recognized to distinguish different reaction mechanism for degradation of organic pollutants. In this study, the dual carbon-bromine isotope effects associated with the anaerobic microbial degradation were first investigated to characterize the reaction mechanisms for BDE-47 and BDE-153. Presence of lower brominated congeners indicated stepwise debromination as the main degradation pathway, with the preferential removal of bromine in para position > meta/ortho position. The pronounced isotope fractionation was observed for both carbon and bromine, with similar carbon (εC) and bromine isotope enrichment factor (εBr) between BDE-47 (εC = -5.98‰, εBr = -2.44‰) and BDE-153 (εC = -5.57‰, εBr = -2.06‰) during the microbial degradation. Compared to εC and εBr, the correlation of carbon and isotope effects (ΛC/Br = Δδ81Br/Δδ13C) was almost the same between BDE-47 (0.436) and BDE-153 (0.435), indicating the similar reaction mechanism. The calculated carbon and bromine apparent kinetic isotope effects (AKIEC and AKIEBr) were 1.0773 and 1.0098 for BDE-47 and 1.0716 and 1.0125 for BDE-153, within range reported for degradation of halogenated compounds following nucleophilic substitution. Combination analysis of degradation products, ΛC/Br and AKIE, all the results pointed to that the anaerobic reductive debromination of BDE-47 and BDE-153 followed the nucleophilic aromatic substitution, with the addition of cofactor to the benzene ring concomitant with dissociation of carbon-bromine bond via the inner-sphere electron transfer, and the cleavage of C-Br bond was the rate-determining step. This study contributed to the development of dual carbon-bromine isotope analysis as a robust approach to probe the fate of PBDEs in contaminated sites.
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Affiliation(s)
- Guoguang Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yu Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; Environmental Information Institute, Dalian Maritime University, Dalian 116026, China.
| | - Xu Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Xu Dong
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Na Jiang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Haixia Wang
- Navigation College, Dalian Maritime University, Dalian 116026, China
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Zhang S, Adrian L, Schüürmann G. Outer-sphere electron transfer does not underpin B 12-dependent olefinic reductive dehalogenation in anaerobes. Phys Chem Chem Phys 2021; 23:27520-27524. [PMID: 34874373 DOI: 10.1039/d1cp04632b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anaerobic microbial B12-dependent reductive dehalogenation may pave a way to remediate soil, sediment, and underground water contaminated with halogenated olefins. The chemical reaction is initiated by electron transfer (ET) from supernucleophilic cob(I)alamin (B12s). However, the inherent mechanism as outer-sphere or inner-sphere route is still under debate. To clarify the possibility of an outer-sphere pathway, we calculated free energy barriers of the initial steps of all outer-sphere ET routes by Marcus theory employing density functional theory (DFT). For 18 fluorinated, chlorinated, and brominated ethenes as representative olefins, 164 of 165 reactions with free energy barriers larger than 20 kcal mol-1 are not feasible under physiological dehalogenase conditions. Moreover, electronic structure analysis of perbromoethene with an outer-sphere free energy barrier of 18.2 kcal mol-1 reveals no ET initiation down to Co⋯Br and Co⋯C distances of 3.15 Å. The results demonstrate that the B12-catalyzed reductive dechlorination of olefins in microbes should proceed through an inner-sphere ET pathway.
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Affiliation(s)
- Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.,UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany.
| | - Lorenz Adrian
- UFZ Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig 04318, Germany. .,Technical University Bergakademie Freiberg, Institute of Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, Germany.
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43
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Reddy BRP, Auffrant A, Gosmini C. Dehalogenation and Desulfonation from Aryl and Alkyl Compounds with a Cobalt Catalyst in the Presence of Alcohol. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Audrey Auffrant
- Laboratoire de Chimie Moléculaire CNRS, École Polytechnique, IP Paris 91128 Palaiseau France
| | - Corinne Gosmini
- Laboratoire de Chimie Moléculaire CNRS, École Polytechnique, IP Paris 91128 Palaiseau France
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Heterologous expression of active Dehalobacter spp. respiratory reductive dehalogenases in Escherichia coli. Appl Environ Microbiol 2021; 88:e0199321. [PMID: 34851719 DOI: 10.1128/aem.01993-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-dependence. There have been a few successful attempts at RDase production in unconventional heterologous hosts, but a robust method has yet to be developed. Here we outline a novel respiratory RDase expression system using Escherichia coli. The overexpression of E. coli's cobamide transport system, btu, and anaerobic expression conditions were found to be essential for production of active RDases from Dehalobacter - an obligate organohalide respiring bacterium. The expression system was validated on six enzymes with amino acid sequence identities as low as 28%. Dehalogenation activity was verified for each RDase by assaying cell-free extracts of small-scale expression cultures on various chlorinated substrates including chloroalkanes, chloroethenes, and hexachlorocyclohexanes. Two RDases, TmrA from Dehalobacter sp. UNSWDHB and HchA from Dehalobacter sp. HCH1, were purified by nickel affinity chromatography. Incorporation of the cobamide and iron-sulfur cluster cofactors was verified; though, the precise cobalamin incorporation could not be determined due to variance between methodologies, and the specific activity of TmrA was consistent with that of the native enzyme. The heterologous expression of respiratory RDases, particularly from obligate organohalide respiring bacteria, has been extremely challenging and unreliable. Here we present a relatively straightforward E. coli expression system that has performed well for a variety of Dehalobacter spp. RDases. IMPORTANCE Understanding microbial reductive dehalogenation is important to refine the global halogen cycle and to improve bioremediation of halogenated contaminants; however, studies of the family of enzymes responsible are limited. Characterization of reductive dehalogenase enzymes has largely eluded researchers due to the lack of a reliable and high-yielding production method. We are presenting an approach to express reductive dehalogenase enzymes from Dehalobacter, a key group of organisms used in bioremediation, in E. coli. This expression system will propel the study of reductive dehalogenases by facilitating their production and isolation, allowing researchers to pursue more in-depth questions about the activity and structure of these enzymes. This platform will also provide a starting point to improve the expression of reductive dehalogenases from many other organisms.
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45
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Abstract
Thousands of heavily fluorinated chemicals are found in the environment, impact human and ecosystem health, and are relatively resistant to biological and chemical degradation. Their persistence in the environment is due to the inability of most microorganisms to biodegrade them. Only a very few examples of polyfluorinated compound biodegradation are known, and the reported rates are very low. This has been mostly attributed to the low chemical reactivity of the C-F bond. This Perspective goes beyond that explanation to highlight microbiological reasons why polyfluorinated compounds resist metabolism. The evolutionary and physiological impediments must be appreciated to better find, study, and harness microbes that degrade polyfluorinated compounds.
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46
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Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
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47
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Sun Q, Zhai Y, Wang W, Gan N, Zhang S, Suo Z, Li H. Molecular recognition patterns between vitamin B12 and human serum albumin explored through STD-NMR and spectroscopic methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119828. [PMID: 33930850 DOI: 10.1016/j.saa.2021.119828] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Ligand-receptor molecular recognitionis the basis of biological process. The Saturation Transfer Difference-NMR (STD-NMR) technique has been recently used to gain qualitative and quantitative information about physiological interactions at atomic-resolution. The molecular recognition patterns between Vitamin B12 (VB12) and human serum albumin (HSA) were investigated by STD-NMR supplemented by other spectroscopies and molecular docking. STD-NMR delivered a complete picture that the substituent groups on the tetrapyrrole ring of VB12 interacted with site III of HSA through binding epitope mapping and competitive probe experiments. STD-NMR and fluorescence results proved the moderate binding capability of VB12 and clarified a static, spontaneous, and temperature-sensitive binding mechanism. 3D-fluorencence, FT-IR and circular dichroism spectra showed a compact protein structure by interacting with VB12. Size distribution and surface hydrophobicity showed the surface properties changes of HSA caused by the binding of VB12. Computer simulation confirmed the recognition mode in theory and was compared with experiments. This work is beneficial for understanding the safety and biological action of VB12, and will attract researchers interested in NMR technology.
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Affiliation(s)
- Qiaomei Sun
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yuanming Zhai
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China.
| | - Wenjing Wang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Na Gan
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Shuangshuang Zhang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zili Suo
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Hui Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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48
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The "beauty in the beast"-the multiple uses of Priestia megaterium in biotechnology. Appl Microbiol Biotechnol 2021; 105:5719-5737. [PMID: 34263356 PMCID: PMC8390425 DOI: 10.1007/s00253-021-11424-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/05/2023]
Abstract
Abstract Over 30 years, the Gram-positive bacterium Priestia megaterium (previously known as Bacillus megaterium) was systematically developed for biotechnological applications ranging from the production of small molecules like vitamin B12, over polymers like polyhydroxybutyrate (PHB) up to the in vivo and in vitro synthesis of multiple proteins and finally whole-cell applications. Here we describe the use of the natural vitamin B12 (cobalamin) producer P. megaterium for the elucidation of the biosynthetic pathway and the subsequent systematic knowledge-based development for production purposes. The formation of PHB, a natural product of P. megaterium and potential petro-plastic substitute, is covered and discussed. Further important biotechnological characteristics of P. megaterium for recombinant protein production including high protein secretion capacity and simple cultivation on value-added carbon sources are outlined. This includes the advanced system with almost 30 commercially available expression vectors for the intracellular and extracellular production of recombinant proteins at the g/L scale. We also revealed a novel P. megaterium transcription-translation system as a complementary and versatile biotechnological tool kit. As an impressive biotechnology application, the formation of various cytochrome P450 is also critically highlighted. Finally, whole cellular applications in plant protection are completing the overall picture of P. megaterium as a versatile giant cell factory. Key points • The use of Priestia megaterium for the biosynthesis of small molecules and recombinant proteins through to whole-cell applications is reviewed. • P. megaterium can act as a promising alternative host in biotechnological production processes.
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49
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Li Y, Zhao HP, Zhu L. Iron Sulfide Enhanced the Dechlorination of Trichloroethene by Dehalococcoides mccartyi Strain 195. Front Microbiol 2021; 12:665281. [PMID: 34140942 PMCID: PMC8203822 DOI: 10.3389/fmicb.2021.665281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
Iron sulfide (FeS) nanoparticles have great potential in environmental remediation. Using the representative species Dehalococcoides mccartyi strain 195 (Dhc 195), the effect of FeS on trichloroethene (TCE) dechlorination was studied with hydrogen and acetate as the electron donor and carbon source, respectively. With the addition of 0.2 mM Fe2+ and S2–, the dechlorination rate of TCE was enhanced from 25.46 ± 1.15 to 37.84 ± 1.89 μmol⋅L–1⋅day–1 by the in situ formed FeS nanoparticles, as revealed through X-ray diffraction. Comparing the tceA gene copy numbers between with FeS and without FeS, real-time polymerase chain reaction (PCR) indicated that the abundance of the tceA gene increased from (2.83 ± 0.13) × 107 to (4.27 ± 0.21) × 108 copies/ml on day 12. The transcriptional activity of key genes involved in the electron transport chain was upregulated after the addition of FeS, including those responsible for the iron–sulfur cluster assembly protein gene (DET1632) and transmembrane transport of iron (DET1503, DET0685), cobalamin (DET0685, DET1139), and molybdenum (DET1161) genes. Meanwhile, the reverse transcription of tceA was increased approximately five times on the 12th day. These upregulations together suggested that the electron transport of D. mccartyi strain 195 was enhanced by FeS for apparent TCE dechlorination. Overall, the present study provided an eco-friendly and effective method to achieve high remediation efficiency for organohalide-polluted groundwater and soil.
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Affiliation(s)
- Yaru Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, China
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50
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Greenhalgh ED, Kunze C, Schubert T, Diekert G, Brunold TC. A Spectroscopically Validated Computational Investigation of Viable Reaction Intermediates in the Catalytic Cycle of the Reductive Dehalogenase PceA. Biochemistry 2021; 60:2022-2032. [PMID: 34132518 DOI: 10.1021/acs.biochem.1c00271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Organisms that produce reductive dehalogenases utilize halogenated aromatic and aliphatic substances as terminal electron acceptors in a process termed organohalide respiration. These organisms can couple the reduction of halogenated substances with the production of ATP. Tetrachloroethylene reductive dehalogenase (PceA) catalyzes the reductive dehalogenation of per- and trichloroethylenes (PCE and TCE, respectively) to primarily cis-dichloroethylene (DCE). The enzymatic conversion of PCE to TCE (and subsequently DCE) could potentially proceed via a mechanism in which the first step involves a single-electron transfer, nucleophilic addition followed by chloride elimination or protonation, or direct attack at the halogen. Difficulties with producing adequate quantities of PceA have greatly hampered direct experimental studies of the reaction mechanism. To overcome these challenges, we have generated computational models of resting and TCE-bound PceA using quantum mechanics/molecular mechanics (QM/MM) calculations and validated these models on the basis of experimental data. Notably, the norpseudo-cob(II)alamin [Co(II)Cbl*] cofactor remains five-coordinate upon binding of the substrate to the enzyme, retaining a loosely bound water on the lower face. Thus, the mechanism for the thermodynamically challenging Co(II) → Co(I)Cbl* reduction used by PceA differs fundamentally from that utilized by adenosyltransferases, which generate four-coordinate Co(II)Cbl species to facilitate access to the Co(I) oxidation state. The same QM/MM computational methodology was then applied to viable reaction intermediates in the catalytic cycle of PceA. The intermediate predicted to possess the lowest energy is that resulting from electron transfer from Co(I)Cbl* to the substrate to yield Co(II)Cbl*, a chloride ion, and a vinylic radical.
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Affiliation(s)
- Elizabeth D Greenhalgh
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Cindy Kunze
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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