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Mondal A, Roy P, Carrannanto J, Datar PM, DiRocco DJ, Hunter K, Marsh ENG. Surveying the scope of aromatic decarboxylations catalyzed by prenylated-flavin dependent enzymes. Faraday Discuss 2024; 252:208-222. [PMID: 38837123 DOI: 10.1039/d4fd00006d] [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: 06/06/2024]
Abstract
The prenylated-flavin mononucleotide-dependent decarboxylases (also known as UbiD-like enzymes) are the most recently discovered family of decarboxylases. The modified flavin facilitates the decarboxylation of unsaturated carboxylic acids through a novel mechanism involving 1,3-dipolar cyclo-addition chemistry. UbiD-like enzymes have attracted considerable interest for biocatalysis applications due to their ability to catalyse (de)carboxylation reactions on a broad range of aromatic substrates at otherwise unreactive carbon centres. There are now ∼35 000 protein sequences annotated as hypothetical UbiD-like enzymes. Sequence similarity network analyses of the UbiD protein family suggests that there are likely dozens of distinct decarboxylase enzymes represented within this family. Furthermore, many of the enzymes so far characterized can decarboxylate a broad range of substrates. Here we describe a strategy to identify potential substrates of UbiD-like enzymes based on detecting enzyme-catalysed solvent deuterium exchange into potential substrates. Using ferulic acid decarboxylase (FDC) as a model system, we tested a diverse range of aromatic and heterocyclic molecules for their ability to undergo enzyme-catalysed H/D exchange in deuterated buffer. We found that FDC catalyses H/D exchange, albeit at generally very low levels, into a wide range of small, aromatic molecules that have little resemblance to its physiological substrate. In contrast, the sub-set of aromatic carboxylic acids that are substrates for FDC-catalysed decarboxylation is much smaller. We discuss the implications of these findings for screening uncharacterized UbiD-like enzymes for novel (de)carboxylase activity.
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Affiliation(s)
- Anushree Mondal
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Pronay Roy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Jaclyn Carrannanto
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Prathamesh M Datar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Daniel J DiRocco
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Katherine Hunter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Datar PM, Roy P, Mondal A, Marsh ENG. Characterization of the N5-dimethylallyl-FMN Intermediate in the Biosynthesis of Prenylated-FMN Catalyzed by UbiX. Biochemistry 2024. [PMID: 39231435 DOI: 10.1021/acs.biochem.4c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Prenylated-FMN (prFMN) is the cofactor used by the UbiD-like family of decarboxylases that catalyzes the decarboxylation of various aromatic and unsaturated carboxylic acids. prFMN is synthesized from reduced FMN and dimethylallyl phosphate (DMAP) by a specialized prenyl transferase, UbiX. UbiX catalyzes the sequential formation of two bonds, the first between N5 of the flavin and C1 of DMAP, and the second between C6 of the flavin and C3 of DMAP. We have examined the reaction of UbiX with both FMN and riboflavin. Although UbiX converts FMN to prFMN, we show that significant amounts of the N5-dimethylallyl-FMN intermediate are released from the enzyme during catalysis. With riboflavin as the substrate, UbiX catalyzes only a partial reaction, resulting in only N5-dimethylallyl-riboflavin being formed. Purification of the N5-dimethylallyl-FMN adduct allowed its structure to be verified by 1H NMR spectroscopy and its reactivity to be investigated. Surprisingly, whereas reduced prFMN oxidizes in seconds to form the stable prFMN semiquinone radical when exposed to air, N5-dimethylallyl-FMN oxidizes much more slowly over several hours; in this case, oxidation is accompanied by spontaneous hydrolysis to regenerate FMN. These studies highlight the important contribution that cyclization of the prenyl-derived ring of prFMN makes to the cofactor's biological activity.
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Nguyen N, Forstater JH, McIntosh JA. Decarboxylation in Natural Products Biosynthesis. JACS AU 2024; 4:2715-2745. [PMID: 39211618 PMCID: PMC11350588 DOI: 10.1021/jacsau.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms and act on a large variety of substrates, making them appealing in terms of biotechnological applications. This Perspective focuses on the occurrence of decarboxylation reactions in natural product biosynthesis and provides a perspective on their applications in biocatalysis for fine chemicals and pharmaceuticals.
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Datar PM, Joshi SY, Deshmukh SA, Marsh ENG. Probing the role of protein conformational changes in the mechanism of prenylated-FMN-dependent phenazine-1-carboxylic acid decarboxylase. J Biol Chem 2024; 300:105621. [PMID: 38176649 PMCID: PMC10850782 DOI: 10.1016/j.jbc.2023.105621] [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: 08/21/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Phenazine-1-carboxylic acid decarboxylase (PhdA) is a prenylated-FMN-dependent (prFMN) enzyme belonging to the UbiD family of decarboxylases. Many UbiD-like enzymes catalyze (de)carboxylation reactions on aromatic rings and conjugated double bonds and are potentially valuable industrial catalysts. We have investigated the mechanism of PhdA using a slow turnover substrate, 2,3-dimethylquinoxaline-5-carboxylic acid (DQCA). Detailed analysis of the pH dependence and solvent deuterium isotope effects associated with the reaction uncovered unusual kinetic behavior. At low substrate concentrations, a substantial inverse solvent isotope effect (SIE) is observed on Vmax/KM of ∼ 0.5 when reaction rates of DQCA in H2O and D2O are compared. Under the same conditions, a normal SIE of 4.15 is measured by internal competition for proton transfer to the product. These apparently contradictory results indicate that the SIE values report on different steps in the mechanism. A proton inventory analysis of the reaction under Vmax/KM and Vmax conditions points to a "medium effect" as the source of the inverse SIE. Molecular dynamics simulations of the effect of D2O on PhdA structure support that D2O reduces the conformational lability of the enzyme and results in a more compact structure, akin to the active, "closed" conformer observed in crystal structures of some UbiD-like enzymes. Consistent with the simulations, PhdA was found to be more stable in D2O and to bind DQCA more tightly, leading to the observed rate enhancement under Vmax/KM conditions.
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Affiliation(s)
- Prathamesh M Datar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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5
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Gahloth D, Fisher K, Marshall S, Leys D. The prFMNH 2-binding chaperone LpdD assists UbiD decarboxylase activation. J Biol Chem 2024; 300:105653. [PMID: 38224946 PMCID: PMC10865409 DOI: 10.1016/j.jbc.2024.105653] [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: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024] Open
Abstract
The UbiD enzyme family of prenylated flavin (prFMN)-dependent reversible decarboxylases is near ubiquitously present in microbes. For some UbiD family members, enzyme activation through prFMNH2 binding and subsequent oxidative maturation of the cofactor readily occurs, both in vivo in a heterologous host and through in vitro reconstitution. However, isolation of the active holo-enzyme has proven intractable for others, notably the canonical Escherichia coli UbiD. We show that E. coli heterologous expression of the small protein LpdD-associated with the UbiD-like gallate decarboxylase LpdC from Lactobacillus plantarum-unexpectedly leads to 3,4-dihydroxybenzoic acid decarboxylation whole-cell activity. This activity was shown to be linked to endogenous E. coli ubiD expression levels. The crystal structure of the purified LpdD reveals a dimeric protein with structural similarity to the eukaryotic heterodimeric proteasome assembly chaperone Pba3/4. Solution studies demonstrate that LpdD protein specifically binds to reduced prFMN species only. The addition of the LpdD-prFMNH2 complex supports reconstitution and activation of the purified E. coli apo-UbiD in vitro, leading to modest 3,4-dihydroxybenzoic acid decarboxylation. These observations suggest that LpdD acts as a prFMNH2-binding chaperone, enabling apo-UbiD activation through enhanced prFMNH2 incorporation and subsequent oxidative maturation. Hence, while a single highly conserved flavin prenyltransferase UbiX is found associated with UbiD enzymes, our observations suggest considerable diversity in UbiD maturation, ranging from robust autocatalytic to chaperone-mediated processes. Unlocking the full (de)carboxylation scope of the UbiD-enzyme family will thus require more than UbiX coexpression.
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Affiliation(s)
- Deepankar Gahloth
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Stephen Marshall
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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Nicoll CR, Alvigini L, Gottinger A, Cecchini D, Mannucci B, Corana F, Mascotti ML, Mattevi A. In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. Nat Catal 2024; 7:148-160. [PMID: 38425362 PMCID: PMC7615680 DOI: 10.1038/s41929-023-01087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/20/2023] [Indexed: 03/02/2024]
Abstract
Metabolons are protein assemblies that perform a series of reactions in a metabolic pathway. However, the general importance and aptitude of metabolons for enzyme catalysis remain poorly understood. In animals, biosynthesis of coenzyme Q is currently attributed to ten different proteins, with COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9 forming the iconic COQ metabolon. Yet several reaction steps conducted by the metabolon remain enigmatic. To elucidate the prerequisites for animal coenzyme Q biosynthesis, we sought to construct the entire metabolon in vitro. Here we show that this approach, rooted in ancestral sequence reconstruction, reveals the enzymes responsible for the uncharacterized steps and captures the biosynthetic pathway in vitro. We demonstrate that COQ8, a kinase, increases and streamlines coenzyme Q production. Our findings provide crucial insight into how biocatalytic efficiency is regulated and enhanced by these biosynthetic engines in the context of the cell.
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Affiliation(s)
- Callum R. Nicoll
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Laura Alvigini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Andrea Gottinger
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Domiziana Cecchini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | | | - Federica Corana
- ’Centro Grandi Strumenti’, University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
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Tong Y, Wei Y, Ju Y, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y, Zhang Y. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria. Cell Chem Biol 2023; 30:1104-1114.e7. [PMID: 37164019 DOI: 10.1016/j.chembiol.2023.04.008] [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: 01/06/2023] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Yingjie Ju
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peishan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yumin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P.R. China
| | - Liqin Li
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Lujuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengnan Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Meining Pharma Inc, 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Zhi Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Wang
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Yiwen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China.
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Werner AZ, Cordell WT, Lahive CW, Klein BC, Singer CA, Tan EC, Ingraham MA, Ramirez KJ, Kim DH, Pedersen JN, Johnson CW, Pfleger BF, Beckham GT, Salvachúa D. Lignin conversion to β-ketoadipic acid by Pseudomonas putida via metabolic engineering and bioprocess development. SCIENCE ADVANCES 2023; 9:eadj0053. [PMID: 37672573 PMCID: PMC10482344 DOI: 10.1126/sciadv.adj0053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here, Pseudomonas putida KT2440 was engineered to convert mixed p-coumaroyl- and coniferyl-type LRCs to β-ketoadipic acid, a precursor for performance-advantaged polymers. Expression of enzymes mediating aromatic O-demethylation, hydroxylation, and ring-opening steps was tuned, and a global regulator was deleted. β-ketoadipate titers of 44.5 and 25 grams per liter and productivities of 1.15 and 0.66 grams per liter per hour were achieved from model LRCs and corn stover-derived LRCs, respectively, the latter representing an overall yield of 0.10 grams per gram corn stover-derived lignin. Technoeconomic analysis of the bioprocess and downstream processing predicted a β-ketoadipate minimum selling price of $2.01 per kilogram, which is cost competitive with fossil carbon-derived adipic acid ($1.10 to 1.80 per kilogram). Overall, this work achieved bioproduction metrics with economic relevance for conversion of lignin-derived streams into a performance-advantaged bioproduct.
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Affiliation(s)
- Allison Z. Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - William T. Cordell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ciaran W. Lahive
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Bruno C. Klein
- Catalytic Carbon Transformation and Scale-Up Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Christine A. Singer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Eric C. D. Tan
- Catalytic Carbon Transformation and Scale-Up Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Morgan A. Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelsey J. Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Dong Hyun Kim
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Jacob Nedergaard Pedersen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Christopher W. Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
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Yin F, Qin Z. Long-Chain Molecules with Agro-Bioactivities and Their Applications. Molecules 2023; 28:5880. [PMID: 37570848 PMCID: PMC10421526 DOI: 10.3390/molecules28155880] [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: 07/10/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Long-chain molecules play a vital role in agricultural production and find extensive use as fungicides, insecticides, acaricides, herbicides, and plant growth regulators. This review article specifically addresses the agricultural biological activities and applications of long-chain molecules. The utilization of long-chain molecules in the development of pesticides is an appealing avenue for designing novel pesticide compounds. By offering valuable insights, this article serves as a useful reference for the design of new long-chain molecules for pesticide applications.
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Affiliation(s)
| | - Zhaohai Qin
- College of Science, China Agricultural University, Beijing 100193, China;
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10
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Li YX, Lin W, Han YH, Wang YQ, Wang T, Zhang H, Zhang Y, Wang SS. Biodegradation of p-hydroxybenzoic acid in Herbaspirillum aquaticum KLS-1 isolated from tailing soil: Characterization and molecular mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131669. [PMID: 37236108 DOI: 10.1016/j.jhazmat.2023.131669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The wide distribution of p-hydroxybenzoic acid (PHBA) in the environments has attracted great concerns due to its potential risks to organisms. Bioremediation is considered a green way to remove PHBA from environment. Here, a new PHBA-degrading bacterium Herbaspirillum aquaticum KLS-1was isolated and its PHBA degradation mechanisms were fully evaluated. Results showed that strain KLS-1 could utilize PHBA as the sole carbon source and completely degrade 500 mg/L PHBA within 18 h. The optimal conditions for bacterial growth and PHBA degradation were pH values of 6.0-8.0, temperatures of 30 °C-35 °C, shaking speed of 180 rpm, Mg2+ concentration of 2.0 mM and Fe2+ concentration of 1.0 mM. Draft genome sequencing and functional gene annotations identified three operons (i.e., pobRA, pcaRHGBD and pcaRIJ) and several free genes possibly participating in PHBA degradation. The key genes pobA, ubiA, fadA, ligK and ubiG involved in the regulation of protocatechuate and ubiquinone (UQ) metabolisms were successfully amplified in strain KLS-1 at mRNA level. Our data suggested that PHBA could be degraded by strain KLS-1 via the protocatechuate ortho-/meta-cleavage pathway and UQ biosynthesis pathway. This study has provided a new PHBA-degrading bacterium for potential bioremediation of PHBA pollution.
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Affiliation(s)
- Yi-Xi Li
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Wei Lin
- College of Life Science, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Yong-He Han
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China.
| | - Yao-Qiang Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Tao Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Hong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Yong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Shan-Shan Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
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11
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Heker I, Haberhauer G, Meckenstock RU. Naphthalene Carboxylation in the Sulfate-Reducing Enrichment Culture N47 Is Proposed to Proceed via 1,3-Dipolar Cycloaddition to the Cofactor Prenylated Flavin Mononucleotide. Appl Environ Microbiol 2023; 89:e0192722. [PMID: 36815794 PMCID: PMC10057960 DOI: 10.1128/aem.01927-22] [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: 11/17/2022] [Accepted: 01/12/2023] [Indexed: 02/24/2023] Open
Abstract
Polycyclic aromatic hydrocarbons are persistent pollutants of anthropogenic or natural origin in the environment and accumulate in anoxic habitats. In this study, we investigated the mechanism of the enzyme naphthalene carboxylase as a model reaction for polycyclic aromatic hydrocarbon activation by carboxylation. An enzyme assay was established with cell extracts of the highly enriched culture N47. In assays without addition of ATP, naphthalene carboxylase catalyzed a stable isotope exchange of the carboxyl group of naphthoate with 13C-labeled bicarbonate buffer, which can only occur via a partial backwards reaction of the naphthalene carboxylase reaction to an intermediate that does not include the carboxyl group. Hence, a new carboxyl group from the labeled bicarbonate is added upon forward reaction to the naphthoate. This indicates that the reaction mechanism consists of two or more steps and that at least the latter steps are reversible and ATP independent. Naphthalene carboxylation assays were carried out in deuterated buffer and revealed the incorporation of 0, 1, 2, or 3 deuterium atoms in the final product naphthoyl-coenzyme A, indicating that the reaction is fully reversible. Putative reaction mechanisms were tested by quantum mechanical calculations. The proposed mechanism of the reaction consists of three steps: the activation of the naphthalene by 1,3-dipolar cycloaddition of the cofactor prFMN to naphthalene, release of a proton and rearomatization producing a stable intermediate, and a carboxylation with a reverse 1,3-dipolar cycloaddition and cleavage of the bond to the cofactor producing 2-naphthoate. IMPORTANCE Pollution with polycyclic aromatic hydrocarbons poses a great hazard to humans and animals, with considerable long-term effects. The anaerobic degradation of polycyclic aromatic hydrocarbons in anoxic zones and anaerobic growth of such organisms is very slow, leading to only poor investigation of the degradation pathways, so far. In this work, we elucidated the mechanism of naphthalene carboxylase, a key enzyme in anaerobic naphthalene degradation. This is the first mechanism proposed for a carboxylase targeting nonsubstituted (polycyclic) aromatic compounds and can serve as a model for the initial activation reaction in the anaerobic degradation of benzene or nonsubstituted polycyclic aromatic hydrocarbons, as well as similar enzymatic reactions from the expanding class of UbiD-like (de)carboxylases.
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Affiliation(s)
- Isabelle Heker
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
| | - Gebhard Haberhauer
- Institute for Organic Chemistry, University Duisburg-Essen, Essen, Germany
| | - Rainer U. Meckenstock
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
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12
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Improved Assessment of Globularity of Protein Structures and the Ellipsoid Profile of the Biological Assemblies from the PDB. Biomolecules 2023; 13:biom13020385. [PMID: 36830752 PMCID: PMC9953691 DOI: 10.3390/biom13020385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
In this paper, we present an update to the ellipsoid profile algorithm (EP), a simple technique for the measurement of the globularity of protein structures without the calculation of molecular surfaces. The globularity property is understood in this context as the ability of the molecule to fill a minimum volume enclosing ellipsoid (MVEE) that approximates its assumed globular shape. The more of the interior of this ellipsoid is occupied by the atoms of the protein, the better are its globularity metrics. These metrics are derived from the comparison of the volume of the voxelized representation of the atoms and the volume of all voxels that can fit inside that ellipsoid (a uniform unit Å cube lattice). The so-called ellipsoid profile shows how the globularity changes with the distance from the center. Two of its values, the so-called ellipsoid indexes, are used to classify the structure as globular, semi-globular or non-globular. Here, we enhance the workflow of the EP algorithm via an improved outlier detection subroutine based on principal component analysis. It is capable of robust distinguishing between the dense parts of the molecules and, for example, disordered chain fragments fully exposed to the solvent. The PCA-based method replaces the current approach based on kernel density estimation. The improved EP algorithm was tested on 2124 representatives of domain superfamilies from SCOP 2.08. The second part of this work is dedicated to the survey of globularity of 3594 representatives of biological assemblies from molecules currently deposited in the PDB and analyzed by the 3DComplex database (monomers and complexes up to 60 chains).
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Kaneshiro AK, Datar PM, Marsh ENG. Negative Cooperativity in the Mechanism of Prenylated-Flavin-Dependent Ferulic Acid Decarboxylase: A Proposal for a "Two-Stroke" Decarboxylation Cycle. Biochemistry 2023; 62:53-61. [PMID: 36521056 DOI: 10.1021/acs.biochem.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ferulic acid decarboxylase (FDC) catalyzes the reversible carboxylation of various substituted phenylacrylic acids to produce the correspondingly substituted styrenes and CO2. FDC is a member of the UbiD family of enzymes that use prenylated-FMN (prFMN) to catalyze decarboxylation reactions on aromatic rings and C-C double bonds. Although a growing number of prFMN-dependent enzymes have been identified, the mechanism of the reaction remains poorly understood. Here, we present a detailed pre-steady-state kinetic analysis of the FDC-catalyzed reaction of prFMN with both styrene and phenylacrylic acid. Based on the pattern of reactivity observed, we propose a "two-stroke" kinetic model in which negative cooperativity between the two subunits of the FDC homodimer plays an important and previously unrecognized role in catalysis. In this model, catalysis is initiated at the high-affinity active site, which reacts with phenylacrylate to yield, after decarboxylation, the covalently bound styrene-prFMN cycloadduct. In the second stage of the catalytic cycle, binding of the second substrate molecule to the low-affinity active site drives a conformational switch that interconverts the high-affinity and low-affinity active sites. This switching of affinity couples the energetically unfavorable cycloelimination of styrene from the first site with the energetically favorable cycloaddition and decarboxylation of phenylacrylate at the second site. We note as a caveat that, at this point, the complexity of the FDC kinetics leaves open other mechanistic interpretations and that further experiments will be needed to more firmly establish or refute our proposal.
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Junghare M, Frey J, Naji KM, Spiteller D, Vaaje-Kolstad G, Schink B. Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate. BMC Microbiol 2022; 22:227. [PMID: 36171563 PMCID: PMC9516798 DOI: 10.1186/s12866-022-02630-x] [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: 04/28/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA. Results Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6 kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg2+ and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between pH 7.0 to 7.5. The optimal temperature was between 25 °C and 37 °C. Denaturation temperature (Tm) of IPCL was found to be at about 63 °C. The apparent KM values for isophthalate, CoA, and ATP were 409 μM, 642 μM, and 3580 μM, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions. Conclusion We have successfully cloned the ipcl gene, expressed and characterized the corresponding IPCL enzyme, which plays a key role in isophthalate activation that initiates its activation and further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02630-x.
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Affiliation(s)
- Madan Junghare
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany. .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway.
| | - Jasmin Frey
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Khalid M Naji
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Dieter Spiteller
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Bernhard Schink
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
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Żaczek S, Dybala-Defratyka A. Unravelling interactions between active site residues and DMAP in the initial steps of prenylated flavin mononucleotide biosynthesis catalyzed by PaUbiX. Biochim Biophys Acta Gen Subj 2022; 1866:130247. [PMID: 36162732 DOI: 10.1016/j.bbagen.2022.130247] [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: 12/28/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Prenylated flavin mononucleotide (prFMN) is a recently discovered, heavily modified flavin compound. It is the only known cofactor that enables enzymatic 1,3-dipolar cycloaddition reactions. It is produced by enzymes from the UbiX family, from flavin mononucleotide and either dimethylallyl mono- or diphosphate. prFMN biosynthesis is currently reported to be initiated by protonation of the substrate by Glu140. METHODS Computational chemistry methods are applied herein - Constant pH MD, classical MD simulations, and QM cluster optimizations. RESULTS Glu140 competes for a single proton with Lys129 prior to prFMN biosynthesis, but it is the latter that adopted a protonated state. Once the prenyl-FMN adduct is formed, Glu140 occurs in a protonated state far more often, while the occupancy of protonated Lys129 does not change. Lys129, Glu140, and Arg122 seem to play a key role in either stabilizing or protonating DMAP phosphate group within the PaUbiX active site throughout initial steps of prFMN biosynthesis. CONCLUSIONS The role of Lys129 in the functioning of PaUbiX is reported for the first time. Glu140 is unlikely to act as a proton donor in prFMN biosynthesis. Instead, Lys129 and Arg122 fulfil this role. Glu140 still plays a role in contributing to hydrogen-bond network. This behavior is most likely conserved throughout the UbiX family due to the structural similarity of the active sites of those proteins. SIGNIFICANCE Mechanistic insights into a crucial biochemical process, the biosynthesis of prFMN, are provided. This study, although purely computational, extends and perfectly complements the knowledge obtained in classical laboratory experiments.
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Affiliation(s)
- Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland.
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Liu P, Zheng Y, Yuan Y, Zhang T, Li Q, Liang Q, Su T, Qi Q. Valorization of Polyethylene Terephthalate to Muconic Acid by Engineering Pseudomonas Putida. Int J Mol Sci 2022; 23:ijms231910997. [PMID: 36232310 PMCID: PMC9569715 DOI: 10.3390/ijms231910997] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Plastic waste is rapidly accumulating in the environment and becoming a huge global challenge. Many studies have highlighted the role of microbial metabolic engineering for the valorization of polyethylene terephthalate (PET) waste. In this study, we proposed a new conceptual scheme for upcycling of PET. We constructed a multifunctional Pseudomonas putida KT2440 to simultaneously secrete PET hydrolase LCC, a leaf-branch compost cutinase, and synthesize muconic acid (MA) using the PET hydrolysate. The final product MA and extracellular LCC can be separated from the supernatant of the culture by ultrafiltration, and the latter was used for the next round of PET hydrolysis. A total of 0.50 g MA was produced from 1 g PET in each cycle of the whole biological processes, reaching 68% of the theoretical conversion. This new conceptual scheme for the valorization of PET waste should have advantages over existing PET upcycling schemes and provides new ideas for the utilization of other macromolecular resources that are difficult to decompose, such as lignin.
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Affiliation(s)
| | | | | | | | | | | | - Tianyuan Su
- Correspondence: (T.S.); (Q.Q.); Tel./Fax: +86-532-58632580 (Q.Q.)
| | - Qingsheng Qi
- Correspondence: (T.S.); (Q.Q.); Tel./Fax: +86-532-58632580 (Q.Q.)
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Xu JJ, Hu M, Yang L, Chen XY. How plants synthesize coenzyme Q. PLANT COMMUNICATIONS 2022; 3:100341. [PMID: 35614856 PMCID: PMC9483114 DOI: 10.1016/j.xplc.2022.100341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Coenzyme Q (CoQ) is a conserved redox-active lipid that has a wide distribution across the domains of life. CoQ plays a key role in the oxidative electron transfer chain and serves as a crucial antioxidant in cellular membranes. Our understanding of CoQ biosynthesis in eukaryotes has come mostly from studies of yeast. Recently, significant advances have been made in understanding CoQ biosynthesis in plants. Unique mitochondrial flavin-dependent monooxygenase and benzenoid ring precursor biosynthetic pathways have been discovered, providing new insights into the diversity of CoQ biosynthetic pathways and the evolution of phototrophic eukaryotes. We summarize research progress on CoQ biosynthesis and regulation in plants and recent efforts to increase the CoQ content in plant foods.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Chenshan Plant Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Mei Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Chenshan Plant Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
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Flavin-enabled reductive and oxidative epoxide ring opening reactions. Nat Commun 2022; 13:4896. [PMID: 35986005 PMCID: PMC9391479 DOI: 10.1038/s41467-022-32641-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/08/2022] [Indexed: 12/23/2022] Open
Abstract
Epoxide ring opening reactions are common and important in both biological processes and synthetic applications and can be catalyzed in a non-redox manner by epoxide hydrolases or reductively by oxidoreductases. Here we report that fluostatins (FSTs), a family of atypical angucyclines with a benzofluorene core, can undergo nonenzyme-catalyzed epoxide ring opening reactions in the presence of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH). The 2,3-epoxide ring in FST C is shown to open reductively via a putative enol intermediate, or oxidatively via a peroxylated intermediate with molecular oxygen as the oxidant. These reactions lead to multiple products with different redox states that possess a single hydroxyl group at C-2, a 2,3-vicinal diol, a contracted five-membered A-ring, or an expanded seven-membered A-ring. Similar reactions also take place in both natural products and other organic compounds harboring an epoxide adjacent to a carbonyl group that is conjugated to an aromatic moiety. Our findings extend the repertoire of known flavin chemistry that may provide new and useful tools for organic synthesis. Epoxide ring opening reactions are important in both biological processes and synthetic applications. Here, the authors show that flavin cofactors can catalyze reductive and oxidative epoxide ring opening reactions and propose the underlying mechanisms.
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High-Level Production of Catechol from Glucose by Engineered Escherichia coli. FERMENTATION 2022. [DOI: 10.3390/fermentation8070344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Catechol (CA) is an aromatic compound with important applications in the fine chemical and pharmaceutical fields. As an alternative strategy to petroleum-based chemical synthesis, the production of catechol by using microbial cell factories has attracted great interest. However, the toxicity of catechol to microbial cells significantly limits the efficient production of bio-based catechol via one-step fermentation. Therefore, in this study, a two-step strategy for the efficient synthesis of CA was designed. Protocatechuic acid (PCA) was first efficiently produced by the engineered Escherichia coli strain AAA01 via fermentation, and then PCA in the fermentative broth was converted into CA by the whole-cell biocatalyst AAA12 with PCA decarboxylase. By optimizing the expression of flavin isoprenyl transferases and protocatechuic acid decarboxylases, the titer of CA increased from 3.4 g/L to 15.8 g/L in 12 h through whole-cell biocatalysis, with a 365% improvement; after further optimizing the reaction conditions for whole-cell biocatalysis, the titer of CA achieved 17.7 g/L within 3 h, which is the highest titer reported so far. This work provides an effective strategy for the green biomanufacturing of toxic compounds by Escherichia coli cell factories.
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Roberts GW, Leys D. Structural insights into UbiD reversible decarboxylation. Curr Opin Struct Biol 2022; 75:102432. [PMID: 35843126 DOI: 10.1016/j.sbi.2022.102432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
Abstract
The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to elucidating the enigmatic mechanism underpinning the conversion of α,β-unsaturated acids by this system. The UbiD component utilises a unique cofactor, prenylated flavin (prFMN), generated by the bespoke action of the associated UbiX flavin prenyltransferase. Structure determination of a range of UbiX/UbiD representatives has revealed a generic mode of action for both the flavin-to-prFMN metamorphosis and the (de)carboxylation. In contrast to the conserved UbiX, the UbiD superfamily is associated with a versatile substrate range. The latter is reflected in the considerable variety of UbiD quaternary structure, dynamic behaviour and active site architecture. Directed evolution of UbiD enzymes has taken advantage of this apparent malleability to generate new variants supporting in vivo hydrocarbon production. Other applications include coupling UbiD to carboxylic acid reductase to convert alkenes into α,β-unsaturated aldehydes via enzymatic CO2 fixation.
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Affiliation(s)
- George W Roberts
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Wang PH, Chen YL, Wu TY, Wu YW, Wang TY, Shih CJ, Wei STS, Lai YL, Liu CX, Chiang YR. Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O 2-fluctuating estuarine sediments. CHEMOSPHERE 2022; 299:134406. [PMID: 35358556 DOI: 10.1016/j.chemosphere.2022.134406] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) represents the most used phthalate plasticizer with an annual production above the millions of tons worldwide. Due to its inadequate disposal, outstanding chemical stability, and extremely low solubility (3 mg/L), endocrine-disrupting DEHP often accumulates in urban estuarine sediments at concentrations above the predicted no-effect concentration (20-100 mg/kg). Our previous study suggested that microbial DEHP degradation in estuarine sediments proceeds synergistically where DEHP side-chain hydrolysis to form phthalic acid represents a bottleneck. Here, we resolved this bottleneck and deconstructed the microbial synergy in O2-fluctuating estuarine sediments. Metagenomic analysis and RNA sequencing suggested that orthologous genes encoding extracellular DEHP hydrolase NCU65476 in Acidovorax sp. strain 210-6 are often flanked by the co-expressed composite transposon and are widespread in aquatic environments worldwide. Therefore, we developed a turbidity-based microplate assay to characterize NCU65476. The optimized assay conditions (with 1 mM Ca2+ and pH 6.0) increased the DEHP hydrolysis rate by a factor of 10. Next, we isolated phthalic acid-degrading Hydrogenophaga spp. and Thauera chlorobenzoica from Guandu estuarine sediment to study the effect of O2(aq) on their metabolic synergy with strain 210-6. The results of co-culture experiments suggested that after DEHP side-chain hydrolysis by strain 210-6, phthalic acid can be degraded by Hydrogenophaga sp. when O2(aq) is above 1 mg/L or degraded by Thauera chlorobenzoica anaerobically. Altogether, our data demonstrates that DEHP could be degraded synergistically in estuarine sediments via divergent pathways responding to O2 availability. The optimized conditions for NCU65476 could facilitate the practice of DEHP bioremediation in estuarine sediments.
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Affiliation(s)
- Po-Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, 320, Taiwan; Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 145-0061, Japan.
| | - Yi-Lung Chen
- Department of Microbiology, Soochow University, Taipei, 106, Taiwan
| | - Tien-Yu Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 106, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 106, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 106, Taiwan
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | | | - Yi-Li Lai
- Biodiversity Research Center, Academia Sinica, Taipei, 106, Taiwan
| | - Cheng-Xuan Liu
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, 320, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 106, Taiwan; Department of Agricultural Chemistry, National Taiwan University, Taipei, 106, Taiwan.
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Gahloth D, Fisher K, Payne KAP, Cliff M, Levy C, Leys D. Structural and biochemical characterization of the prenylated flavin mononucleotide-dependent indole-3-carboxylic acid decarboxylase. J Biol Chem 2022; 298:101771. [PMID: 35218772 PMCID: PMC8988006 DOI: 10.1016/j.jbc.2022.101771] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 02/08/2023] Open
Abstract
The ubiquitous UbiD family of reversible decarboxylases is implicated in a wide range of microbial processes and depends on the prenylated flavin mononucleotide cofactor for catalysis. However, only a handful of UbiD family members have been characterized in detail, and comparison between these has suggested considerable variability in enzyme dynamics and mechanism linked to substrate specificity. In this study, we provide structural and biochemical insights into the indole-3-carboxylic acid decarboxylase, representing an UbiD enzyme activity distinct from those previously studied. Structural insights from crystal structure determination combined with small-angle X-ray scattering measurements reveal that the enzyme likely undergoes an open-closed transition as a consequence of domain motion, an event that is likely coupled to catalysis. We also demonstrate that the indole-3-carboxylic acid decarboxylase can be coupled with carboxylic acid reductase to produce indole-3-carboxyaldehyde from indole + CO2 under ambient conditions. These insights provide further evidence for a common mode of action in the widespread UbiD enzyme family.
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Affiliation(s)
- Deepankar Gahloth
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Matthew Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Colin Levy
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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25
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Ishibashi Y, Matsushima N, Ito T, Hemmi H. Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Biosci Biotechnol Biochem 2022; 86:246-253. [PMID: 34864834 DOI: 10.1093/bbb/zbab205] [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: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 11/12/2022]
Abstract
Nudix hydrolases typically catalyze the hydrolysis of nucleoside diphosphate linked to moiety X and yield nucleoside monophosphate and X-phosphate, while some of them hydrolyze a terminal diphosphate group of non-nucleosidic compounds and convert it into a phosphate group. Although the number of Nudix hydrolases is usually limited in archaea comparing with those in bacteria and eukaryotes, the physiological functions of most archaeal Nudix hydrolases remain unknown. In this study, a Nudix hydrolase family protein, MM_2582, from the methanogenic archaeon Methanosarcina mazei was recombinantly expressed in Escherichia coli, purified, and characterized. This recombinant protein shows higher hydrolase activity toward isopentenyl diphosphate and short-chain prenyl diphosphates than that toward nucleosidic compounds. Kinetic studies demonstrated that the archaeal enzyme prefers isopentenyl diphosphate and dimethylallyl diphosphate, which suggests its role in the biosynthesis of prenylated flavin mononucleotide, a recently discovered coenzyme that is required, for example, in the archaea-specific modified mevalonate pathway.
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Affiliation(s)
- Yumi Ishibashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Natsumi Matsushima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Tomokazu Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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26
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Bloor S, Michurin I, Titchiner GR, Leys D. Prenylated flavins: structures and mechanisms. FEBS J 2022; 290:2232-2245. [PMID: 35073609 DOI: 10.1111/febs.16371] [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] [Received: 11/22/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
The UbiX/UbiD system is widespread in microbes and responsible for the reversible decarboxylation of unsaturated carboxylic acids. The UbiD enzyme catalyzes this unusual reaction using a prenylated flavin (prFMN) as cofactor, the latter formed by the flavin prenyltransferase UbiX. A detailed picture of the biochemistry of flavin prenylation, oxidative maturation, and covalent catalysis underpinning reversible decarboxylation is emerging. This reveals the prFMN cofactor can undergo a wide range of transformations, complemented by considerable UbiD-variability. These provide a blueprint for biotechnological applications aimed at producing hydrocarbons or aromatic C-H activation through carboxylation.
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Affiliation(s)
- Samuel Bloor
- Department of Chemistry, Manchester Institute of Biotechnology, UK
| | | | | | - David Leys
- Department of Chemistry, Manchester Institute of Biotechnology, UK
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27
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Ohtsu H, Takaoka M, Tezuka Y, Tsuge K, Tanaka K. An NAD +-type earth-abundant metal complex enabling photo-driven alcohol oxidation. Chem Commun (Camb) 2021; 57:13574-13577. [PMID: 34850789 DOI: 10.1039/d1cc04665a] [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
For the first time, an NAD+-type earth-abundant metal complex [Zn(pbn)2(H2O)](ClO4)2 (1) was found to exhibit photo-induced oxidizing ability to convert various primary and secondary alcohols to the corresponding aldehyde and ketone compounds. In addition, a two-electron-reduced Zn(II) complex [Zn(pbnH-pbnH)(ClO4)2] (1red) comprising the novel C-C coupling ligand, obtained by the photo-induced oxidation of alcohols by 1, was successfully isolated and completely characterized. We clarified that the photochemical oxidation of alcohols by 1 to produce 1red proceeds via an electron transfer followed by proton transfer mechanism as elucidated by kinetic analysis on the basis of absorption spectroscopic measurements.
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Affiliation(s)
- Hideki Ohtsu
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
| | - Mikio Takaoka
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
| | - Yosuke Tezuka
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
| | - Kiyoshi Tsuge
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
| | - Koji Tanaka
- Institute for Integrated Cell-Material Science, Institute for Advanced Study, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Graduate School of Life Science, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
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28
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Del Rio Flores A, Twigg FF, Du Y, Cai W, Aguirre DQ, Sato M, Dror MJ, Narayanamoorthy M, Geng J, Zill NA, Zhai R, Zhang W. Biosynthesis of triacsin featuring an N-hydroxytriazene pharmacophore. Nat Chem Biol 2021; 17:1305-1313. [PMID: 34725510 PMCID: PMC8605994 DOI: 10.1038/s41589-021-00895-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing, hydrazine-forming enzyme (Tri28) and a nitrite-utilizing, N-nitrosating enzyme (Tri17). This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Frederick F Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Daniel Q Aguirre
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | | | - Jiaxin Geng
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States.
- Chan Zuckerberg Biohub, San Francisco, CA, United States.
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29
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Datar PM, Marsh ENG. Decarboxylation of Aromatic Carboxylic Acids by the Prenylated-FMN-dependent Enzyme Phenazine-1-carboxylic Acid Decarboxylase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Saaret A, Villiers B, Stricher F, Anissimova M, Cadillon M, Spiess R, Hay S, Leys D. Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production. Nat Commun 2021; 12:5300. [PMID: 34489427 PMCID: PMC8421414 DOI: 10.1038/s41467-021-25598-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group. Isobutene is a high value gaseous alkene that is widely used as fuel additive and a chemical building block. Here, the authors report an alternative pathway for isobutene bioproduction by directed evolution of prenylated FMN-dependent ferulic acid decarboxylase.
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Affiliation(s)
- Annica Saaret
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | | | | | | | | | - Reynard Spiess
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK.
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31
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Marshall SA, Payne KAP, Fisher K, Titchiner GR, Levy C, Hay S, Leys D. UbiD domain dynamics underpins aromatic decarboxylation. Nat Commun 2021; 12:5065. [PMID: 34417452 PMCID: PMC8379154 DOI: 10.1038/s41467-021-25278-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
The widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.
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Affiliation(s)
- Stephen A. Marshall
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK ,grid.4991.50000 0004 1936 8948Present Address: Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Karl A. P. Payne
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel R. Titchiner
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Colin Levy
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
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32
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Bou-Nader C, Stull FW, Pecqueur L, Simon P, Guérineau V, Royant A, Fontecave M, Lombard M, Palfey BA, Hamdane D. An enzymatic activation of formaldehyde for nucleotide methylation. Nat Commun 2021; 12:4542. [PMID: 34315871 PMCID: PMC8316439 DOI: 10.1038/s41467-021-24756-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Frederick W Stull
- Programs in Chemical Biology and the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Philippe Simon
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Vincent Guérineau
- CNRS, Institut de Chimie des Substances Naturelles UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Antoine Royant
- CEA, CNRS, Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Grenoble, France.,European Synchrotron Radiation Facility, Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Bruce A Palfey
- Programs in Chemical Biology and the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France.
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33
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Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments. mSystems 2021; 6:e0035821. [PMID: 34100638 PMCID: PMC8269228 DOI: 10.1128/msystems.00358-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase—key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively—are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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35
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Kawanabe K, Aono R, Kino K. 2,5-Furandicarboxylic acid production from furfural by sequential biocatalytic reactions. J Biosci Bioeng 2021; 132:18-24. [PMID: 33846091 DOI: 10.1016/j.jbiosc.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
2,5-Furandicarboxylic acid (FDCA) is a valuable compound that can be synthesized from biomass-derived hydroxymethylfurfural (HMF), and holds great potential as a promising replacement for petroleum-based terephthalic acid in the production of polyamides, polyesters, and polyurethanes used universally. However, an economical large-scale production strategy for HMF from lignocellulosic biomass is yet to be established. This study aimed to design a synthetic pathway that can yield FDCA from furfural, whose industrial production from lignocellulosic biomass has already been established. This artificial pathway consists of an oxidase and a prenylated flavin mononucleotide (prFMN)-dependent reversible decarboxylase, catalyzing furfural oxidation and carboxylation of 2-furoic acid, respectively. The prFMN-dependent reversible decarboxylase was identified in an isolated strain, Paraburkholderia fungorum KK1, whereas an HMF oxidase from Methylovorus sp. MP688 exhibited furfural oxidation activity and was used as a furfural oxidase. Using Escherichia coli cells coexpressing these proteins, as well as a flavin prenyltransferase, FDCA could be produced from furfural via 2-furoic acid in one pot.
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Affiliation(s)
- Kazuki Kawanabe
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Riku Aono
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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36
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Burgardt A, Moustafa A, Persicke M, Sproß J, Patschkowski T, Risse JM, Peters-Wendisch P, Lee JH, Wendisch VF. Coenzyme Q 10 Biosynthesis Established in the Non-Ubiquinone Containing Corynebacterium glutamicum by Metabolic Engineering. Front Bioeng Biotechnol 2021; 9:650961. [PMID: 33859981 PMCID: PMC8042324 DOI: 10.3389/fbioe.2021.650961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Coenzyme Q10 (CoQ10) serves as an electron carrier in aerobic respiration and has become an interesting target for biotechnological production due to its antioxidative effect and benefits in supplementation to patients with various diseases. For the microbial production, so far only bacteria have been used that naturally synthesize CoQ10 or a related CoQ species. Since the whole pathway involves many enzymatic steps and has not been fully elucidated yet, the set of genes required for transfer of CoQ10 synthesis to a bacterium not naturally synthesizing CoQ species remained unknown. Here, we established CoQ10 biosynthesis in the non-ubiquinone-containing Gram-positive Corynebacterium glutamicum by metabolic engineering. CoQ10 biosynthesis involves prenylation and, thus, requires farnesyl diphosphate as precursor. A carotenoid-deficient strain was engineered to synthesize an increased supply of the precursor molecule farnesyl diphosphate. Increased farnesyl diphosphate supply was demonstrated indirectly by increased conversion to amorpha-4,11-diene. To provide the first CoQ10 precursor decaprenyl diphosphate (DPP) from farnesyl diphosphate, DPP synthase gene ddsA from Paracoccus denitrificans was expressed. Improved supply of the second CoQ10 precursor, para-hydroxybenzoate (pHBA), resulted from metabolic engineering of the shikimate pathway. Prenylation of pHBA with DPP and subsequent decarboxylation, hydroxylation, and methylation reactions to yield CoQ10 was achieved by expression of ubi genes from Escherichia coli. CoQ10 biosynthesis was demonstrated in shake-flask cultivation and verified by liquid chromatography mass spectrometry analysis. To the best of our knowledge, this is the first report of CoQ10 production in a non-ubiquinone-containing bacterium.
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Affiliation(s)
- Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ayham Moustafa
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Thomas Patschkowski
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Petra Peters-Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Major in Food Science & Biotechnology, School of Food Biotechnology & Nutrition, Kyungsung University, Busan, South Korea
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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Payne KAP, Marshall SA, Fisher K, Rigby SEJ, Cliff MJ, Spiess R, Cannas DM, Larrosa I, Hay S, Leys D. Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence. ACS Catal 2021; 11:2865-2878. [PMID: 33763291 PMCID: PMC7976604 DOI: 10.1021/acscatal.0c05042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/04/2021] [Indexed: 11/29/2022]
Abstract
The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN-imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.
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Affiliation(s)
- Karl A. P. Payne
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen A. Marshall
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Reynard Spiess
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Diego M. Cannas
- Department of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Igor Larrosa
- Department of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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38
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Yang Q, Guo X, Liu Y, Jiang H. Biocatalytic C-C Bond Formation for One Carbon Resource Utilization. Int J Mol Sci 2021; 22:ijms22041890. [PMID: 33672882 PMCID: PMC7918591 DOI: 10.3390/ijms22041890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022] Open
Abstract
The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO2, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.
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Affiliation(s)
- Qiaoyu Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxian Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yuwan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
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39
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Mendes V, Green SR, Evans JC, Hess J, Blaszczyk M, Spry C, Bryant O, Cory-Wright J, Chan DSH, Torres PHM, Wang Z, Nahiyaan N, O’Neill S, Damerow S, Post J, Bayliss T, Lynch SL, Coyne AG, Ray PC, Abell C, Rhee KY, Boshoff HIM, Barry CE, Mizrahi V, Wyatt PG, Blundell TL. Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site. Nat Commun 2021; 12:143. [PMID: 33420031 PMCID: PMC7794376 DOI: 10.1038/s41467-020-20224-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 11/18/2020] [Indexed: 02/02/2023] Open
Abstract
Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.
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Affiliation(s)
- Vitor Mendes
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Simon R. Green
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Joanna C. Evans
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Jeannine Hess
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Michal Blaszczyk
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Christina Spry
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Owain Bryant
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - James Cory-Wright
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Daniel S-H. Chan
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Pedro H. M. Torres
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Zhe Wang
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Navid Nahiyaan
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Sandra O’Neill
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Sebastian Damerow
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - John Post
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Tracy Bayliss
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Sasha L. Lynch
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Anthony G. Coyne
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Peter C. Ray
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Chris Abell
- grid.5335.00000000121885934Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Kyu Y. Rhee
- grid.5386.8000000041936877XDivision of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Helena I. M. Boshoff
- grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Clifton E. Barry
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa ,grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Valerie Mizrahi
- grid.7836.a0000 0004 1937 1151MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Paul G. Wyatt
- grid.8241.f0000 0004 0397 2876Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH Scotland UK
| | - Tom L. Blundell
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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40
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The In Vitro Production of prFMN for Reconstitution of UbiD Enzymes. Methods Mol Biol 2021; 2280:219-227. [PMID: 33751438 DOI: 10.1007/978-1-0716-1286-6_14] [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: 01/25/2023]
Abstract
Prenylated flavin (prFMN) is a modified FMN cofactor, the isoalloxazine is extended by an additional six membered nonaromatic ring. The modification confers azomethine ylide characteristics on the oxidised prFMN, allowing it to support the reversible nonoxidative decarboxylation of unsaturated acids by the UbiD family of decarboxylases. In absence of a chemical synthesis route for prFMN, enzymatic production by the flavin prenyltransferase, UbiX, is required for in vitro reconstitution of prFMN-dependent enzymes. Here we provide an overview of the methods for producing prFMN in vitro using the flavin prenyltransferase UbiX, and the subsequent reconstitution and activation of UbiD enzymes.
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41
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Toplak M, Matthews A, Teufel R. The devil is in the details: The chemical basis and mechanistic versatility of flavoprotein monooxygenases. Arch Biochem Biophys 2020; 698:108732. [PMID: 33358998 DOI: 10.1016/j.abb.2020.108732] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023]
Abstract
The ubiquitous flavoenzymes commonly catalyze redox chemistry such as the monooxygenation of organic substrates and are both widely utilized in nature (e.g., in primary and secondary metabolism) and of significant industrial interest. In this work, we highlight the structural and mechanistic characteristics of the distinct types of flavoprotein monooxygenases (FPMOs). We thereby illustrate the chemical basis of FPMO catalysis, which enables reactions such as (aromatic) hydroxylation, epoxidation, (de)halogenation, heteroatom oxygenation, Baeyer-Villiger oxidation, α-hydroxylation of ketones, or non-oxidative carbon-hetero bond cleavage. This seemingly unmatched versatility in oxygenation chemistry results from extensive fine-tuning and regiospecific functionalization of the flavin cofactor that is tightly controlled by the surrounding protein matrix. Accordingly, FPMOs steer the formation of covalent flavin-oxygen adducts for oxygen transfer in the form of the classical flavin-C4a-(hydro)peroxide or the recently discovered N5-functionalized flavins (i.e. the flavin-N5-oxide and the flavin-N5-peroxide), while in rare cases covalent oxygen adduct formation may be foregone entirely. Finally, we speculate about hitherto undiscovered flavin-mediated oxygenation reactions and compare FPMOs to cytochrome P450 monooxygenases, before addressing open questions and challenges for the future investigation of FPMOs.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Arne Matthews
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.
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42
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Kaneshiro AK, Koebke KJ, Zhao C, Ferguson KL, Ballou DP, Palfey BA, Ruotolo BT, Marsh ENG. Kinetic Analysis of Transient Intermediates in the Mechanism of Prenyl-Flavin-Dependent Ferulic Acid Decarboxylase. Biochemistry 2020; 60:125-134. [PMID: 33342208 DOI: 10.1021/acs.biochem.0c00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferulic acid decarboxylase catalyzes the decarboxylation of various substituted phenylacrylic acids to their corresponding styrene derivatives and CO2 using the recently discovered cofactor prenylated FMN (prFMN). The mechanism involves an unusual 1,3-dipolar cycloaddition reaction between prFMN and the substrate to generate a cycloadduct capable of undergoing decarboxylation. Using native mass spectrometry, we show the enzyme forms a stable prFMN-styrene cycloadduct that accumulates on the enzyme during turnover. Pre-steady state kinetic analysis of the reaction using ultraviolet-visible stopped-flow spectroscopy reveals a complex pattern of kinetic behavior, best described by a half-of-sites model involving negative cooperativity between the two subunits of the dimeric enzyme. For the reactive site, the cycloadduct of prFMN with phenylacylic acid is formed with a kapp of 131 s-1. This intermediate converts to the prFMN-styrene cycloadduct with a kapp of 75 s-1. Cycloelimination of the prFMN-styrene cycloadduct to generate styrene and free enzyme appears to determine kcat for the overall reaction, which is 11.3 s-1.
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43
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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44
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Balaikaite A, Chisanga M, Fisher K, Heyes DJ, Spiess R, Leys D. Ferulic Acid Decarboxylase Controls Oxidative Maturation of the Prenylated Flavin Mononucleotide Cofactor. ACS Chem Biol 2020; 15:2466-2475. [PMID: 32840348 DOI: 10.1021/acschembio.0c00456] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered modified flavin cofactor containing an additional nonaromatic ring, connected to the N5 and C6 atoms. This cofactor underpins reversible decarboxylation catalyzed by members of the widespread UbiD enzyme family and is produced by the flavin prenyltransferase UbiX. Oxidative maturation of the UbiX product prFMNH2 to the corresponding oxidized prFMNiminium is required for ferulic acid decarboxylase (Fdc1; a UbiD-type enzyme) activity. However, it is unclear what role the Fdc1 enzyme plays in this process. Here, we demonstrate that, in the absence of Fdc1, prFMNH2 oxidation by O2 proceeds via a transient semiquinone prFMNradical species and culminates in a remarkably stable prFMN-hydroperoxide species. Neither forms of prFMN are able to support Fdc1 activity. Instead, enzyme activation using O2-mediated oxidation requires prFMNH2 binding prior to oxygen exposure, confirming that UbiD enzymes play a role in O2-mediated oxidative maturation. In marked contrast, alternative oxidants such as potassium ferricyanide support prFMNiminium formation both in solution and in Fdc1.
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Affiliation(s)
- Arune Balaikaite
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Malama Chisanga
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Department of Chemistry, School of Mathematics and Natural Sciences, Copperbelt University, Kitwe, Zambia
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Reynard Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
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45
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He H, Bian G, Herbst-Gervasoni CJ, Mori T, Shinsky SA, Hou A, Mu X, Huang M, Cheng S, Deng Z, Christianson DW, Abe I, Liu T. Discovery of the cryptic function of terpene cyclases as aromatic prenyltransferases. Nat Commun 2020; 11:3958. [PMID: 32769971 PMCID: PMC7414894 DOI: 10.1038/s41467-020-17642-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/08/2020] [Indexed: 11/25/2022] Open
Abstract
Catalytic versatility is an inherent property of many enzymes. In nature, terpene cyclases comprise the foundation of molecular biodiversity as they generate diverse hydrocarbon scaffolds found in thousands of terpenoid natural products. Here, we report that the catalytic activity of the terpene cyclases AaTPS and FgGS can be switched from cyclase to aromatic prenyltransferase at basic pH to generate prenylindoles. The crystal structures of AaTPS and FgGS provide insights into the catalytic mechanism of this cryptic function. Moreover, aromatic prenyltransferase activity discovered in other terpene cyclases indicates that this cryptic function is broadly conserved among the greater family of terpene cyclases. We suggest that this cryptic function is chemoprotective for the cell by regulating isoprenoid diphosphate concentrations so that they are maintained below toxic thresholds.
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Affiliation(s)
- Haibing He
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Guangkai Bian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Corey J Herbst-Gervasoni
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323, USA
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Stephen A Shinsky
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323, USA
| | - Anwei Hou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xin Mu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Minjian Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shu Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323, USA.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan.
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, China.
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46
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Aleku GA, Saaret A, Bradshaw-Allen RT, Derrington SR, Titchiner GR, Gostimskaya I, Gahloth D, Parker DA, Hay S, Leys D. Enzymatic C–H activation of aromatic compounds through CO2 fixation. Nat Chem Biol 2020; 16:1255-1260. [DOI: 10.1038/s41589-020-0603-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022]
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47
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Abstract
The reversible (de)carboxylation of unsaturated carboxylic acids is carried out by the UbiX-UbiD system, ubiquitously present in microbes. The biochemical basis of this challenging reaction has recently been uncovered by the discovery of the UbiD cofactor, prenylated FMN (prFMN). This heavily modified flavin is synthesized by the flavin prenyltransferase UbiX, which catalyzes the non-metal dependent prenyl transfer from dimethylallyl(pyro)phosphate (DMAP(P)) to the flavin N5 and C6 positions, creating a fourth non-aromatic ring. Following prenylation, prFMN undergoes oxidative maturation to form the iminium species required for UbiD activity. prFMNiminium acts as a prostethic group and is bound via metal ion mediated interactions between UbiD and the prFMNiminium phosphate moiety. The modified isoalloxazine ring is place adjacent to the E(D)-R-E UbiD signature sequent motif. The fungal ferulic acid decarboxylase Fdc from Aspergillus niger has emerged as a UbiD-model system, and has yielded atomic level insight into the prFMNiminium mediated (de)carboxylation. A wealth of data now supports a mechanism reliant on reversible 1,3 dipolar cycloaddition between substrate and cofactor for this enzyme. This poses the intriguing question whether a similar mechanism is used by all UbiD enzymes, especially those that act as carboxylases on inherently more difficult substrates such as phenylphosphate or benzene/naphthalene. Indeed, considerable variability in terms of oligomerization, domain motion and active site structure is now reported for the UbiD family.
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Affiliation(s)
- Annica Saaret
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Arune Balaikaite
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom.
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48
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Batyrova KA, Khusnutdinova AN, Wang PH, Di Leo R, Flick R, Edwards EA, Savchenko A, Yakunin AF. Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation. ACS Chem Biol 2020; 15:1874-1882. [PMID: 32579338 DOI: 10.1021/acschembio.0c00136] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible UbiD-like (de)carboxylases represent a large family of mostly uncharacterized enzymes, which require the recently discovered prenylated FMN (prFMN) cofactor for activity. Functional characterization of novel UbiDs is hampered by a lack of robust protocols for prFMN generation and UbiD activation. Here, we report two systems for in vitro and in vivo FMN prenylation and UbiD activation under aerobic conditions. The in vitro one-pot prFMN cascade includes five enzymes: FMN prenyltransferase (UbiX), prenol kinase, polyphosphate kinase, formate dehydrogenase, and FMN reductase, which use prenol, polyphosphate, formate, ATP, NAD+, and FMN as substrates and cofactors. Under aerobic conditions, this cascade produced prFMN from FMN with over 98% conversion and activated purified ferulic acid decarboxylase Fdc1 from Aspergillus niger and protocatechuic acid decarboxylase ENC0058 from Enterobacter cloaceae. The in vivo system for FMN prenylation and UbiD activation is based on the coexpression of Fdc1 and UbiX in Escherichia coli cells under aerobic conditions in the presence of prenol. The in vitro and in vivo FMN prenylation cascades will facilitate functional characterization of novel UbiDs and their applications.
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Affiliation(s)
- Khorcheska A. Batyrova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom
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49
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Abby SS, Kazemzadeh K, Vragniau C, Pelosi L, Pierrel F. Advances in bacterial pathways for the biosynthesis of ubiquinone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148259. [PMID: 32663475 DOI: 10.1016/j.bbabio.2020.148259] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes of the mitochondrial pathway that produces ubiquinone are highly similar across eukaryotes, recent results point to a rather high diversity of pathways in bacteria. This review focuses on ubiquinone in bacteria, highlighting newly discovered functions and detailing the proteins that are known to participate to its biosynthetic pathways. Novel results showing that ubiquinone can be produced by a pathway independent of dioxygen suggest that ubiquinone may participate to anaerobiosis, in addition to its well-established role for aerobiosis. We also discuss the supramolecular organization of ubiquinone biosynthesis proteins and we summarize the current understanding of the evolution of the ubiquinone pathways relative to those of other isoprenoid quinones like menaquinone and plastoquinone.
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Affiliation(s)
- Sophie Saphia Abby
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Charles Vragniau
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.
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50
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Fino C, Vestergaard M, Ingmer H, Pierrel F, Gerdes K, Harms A. PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10. Microbiologyopen 2020; 9:e1064. [PMID: 32558363 PMCID: PMC7424257 DOI: 10.1002/mbo3.1064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotic‐tolerant persisters are often implicated in treatment failure of chronic and relapsing bacterial infections, but the underlying molecular mechanisms have remained elusive. Controversies revolve around the relative contribution of specific genetic switches called toxin–antitoxin (TA) modules and global modulation of cellular core functions such as slow growth. Previous studies on uropathogenic Escherichia coli observed impaired persister formation for mutants lacking the pasTI locus that had been proposed to encode a TA module. Here, we show that pasTI is not a TA module and that the supposed toxin PasT is instead the bacterial homolog of mitochondrial protein Coq10 that enables the functionality of the respiratory electron carrier ubiquinone as a “lipid chaperone.” Consistently, pasTI mutants show pleiotropic phenotypes linked to defective electron transport such as decreased membrane potential and increased sensitivity to oxidative stress. We link impaired persister formation of pasTI mutants to a global distortion of cellular stress responses due to defective respiration. Remarkably, the ectopic expression of human coq10 largely complements the respiratory defects and decreased persister levels of pasTI mutants. Our work suggests that PasT/Coq10 has a central role in respiratory electron transport that is conserved from bacteria to humans and sustains bacterial tolerance to antibiotics.
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Affiliation(s)
- Cinzia Fino
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hanne Ingmer
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabien Pierrel
- CNRS, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Kenn Gerdes
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Harms
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Focal Area of Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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