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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Barroso GT, Garcia AA, Knapp M, Boggs DG, Bridwell-Rabb J. Purification and characterization of a Rieske oxygenase and its NADH-regenerating partner proteins. Methods Enzymol 2024; 703:215-242. [PMID: 39260997 DOI: 10.1016/bs.mie.2024.05.015] [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] [Indexed: 09/13/2024]
Abstract
The Rieske non-heme iron oxygenases (Rieske oxygenases) comprise a class of metalloenzymes that are involved in the biosynthesis of complex natural products and the biodegradation of aromatic pollutants. Despite this desirable catalytic repertoire, industrial implementation of Rieske oxygenases has been hindered by the multicomponent nature of these enzymes and their requirement for expensive reducing equivalents in the form of a reduced nicotinamide adenine dinucleotide cosubstrate (NAD(P)H). Fortunately, however, some Rieske oxygenases co-occur with accessory proteins, that through a downstream reaction, recycle the needed NAD(P)H for catalysis. As these pathways and accessory proteins are attractive for bioremediation applications and enzyme engineering campaigns, herein, we describe methods for assembling Rieske oxygenase pathways in vitro. Further, using the TsaMBCD pathway as a model system, in this chapter, we provide enzymatic, spectroscopic, and crystallographic methods that can be adapted to explore both Rieske oxygenases and their co-occurring accessory proteins.
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Affiliation(s)
- Gage T Barroso
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | | | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
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3
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de Kok NAW, Miao H, Schmidt S. In vitro analysis of the three-component Rieske oxygenase cumene dioxygenase from Pseudomonas fluorescens IP01. Methods Enzymol 2024; 703:167-192. [PMID: 39260995 DOI: 10.1016/bs.mie.2024.05.013] [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] [Indexed: 09/13/2024]
Abstract
Rieske non-heme iron-dependent oxygenases (ROs) are a versatile group of enzymes traditionally associated with the degradation of aromatic xenobiotics. In addition, ROs have been found to play key roles in natural product biosynthesis, displaying a wide catalytic diversity with typically high regio- and stereo- selectivity. However, the detailed characterization of ROs presents formidable challenges due to their complex structural and functional properties, including their multi-component composition, cofactor dependence, and susceptibility to reactive oxygen species. In addition, the substrate availability of natural product biosynthetic intermediates, the limited solubility of aromatic hydrocarbons, and the radical-mediated reaction mechanism can further complicate functional assays. Despite these challenges, ROs hold immense potential as biocatalysts for pharmaceutical applications and bioremediation. Using cumene dioxygenase (CDO) from Pseudomonas fluorescens IP01 as a model enzyme, this chapter details techniques for characterizing ROs that oxyfunctionalize aromatic hydrocarbons. Moreover, potential pitfalls, anticipated complications, and proposed solutions for the characterization of novel ROs are described, providing a framework for future RO research and strategies for studying this enzyme class. In particular, we describe the methods used to obtain CDO, from construct design to expression conditions, followed by a purification procedure, and ultimately activity determination through various activity assays.
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Affiliation(s)
- Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Hui Miao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
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4
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Su L, Souaibou Y, Hôtel L, Paris C, Weissman KJ, Aigle B. Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways. Appl Environ Microbiol 2024; 90:e0211523. [PMID: 38323847 PMCID: PMC10952394 DOI: 10.1128/aem.02115-23] [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: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.
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Affiliation(s)
- Li Su
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Yaouba Souaibou
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
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5
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Guth FM, Lindner F, Rydzek S, Peil A, Friedrich S, Hauer B, Hahn F. Rieske Oxygenase-Catalyzed Oxidative Late-Stage Functionalization during Complex Antifungal Polyketide Biosynthesis. ACS Chem Biol 2023; 18:2450-2456. [PMID: 37948749 DOI: 10.1021/acschembio.3c00498] [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: 11/12/2023]
Abstract
Rieske oxygenases (ROs) from natural product biosynthetic pathways are a poorly studied group of enzymes with significant potential as oxidative functionalization biocatalysts. A study on the ROs JerL, JerP, and AmbP from the biosynthetic pathways of jerangolid A and ambruticin VS-3 is described. Their activity was successfully reconstituted using whole-cell bioconversion systems coexpressing the ROs and their respective natural flavin-dependent reductase (FDR) partners. Feeding authentic biosynthetic intermediates and synthetic surrogates to these strains confirmed the involvement of the ROs in hydroxymethylpyrone and dihydropyran formation and revealed crucial information about the RO's substrate specificity. The pronounced dependence of JerL and JerP on the presence of a methylenolether allowed the precise temporal assignment of RO catalysis to the ultimate steps of jerangolid biosynthesis. JerP and AmbP stand out among the biosynthetic ROs studied so far for their ability to catalyze clean tetrahydropyran desaturation without further functionalizing the formed electron-rich double bonds. This work highlights the remarkable ability of ROs to highly selectively oxidize complex molecular scaffolds.
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Affiliation(s)
- Florian M Guth
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Simon Rydzek
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Andreas Peil
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Steffen Friedrich
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
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6
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Mori A, Hirata Y, Kishida M, Mori Y, Kondo A, Noda S, Tanaka T. p-Nitrobenzoate production from glucose by utilizing p-aminobenzoate N-oxygenase: AurF. Enzyme Microb Technol 2023; 171:110321. [PMID: 37696175 DOI: 10.1016/j.enzmictec.2023.110321] [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: 06/19/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023]
Abstract
Nitroaromatic compounds are widely used in industry, but their production is associated with issues such as the hazardousness of the process and low regioselectivity. Here, we successfully demonstrated the production of p-nitrobenzoate (PNBA) from glucose by constructing p-aminobenzoate N-oxygenase AurF-expressing E. coli. We generated this strain, which we named PN-1 by disrupting four genes involved in PNBA degradation: nfsA, nfsB, nemA, and azoR. We then expressed AurF from Streptomyces thioluteus in this strain, which resulted in the production of 945 mg/L PNBA in the presence of 1 g/L p-aminobenzoate. Direct production of PNBA from glucose was achieved by co-expressing the pabA, pabB, and pabC, as well as aurF, resulting in the production of 393 mg/L PNBA from 20 g/L glucose. To improve the PNBA titer, we disrupted genes involved in competing pathways: pheA, tyrA, trpE, pykA, and pykF. The resultant strain PN-4Ap produced 975 mg/L PNBA after 72 h of cultivation. These results highlight the potential of using microorganisms to produce other nitroaromatic compounds.
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Affiliation(s)
- Ayana Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Mayumi Kishida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Shuhei Noda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [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: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Wang X, Lin X, Jiang Y, Qin X, Ma N, Yao F, Dong S, Liu C, Feng Y, Jin L, Xian M, Cong Z. Engineering Cytochrome P450BM3 Enzymes for Direct Nitration of Unsaturated Hydrocarbons. Angew Chem Int Ed Engl 2023; 62:e202217678. [PMID: 36660956 DOI: 10.1002/anie.202217678] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Applications of the peroxidase activity of cytochrome P450 enzymes in synthetic chemistry remain largely unexplored. We present herein a protein engineering strategy to increase cytochrome P450BM3 peroxidase activity for the direct nitration of aromatic compounds and terminal aryl-substituted olefins in the presence of a dual-functional small molecule (DFSM). Site-directed mutations of key active-site residues allowed the efficient regulation of steric effects to limit substrate access and, thus, a significant decrease in monooxygenation activity and increase in peroxidase activity. Nitration of several phenol and aniline compounds also yielded ortho- and para-nitration products with moderate-to-high total turnover numbers. Besides direct aromatic nitration by P450 variants using nitrite as a nitrating agent, we also demonstrated the use of the DFSM-facilitated P450 peroxidase system for the nitration of the vinyl group of styrene and its derivatives.
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Affiliation(s)
- Xiling Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xiaodan Lin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Department of Chemistry, Yanbian University Yanji, Jilin, 133002, China
| | - Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuquan Yao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Longyi Jin
- Department of Chemistry, Yanbian University Yanji, Jilin, 133002, China
| | - Mo Xian
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Hu WY, Li K, Weitz A, Wen A, Kim H, Murray JC, Cheng R, Chen B, Naowarojna N, Grinstaff MW, Elliott SJ, Chen JS, Liu P. Light-Driven Oxidative Demethylation Reaction Catalyzed by a Rieske-Type Non-heme Iron Enzyme Stc2. ACS Catal 2022; 12:14559-14570. [PMID: 37168530 PMCID: PMC10168674 DOI: 10.1021/acscatal.2c04232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rieske-type non-heme iron oxygenases/oxidases catalyze a wide range of transformations. Their applications in bioremediation or biocatalysis face two key barriers: the need of expensive NAD(P)H as a reductant and a proper reductase to mediate the electron transfer from NAD(P)H to the oxygenases. To bypass the need of both the reductase and NAD(P)H, using Rieske-type oxygenase (Stc2) catalyzed oxidative demethylation as the model system, we report Stc2 photocatalysis using eosin Y/sulfite as the photosensitizer/sacrificial reagent pair. In a flow-chemistry setting to separate the photo-reduction half-reaction and oxidation half-reaction, Stc2 photo-biocatalysis outperforms the Stc2-NAD(P)H-reductase (GbcB) system. In addition, in a few other selected Rieske enzymes (NdmA, CntA, and GbcA), and a flavin-dependent enzyme (iodotyrosine deiodinase, IYD), the eosin Y/sodium sulfite photo-reduction pair could also serve as the NAD(P)H-reductase surrogate to support catalysis, which implies the potential applicability of this photo-reduction system to other redox enzymes.
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Affiliation(s)
- Wei-Yao Hu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Kelin Li
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Andrew Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Aiwen Wen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Hyomin Kim
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jessica C. Murray
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Baixiong Chen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Mark W. Grinstaff
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jie-Sheng Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
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11
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Srivastava AK, Srivastava R, Sharma A, Bharati AP, Yadav J, Singh AK, Tiwari PK, Srivatava AK, Chakdar H, Kashyap PL, Saxena AK. Transcriptome Analysis to Understand Salt Stress Regulation Mechanism of Chromohalobacter salexigens ANJ207. Front Microbiol 2022; 13:909276. [PMID: 35847097 PMCID: PMC9279137 DOI: 10.3389/fmicb.2022.909276] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Soil salinity is one of the major global issues affecting soil quality and agricultural productivity. The plant growth-promoting halophilic bacteria that can thrive in regions of high salt (NaCl) concentration have the ability to promote the growth of plants in salty environments. In this study, attempts have been made to understand the salinity adaptation of plant growth-promoting moderately halophilic bacteria Chromohalobacter salexigens ANJ207 at the genetic level through transcriptome analysis. In order to identify the stress-responsive genes, the transcriptome sequencing of C. salexigens ANJ207 under different salt concentrations was carried out. Among the 8,936 transcripts obtained, 93 were upregulated while 1,149 were downregulated when the NaCl concentration was increased from 5 to 10%. At 10% NaCl concentration, genes coding for lactate dehydrogenase, catalase, and OsmC-like protein were upregulated. On the other hand, when salinity was increased from 10 to 25%, 1,954 genes were upregulated, while 1,287 were downregulated. At 25% NaCl, genes coding for PNPase, potassium transporter, aconitase, excinuclease subunit ABC, and transposase were found to be upregulated. The quantitative real-time PCR analysis showed an increase in the transcript of genes related to the biosynthesis of glycine betaine coline genes (gbcA, gbcB, and L-pro) and in the transcript of genes related to the uptake of glycine betaine (OpuAC, OpuAA, and OpuAB). The transcription of the genes involved in the biosynthesis of L-hydroxyproline (proD and proS) and one stress response proteolysis gene for periplasmic membrane stress sensing (serP) were also found to be increased. The presence of genes for various compatible solutes and their increase in expression at the high salt concentration indicated that a coordinated contribution by various compatible solutes might be responsible for salinity adaptation in ANJ207. The investigation provides new insights into the functional roles of various genes involved in salt stress tolerance and oxidative stress tolerance produced by high salt concentration in ANJ207 and further support the notion regarding the utilization of bacterium and their gene(s) in ameliorating salinity problem in agriculture.
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Affiliation(s)
- Alok Kumar Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Ruchi Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anjney Sharma
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Akhilendra Pratap Bharati
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India.,Department of Life Science and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Jagriti Yadav
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Alok Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Praveen Kumar Tiwari
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anchal Kumar Srivatava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Hillol Chakdar
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Prem Lal Kashyap
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Kumar Saxena
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Mau, India
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12
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Nóbile ML, Stricker AM, Marchesano L, Iribarren AM, Lewkowicz ES. N-oxygenation of amino compounds: Early stages in its application to the biocatalyzed preparation of bioactive compounds. Biotechnol Adv 2021; 51:107726. [PMID: 33675955 DOI: 10.1016/j.biotechadv.2021.107726] [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: 11/16/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Among the compounds that contain unusual functional groups, nitro is perhaps one of the most interesting due to the valuable properties it confers on pharmaceuticals and explosives. Traditional chemistry has for many years used environmentally unfriendly strategies; in contrast, the biocatalyzed production of this type of products offers a promising alternative. The small family of enzymes formed by N-oxygenases allows the conversion of an amino group to a nitro through the sequential addition of oxygen. These enzymes also make it possible to obtain other less oxidized N-O functions, such as hydroxylamine or nitroso, present in intermediate or final products. The current substrates on which these enzymes are reported to work encompass a few aromatic molecules and sugars. The unique characteristics of N-oxygenases and the great economic value of the products that they could generate, place them in a position of very high scientific and industrial interest. The most important and best studied N-oxygenases will be presented here.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Lucas Marchesano
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
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13
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Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y. Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer. J Biol Chem 2020; 296:100038. [PMID: 33158989 PMCID: PMC7948474 DOI: 10.1074/jbc.ra120.016019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease, and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail α3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located >40 Å apart in the same monomer but adjacent in two neighboring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in intersubunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut.
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Affiliation(s)
- Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology & Photon Science Institute, The University of Manchester, Manchester, UK
| | | | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK.
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14
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Mao S, Song Z, Wu M, Wang X, Lu F, Qin HM. Expression, Purification, Refolding, and Characterization of a Neverland Protein From Caenorhabditis elegans. Front Bioeng Biotechnol 2020; 8:593041. [PMID: 33195160 PMCID: PMC7609953 DOI: 10.3389/fbioe.2020.593041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/24/2020] [Indexed: 11/23/2022] Open
Abstract
Steroid hormones that serve as vital compounds are necessary for the development and metabolism of a variety of organisms. The neverland (NVD) family genes encode the conserved Rieske-type oxygenases, which are accountable for the dehydrogenation during the synthesis and regulation of steroid hormones. However, the His-tagged NVD protein from Caenorhabditis elegans expresses as inclusion bodies in Escherichia coli BL21 (DE3). This bottleneck can be solved through refolding by urea or the introduction of a maltose-binding protein (MBP) tag at the N-terminus. Through further research on purification after the introduction of a MBP tag at the N-terminus, the CD measurement and fluorescence-based thermal shift assay indicated that MBP was favorable for the NVD proteins' solubility and stability, which may be beneficial for the large-scale manufacture of NVD protein for further research. The structural model contained the Rieske [2Fe-2S] domain and non-heme iron-binding motif, which were similar to 3-ketosteroid 9 α-hydroxylase.
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Affiliation(s)
- Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
| | - Zhan Song
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Mian Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaorui Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
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15
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Massmig M, Reijerse E, Krausze J, Laurich C, Lubitz W, Jahn D, Moser J. Carnitine metabolism in the human gut: characterization of the two-component carnitine monooxygenase CntAB from Acinetobacter baumannii. J Biol Chem 2020; 295:13065-13078. [PMID: 32694223 DOI: 10.1074/jbc.ra120.014266] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/24/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial formation of trimethylamine (TMA) from carnitine in the gut microbiome has been linked to cardiovascular disease. During this process, the two-component carnitine monooxygenase (CntAB) catalyzes the oxygen-dependent cleavage of carnitine to TMA and malic semialdehyde. Individual redox states of the reductase CntB and the catalytic component CntA were investigated based on mutagenesis and electron paramagnetic resonance (EPR) spectroscopic approaches. Protein ligands of the flavin mononucleotide (FMN) and the plant-type [2Fe-2S] cluster of CntB and also of the Rieske-type [2Fe-2S] cluster and the mononuclear [Fe] center of CntA were identified. EPR spectroscopy of variant CntA proteins suggested a hierarchical metallocenter maturation, Rieske [2Fe-2S] followed by the mononuclear [Fe] center. NADH-dependent electron transfer via the redox components of CntB and within the trimeric CntA complex for the activation of molecular oxygen was investigated. EPR experiments indicated that the two electrons from NADH were allocated to the plant-type [2Fe-2S] cluster and to FMN in the form of a flavin semiquinone radical. Single-turnover experiments of this reduced CntB species indicated the translocation of the first electron onto the [Fe] center and the second electron onto the Rieske-type [2Fe-2S] cluster of CntA to finally allow for oxygen activation as a basis for carnitine cleavage. EPR spectroscopic investigation of CntA variants indicated an unusual intermolecular electron transfer between the subunits of the CntA trimer via the "bridging" residue Glu-205. On the basis of these data, a redox catalytic cycle for carnitine monooxygenase was proposed.
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Affiliation(s)
- Marco Massmig
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Edward Reijerse
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Joern Krausze
- Institute of Plant Biology, Technical University Braunschweig, Braunschweig, Germany
| | - Christoph Laurich
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology, Braunschweig, Germany
| | - Jürgen Moser
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany.
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16
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Rogers MS, Lipscomb JD. Salicylate 5-Hydroxylase: Intermediates in Aromatic Hydroxylation by a Rieske Monooxygenase. Biochemistry 2019; 58:5305-5319. [PMID: 31066545 PMCID: PMC6856394 DOI: 10.1021/acs.biochem.9b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rieske oxygenases (ROs) catalyze a large range of oxidative chemistry. We have shown that cis-dihydrodiol-forming Rieske dioxygenases first react with their aromatic substrates via an active site nonheme Fe(III)-superoxide; electron transfer from the Rieske cluster then completes the product-forming reaction. Alternatively, two-electron-reduced Fe(III)-peroxo or hydroxo-Fe(V)-oxo activated oxygen intermediates are possible and may be utilized by other ROs to expand the catalytic range. Here, the reaction of a Rieske monooxygenase, salicylate 5-hydroxylase, that does not form a cis-dihydrodiol is examined. Single-turnover kinetic studies show fast binding of salicylate and O2. Transfer of the Rieske electron required to form the gentisate product occurs through bonds over ∼12 Å and must also be very fast. However, the observed rate constant for this reaction is much slower than expected and sensitive to substrate type. This suggests that initial reaction with salicylate occurs using the same Fe(III)-superoxo-level intermediate as Rieske dioxygenases and that this reaction limits the observed rate of electron transfer. A transient intermediate (λmax = 700 nm) with an electron paramagnetic resonance (EPR) at g = 4.3 is observed after the product is formed in the active site. The use of 17O2 (I = 5/2) results in hyperfine broadening of the g = 4.3 signal, showing that gentisate binds to the mononuclear iron via its C5-OH in the intermediate. The chromophore and EPR signal allow study of product release in the catalytic cycle. Comparison of the kinetics of single- and multiple-turnover reactions shows that re-reduction of the metal centers accelerates product release ∼300-fold, providing insight into the regulatory mechanism of ROs.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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17
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Pawar S, Chaudhari A. Pyrrolnitrin from Rhizospheric Serratia marcescens NCIM 5696: Optimization of Process Parameters Using Statistical Tools and Seed-Applied Bioprotectants for Vigna radiata (L.) Against Fusarium oxysporum MTCC 9913. Appl Biochem Biotechnol 2019; 190:803-825. [PMID: 31493159 DOI: 10.1007/s12010-019-03123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
The extensive use of chemical fungicide in the health and agriculture sectors has increased environmental concerns and promoted an extensive search for alternative bioactives from the microbial system. In the present study, two rhizospheric strains of Serratia spp. (TO-2 and TW-3) have been shown to secrete pyrrolnitrin (PRN) in the range of 11.35 to 35.97 μg ml-1 using MSG and MSD medium after 72 h under static and shake conditions, respectively, but thereafter marginally declined in 96 to 240 h. Alternative one variable assortment at a time (OVAT) for PRN secretion by TW-3 yielded 59.27 μg ml-1 using (gl-1) glycerol (20), monosodium glutamate (14), KH2PO4 (14), NH4Cl (3), Na2HPO4 (4), and MgSO4 (0.3) at pH 7, 120 rpm within 72 h. Further, the Placket-Burman Design (PBD) identified KH2PO4, glycerol, pH, and monosodium glutamate as significant variables and optimized by centered composite design. Accordingly, 3% glycerol, 1.72% KH2PO4, 1.1% monosodium glutamate, 0.4% Na2HPO4, 0.03% MgSO4, 0.05% FeSO4, and 0.01% ZnSO4 were found to enhance the yield of PRN to 96.54 μg ml-1 by TW-3 in 72 h, 120 rpm. Thus, the statistical tool employed in the present study showed a threefold hike in PRN secretion over the OVAT approach, thereby indicating the scope for more PRN production from rhizobacteria. Further, seed application of low PRN (30 μg ml-1) concentration in treatments I and II showed > 90% germination in the initial seed germination and pot assay with the Fusarium oxysporum challenge compared to the control. Also, various growth parameters calculated during 11 days of experiment were significantly increased compared to the negative control (seed + fungus) in both treatments. Thus, the application of PRN at a low concentration to seeds of Vigna radiata (L.) offered protection against the phytopathogenic F. oxysporum MTCC 9913 challenge, suggesting biocontrol activity potential for use in agriculture soils particularly salt-affected soil.
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Affiliation(s)
- Shraddha Pawar
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, 425001, India
| | - Ambalal Chaudhari
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, 425001, India.
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18
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Pawar S, Chaudhari A, Prabha R, Shukla R, Singh DP. Microbial Pyrrolnitrin: Natural Metabolite with Immense Practical Utility. Biomolecules 2019; 9:E443. [PMID: 31484394 PMCID: PMC6769897 DOI: 10.3390/biom9090443] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Pyrrolnitrin (PRN) is a microbial pyrrole halometabolite of immense antimicrobial significance for agricultural, pharmaceutical and industrial implications. The compound and its derivatives have been isolated from rhizospheric fluorescent or non-fluorescent pseudomonads, Serratia and Burkholderia. They are known to confer biological control against a wide range of phytopathogenic fungi, and thus offer strong plant protection prospects against soil and seed-borne phytopathogenic diseases. Although chemical synthesis of PRN has been obtained using different steps, microbial production is still the most useful option for producing this metabolite. In many of the plant-associated isolates of Serratia and Burkholderia, production of PRN is dependent on the quorum-sensing regulation that usually involves N-acylhomoserine lactone (AHL) autoinducer signals. When applied on the organisms as antimicrobial agent, the molecule impedes synthesis of key biomolecules (DNA, RNA and protein), uncouples with oxidative phosphorylation, inhibits mitotic division and hampers several biological mechanisms. With its potential broad-spectrum activities, low phototoxicity, non-toxic nature and specificity for impacts on non-target organisms, the metabolite has emerged as a lead molecule of industrial importance, which has led to developing cost-effective methods for the biosynthesis of PRN using microbial fermentation. Quantum of work narrating focused research efforts in the emergence of this potential microbial metabolite is summarized here to present a consolidated, sequential and updated insight into the chemistry, biology and applicability of this natural molecule.
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Affiliation(s)
- Shraddha Pawar
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India.
| | - Ambalal Chaudhari
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425001, India.
| | - Ratna Prabha
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275101, India.
| | - Renu Shukla
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275101, India.
| | - Dhananjaya P Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275101, India.
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19
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Hedges JB, Ryan KS. In vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jason B. Hedges
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
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20
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Hedges JB, Ryan KS. In vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angew Chem Int Ed Engl 2019; 58:11647-11651. [DOI: 10.1002/anie.201903500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/23/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jason B. Hedges
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
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21
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Ng TL, Rohac R, Mitchell AJ, Boal AK, Balskus EP. An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. Nature 2019; 566:94-99. [PMID: 30728519 PMCID: PMC6369591 DOI: 10.1038/s41586-019-0894-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/12/2018] [Indexed: 12/31/2022]
Abstract
Small molecules containing the N-nitroso group, such as the bacterial natural product streptozotocin, are prominent carcinogens1,2 and important cancer chemotherapeutics3,4. Despite the considerable importance of this functional group to human health, enzymes dedicated to the assembly of the N-nitroso unit have not been identified. Here we show that SznF, a metalloenzyme from the biosynthesis of streptozotocin, catalyses an oxidative rearrangement of the guanidine group of Nω-methyl-L-arginine to generate an N-nitrosourea product. Structural characterization and mutagenesis of SznF reveal two separate active sites that promote distinct steps in this transformation using different iron-containing metallocofactors. This biosynthetic reaction, which has little precedent in enzymology or organic synthesis, expands the catalytic capabilities of non-haem-iron-dependent enzymes to include N-N bond formation. We find that biosynthetic gene clusters that encode SznF homologues are widely distributed among bacteria-including environmental organisms, plant symbionts and human pathogens-which suggests an unexpectedly diverse and uncharacterized microbial reservoir of bioactive N-nitroso metabolites.
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Affiliation(s)
- Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Roman Rohac
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Andrew J Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Amie K Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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22
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Wei W, Siegbahn PEM, Liao R. Mechanism of the Dinuclear Iron Enzymep‐Aminobenzoate N‐oxygenase from Density Functional Calculations. ChemCatChem 2018. [DOI: 10.1002/cctc.201801072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen‐Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm University Stockholm SE-10691 Sweden
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
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23
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Lukowski AL, Ellinwood DC, Hinze ME, DeLuca RJ, Du Bois J, Hall S, Narayan ARH. C-H Hydroxylation in Paralytic Shellfish Toxin Biosynthesis. J Am Chem Soc 2018; 140:11863-11869. [PMID: 30192526 PMCID: PMC6558983 DOI: 10.1021/jacs.8b08901] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The remarkable degree of synthetic selectivity found in Nature is exemplified by the biosynthesis of paralytic shellfish toxins such as saxitoxin. The polycyclic core shared by saxitoxin and its relatives is assembled and subsequently elaborated through the installation of hydroxyl groups with exquisite precision that is not possible to replicate with traditional synthetic methods. Here, we report the identification of the enzymes that carry out a subset of C-H functionalizations involved in paralytic shellfish toxin biosynthesis. We have shown that three Rieske oxygenases mediate hydroxylation reactions with perfect site- and stereoselectivity. Specifically, the Rieske oxygenase SxtT is responsible for selective hydroxylation of a tricyclic precursor to the famous natural product saxitoxin, and a second Rieske oxygenase, GxtA, selectively hydroxylates saxitoxin to access the oxidation pattern present in gonyautoxin natural products. Unexpectedly, a third Rieske oxygenase, SxtH, does not hydroxylate tricyclic intermediates, but rather a linear substrate prior to tricycle formation, rewriting the biosynthetic route to paralytic shellfish toxins. Characterization of SxtT, SxtH, and GxtA is the first demonstration of enzymes carrying out C-H hydroxylation reactions in paralytic shellfish toxin biosynthesis. Additionally, the reactions of these oxygenases with a suite of saxitoxin-related molecules are reported, highlighting the substrate promiscuity of these catalysts and the potential for their application in the synthesis of natural and unnatural saxitoxin congeners.
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Affiliation(s)
- April L. Lukowski
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Duncan C. Ellinwood
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Meagan E. Hinze
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Ryan J. DeLuca
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - J. Du Bois
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Sherwood Hall
- United States Food and Drug Administration, College Park, Maryland 20740
| | - Alison R. H. Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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Glycine Betaine Monooxygenase, an Unusual Rieske-Type Oxygenase System, Catalyzes the Oxidative N-Demethylation of Glycine Betaine in Chromohalobacter salexigens DSM 3043. Appl Environ Microbiol 2018; 84:AEM.00377-18. [PMID: 29703733 DOI: 10.1128/aem.00377-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/20/2018] [Indexed: 11/20/2022] Open
Abstract
Although some bacteria, including Chromohalobacter salexigens DSM 3043, can use glycine betaine (GB) as a sole source of carbon and energy, little information is available about the genes and their encoded proteins involved in the initial step of the GB degradation pathway. In the present study, the results of conserved domain analysis, construction of in-frame deletion mutants, and an in vivo functional complementation assay suggested that the open reading frames Csal_1004 and Csal_1005, designated bmoA and bmoB, respectively, may act as the terminal oxygenase and the ferredoxin reductase genes in a novel Rieske-type oxygenase system to convert GB to dimethylglycine in C. salexigens DSM 3043. To further verify their function, BmoA and BmoB were heterologously overexpressed in Escherichia coli, and 13C nuclear magnetic resonance analysis revealed that dimethylglycine was accumulated in E. coli BL21(DE3) expressing BmoAB or BmoA. In addition, His-tagged BmoA and BmoB were individually purified to electrophoretic homogeneity and estimated to be a homotrimer and a monomer, respectively. In vitro biochemical analysis indicated that BmoB is an NADH-dependent flavin reductase with one noncovalently bound flavin adenine dinucleotide (FAD) as its prosthetic group. In the presence of BmoB, NADH, and flavin, BmoA could aerobically degrade GB to dimethylglycine with the concomitant production of formaldehyde. BmoA exhibited strict substrate specificity for GB, and its demethylation activity was stimulated by Fe2+ Phylogenetic analysis showed that BmoA belongs to group V of the Rieske nonheme iron oxygenase (RO) family, and all the members in this group were able to use quaternary ammonium compounds as substrates.IMPORTANCE GB is widely distributed in nature. In addition to being accumulated intracellularly as a compatible solute to deal with osmotic stress, it can be utilized by many bacteria as a source of carbon and energy. However, very limited knowledge is presently available about the molecular and biochemical mechanisms for the initial step of the aerobic GB degradation pathway in bacteria. Here, we report the molecular and biochemical characterization of a novel two-component Rieske-type monooxygenase system, GB monooxygenase (BMO), which is responsible for oxidative demethylation of GB to dimethylglycine in C. salexigens DSM 3043. The results gained in this study extend our knowledge on the catalytic reaction of microbial GB degradation to dimethylglycine.
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25
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Zhang L, Xu Y, Makris TM, Wang Q. Enhanced Arylamine N-Oxygenase Activity of Polymer–Enzyme Assemblies by Facilitating Electron-Transferring Efficiency. Biomacromolecules 2018; 19:918-925. [DOI: 10.1021/acs.biomac.7b01706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Yanmei Xu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
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26
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Perry C, de los Santos EC, Alkhalaf LM, Challis GL. Rieske non-heme iron-dependent oxygenases catalyse diverse reactions in natural product biosynthesis. Nat Prod Rep 2018; 35:622-632. [DOI: 10.1039/c8np00004b] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The role played by Rieske non-heme iron-dependent oxygenases in natural product biosyntheses is reviewed, with particular focus on experimentally characterised examples.
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Affiliation(s)
| | | | | | - Gregory L. Challis
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL
- UK
- Warwick Integrative Synthetic Biology Centre
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27
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Kalnins G, Sevostjanovs E, Hartmane D, Grinberga S, Tars K. CntA oxygenase substrate profile comparison and oxygen dependency of TMA production in Providencia rettgeri. J Basic Microbiol 2017; 58:52-59. [PMID: 29110324 DOI: 10.1002/jobm.201700428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/05/2017] [Accepted: 10/12/2017] [Indexed: 01/22/2023]
Abstract
CntA oxygenase is a Rieske 2S-2Fe cluster-containing protein that has been previously described as able to produce trimethylamine (TMA) from carnitine, gamma-butyrobetaine, glycine betaine, and in one case, choline. TMA found in humans is exclusively of bacterial origin, and its metabolite, trimethylamine oxide (TMAO), has been associated with atherosclerosis and heart and renal failure. We isolated four different Rieske oxygenases and determined that there are no significant differences in their substrate panels. All three had high activity toward carnitine/gamma-butyrobetaine, medium activity toward glycine betaine, and very low activity toward choline. We tested the influence of low oxygen concentrations on TMA production in CntA-containing Providencia rettgeri cell cultures and discovered that this process, although dependent on the amount of oxygen, is still feasible in environments with 1 and 0.2% oxygen, which is comparable to oxygen levels in some parts of the digestive system.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Dace Hartmane
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Faculty of Biology, University of Latvia, Riga, Latvia
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Wang C, Chen H. Convergent Theoretical Prediction of Reactive Oxidant Structures in Diiron Arylamine Oxygenases AurF and CmlI: Peroxo or Hydroperoxo? J Am Chem Soc 2017; 139:13038-13046. [DOI: 10.1021/jacs.7b06343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chao Wang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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29
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Tomita H, Katsuyama Y, Minami H, Ohnishi Y. Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem 2017; 292:15859-15869. [PMID: 28774961 DOI: 10.1074/jbc.m117.791269] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Rufomycin is a circular heptapeptide with anti-mycobacterial activity and is produced by Streptomyces atratus ATCC 14046. Its structure contains three non-proteinogenic amino acids, N-dimethylallyltryptophan, trans-2-crotylglycine, and 3-nitrotyrosine (3NTyr). Although the rufomycin structure was already reported in the 1960s, its biosynthesis, including 3NTyr generation, remains unclear. To elucidate the rufomycin biosynthetic pathway, we assembled a draft genome sequence of S. atratus and identified the rufomycin biosynthetic gene cluster (ruf cluster), consisting of 20 ORFs (rufA-rufT). We found a putative heptamodular nonribosomal peptide synthetase encoded by rufT, a putative tryptophan N-dimethylallyltransferase encoded by rufP, and a putative trimodular type I polyketide synthase encoded by rufEF Moreover, the ruf cluster contains an apparent operon harboring putative cytochrome P450 (rufO) and nitric oxide synthase (rufN) genes. A similar operon, txtDE, is responsible for the formation of 4-nitrotryptophan in thaxtomin biosynthesis; the cytochrome P450 TxtE catalyzes the 4-nitration of Trp. Therefore, we hypothesized that RufO should catalyze the Tyr 3-nitration. Disruption of rufO abolished rufomycin production by S. atratus, which was restored when 3NTyr was added to the culture medium of the disruptant. Recombinant RufO protein exhibited Tyr 3-nitration activity both in vitro and in vivo Spectroscopic analysis further revealed that RufO recognizes Tyr as the substrate with a dissociation constant of ∼0.1 μm These results indicate that RufO is an unprecedented cytochrome P450 that catalyzes Tyr nitration. Taken together with the results of an in silico analysis of the ruf cluster, we propose a rufomycin biosynthetic pathway in S. atratus.
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Affiliation(s)
- Hiroya Tomita
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657.,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Yohei Katsuyama
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Hiromichi Minami
- the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasuo Ohnishi
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
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30
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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31
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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32
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Knoot CJ, Kovaleva EG, Lipscomb JD. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway. J Biol Inorg Chem 2016; 21:589-603. [PMID: 27229511 PMCID: PMC4994471 DOI: 10.1007/s00775-016-1363-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/16/2016] [Indexed: 11/28/2022]
Abstract
The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form.
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Affiliation(s)
- Cory J Knoot
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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33
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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34
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Komor AJ, Rivard BS, Fan R, Guo Y, Que L, Lipscomb JD. Mechanism for Six-Electron Aryl-N-Oxygenation by the Non-Heme Diiron Enzyme CmlI. J Am Chem Soc 2016; 138:7411-21. [PMID: 27203126 PMCID: PMC4914076 DOI: 10.1021/jacs.6b03341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ultimate step in chloramphenicol (CAM) biosynthesis is a six-electron oxidation of an aryl-amine precursor (NH2-CAM) to the aryl-nitro group of CAM catalyzed by the non-heme diiron cluster-containing oxygenase CmlI. Upon exposure of the diferrous cluster to O2, CmlI forms a long-lived peroxo intermediate, P, which reacts with NH2-CAM to form CAM. Since P is capable of at most a two-electron oxidation, the overall reaction must occur in several steps. It is unknown whether P is the oxidant in each step or whether another oxidizing species participates in the reaction. Mass spectrometry product analysis of reactions under (18)O2 show that both oxygen atoms in the nitro function of CAM derive from O2. However, when the single-turnover reaction between (18)O2-P and NH2-CAM is carried out in an (16)O2 atmosphere, CAM nitro groups contain both (18)O and (16)O, suggesting that P can be reformed during the reaction sequence. Such reformation would require reduction by a pathway intermediate, shown here to be NH(OH)-CAM. Accordingly, the aerobic reaction of NH(OH)-CAM with diferric CmlI yields P and then CAM without an external reductant. A catalytic cycle is proposed in which NH2-CAM reacts with P to form NH(OH)-CAM and diferric CmlI. Then the NH(OH)-CAM rereduces the enzyme diiron cluster, allowing P to reform upon O2 binding, while itself being oxidized to NO-CAM. Finally, the reformed P oxidizes NO-CAM to CAM with incorporation of a second O2-derived oxygen atom. The complete six-electron oxidation requires only two exogenous electrons and could occur in one active site.
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Affiliation(s)
- Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Brent S. Rivard
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - John D. Lipscomb
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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35
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Zuo R, Zhang Y, Huguet‐Tapia JC, Mehta M, Dedic E, Bruner SD, Loria R, Ding Y. An artificial self‐sufficient cytochrome P450 directly nitrates fluorinated tryptophan analogs with a different regio‐selectivity. Biotechnol J 2016; 11:624-32. [DOI: 10.1002/biot.201500416] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/16/2015] [Accepted: 12/23/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Ran Zuo
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida Gainesville Florida USA
| | - Yi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida Gainesville Florida USA
| | - Jose C. Huguet‐Tapia
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida Gainesville Florida USA
| | - Mishal Mehta
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida Gainesville Florida USA
| | - Evelina Dedic
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida Gainesville Florida USA
| | - Steven D. Bruner
- Department of Chemistry, University of Florida Gainesville Florida USA
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida Gainesville Florida USA
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida Gainesville Florida USA
| | - Yousong Ding
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida Gainesville Florida USA
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida Gainesville Florida USA
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36
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Ding XB, Brimble MA, Furkert DP. Nitropyrrole natural products: isolation, biosynthesis and total synthesis. Org Biomol Chem 2016; 14:5390-401. [DOI: 10.1039/c5ob02599k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of the isolation, biological activity, biosynthesis and chemical synthesis of nitropyrrole-containing natural products reported to date, including the pyrrolomycins, heronapyrroles and nitropyrrolins.
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Affiliation(s)
- Xiao-Bo Ding
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Daniel P. Furkert
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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37
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Patil VV, Shankarling GS. Steric-Hindrance-Induced Regio- and Chemoselective Oxidation of Aromatic Amines. J Org Chem 2015. [DOI: 10.1021/acs.joc.5b00582] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vilas Venunath Patil
- Department of Dyestuff Technology, Institute of Chemical Technology, N. P. Marg, Matunga, Mumbai 400019, India
| | - Ganapati Subray Shankarling
- Department of Dyestuff Technology, Institute of Chemical Technology, N. P. Marg, Matunga, Mumbai 400019, India
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38
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39
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Indest KJ, Eberly JO, Hancock DE. Expression and characterization of an N-oxygenase from Rhodococcus jostii RHAI. J GEN APPL MICROBIOL 2015; 61:217-23. [DOI: 10.2323/jgam.61.217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karl J. Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Jed O. Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Dawn E. Hancock
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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40
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Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. J Biol Chem 2014; 289:25523-36. [PMID: 25049233 DOI: 10.1074/jbc.m114.575886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.
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Affiliation(s)
| | - Liam J Worrall
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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41
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Hillwig ML, Zhu Q, Liu X. Biosynthesis of ambiguine indole alkaloids in cyanobacterium Fischerella ambigua. ACS Chem Biol 2014; 9:372-7. [PMID: 24180436 DOI: 10.1021/cb400681n] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ambiguines belong to a family of hapalindole-type indole alkaloid natural products, with many of the members possessing up to eight consecutive carbon stereocenters in a fused pentacyclic 6-6-6-5-7 ring scaffold. Here, we report the identification of a 42 kbp ambiguine (amb) biosynthetic gene cluster that harbors 32 protein-coding genes in its native producer Fischerella ambigua UTEX1903. Association of the amb cluster with ambiguine biosynthesis was confirmed by both bioinformatic analysis and in vitro characterizations of enzymes responsible for 3-((Z)-2'-isocyanoethenyl) indole and geranyl pyrophosphate biosynthesis and a C-2 indole dimethylallyltransferase that regiospecifically tailors hapalindole G to ambiguine A. The presence of five nonheme iron-dependent oxygenase coding genes (including four Rieske-type oxygenases) within the amb cluster suggests late-stage C-H activations are likely responsible for the structural diversities of ambiguines by regio- and stereospecific chlorination, hydroxylation, epoxidation, and sp(2)-sp(3) C-C bond formation.
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Affiliation(s)
- Matthew L. Hillwig
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Qin Zhu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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42
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Abstract
Important biomimetic steps in natural product synthesis have been promoted by transition metals, as exemplified by this beautiful ruthenium-catalyzed rearrangement of an endoperoxide into elysiapyrone A. Such reactions are supposed to occur during the biosynthesis, yet under different catalysis conditions.
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Affiliation(s)
- Xu-Wen Li
- Muséum National d'Histoire Naturelle and Centre National de la Recherche Scientifique
- Unité “Molécules de Communication et Adaptation des Micro-organismes” (UMR 7245 CNRS-MNHN)
- 75005 Paris, France
| | - Bastien Nay
- Muséum National d'Histoire Naturelle and Centre National de la Recherche Scientifique
- Unité “Molécules de Communication et Adaptation des Micro-organismes” (UMR 7245 CNRS-MNHN)
- 75005 Paris, France
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43
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Barry SM, Challis GL. Mechanism and Catalytic Diversity of Rieske Non-Heme Iron-Dependent Oxygenases. ACS Catal 2013; 3. [PMID: 24244885 DOI: 10.1021/cs400087p] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rieske non-heme iron-dependent oxygenases are important enzymes that catalyze a wide variety of reactions in the biodegradation of xenobiotics and the biosynthesis of bioactive natural products. In this perspective article, we summarize recent efforts to elucidate the catalytic mechanisms of Rieske oxygenases and highlight the diverse range of reactions now known to be catalyzed by such enzymes.
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Affiliation(s)
- Sarah M. Barry
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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44
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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45
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Abstract
The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC-MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.
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Affiliation(s)
- Haige Lu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Emmanuel Chanco
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA ; Department of Chemistry, University of Illinois at Urbana-Champaign, USA
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46
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Mechanistic studies on the flavin:NADH reductase (PrnF) from Pseudomonas fluorescens involved in arylamine oxygenation. Bioorg Med Chem Lett 2012; 22:1344-7. [DOI: 10.1016/j.bmcl.2011.12.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/12/2011] [Accepted: 12/14/2011] [Indexed: 11/22/2022]
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47
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Weeks AM, Chang MCY. Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry 2011; 50:5404-18. [PMID: 21591680 DOI: 10.1021/bi200416g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Living organisms have evolved a vast array of catalytic functions that make them ideally suited for the production of medicinally and industrially relevant small-molecule targets. Indeed, native metabolic pathways in microbial hosts have long been exploited and optimized for the scalable production of both fine and commodity chemicals. Our increasing capacity for DNA sequencing and synthesis has revealed the molecular basis for the biosynthesis of a variety of complex and useful metabolites and allows the de novo construction of novel metabolic pathways for the production of new and exotic molecular targets in genetically tractable microbes. However, the development of commercially viable processes for these engineered pathways is currently limited by our ability to quickly identify or engineer enzymes with the correct reaction and substrate selectivity as well as the speed by which metabolic bottlenecks can be determined and corrected. Efforts to understand the relationship among sequence, structure, and function in the basic biochemical sciences can advance these goals for synthetic biology applications while also serving as an experimental platform for elucidating the in vivo specificity and function of enzymes and reconstituting complex biochemical traits for study in a living model organism. Furthermore, the continuing discovery of natural mechanisms for the regulation of metabolic pathways has revealed new principles for the design of high-flux pathways with minimized metabolic burden and has inspired the development of new tools and approaches to engineering synthetic pathways in microbial hosts for chemical production.
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Affiliation(s)
- Amy M Weeks
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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48
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Tiwari MK, Lee JK, Moon HJ, Zhao H. Further biochemical studies on aminopyrrolnitrin oxygenase (PrnD). Bioorg Med Chem Lett 2011; 21:2873-6. [DOI: 10.1016/j.bmcl.2011.03.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/18/2011] [Accepted: 03/22/2011] [Indexed: 11/30/2022]
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49
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Sydor PK, Barry SM, Odulate OM, Barona-Gomez F, Haynes SW, Corre C, Song L, Challis GL. Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes. Nat Chem 2011; 3:388-92. [PMID: 21505498 PMCID: PMC3085852 DOI: 10.1038/nchem.1024] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/07/2011] [Indexed: 11/16/2022]
Abstract
Oxidative cyclizations, exemplified by the biosynthetic assembly of the penicillin nucleus from a tripeptide precursor, are arguably the most synthetically-powerful implementation of C-H activation reactions in Nature. Here we show that Rieske oxygenase-like enzymes mediate regio and stereodivergent oxidative cyclizations to form 10- and 12-membered carbocyclic rings in the key steps of the biosynthesis of the antibiotics streptorubin B and metacycloprodigiosin, respectively. These reactions represent the first examples of oxidative carbocyclizations catalyzed by non-heme iron-dependent oxidases and define a novel type of catalytic activity for Rieske enzymes. A better understanding of how these enzymes achieve such remarkable regio and stereocontrol in the functionalization of unactivated hydrocarbon chains will greatly facilitate the development of selective manmade C-H activation catalysts.
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Affiliation(s)
- Paulina K Sydor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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50
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Platter E, Lawson M, Marsh C, Sazinsky MH. Characterization of a non-ribosomal peptide synthetase-associated diiron arylamine N-oxygenase from Pseudomonas syringae pv. phaseolicola. Arch Biochem Biophys 2011; 508:39-45. [DOI: 10.1016/j.abb.2011.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/10/2011] [Accepted: 01/12/2011] [Indexed: 11/16/2022]
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