1
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Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [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: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
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Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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2
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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3
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Jaroensuk J, Chuaboon L, Chaiyen P. Biochemical reactions for in vitro ATP production and their applications. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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4
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Pfister P, Zarzycki J, Erb TJ. Structural Basis for a Cork-Up Mechanism of the Intra-Molecular Mesaconyl-CoA Transferase. Biochemistry 2023; 62:75-84. [PMID: 36535006 DOI: 10.1021/acs.biochem.2c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mesaconyl-CoA transferase (Mct) is one of the key enzymes of the 3-hydroxypropionate (3HP) bi-cycle for autotrophic CO2 fixation. Mct is a family III/Frc family CoA transferase that catalyzes an unprecedented intra-molecular CoA transfer from the C1-carboxyl group to the C4-carboxyl group of mesaconate at catalytic efficiencies >106 M-1 s-1. Here, we show that the reaction of Mct proceeds without any significant release of free CoA or the transfer to external acceptor acids. Mct catalyzes intra-molecular CoA transfers at catalytic efficiencies that are at least more than 6 orders of magnitude higher compared to inter-molecular CoA transfers, demonstrating that the enzyme exhibits exquisite control over its reaction. To understand the molecular basis of the intra-molecular CoA transfer in Mct, we solved crystal structures of the enzyme from Chloroflexus aurantiacus in its apo form, as well as in complex with mesaconyl-CoA and several covalently enzyme-bound intermediates of CoA and mesaconate at the catalytically active residue Asp165. Based on these structures, we propose a reaction mechanism for Mct that is similar to inter-molecular family III/Frc family CoA transferases. However, in contrast to the latter that undergo opening and closing cycles during the reaction to exchange substrates, the central cavity of Mct remains sealed ("corked-up") by the CoA moiety, strongly favoring the intra-molecular CoA transfer between the C1 and the C4 position of mesaconate.
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Affiliation(s)
- Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch Straße 14, 35032 Marburg, Germany
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5
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Diehl C, Gerlinger PD, Paczia N, Erb TJ. Synthetic anaplerotic modules for the direct synthesis of complex molecules from CO 2. Nat Chem Biol 2023; 19:168-175. [PMID: 36470994 PMCID: PMC9889269 DOI: 10.1038/s41589-022-01179-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/22/2022] [Indexed: 12/12/2022]
Abstract
Anaplerosis is an essential feature of metabolism that allows the continuous operation of natural metabolic networks, such as the citric acid cycle, by constantly replenishing drained intermediates. However, this concept has not been applied to synthetic in vitro metabolic networks, thus far. Here we used anaplerotic strategies to directly access the core sequence of the CETCH cycle, a new-to-nature in vitro CO2-fixation pathway that features several C3-C5 biosynthetic precursors. We drafted four different anaplerotic modules that use CO2 to replenish the CETCH cycle's intermediates and validated our designs by producing 6-deoxyerythronolide B (6-DEB), the C21-macrolide backbone of erythromycin. Our best design allowed the carbon-positive synthesis of 6-DEB via 54 enzymatic reactions in vitro at yields comparable to those with isolated 6-DEB polyketide synthase (DEBS). Our work showcases how new-to-nature anaplerotic modules can be designed and tailored to enhance and expand the synthetic capabilities of complex catalytic in vitro reaction networks.
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Affiliation(s)
- Christoph Diehl
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Patrick D. Gerlinger
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- grid.419554.80000 0004 0491 8361Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J. Erb
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany ,grid.452532.7SYNMIKRO Center for Synthetic Microbiology, Marburg, Germany
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6
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Geyer K, Hartmann S, Singh RR, Erb TJ. Multiple Functions of the Type II Thioesterase Associated with the Phoslactomycin Polyketide Synthase. Biochemistry 2022; 61:2662-2671. [DOI: 10.1021/acs.biochem.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Steffen Hartmann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Randolph R. Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, L-4367 Belvaux, Luxembourg
| | - Tobias J. Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch-Street 16, D-35043 Marburg, Germany
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7
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Schühle K, Saft M, Vögeli B, Erb TJ, Heider J. Benzylmalonyl-CoA dehydrogenase, an enzyme involved in bacterial auxin degradation. Arch Microbiol 2021; 203:4149-4159. [PMID: 34059946 PMCID: PMC8360864 DOI: 10.1007/s00203-021-02406-3] [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: 03/24/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
A novel acyl-CoA dehydrogenase involved in degradation of the auxin indoleacetate by Aromatoleum aromaticum was identified as a decarboxylating benzylmalonyl-CoA dehydrogenase (IaaF). It is encoded within the iaa operon coding for enzymes of indoleacetate catabolism. Using enzymatically produced benzylmalonyl-CoA, the reaction was characterized as simultaneous oxidation and decarboxylation of benzylmalonyl-CoA to cinnamoyl-CoA and CO2. Oxygen served as electron acceptor and was reduced to H2O2, whereas electron transfer flavoprotein or artificial dyes serving as electron acceptors for other acyl-CoA dehydrogenases were not used. The enzyme is homotetrameric, contains an FAD cofactor and is enantiospecific in benzylmalonyl-CoA turnover. It shows high catalytic efficiency and strong substrate inhibition with benzylmalonyl-CoA, but otherwise accepts only a few medium-chain alkylmalonyl-CoA compounds as alternative substrates with low activities. Its reactivity of oxidizing 2-carboxyacyl-CoA with simultaneous decarboxylation is unprecedented and indicates a modified reaction mechanism for acyl-CoA dehydrogenases, where elimination of the 2-carboxy group replaces proton abstraction from C2.
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Affiliation(s)
- Karola Schühle
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Martin Saft
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Marburg, Germany
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany. .,LOEWE-Center for Synthetic Microbiology, Marburg, Germany.
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8
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Kalkreuter E, Bingham KS, Keeler AM, Lowell AN, Schmidt JJ, Sherman DH, Williams GJ. Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase. Nat Commun 2021; 12:2193. [PMID: 33850151 PMCID: PMC8044089 DOI: 10.1038/s41467-021-22497-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/26/2021] [Indexed: 11/28/2022] Open
Abstract
Polyketides, one of the largest classes of natural products, are often clinically relevant. The ability to engineer polyketide biosynthesis to produce analogs is critically important. Acyltransferases (ATs) of modular polyketide synthases (PKSs) catalyze the installation of malonyl-CoA extenders into polyketide scaffolds. ATs have been targeted extensively to site-selectively introduce various extenders into polyketides. Yet, a complete inventory of AT residues responsible for substrate selection has not been established, limiting the scope of AT engineering. Here, molecular dynamics simulations are used to prioritize ~50 mutations within the active site of EryAT6 from erythromycin biosynthesis, leading to identification of two previously unexplored structural motifs. Exchanging both motifs with those from ATs with alternative extender specificities provides chimeric PKS modules with expanded and inverted substrate specificity. Our enhanced understanding of AT substrate selectivity and application of this motif-swapping strategy are expected to advance our ability to engineer PKSs towards designer polyketides.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Kyle S Bingham
- Department of Chemistry, NC State University, Raleigh, NC, USA
- UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Aaron M Keeler
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jennifer J Schmidt
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA.
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9
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Bernhardsgrütter I, Stoffel GM, Miller TE, Erb TJ. CO 2-converting enzymes for sustainable biotechnology: from mechanisms to application. Curr Opin Biotechnol 2021; 67:80-87. [PMID: 33508634 DOI: 10.1016/j.copbio.2021.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/20/2020] [Accepted: 01/05/2021] [Indexed: 01/28/2023]
Abstract
To realize a circular, carbon-neutral economy, it will become important to utilize the greenhouse gas CO2 as a sustainable carbon source. Carboxylases, the enzymes that capture and convert gaseous CO2 are the prime candidates to pave the way towards realizing this vision of a CO2-based bio-economy. In the last couple of years, the interest in using and engineering carboxylases has been steadily growing. Here, we discuss how basic research on the mechanism of CO2 binding and activation by carboxylases opened the way to develop new-to-nature CO2-fixing enzymes that found application in the development of synthetic CO2-fixation pathways and their further realization in vitro and in vivo. These pioneering efforts in the field pave the way to realize a diverse CO2-fixation biochemistry that can find application in biocatalysis, biotechnology, and artificial photosynthesis.
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Affiliation(s)
- Iria Bernhardsgrütter
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Gabriele Mm Stoffel
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tarryn E Miller
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; Center for Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.
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10
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Malico AA, Nichols L, Williams GJ. Synthetic biology enabling access to designer polyketides. Curr Opin Chem Biol 2020; 58:45-53. [PMID: 32758909 DOI: 10.1016/j.cbpa.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/08/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022]
Abstract
The full potential of polyketide discovery has yet to be reached owing to a lack of suitable technologies and knowledge required to advance engineering of polyketide biosynthesis. Recent investigations on the discovery, enhancement, and non-natural use of these biosynthetic gene clusters via computational biology, metabolic engineering, structural biology, and enzymology-guided approaches have facilitated improved access to designer polyketides. Here, we discuss recent successes in gene cluster discovery, host strain engineering, precursor-directed biosynthesis, combinatorial biosynthesis, polyketide tailoring, and high-throughput synthetic biology, as well as challenges and outlooks for rapidly generating useful target polyketides.
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Affiliation(s)
- Alexandra A Malico
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States
| | - Lindsay Nichols
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States; Comparative Medicine Institute, NC State University, Raleigh, NC, 27695, United States.
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11
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Abstract
This chapter represents a journey through flavoprotein oxidases. The purpose is to excite the reader curiosity regarding this class of enzymes by showing their diverse applications. We start with a brief overview on oxidases to then introduce flavoprotein oxidases and elaborate on the flavin cofactors, their redox and spectroscopic characteristics, and their role in the catalytic mechanism. The six major flavoprotein oxidase families will be described, giving examples of their importance in biology and their biotechnological uses. Specific attention will be given to a few selected flavoprotein oxidases that are not extensively discussed in other chapters of this book. Glucose oxidase, cholesterol oxidase, 5-(hydroxymethyl)furfural (HMF) oxidase and methanol oxidase are four examples of oxidases belonging to the GMC-like flavoprotein oxidase family and that have been shown to be valuable biocatalysts. Their structural and mechanistic features and recent enzyme engineering will be discussed in details. Finally we give a look at the current trend in research and conclude with a future outlook.
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Affiliation(s)
- Caterina Martin
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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12
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Zhou S, Hao T, Xu S, Deng Y. Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds. Biotechnol Adv 2020; 43:107575. [PMID: 32512221 DOI: 10.1016/j.biotechadv.2020.107575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shumin Xu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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13
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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14
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Alanjary M, Cano-Prieto C, Gross H, Medema MH. Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. Nat Prod Rep 2019; 36:1249-1261. [PMID: 31259995 DOI: 10.1039/c9np00021f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
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Affiliation(s)
- Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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15
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Kalkreuter E, Keeler AM, Malico AA, Bingham KS, Gayen AK, Williams GJ. Development of a Genetically Encoded Biosensor for Detection of Polyketide Synthase Extender Units in Escherichia coli. ACS Synth Biol 2019; 8:1391-1400. [PMID: 31134799 PMCID: PMC6915837 DOI: 10.1021/acssynbio.9b00078] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The scaffolds of polyketides are constructed via assembly of extender units based on malonyl-CoA and its derivatives that are substituted at the C2-position with diverse chemical functionality. Subsequently, a transcription-factor-based biosensor for malonyl-CoA has proven to be a powerful tool for detecting malonyl-CoA, facilitating the dynamic regulation of malonyl-CoA biosynthesis and guiding high-throughput engineering of malonyl-CoA-dependent processes. Yet, a biosensor for the detection of malonyl-CoA derivatives has yet to be reported, severely restricting the application of high-throughput synthetic biology approaches to engineering extender unit biosynthesis and limiting the ability to dynamically regulate the biosynthesis of polyketide products that are dependent on such α-carboxyacyl-CoAs. Herein, the FapR biosensor was re-engineered and optimized for a range of mCoA concentrations across a panel of E. coli strains. The effector specificity of FapR was probed by cell-free transcription-translation, revealing that a variety of non-native and non-natural acyl-thioesters are FapR effectors. This FapR promiscuity proved sufficient for the detection of the polyketide extender unit methylmalonyl-CoA in E. coli, providing the first reported genetically encoded biosensor for this important metabolite. As such, the previously unknown broad effector promiscuity of FapR provides a platform to develop new tools and approaches that can be leveraged to overcome limitations of pathways that construct diverse α-carboxyacyl-CoAs and those that are dependent on them, including biofuels, antibiotics, anticancer drugs, and other value-added products.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
- Present address: Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Aaron M. Keeler
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Alexandra A. Malico
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Kyle S. Bingham
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Present address: UNC Chapel Hill School of Medicine, Chapel Hill, North Carolina 27516, United States
| | - Anuran K. Gayen
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Gavin J. Williams
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
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16
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Zhang F, Shi T, Ji H, Ali I, Huang S, Deng Z, Min Q, Bai L, Zhao Y, Zheng J. Structural Insights into the Substrate Specificity of Acyltransferases from Salinomycin Polyketide Synthase. Biochemistry 2019; 58:2978-2986. [PMID: 31199122 DOI: 10.1021/acs.biochem.9b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Salinomycin with antibacterial and anticoccidial activities is a commercial polyether polyketide widely used in animal husbandry as a food additive. Malonyl-CoA (MCoA), methylmalonyl-CoA (MMCoA), and ethylmalonyl-CoA (EMCoA) are used as extension units in its biosynthesis. To understand how the salinomycin modular polyketide synthase (PKS) strictly discriminates among these extension units, the acyltransferase (AT) domains selecting MCoA, MMCoA, and EMCoA were structurally characterized. Molecular dynamics simulations of the AT structures helped to reveal the key interactions involved in enzyme-substrate recognitions, which enabled the engineering of AT mutants with switched specificity. The catalytic efficiencies ( kcat/ Km) of these AT mutants are comparable with those of the wild-type AT domains. These results set the stage for engineering the AT substrate specificity of modular PKSs.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Shuxin Huang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qing Min
- Pharmacy School , Hubei University of Science and Technology , Hubei , Xianning 437100 , China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
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17
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Bernhardsgrütter I, Schell K, Peter DM, Borjian F, Saez DA, Vöhringer-Martinez E, Erb TJ. Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO 2-Binding Potential of Reductases. J Am Chem Soc 2019; 141:9778-9782. [PMID: 31188584 PMCID: PMC6650136 DOI: 10.1021/jacs.9b03431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Developing new carbon
dioxide (CO2) fixing enzymes is
a prerequisite to create new biocatalysts for diverse applications
in chemistry, biotechnology and synthetic biology. Here we used bioinformatics
to identify a “sleeping carboxylase function” in the
superfamily of medium-chain dehydrogenases/reductases (MDR), i.e.
enzymes that possess a low carboxylation side activity next to their
original enzyme reaction. We show that propionyl-CoA synthase from Erythrobacter sp. NAP1, as well as an acrylyl-CoA
reductase from Nitrosopumilus maritimus possess carboxylation yields of 3 ± 1 and 4.5 ± 0.9%.
We use rational design to engineer these enzymes further into carboxylases
by increasing interactions of the proteins with CO2 and
suppressing diffusion of water to the active site. The engineered
carboxylases show improved CO2-binding and kinetic parameters
comparable to naturally existing CO2-fixing enzymes. Our
results provide a strategy to develop novel CO2-fixing
enzymes and shed light on the emergence of natural carboxylases during
evolution.
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Affiliation(s)
- Iria Bernhardsgrütter
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Kristina Schell
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Dominik M Peter
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Farshad Borjian
- Institute for Molecular Microbiology and Biotechnology, University of Münster , Corrensstr. 3 , D-48149 Münster , Germany
| | - David Adrian Saez
- Departamento de Físico Química, Facultad de Ciencias Químicas , Universidad de Concepción , 1290 Concepción , Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas , Universidad de Concepción , 1290 Concepción , Chile
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany.,LOEWE Center for Synthetic Microbiology (Synmikro) , Karl-von-Frisch-Straße 16 , D-35043 Marburg , Germany
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18
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Kalkreuter E, CroweTipton JM, Lowell AN, Sherman DH, Williams GJ. Engineering the Substrate Specificity of a Modular Polyketide Synthase for Installation of Consecutive Non-Natural Extender Units. J Am Chem Soc 2019; 141:1961-1969. [PMID: 30676722 DOI: 10.1021/jacs.8b10521] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is significant interest in diversifying the structures of polyketides to create new analogues of these bioactive molecules. This has traditionally been done by focusing on engineering the acyltransferase (AT) domains of polyketide synthases (PKSs) responsible for the incorporation of malonyl-CoA extender units. Non-natural extender units have been utilized by engineered PKSs previously; however, most of the work to date has been accomplished with ATs that are either naturally promiscuous and/or located in terminal modules lacking downstream bottlenecks. These limitations have prevented the engineering of ATs with low native promiscuity and the study of any potential gatekeeping effects by domains downstream of an engineered AT. In an effort to address this gap in PKS engineering knowledge, the substrate preferences of the final two modules of the pikromycin PKS were compared for several non-natural extender units and through active site mutagenesis. This led to engineering of the methylmalonyl-CoA specificity of both modules and inversion of their selectivity to prefer consecutive non-natural derivatives. Analysis of the product distributions of these bimodular reactions revealed unexpected metabolites resulting from gatekeeping by the downstream ketoreductase and ketosynthase domains. Despite these new bottlenecks, AT engineering provided the first full-length polyketide products incorporating two non-natural extender units. Together, this combination of tandem AT engineering and the identification of previously poorly characterized bottlenecks provides a platform for future advancements in the field.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
| | - Jared M CroweTipton
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Chemistry and Department of Microbiology & Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gavin J Williams
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
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19
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Carpenter SM, Williams GJ. Extender Unit Promiscuity and Orthogonal Protein Interactions of an Aminomalonyl-ACP Utilizing Trans-Acyltransferase from Zwittermicin Biosynthesis. ACS Chem Biol 2018; 13:3361-3373. [PMID: 30484625 DOI: 10.1021/acschembio.8b00867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trans-acting acyltransferases (trans-ATs) are standalone enzymes that select and deliver extender units to polyketide synthase assembly lines. Accordingly, there is interest in leveraging trans-ATs as tools to regioselectively diversify polyketide structures. Yet, little is known regarding the extender unit and acyl carrier protein (ACP) specificity of trans-ATs, particularly those that utilize unusual ACP-linked extender units. For example, the biosynthesis of the antibiotic zwittermicin involves the trans-AT ZmaF, which is responsible for installing a rare ACP-linked aminomalonyl extender unit. Here, we developed a method to access a panel of non-natural and non-native ACP-linked extender units and used it to probe the promiscuity of ZmaF, revealing one of the most promiscuous ATs characterized to date. Furthermore, we demonstrated that ZmaF is highly orthogonal with respect to its ACP specificity, and the ability of ZmaF to trans-complement noncognate PKS modules was also explored. Together, these results set the stage for further engineering ZmaF as a tool for polyketide diversification.
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Affiliation(s)
- Samantha M. Carpenter
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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