1
|
Gahloth D, Fisher K, Marshall S, Leys D. The prFMNH 2-binding chaperone LpdD assists UbiD decarboxylase activation. J Biol Chem 2024; 300:105653. [PMID: 38224946 PMCID: PMC10865409 DOI: 10.1016/j.jbc.2024.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024] Open
Abstract
The UbiD enzyme family of prenylated flavin (prFMN)-dependent reversible decarboxylases is near ubiquitously present in microbes. For some UbiD family members, enzyme activation through prFMNH2 binding and subsequent oxidative maturation of the cofactor readily occurs, both in vivo in a heterologous host and through in vitro reconstitution. However, isolation of the active holo-enzyme has proven intractable for others, notably the canonical Escherichia coli UbiD. We show that E. coli heterologous expression of the small protein LpdD-associated with the UbiD-like gallate decarboxylase LpdC from Lactobacillus plantarum-unexpectedly leads to 3,4-dihydroxybenzoic acid decarboxylation whole-cell activity. This activity was shown to be linked to endogenous E. coli ubiD expression levels. The crystal structure of the purified LpdD reveals a dimeric protein with structural similarity to the eukaryotic heterodimeric proteasome assembly chaperone Pba3/4. Solution studies demonstrate that LpdD protein specifically binds to reduced prFMN species only. The addition of the LpdD-prFMNH2 complex supports reconstitution and activation of the purified E. coli apo-UbiD in vitro, leading to modest 3,4-dihydroxybenzoic acid decarboxylation. These observations suggest that LpdD acts as a prFMNH2-binding chaperone, enabling apo-UbiD activation through enhanced prFMNH2 incorporation and subsequent oxidative maturation. Hence, while a single highly conserved flavin prenyltransferase UbiX is found associated with UbiD enzymes, our observations suggest considerable diversity in UbiD maturation, ranging from robust autocatalytic to chaperone-mediated processes. Unlocking the full (de)carboxylation scope of the UbiD-enzyme family will thus require more than UbiX coexpression.
Collapse
Affiliation(s)
- Deepankar Gahloth
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Stephen Marshall
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
2
|
Vilbert AC, Kontur WS, Gille D, Noguera DR, Donohue TJ. Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics. Appl Environ Microbiol 2024; 90:e0166023. [PMID: 38117061 PMCID: PMC10807440 DOI: 10.1128/aem.01660-23] [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: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.
Collapse
Affiliation(s)
- Avery C. Vilbert
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wayne S. Kontur
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Derek Gille
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
3
|
Kaneshiro AK, Datar PM, Marsh ENG. Negative Cooperativity in the Mechanism of Prenylated-Flavin-Dependent Ferulic Acid Decarboxylase: A Proposal for a "Two-Stroke" Decarboxylation Cycle. Biochemistry 2023; 62:53-61. [PMID: 36521056 DOI: 10.1021/acs.biochem.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ferulic acid decarboxylase (FDC) catalyzes the reversible carboxylation of various substituted phenylacrylic acids to produce the correspondingly substituted styrenes and CO2. FDC is a member of the UbiD family of enzymes that use prenylated-FMN (prFMN) to catalyze decarboxylation reactions on aromatic rings and C-C double bonds. Although a growing number of prFMN-dependent enzymes have been identified, the mechanism of the reaction remains poorly understood. Here, we present a detailed pre-steady-state kinetic analysis of the FDC-catalyzed reaction of prFMN with both styrene and phenylacrylic acid. Based on the pattern of reactivity observed, we propose a "two-stroke" kinetic model in which negative cooperativity between the two subunits of the FDC homodimer plays an important and previously unrecognized role in catalysis. In this model, catalysis is initiated at the high-affinity active site, which reacts with phenylacrylate to yield, after decarboxylation, the covalently bound styrene-prFMN cycloadduct. In the second stage of the catalytic cycle, binding of the second substrate molecule to the low-affinity active site drives a conformational switch that interconverts the high-affinity and low-affinity active sites. This switching of affinity couples the energetically unfavorable cycloelimination of styrene from the first site with the energetically favorable cycloaddition and decarboxylation of phenylacrylate at the second site. We note as a caveat that, at this point, the complexity of the FDC kinetics leaves open other mechanistic interpretations and that further experiments will be needed to more firmly establish or refute our proposal.
Collapse
|
4
|
Couillaud J, Amouric A, Courvoisier-Dezord E, Leydet L, Schweitzer N, Rosso MN, Hage H, Loussouarn-Yvon M, Vincentelli R, Petit JL, de Berardinis V, Attolini M, Maresca M, Duquesne K, Iacazio G. In vitro Applications of the Terpene Mini-Path 2.0. Chembiochem 2022; 23:e202200595. [PMID: 36269004 DOI: 10.1002/cbic.202200595] [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: 10/18/2022] [Revised: 10/21/2022] [Indexed: 01/25/2023]
Abstract
In 2019 four groups reported independently the development of a simplified enzymatic access to the diphosphates (IPP and DMAPP) of isopentenol and dimethylallyl alcohol (IOH and DMAOH). The former are the two universal precursors of all terpenes. We report here on an improved version of what we call the terpene mini-path as well as its use in enzymatic cascades in combination with various transferases. The goal of this study is to demonstrate the in vitro utility of the TMP in, i) synthesizing various natural terpenes, ii) revealing the product selectivity of an unknown terpene synthase, or iii) generating unnatural cyclobutylated terpenes.
Collapse
Affiliation(s)
- Julie Couillaud
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, SWEDEN
| | - Agnès Amouric
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | | | - Létitia Leydet
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | - Nicolas Schweitzer
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Hayat Hage
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Margot Loussouarn-Yvon
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009, Marseille, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mireille Attolini
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | - Marc Maresca
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | - Katia Duquesne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| | - Gilles Iacazio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13009, Marseille, France
| |
Collapse
|
5
|
Żaczek S, Dybala-Defratyka A. Unravelling interactions between active site residues and DMAP in the initial steps of prenylated flavin mononucleotide biosynthesis catalyzed by PaUbiX. Biochim Biophys Acta Gen Subj 2022; 1866:130247. [PMID: 36162732 DOI: 10.1016/j.bbagen.2022.130247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Prenylated flavin mononucleotide (prFMN) is a recently discovered, heavily modified flavin compound. It is the only known cofactor that enables enzymatic 1,3-dipolar cycloaddition reactions. It is produced by enzymes from the UbiX family, from flavin mononucleotide and either dimethylallyl mono- or diphosphate. prFMN biosynthesis is currently reported to be initiated by protonation of the substrate by Glu140. METHODS Computational chemistry methods are applied herein - Constant pH MD, classical MD simulations, and QM cluster optimizations. RESULTS Glu140 competes for a single proton with Lys129 prior to prFMN biosynthesis, but it is the latter that adopted a protonated state. Once the prenyl-FMN adduct is formed, Glu140 occurs in a protonated state far more often, while the occupancy of protonated Lys129 does not change. Lys129, Glu140, and Arg122 seem to play a key role in either stabilizing or protonating DMAP phosphate group within the PaUbiX active site throughout initial steps of prFMN biosynthesis. CONCLUSIONS The role of Lys129 in the functioning of PaUbiX is reported for the first time. Glu140 is unlikely to act as a proton donor in prFMN biosynthesis. Instead, Lys129 and Arg122 fulfil this role. Glu140 still plays a role in contributing to hydrogen-bond network. This behavior is most likely conserved throughout the UbiX family due to the structural similarity of the active sites of those proteins. SIGNIFICANCE Mechanistic insights into a crucial biochemical process, the biosynthesis of prFMN, are provided. This study, although purely computational, extends and perfectly complements the knowledge obtained in classical laboratory experiments.
Collapse
Affiliation(s)
- Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland.
| |
Collapse
|
6
|
Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
Collapse
Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
| |
Collapse
|
7
|
Akutsu M, Abe N, Sakamoto C, Kurimoto Y, Sugita H, Tanaka M, Higuchi Y, Sakamoto K, Kamimura N, Kurihara H, Masai E, Sonoki T. Pseudomonas sp. NGC7 as a microbial chassis for glucose-free muconate production from a variety of lignin-derived aromatics and its application to the production from sugar cane bagasse alkaline extract. BIORESOURCE TECHNOLOGY 2022; 359:127479. [PMID: 35714780 DOI: 10.1016/j.biortech.2022.127479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
cis,cis-Muconate (ccMA) is a promising platform for use in synthesizing various polymers. A glucose-free ccMA production using Pseudomonas sp. NGC7 from hardwood lignin-derived aromatic compounds was previously reported. In that system, syringyl nucleus compounds were essential for growth. Here, it is shown that NGC7 is available for glucose-free ccMA production even from a mixture of lignin-derived aromatics that does not contain syringyl nucleus compounds. By introducing a gene set for the protocatechuate (PCA)-shunt consisting of PCA 3,4-dioxygenase and PCA decarboxylase into an NGC7-derived strain deficient in PCA 3,4-dioxygenase and ccMA cycloisomerase, it was succeeded in constructing a ccMA-producing strain that grows on a lignin-derived aromatics mixture containing no syringyl nucleus compounds. Finally, it is demonstrated that the engineered strain produced ccMA from sugar cane bagasse alkaline extract in 18.7 mol%. NGC7 is thus shown to be a promising microbial chassis for biochemicals production from lignin-derived aromatics.
Collapse
Affiliation(s)
- Miho Akutsu
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Nanase Abe
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Chiho Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuki Kurimoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Haruka Sugita
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Makoto Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yudai Higuchi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kimitoshi Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Hiroyuki Kurihara
- Toray Industries, Inc, New Frontiers Research Laboratories, Kamakura, Kanagawa 248-0036, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Tomonori Sonoki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.
| |
Collapse
|
8
|
Roberts GW, Leys D. Structural insights into UbiD reversible decarboxylation. Curr Opin Struct Biol 2022; 75:102432. [PMID: 35843126 DOI: 10.1016/j.sbi.2022.102432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
Abstract
The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to elucidating the enigmatic mechanism underpinning the conversion of α,β-unsaturated acids by this system. The UbiD component utilises a unique cofactor, prenylated flavin (prFMN), generated by the bespoke action of the associated UbiX flavin prenyltransferase. Structure determination of a range of UbiX/UbiD representatives has revealed a generic mode of action for both the flavin-to-prFMN metamorphosis and the (de)carboxylation. In contrast to the conserved UbiX, the UbiD superfamily is associated with a versatile substrate range. The latter is reflected in the considerable variety of UbiD quaternary structure, dynamic behaviour and active site architecture. Directed evolution of UbiD enzymes has taken advantage of this apparent malleability to generate new variants supporting in vivo hydrocarbon production. Other applications include coupling UbiD to carboxylic acid reductase to convert alkenes into α,β-unsaturated aldehydes via enzymatic CO2 fixation.
Collapse
Affiliation(s)
- George W Roberts
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
9
|
Toolbox for the structure-guided evolution of ferulic acid decarboxylase (FDC). Sci Rep 2022; 12:3347. [PMID: 35232989 PMCID: PMC8888657 DOI: 10.1038/s41598-022-07110-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022] Open
Abstract
The interest towards ferulic acid decarboxylase (FDC), piqued by the enzyme's unique 1,3-dipolar cycloaddition mechanism and its atypic prFMN cofactor, provided several applications of the FDC mediated decarboxylations, such as the synthesis of styrenes, or its diverse derivatives, including 1,3-butadiene and the enzymatic activation of C-H bonds through the reverse carboligation reactions. While rational design-based protein engineering was successfully employed for tailoring FDC towards diverse substrates of interest, the lack of high-throughput FDC-activity assay hinders its directed evolution-based protein engineering. Herein we report a toolbox, useful for the directed evolution based and/or structure-guided protein engineering of FDC, which was validated representatively on the well described FDC, originary from Saccharomyces cerevisiae (ScFDC). Accordingly, the developed fluorescent plate-assay allows in premiere the FDC-activity screens of a mutant library in a high-throughput manner. Moreover, using the plate-assay for the activity screens of a rationally designed 23-membered ScFDC variant library against a substrate panel comprising of 16, diversely substituted cinnamic acids, revealed several variants of improved activity. The superior catalytic properties of the hits revealed by the plate-assay, were also supported by the conversion values from their analytical scale biotransformations. The computational results further endorsed the experimental findings, showing inactive binding poses of several non-transformed substrate analogues within the active site of the wild-type ScFDC, but favorable ones within the catalytic site of the variants of improved activity. The results highlight several 'hot-spot' residues involved in substrate specificity modulation of FDC, such as I189, I330, F397, I398 or Q192, of which mutations to sterically less demanding residues increased the volume of the active site, thus facilitated proper binding and increased conversions of diverse non-natural substrates. Upon revealing which mutations improve the FDC activity towards specific substrate analogues, we also provide key for the rational substrate-tailoring of FDC.
Collapse
|
10
|
|
11
|
Bloor S, Michurin I, Titchiner GR, Leys D. Prenylated flavins: structures and mechanisms. FEBS J 2022; 290:2232-2245. [PMID: 35073609 DOI: 10.1111/febs.16371] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
The UbiX/UbiD system is widespread in microbes and responsible for the reversible decarboxylation of unsaturated carboxylic acids. The UbiD enzyme catalyzes this unusual reaction using a prenylated flavin (prFMN) as cofactor, the latter formed by the flavin prenyltransferase UbiX. A detailed picture of the biochemistry of flavin prenylation, oxidative maturation, and covalent catalysis underpinning reversible decarboxylation is emerging. This reveals the prFMN cofactor can undergo a wide range of transformations, complemented by considerable UbiD-variability. These provide a blueprint for biotechnological applications aimed at producing hydrocarbons or aromatic C-H activation through carboxylation.
Collapse
Affiliation(s)
- Samuel Bloor
- Department of Chemistry, Manchester Institute of Biotechnology, UK
| | | | | | - David Leys
- Department of Chemistry, Manchester Institute of Biotechnology, UK
| |
Collapse
|
12
|
Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate. Metab Eng 2022; 70:31-42. [PMID: 34982998 DOI: 10.1016/j.ymben.2021.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Overall, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.
Collapse
|
13
|
Couillaud J, Duquesne K, Iacazio G. Extension of the Terpene Chemical Space: the Very First Biosynthetic Steps. Chembiochem 2021; 23:e202100642. [PMID: 34905641 DOI: 10.1002/cbic.202100642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Indexed: 11/06/2022]
Abstract
The structural diversity of terpenes is particularly notable and many studies are carried out to increase it further. In the terpene biosynthetic pathway this diversity is accessible from only two common precursors, i. e. isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Methods recently developed (e. g. the Terpene Mini Path) have allowed DMAPP and IPP to be obtained from a two-step enzymatic conversion of industrially available isopentenol (IOH) and dimethylallyl alcohol (DMAOH) into their corresponding diphosphates. Easily available IOH and DMAOH analogues then offer quick access to modified terpenoids thus avoiding the tedious chemical synthesis of unnatural diphosphates. The aim of this minireview is to cover the literature devoted to the use of these analogues for widening the accessible terpene chemical space.
Collapse
Affiliation(s)
- Julie Couillaud
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France.,Actual address: Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katia Duquesne
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
| | - Gilles Iacazio
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
| |
Collapse
|
14
|
Couillaud J, Leydet L, Duquesne K, Iacazio G. The Terpene Mini-Path, a New Promising Alternative for Terpenoids Bio-Production. Genes (Basel) 2021; 12:genes12121974. [PMID: 34946923 PMCID: PMC8701039 DOI: 10.3390/genes12121974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/25/2023] Open
Abstract
Terpenoids constitute the largest class of natural compounds and are extremely valuable from an economic point of view due to their extended physicochemical properties and biological activities. Due to recent environmental concerns, terpene extraction from natural sources is no longer considered as a viable option, and neither is the chemical synthesis to access such chemicals due to their sophisticated structural characteristics. An alternative to produce terpenoids is the use of biotechnological tools involving, for example, the construction of enzymatic cascades (cell-free synthesis) or a microbial bio-production thanks to metabolic engineering techniques. Despite outstanding successes, these approaches have been hampered by the length of the two natural biosynthetic routes (the mevalonate and the methyl erythritol phosphate pathways), leading to dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP), the two common universal precursors of all terpenoids. Recently, we, and others, developed what we called the terpene mini-path, a robust two enzyme access to DMAPP and IPP starting from their corresponding two alcohols, dimethylallyl alcohol and isopentenol. The aim here is to present the potential of this artificial bio-access to terpenoids, either in vitro or in vivo, through a review of the publications appearing since 2016 on this very new and fascinating field of investigation.
Collapse
Affiliation(s)
- Julie Couillaud
- Centrale Marseille, CNRS, iSm2 Marseille, ISM2 UMR 7313, Aix-Marseille Université, Av. Escadrille Normandie-Niemen, 13013 Marseille, France; (J.C.); (L.L.); (K.D.)
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Létitia Leydet
- Centrale Marseille, CNRS, iSm2 Marseille, ISM2 UMR 7313, Aix-Marseille Université, Av. Escadrille Normandie-Niemen, 13013 Marseille, France; (J.C.); (L.L.); (K.D.)
| | - Katia Duquesne
- Centrale Marseille, CNRS, iSm2 Marseille, ISM2 UMR 7313, Aix-Marseille Université, Av. Escadrille Normandie-Niemen, 13013 Marseille, France; (J.C.); (L.L.); (K.D.)
| | - Gilles Iacazio
- Centrale Marseille, CNRS, iSm2 Marseille, ISM2 UMR 7313, Aix-Marseille Université, Av. Escadrille Normandie-Niemen, 13013 Marseille, France; (J.C.); (L.L.); (K.D.)
- Correspondence:
| |
Collapse
|
15
|
Ishibashi Y, Matsushima N, Ito T, Hemmi H. Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Biosci Biotechnol Biochem 2021; 86:246-253. [PMID: 34864834 DOI: 10.1093/bbb/zbab205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 11/12/2022]
Abstract
Nudix hydrolases typically catalyze the hydrolysis of nucleoside diphosphate linked to moiety X and yield nucleoside monophosphate and X-phosphate, while some of them hydrolyze a terminal diphosphate group of non-nucleosidic compounds and convert it into a phosphate group. Although the number of Nudix hydrolases is usually limited in archaea comparing with those in bacteria and eukaryotes, the physiological functions of most archaeal Nudix hydrolases remain unknown. In this study, a Nudix hydrolase family protein, MM_2582, from the methanogenic archaeon Methanosarcina mazei was recombinantly expressed in Escherichia coli, purified, and characterized. This recombinant protein shows higher hydrolase activity toward isopentenyl diphosphate and short-chain prenyl diphosphates than that toward nucleosidic compounds. Kinetic studies demonstrated that the archaeal enzyme prefers isopentenyl diphosphate and dimethylallyl diphosphate, which suggests its role in the biosynthesis of prenylated flavin mononucleotide, a recently discovered coenzyme that is required, for example, in the archaea-specific modified mevalonate pathway.
Collapse
Affiliation(s)
- Yumi Ishibashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Natsumi Matsushima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Tomokazu Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| |
Collapse
|
16
|
Vignali E, Pollegioni L, Di Nardo G, Valetti F, Gazzola S, Gilardi G, Rosini E. Multi‐Enzymatic Cascade Reactions for the Synthesis of
cis,cis
‐Muconic Acid. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Elisa Vignali
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Silvia Gazzola
- Department of Science and High Technology University of Insubria Via Valleggio 9 22100 Como Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
| |
Collapse
|
17
|
Datar PM, Marsh ENG. Decarboxylation of Aromatic Carboxylic Acids by the Prenylated-FMN-dependent Enzyme Phenazine-1-carboxylic Acid Decarboxylase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
18
|
Phan HV, Kurisu F, Kiba K, Furumai H. Optimized Cultivation and Syntrophic Relationship of Anaerobic Benzene-Degrading Enrichment Cultures under Methanogenic Conditions. Microbes Environ 2021; 36. [PMID: 34433738 PMCID: PMC8446749 DOI: 10.1264/jsme2.me21028] [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] [Indexed: 11/26/2022] Open
Abstract
Current challenges in the anaerobic bioremediation of benzene are the lack of capable cultures and limited knowledge on the biodegradation pathway. Under methanogenic conditions, benzene may be mineralized by syntrophic interactions between microorganisms, which are poorly understood. The present study developed an optimized formula for anoxic medium to successfully promote the growth of the putative benzene degrader Deltaproteobacterium Hasda-A and enhance the benzene degradation activity of methanogenic enrichment cultures. Within 70 d of incubation, the benzene degradation activity and relative abundance of Hasda-A in cultures in the new defined medium increased from 0.5 to >3 mg L–1 d–1 and from 2.5% to >17%, respectively. Together with Hasda-A, we found a strong positive relationship between the abundances of superphylum OD1 bacteria, three methanogens (Methanoregula, Methanolinea, and Methanosaeta) and benzene degradation activity. The syntrophic relationship between these microbial taxa and Hasda-A was then demonstrated in a correlation analysis of longitudinal data. The involvement of methanogenesis in anaerobic benzene mineralization was confirmed by inhibition experiments. The high benzene degradation activity and growth of Hasda-A were quickly recovered in successive dilutions of enrichment cultures, proving the feasibility of using the medium developed in the present study to produce highly capable cultures. The present results will facilitate practical applications in bioremediation and research on the molecular mechanisms underlying benzene activation and syntrophic interactions in benzene mineralization.
Collapse
Affiliation(s)
- Hop V Phan
- JSPS International Research Fellow, Research Center for Water Environment Technology, The University of Tokyo
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, The University of Tokyo
| | - Koichiro Kiba
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo
| |
Collapse
|
19
|
Mori Y, Noda S, Shirai T, Kondo A. Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. Nat Commun 2021; 12:2195. [PMID: 33850144 PMCID: PMC8044207 DOI: 10.1038/s41467-021-22504-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO-stat fed-batch fermentation, we produce 2.13 ± 0.17 g L-1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.
Collapse
Affiliation(s)
- Yutaro Mori
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan.
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| |
Collapse
|
20
|
Kaneshiro AK, Koebke KJ, Zhao C, Ferguson KL, Ballou DP, Palfey BA, Ruotolo BT, Marsh ENG. Kinetic Analysis of Transient Intermediates in the Mechanism of Prenyl-Flavin-Dependent Ferulic Acid Decarboxylase. Biochemistry 2020; 60:125-134. [PMID: 33342208 DOI: 10.1021/acs.biochem.0c00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferulic acid decarboxylase catalyzes the decarboxylation of various substituted phenylacrylic acids to their corresponding styrene derivatives and CO2 using the recently discovered cofactor prenylated FMN (prFMN). The mechanism involves an unusual 1,3-dipolar cycloaddition reaction between prFMN and the substrate to generate a cycloadduct capable of undergoing decarboxylation. Using native mass spectrometry, we show the enzyme forms a stable prFMN-styrene cycloadduct that accumulates on the enzyme during turnover. Pre-steady state kinetic analysis of the reaction using ultraviolet-visible stopped-flow spectroscopy reveals a complex pattern of kinetic behavior, best described by a half-of-sites model involving negative cooperativity between the two subunits of the dimeric enzyme. For the reactive site, the cycloadduct of prFMN with phenylacylic acid is formed with a kapp of 131 s-1. This intermediate converts to the prFMN-styrene cycloadduct with a kapp of 75 s-1. Cycloelimination of the prFMN-styrene cycloadduct to generate styrene and free enzyme appears to determine kcat for the overall reaction, which is 11.3 s-1.
Collapse
|
21
|
Balaikaite A, Chisanga M, Fisher K, Heyes DJ, Spiess R, Leys D. Ferulic Acid Decarboxylase Controls Oxidative Maturation of the Prenylated Flavin Mononucleotide Cofactor. ACS Chem Biol 2020; 15:2466-2475. [PMID: 32840348 DOI: 10.1021/acschembio.0c00456] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered modified flavin cofactor containing an additional nonaromatic ring, connected to the N5 and C6 atoms. This cofactor underpins reversible decarboxylation catalyzed by members of the widespread UbiD enzyme family and is produced by the flavin prenyltransferase UbiX. Oxidative maturation of the UbiX product prFMNH2 to the corresponding oxidized prFMNiminium is required for ferulic acid decarboxylase (Fdc1; a UbiD-type enzyme) activity. However, it is unclear what role the Fdc1 enzyme plays in this process. Here, we demonstrate that, in the absence of Fdc1, prFMNH2 oxidation by O2 proceeds via a transient semiquinone prFMNradical species and culminates in a remarkably stable prFMN-hydroperoxide species. Neither forms of prFMN are able to support Fdc1 activity. Instead, enzyme activation using O2-mediated oxidation requires prFMNH2 binding prior to oxygen exposure, confirming that UbiD enzymes play a role in O2-mediated oxidative maturation. In marked contrast, alternative oxidants such as potassium ferricyanide support prFMNiminium formation both in solution and in Fdc1.
Collapse
Affiliation(s)
- Arune Balaikaite
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Malama Chisanga
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Department of Chemistry, School of Mathematics and Natural Sciences, Copperbelt University, Kitwe, Zambia
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Reynard Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| |
Collapse
|
22
|
Abstract
Flavin-dependent enzymes catalyze a wide variety of biological reactions that are important for all types of living organisms. Knowledge gained from studying the chemistry and biological functions of flavins and flavin-dependent enzymes has continuously made significant contributions to the development of the fields of enzymology and metabolism from the 1970s until now. The enzymes have been applied in various applications such as use as biocatalysts in synthetic processes for the chemical and pharmaceutical industries or in the biodetoxification and bioremediation of toxic or unwanted compounds, and as biosensors or biodetection tools for quantifying various agents of interest. Many flavin-dependent enzymes are also prime targets for drug development. Based on their reaction mechanisms, they can be classified into five categories: oxidase, dehydrogenase, monooxygenase, reductase, and redox neutral flavin-dependent enzymes. In this chapter, the general properties of flavin-dependent enzymes and the nature of their chemical reactions are discussed, along with their practical applications.
Collapse
|
23
|
Abstract
The reversible (de)carboxylation of unsaturated carboxylic acids is carried out by the UbiX-UbiD system, ubiquitously present in microbes. The biochemical basis of this challenging reaction has recently been uncovered by the discovery of the UbiD cofactor, prenylated FMN (prFMN). This heavily modified flavin is synthesized by the flavin prenyltransferase UbiX, which catalyzes the non-metal dependent prenyl transfer from dimethylallyl(pyro)phosphate (DMAP(P)) to the flavin N5 and C6 positions, creating a fourth non-aromatic ring. Following prenylation, prFMN undergoes oxidative maturation to form the iminium species required for UbiD activity. prFMNiminium acts as a prostethic group and is bound via metal ion mediated interactions between UbiD and the prFMNiminium phosphate moiety. The modified isoalloxazine ring is place adjacent to the E(D)-R-E UbiD signature sequent motif. The fungal ferulic acid decarboxylase Fdc from Aspergillus niger has emerged as a UbiD-model system, and has yielded atomic level insight into the prFMNiminium mediated (de)carboxylation. A wealth of data now supports a mechanism reliant on reversible 1,3 dipolar cycloaddition between substrate and cofactor for this enzyme. This poses the intriguing question whether a similar mechanism is used by all UbiD enzymes, especially those that act as carboxylases on inherently more difficult substrates such as phenylphosphate or benzene/naphthalene. Indeed, considerable variability in terms of oligomerization, domain motion and active site structure is now reported for the UbiD family.
Collapse
Affiliation(s)
- Annica Saaret
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Arune Balaikaite
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
24
|
Batyrova KA, Khusnutdinova AN, Wang PH, Di Leo R, Flick R, Edwards EA, Savchenko A, Yakunin AF. Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation. ACS Chem Biol 2020; 15:1874-1882. [PMID: 32579338 DOI: 10.1021/acschembio.0c00136] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible UbiD-like (de)carboxylases represent a large family of mostly uncharacterized enzymes, which require the recently discovered prenylated FMN (prFMN) cofactor for activity. Functional characterization of novel UbiDs is hampered by a lack of robust protocols for prFMN generation and UbiD activation. Here, we report two systems for in vitro and in vivo FMN prenylation and UbiD activation under aerobic conditions. The in vitro one-pot prFMN cascade includes five enzymes: FMN prenyltransferase (UbiX), prenol kinase, polyphosphate kinase, formate dehydrogenase, and FMN reductase, which use prenol, polyphosphate, formate, ATP, NAD+, and FMN as substrates and cofactors. Under aerobic conditions, this cascade produced prFMN from FMN with over 98% conversion and activated purified ferulic acid decarboxylase Fdc1 from Aspergillus niger and protocatechuic acid decarboxylase ENC0058 from Enterobacter cloaceae. The in vivo system for FMN prenylation and UbiD activation is based on the coexpression of Fdc1 and UbiX in Escherichia coli cells under aerobic conditions in the presence of prenol. The in vitro and in vivo FMN prenylation cascades will facilitate functional characterization of novel UbiDs and their applications.
Collapse
Affiliation(s)
- Khorcheska A. Batyrova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom
| |
Collapse
|
25
|
Johnson LA, Dunbabin A, Benton JCR, Mart RJ, Allemann RK. Modular Chemoenzymatic Synthesis of Terpenes and their Analogues. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Luke A. Johnson
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | - Alice Dunbabin
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | | | - Robert J. Mart
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | | |
Collapse
|
26
|
Dabravolski S. Multi-faceted nature of the tRNA isopentenyltransferase. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:475-485. [PMID: 32345433 DOI: 10.1071/fp19255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/26/2019] [Indexed: 06/11/2023]
Abstract
Transfer RNA isopentenylation an adenine 37 position (A37) is a universal modification known in prokaryotes and eukaryotes. A set of highly homologous enzymes catalyse a series of reactions, leading to tRNA modifications, aimed to increase adaptation to environmental condition through the control of translation efficiency and reading frame maintenance. Transfer RNA-isopentenylation-related (TI-related) functions are well studied in bacteria, mitochondria of yeast and human, but completely unexplored in plants. Transfer RNA-isopentenylation-unrelated (TI-unrelated) functions participate in adaptation to environmental stresses via the regulation of sterol metabolism, gene silencing/suppression and amyloid fibrils formation. TI-unrelated functions are mostly studied in yeast. Finally, the degradation of A37-modified tRNA releases a set of bioactive compounds known as cis-cytokinins. Although all organisms are able to produce cis-cytokinins, its physiological role is still a matter of debates. For several species of bacteria and fungi, cis-cytokinins are known to play a crucial role in pathogenesis. In mammalian and human models cis-cytokinins have tumour-suppressing and anti-inflammation effects. This review aims to summarise current knowledge of the TI-related and TI-unrelated functions and main bioactive by-products of isopentenylated tRNA degradation.
Collapse
Affiliation(s)
- Siarhei Dabravolski
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 78371 Olomouc, Czech Republic.
| |
Collapse
|
27
|
Johnson LA, Dunbabin A, Benton JCR, Mart RJ, Allemann RK. Modular Chemoenzymatic Synthesis of Terpenes and their Analogues. Angew Chem Int Ed Engl 2020; 59:8486-8490. [DOI: 10.1002/anie.202001744] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Luke A. Johnson
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | - Alice Dunbabin
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | | | - Robert J. Mart
- School of Chemistry Cardiff University Park Place Cardiff CF10 3AT UK
| | | |
Collapse
|
28
|
Reconstruction of the "Archaeal" Mevalonate Pathway from the Methanogenic Archaeon Methanosarcina mazei in Escherichia coli Cells. Appl Environ Microbiol 2020; 86:AEM.02889-19. [PMID: 31924615 DOI: 10.1128/aem.02889-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
The mevalonate pathway is a well-known metabolic route that provides biosynthetic precursors for myriad isoprenoids. An unexpected variety of the pathway has been discovered from recent studies on microorganisms, mainly on archaea. The most recently discovered example, called the "archaeal" mevalonate pathway, is a modified version of the canonical eukaryotic mevalonate pathway and was elucidated in our previous study using the hyperthermophilic archaeon Aeropyrum pernix This pathway comprises four known enzymes that can produce mevalonate 5-phosphate from acetyl coenzyme A, two recently discovered enzymes designated phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, and two more known enzymes, i.e., isopentenyl phosphate kinase and isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase. To show its wide distribution in archaea and to confirm if its enzyme configuration is identical among species, the putative genes of a lower portion of the pathway-from mevalonate to isopentenyl pyrophosphate-were isolated from the methanogenic archaeon Methanosarcina mazei, which is taxonomically distant from A. pernix, and were introduced into an engineered Escherichia coli strain that produces lycopene, a red carotenoid pigment. Lycopene production, as a measure of isoprenoid productivity, was enhanced when the cells were grown semianaerobically with the supplementation of mevalonolactone, which demonstrates that the archaeal pathway can function in bacterial cells to convert mevalonate into isopentenyl pyrophosphate. Gene deletion and complementation analysis using the carotenogenic E. coli strain suggests that both phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase from M. mazei are required for the enhancement of lycopene production.IMPORTANCE Two enzymes that have recently been identified from the hyperthermophilic archaeon A. pernix as components of the archaeal mevalonate pathway do not require ATP for their reactions. This pathway, therefore, might consume less energy than other mevalonate pathways to produce precursors for isoprenoids. Thus, the pathway might be applicable to metabolic engineering and production of valuable isoprenoids that have application as pharmaceuticals. The archaeal mevalonate pathway was successfully reconstructed in E. coli cells by introducing several genes from the methanogenic or hyperthermophilic archaeon, which demonstrated that the pathway requires the same components even in distantly related archaeal species and can function in bacterial cells.
Collapse
|
29
|
Ward VC, Chatzivasileiou AO, Stephanopoulos G. Cell free biosynthesis of isoprenoids from isopentenol. Biotechnol Bioeng 2019; 116:3269-3281. [DOI: 10.1002/bit.27146] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Valerie C.A. Ward
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts
- Department of Chemical Engineering University of Waterloo Waterloo Ontario Canada
| | | | - Gregory Stephanopoulos
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts
| |
Collapse
|
30
|
Bandari C, Scull EM, Bavineni T, Nimmo SL, Gardner ED, Bensen RC, Burgett AW, Singh S. FgaPT2, a biocatalytic tool for alkyl-diversification of indole natural products. MEDCHEMCOMM 2019; 10:1465-1475. [PMID: 31534661 PMCID: PMC6748273 DOI: 10.1039/c9md00177h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
Abstract
Demonstration of FgaPT2 catalyzed alkyl-diversification of indole containing natural products.
Aromatic prenyltransferases from natural product biosynthetic pathways display relaxed specificity for their aromatic substrates. While a growing body of evidence suggests aromatic prenyltransferases to be more tolerant towards their alkyl-donor substrates, most studies aimed at probing their donor-substrate specificity are limited to only a small set of alkyl pyrophosphate donors, restricting their broader utility as biocatalysts for synthetic applications. Here, we assess the donor substrate specificity of an l-tryptophan C4-prenyltransferase, also known as C4-dimethylallyltryptophan synthase, FgaPT2 from Aspergillus fumigatus, using an array of 34 synthetic unnatural alkyl-pyrophosphate analogues, and demonstrate FgaPT2 can catalyze the transfer of 25 of the 34 non-native alkyl groups from their corresponding synthetic alkyl-pyrophosphate analogues at N1, C3, C4 and C5 position of tryptophan in a normal and reverse manner. The kinetic studies and regio-chemical analysis of the alkyl-l-tryptophan products suggest that the alkyl-donor transfer by FgaPT2 is a function of the stability of the carbocation and the steric factors in the active site of the enzyme. Further, to demonstrate the biocatalytic utility of FgaPT2, this study also highlights the FgaPT2-catalyzed synthesis of a small set of alkyl-diversified indolocarbazole analogues. These results reveal FgaPT2 to be more tolerant to diverse non-native alkyl-donor substrates beyond their known acceptor substrate promiscuity and set the stage for its development as a novel biocatalytic tool for the differential alkylation of natural products for drug discovery and other synthetic applications.
Collapse
Affiliation(s)
- Chandrasekhar Bandari
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Erin M Scull
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Tejaswi Bavineni
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Susan L Nimmo
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Eric D Gardner
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Ryan C Bensen
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Anthony W Burgett
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Shanteri Singh
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| |
Collapse
|
31
|
Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
Collapse
Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| |
Collapse
|
32
|
Marshall SA, Payne KAP, Fisher K, White MD, Ní Cheallaigh A, Balaikaite A, Rigby SEJ, Leys D. The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun 2019; 10:2357. [PMID: 31142738 PMCID: PMC6541611 DOI: 10.1038/s41467-019-10220-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022] Open
Abstract
The UbiX-UbiD enzymes are widespread in microbes, acting in concert to decarboxylate alpha-beta unsaturated carboxylic acids using a highly modified flavin cofactor, prenylated FMN (prFMN). UbiX serves as the flavin prenyltransferase, extending the isoalloxazine ring system with a fourth non-aromatic ring, derived from sequential linkage between a dimethylallyl moiety and the FMN N5 and C6. Using structure determination and solution studies of both dimethylallyl monophosphate (DMAP) and dimethyallyl pyrophosphate (DMAPP) dependent UbiX enzymes, we reveal the first step, N5-C1' bond formation, is contingent on the presence of a dimethylallyl substrate moiety. Hence, an SN1 mechanism similar to other prenyltransferases is proposed. Selected variants of the (pyro)phosphate binding site are unable to catalyse subsequent Friedel-Crafts alkylation of the flavin C6, but can be rescued by addition of (pyro)phosphate. Thus, retention of the (pyro)phosphate leaving group is required for C6-C3' bond formation, resembling pyrophosphate initiated class I terpene cyclase reaction chemistry.
Collapse
Affiliation(s)
- Stephen A Marshall
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mark D White
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, New South Wales, Australia
| | - Aisling Ní Cheallaigh
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- Centre for Synthesis and Chemical Biology, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Arune Balaikaite
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
| |
Collapse
|
33
|
Khusnutdinova AN, Xiao J, Wang PH, Batyrova KA, Flick R, Edwards EA, Yakunin AF. Prenylated FMN: Biosynthesis, purification, and Fdc1 activation. Methods Enzymol 2019; 620:469-488. [PMID: 31072498 DOI: 10.1016/bs.mie.2019.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered flavin cofactor produced by the UbiX family of FMN prenyltransferases, and is required for the activity of UbiD-like reversible decarboxylases. The latter enzymes are known to be involved in ubiquinone biosynthesis and biotransformation of lignin, aromatic compounds, and unsaturated aliphatic acids. However, exploration of uncharacterized UbiD proteins for biotechnological applications is hindered by our limited knowledge about the biochemistry of prFMN and prFMN-dependent enzymes. Here, we describe experimental protocols and considerations for the biosynthesis of prFMN in vivo and in vitro, in addition to cofactor extraction and application for activation of UbiD proteins.
Collapse
Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Johnny Xiao
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, United Kingdom.
| |
Collapse
|
34
|
Marshall SA, Payne KAP, Fisher K, Gahloth D, Bailey SS, Balaikaite A, Saaret A, Gostimskaya I, Aleku G, Huang H, Rigby SEJ, Procter D, Leys D. Heterologous production, reconstitution and EPR spectroscopic analysis of prFMN dependent enzymes. Methods Enzymol 2019; 620:489-508. [PMID: 31072499 DOI: 10.1016/bs.mie.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent discovery of the prenylated FMN (prFMN) cofactor has led to a renewed interest in the prFMN-dependent UbiD family of enzymes. The latter catalyses the reversible decarboxylation of alpha-beta unsaturated carboxylic acids and features widely in microbial metabolism. The flavin prenyltransferase UbiX synthesizes prFMN from reduced FMN and phosphorylated dimethylallyl precursors. Oxidative maturation of the resulting prFMNreduced species to the active prFMNiminium form is required for UbiD activity. Heterologous production of active holo-UbiD requires co-expression of UbiX, but the levels of prFMN incorporation and oxidative maturation appear variable. Detailed protocols and strategies for in vitro reconstitution and oxidative maturation of UbiD are presented that can yield an alternative source of active holo-UbiD for biochemical studies.
Collapse
Affiliation(s)
- Stephen A Marshall
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl A P Payne
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl Fisher
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Deepankar Gahloth
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samuel S Bailey
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Arune Balaikaite
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Annica Saaret
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Irina Gostimskaya
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Godwin Aleku
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Huanming Huang
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Stephen E J Rigby
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Procter
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- School of Chemistry, University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
35
|
Junghare M, Spiteller D, Schink B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME JOURNAL 2019; 13:1252-1268. [PMID: 30647456 DOI: 10.1038/s41396-019-0348-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022]
Abstract
Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.
Collapse
Affiliation(s)
- Madan Junghare
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Dieter Spiteller
- Chemical Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| |
Collapse
|
36
|
Leys D. Flavin metamorphosis: cofactor transformation through prenylation. Curr Opin Chem Biol 2018; 47:117-125. [PMID: 30326424 DOI: 10.1016/j.cbpa.2018.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/28/2022]
Abstract
Prenylated flavin (prFMN) is a recently discovered cofactor that underpins catalysis in the ubiquitous microbial UbiDX system. UbiX acts as a flavin prenyltransferase while UbiD is a prFMN-dependent reversible (de)carboxylase. The extensive modification of flavin by prenylation, and the consecutive oxidation to the prFMNiminium azomethine ylide, leads to cofactor metamorphosis. While prFMN is no longer able to perform N5-based classical flavin chemistry, it is capable of forming cycloadducts with dipolarophiles, long-lived C4a-based radical species as well as undergoing extensive light driven isomerization. An ever-expanding range of distinct prFMN forms hints at the possibility of novel prFMN driven biochemistry yet to be discovered.
Collapse
Affiliation(s)
- David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, UK.
| |
Collapse
|
37
|
Żaczek S, Kowalska J, Dybala-Defratyka A. Ligand-Driven Conformational Dynamics Influences Selectivity of UbiX. Chembiochem 2018; 19:2403-2409. [PMID: 30136768 DOI: 10.1002/cbic.201800389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 12/31/2022]
Abstract
Up until now, it has remained elusive as to why the flavin prenyltransferase UbiX requires dimethylallyl monophosphate (DMAP) as one of its cosubstrates instead of dimethylallyl pyrophosphate (DMAPP), even though the former is not used in metabolic pathways, while the latter is a common isoprenoid precursor. Herein, mainly on the basis of molecular dynamics (MD) simulations, we demonstrate that the selectivity of UbiX may be governed by its conformational dynamics. The hydrogen-bonding network of UbiX does not facilitate a proper encompassing of DMAPP. This induces significant conformational changes of the enzyme that result mostly in unreactive trajectories, whereas DMAP remains at a catalytically competent position throughout the performed simulations. Within the presented study, we provide a justification for the atypical selectivity of UbiX.
Collapse
Affiliation(s)
- Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Justyna Kowalska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| |
Collapse
|
38
|
Annaval T, Han L, Rudolf JD, Xie G, Yang D, Chang CY, Ma M, Crnovcic I, Miller MD, Soman J, Xu W, Phillips GN, Shen B. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway. ACS Chem Biol 2018; 13:2728-2738. [PMID: 30152678 DOI: 10.1021/acschembio.8b00673] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tautomycetin (TTN) is a polyketide natural product featuring a terminal alkene. Functional characterization of the genes within the ttn gene cluster from Streptomyces griseochromogenes established the biosynthesis of the TTN polyketide backbone, its dialkylmaleic anhydride moiety, the coupling of the two moieties to form the nascent intermediate TTN F-1, and the tailoring steps converting TTN F-1 to TTN. Here, we report biochemical and structural characterization of TtnD, a prenylated FMN (prFMN)-dependent decarboxylase belonging to the UbiD family that catalyzes the penultimate step of TTN biosynthesis. TtnD catalyzes decarboxylation of TTN D-1 to TTN I-1, utilizing prFMN as a cofactor generated by the TtnC flavin prenyltransferase; both TtnD and TtnC are encoded within the ttn biosynthetic gene cluster. TtnD exhibits substrate promiscuity but accepts only TTN D-1 congeners that feature an α,β-unsaturated acid, supporting the [3+2] cycloaddition mechanism during catalysis that requires the double bond of an α,β-unsaturated acid substrate. TtnD shares a similar overall structure with other members of the UbiD family but forms a homotetramer in solution. Each protomer is composed of three domains with the active site located between the middle and C-terminal domains; R169-E272-E277, constituting the catalytic triad, and E228, involved in Mn(II)-mediated binding of prFMN, were confirmed by site-directed mutagenesis. TtnD represents the first example of a prFMN-dependent decarboxylase involved in polyketide biosynthesis, expanding the substrate scope of the UbiD family of decarboxylases beyond simple aromatic and cinnamic acids. TtnD and its homologues are widespread in nature and could be exploited as biocatalysts for organic synthesis.
Collapse
Affiliation(s)
- Thibault Annaval
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | | | - Jeffrey D. Rudolf
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Guangbo Xie
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | | | | | | | | | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
39
|
Pyne ME, Narcross L, Melgar M, Kevvai K, Mookerjee S, Leite GB, Martin VJJ. An Engineered Aro1 Protein Degradation Approach for Increased cis,cis-Muconic Acid Biosynthesis in Saccharomyces cerevisiae. Appl Environ Microbiol 2018; 84:e01095-18. [PMID: 29934332 PMCID: PMC6102976 DOI: 10.1128/aem.01095-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/16/2018] [Indexed: 12/11/2022] Open
Abstract
Muconic acid (MA) is a chemical building block and precursor to adipic and terephthalic acids used in the production of nylon and polyethylene terephthalate polymer families. Global demand for these important materials, coupled to their dependence on petrochemical resources, provides substantial motivation for the microbial synthesis of MA and its derivatives. In this context, the Saccharomyces cerevisiae yeast shikimate pathway can be sourced as a precursor for the formation of MA. Here we report a novel strategy to balance MA pathway performance with aromatic amino acid prototrophy by destabilizing Aro1 through C-terminal degron tagging. Coupling of a composite MA production pathway to degron-tagged Aro1 in an aro3Δ aro4Δ mutant background led to the accumulation of 5.6 g/liter protocatechuic acid (PCA). However, metabolites downstream of PCA were not detected, despite the inclusion of genes mediating their biosynthesis. Because CEN.PK family strains of S. cerevisiae lack the activity of Pad1, a key enzyme supporting PCA decarboxylase activity, chromosomal expression of intact PAD1 alleviated this bottleneck, resulting in nearly stoichiometric conversion (95%) of PCA to downstream products. In a fed-batch bioreactor, the resulting strain produced 1.2 g/liter MA under prototrophic conditions and 5.1 g/liter MA when supplemented with amino acids, corresponding to a yield of 58 mg/g sugar.IMPORTANCE Previous efforts to engineer a heterologous MA pathway in Saccharomyces cerevisiae have been hindered by a bottleneck at the PCA decarboxylation step and the creation of aromatic amino acid auxotrophy through deleterious manipulation of the pentafunctional Aro1 protein. In light of these studies, this work was undertaken with the central objective of preserving amino acid prototrophy, which we achieved by employing an Aro1 degradation strategy. Moreover, resolution of the key PCA decarboxylase bottleneck, as detailed herein, advances our understanding of yeast MA biosynthesis and will guide future strain engineering efforts. These strategies resulted in the highest titer reported to date for muconic acid produced in yeast. Overall, our study showcases the effectiveness of careful tuning of yeast Aro1 activity and the importance of host-pathway dynamics.
Collapse
Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Mindy Melgar
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Shoham Mookerjee
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Gustavo B Leite
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| |
Collapse
|