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Ren H, Huang C, Pan Y, Dommaraju SR, Cui H, Li M, Gadgil MG, Mitchell DA, Zhao H. Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides. Nat Chem 2024:10.1038/s41557-024-01491-3. [PMID: 38528101 DOI: 10.1038/s41557-024-01491-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries. However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machinery from other natural product families. Here we report lipoavitides, a class of RiPP/fatty-acid hybrid lipopeptides that display a unique, putatively membrane-targeting 4-hydroxy-2,4-dimethylpentanoyl (HMP)-modified N terminus. The HMP is formed via condensation of isobutyryl-coenzyme A (isobutyryl-CoA) and methylmalonyl-CoA catalysed by a 3-ketoacyl-(acyl carrier protein) synthase III enzyme, followed by successive tailoring reactions in the fatty acid biosynthetic pathway. The HMP and RiPP substructures are then connected by an acyltransferase exhibiting promiscuous activity towards the fatty acyl and RiPP substrates. Overall, the discovery of lipoavitides contributes a prototype of RiPP/fatty-acid hybrids and provides possible enzymatic tools for lipopeptide bioengineering.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuwei Pan
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shravan R Dommaraju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Maolin Li
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mayuresh G Gadgil
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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2
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Seo K, Shu W, Rückert-Reed C, Gerlinger P, Erb TJ, Kalinowski J, Wittmann C. From waste to health-supporting molecules: biosynthesis of natural products from lignin-, plastic- and seaweed-based monomers using metabolically engineered Streptomyces lividans. Microb Cell Fact 2023; 22:262. [PMID: 38114944 PMCID: PMC10731712 DOI: 10.1186/s12934-023-02266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Transforming waste and nonfood materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry to optimize the use of resources while reducing environmental footprint. However, despite these advancements, the production of high-value natural products often continues to depend on the use of first-generation substrates, underscoring the intricate processes and specific requirements of their biosyntheses. This is also true for Streptomyces lividans, a renowned host organism celebrated for its capacity to produce a wide array of natural products, which is attributed to its genetic versatility and potent secondary metabolic activity. Given this context, it becomes imperative to assess and optimize this microorganism for the synthesis of natural products specifically from waste and nonfood substrates. RESULTS We metabolically engineered S. lividans to heterologously produce the ribosomally synthesized and posttranslationally modified peptide bottromycin, as well as the polyketide pamamycin. The modified strains successfully produced these compounds using waste and nonfood model substrates such as protocatechuate (derived from lignin), 4-hydroxybenzoate (sourced from plastic waste), and mannitol (from seaweed). Comprehensive transcriptomic and metabolomic analyses offered insights into how these substrates influenced the cellular metabolism of S. lividans. In terms of production efficiency, S. lividans showed remarkable tolerance, especially in a fed-batch process using a mineral medium containing the toxic aromatic 4-hydroxybenzoate, which led to enhanced and highly selective bottromycin production. Additionally, the strain generated a unique spectrum of pamamycins when cultured in mannitol-rich seaweed extract with no additional nutrients. CONCLUSION Our study showcases the successful production of high-value natural products based on the use of varied waste and nonfood raw materials, circumventing the reliance on costly, food-competing resources. S. lividans exhibited remarkable adaptability and resilience when grown on these diverse substrates. When cultured on aromatic compounds, it displayed a distinct array of intracellular CoA esters, presenting promising avenues for polyketide production. Future research could be focused on enhancing S. lividans substrate utilization pathways to process the intricate mixtures commonly found in waste and nonfood sources more efficiently.
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Affiliation(s)
- Kyoyoung Seo
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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3
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Paulsel TQ, Williams GJ. Current State-of-the-Art Toward Chemoenzymatic Synthesis of Polyketide Natural Products. Chembiochem 2023; 24:e202300386. [PMID: 37615926 PMCID: PMC10964317 DOI: 10.1002/cbic.202300386] [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: 05/23/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
Polyketide natural products have significant promise as pharmaceutical targets for human health and as molecular tools to probe disease and complex biological systems. While the biosynthetic logic of polyketide synthases (PKS) is well-understood, biosynthesis of designer polyketides remains challenging due to several bottlenecks, including substrate specificity constraints, disrupted protein-protein interactions, and protein solubility and folding issues. Focusing on substrate specificity, PKSs are typically interrogated using synthetic thioesters. PKS assembly lines and their products offer a wealth of information when studied in a chemoenzymatic fashion. This review provides an overview of the past two decades of polyketide chemoenzymatic synthesis and their contributions to the field of chemical biology. These synthetic strategies have successfully yielded natural product derivatives while providing critical insights into enzymatic promiscuity and mechanistic activity.
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Affiliation(s)
- Thaddeus Q Paulsel
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
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4
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Ren H, Huang C, Pan Y, Cui H, Dommaraju SR, Mitchell DA, Zhao H. Non-modular Fatty Acid Synthases Yield Unique Acylation in Ribosomal Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564083. [PMID: 37961664 PMCID: PMC10634828 DOI: 10.1101/2023.10.25.564083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries 1, 2 . However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machineries from other natural product families 3-8 . Here, we report lipoavitides, a class of RiPP/fatty acid hybrid lipopeptides that display a unique, membrane-targeting 4-hydroxy-2,4-dimethylpentanoyl (HMP)-modified N -terminus. The HMP is formed via condensation of isobutyryl-CoA and methylmalonyl-CoA catalyzed by a 3-ketoacyl-ACP synthase III enzyme, followed by successive tailoring reactions in the fatty acid biosynthetic pathway. The HMP and RiPP substructures are then connected by an acyltransferase exhibiting promiscuous activity towards the fatty acyl and RiPP substrates. Overall, the discovery of lipoavitides contributes a prototype of RiPP/fatty acid hybrids and provides possible enzymatic tools for lipopeptide bioengineering.
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5
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Fraser OA, Namitz KEW, Showalter SA. Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors. Methods 2023; 218:72-83. [PMID: 37524235 PMCID: PMC10528339 DOI: 10.1016/j.ymeth.2023.07.010] [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: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
Post-translational modifications (PTMs) are reversible chemical modifications that can modulate protein structure and function. Methylation and acetylation are two such PTMs with integral and well-characterized biological roles, including modulation of chromatin structure; and unknown or poorly understood roles, exemplified by the influence of these PTMs on transcription factor structure and function. The need for biological insights into the function of these PTMs motivates the development of a nondestructive and label-free method that enables pursuit of molecular mechanisms. Here, we present a protocol for implementing nuclear magnetic resonance (NMR) methods that allow for unambiguous detection of methylation and acetylation events and demonstrate their utility by observing these marks on histone H3 tail as a model system. We leverage strategic isotopic enrichment of cofactor and peptide for visualization by [1H, 13C]-HSQC and 13C direct-detect NMR measurements. Finally, we present 13C-labeling schemes that facilitate one-dimensional NMR experiments, which combine reduced measurement time relative to two-dimensional spectroscopy with robust filtering of background signals that would otherwise create spectral crowding or limit detection of low-abundance analytes.
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Affiliation(s)
- Olivia A Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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6
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Kremer K, Meier D, Theis L, Miller S, Rost-Nasshan A, Naing YT, Zarzycki J, Paczia N, Serrania J, Blumenkamp P, Goesmann A, Becker A, Thanbichler M, Hochberg GKA, Carter MS, Erb TJ. Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway. Appl Environ Microbiol 2023:e0023823. [PMID: 37318336 PMCID: PMC10370305 DOI: 10.1128/aem.00238-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. IMPORTANCE Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.
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Affiliation(s)
- Katharina Kremer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Lisa Theis
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stephanie Miller
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | | | - Yadanar T Naing
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for terrestrial Microbiology, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anke Becker
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K A Hochberg
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, University of Marburg, Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael S Carter
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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7
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Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ. Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis. Biochemistry 2023. [PMID: 37207322 DOI: 10.1021/acs.biochem.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Succinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO2-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP+ and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology.
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Affiliation(s)
- Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Eric Hammarlund
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Martina Carrillo
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch Str., 14, 35032 Marburg, Germany
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8
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Fraser OA, Dewing SM, Usher ET, George C, Showalter SA. A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins. Front Mol Biosci 2023; 9:1074743. [PMID: 36685286 PMCID: PMC9853081 DOI: 10.3389/fmolb.2022.1074743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.
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Affiliation(s)
- Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Sophia M. Dewing
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Emery T. Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Christy George
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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9
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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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10
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Abstract
The traditional textbook describes ubiquitylation as the conjugation of ubiquitin to a target by forming a covalent bond connecting ubiquitin's carboxy-terminal glycine residue with an acceptor amino acid like lysine or amino-terminal methionine in the substrate protein. While this adequately depicts a significant fraction of cellular ubiquitylation processes, a growing number of ubiquitin modifications do not follow this rule. Recent data demonstrate that ubiquitin can also be efficiently attached to other amino acids, such as cysteine, serine, and threonine, via ester bonding. Initially observed for a virus-encoded ubiquitin ligase, which targets a cysteine residue in a host protein to initiate its degradation, ester-linked ubiquitylation is now shown to also drive regular cellular processes. These ubiquitylation events expand the complexity and diversity of ubiquitin signaling and broaden the capability of cellular messages in the so-called ubiquitin code. Still, questions on the prevalence, relevance, and involvement in physiological and cellular functions await clearing. In this review, we aim to summarize our knowledge on ester-linked ubiquitylation and introduce experimental strategies to circumvent technical issues that complicate analysis of this uncommon posttranslational modification.
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Affiliation(s)
- Alba Ferri-Blazquez
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Ernst Jarosch
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholz Association, Berlin Buch, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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11
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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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12
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Thioester-mediated biocatalytic amide bond synthesis with in situ thiol recycling. Nat Catal 2022. [DOI: 10.1038/s41929-022-00889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Bacterial Hydratases Involved in Steroid Side Chain Degradation Have Distinct Substrate Specificities. J Bacteriol 2022; 204:e0023622. [PMID: 36000836 PMCID: PMC9491828 DOI: 10.1128/jb.00236-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinobacterial MaoC family enoyl coenzyme A (CoA) hydratases catalyze the addition of water across the double bond of CoA esters during steroid side chain catabolism. We determined that heteromeric MaoC type hydratases, exemplified by ChsH1-ChsH2Mtb of Mycobacterium tuberculosis and CasM-CasORjost from Rhodococcus jostii RHA1, are specific toward a 3-carbon side chain steroid metabolite, consistent with their roles in the last β-oxidation cycle of steroid side chain degradation. Hydratases containing two fused MaoC domains are responsible for the degradation of longer steroid side chains. These hydratases, encoded in the cholesterol degradation gene clusters of M. tuberculosis and R. jostii RHA1, have broad specificity and were able to catalyze the hydration of the 5-carbon side chain of both cholesterol and bile acid metabolites. Surprisingly, the homologous hydratases from the bile acid degradation pathway have low catalytic efficiencies or no activity toward the 5-carbon side chain bile acid metabolites, cholyl-enoyl-CoA, lithocholyl-enoyl-CoA, and chenodeoxycholyl-enoyl-CoA. Instead, these hydratases preferred a cholate metabolite with oxidized steroid rings and a planar ring structure. Together, the results suggest that ring oxidation occurs prior to side chain degradation in the actinobacterial bile acid degradation pathway. IMPORTANCE Characterization of the substrate specificity of hydratases described here will facilitate the development of specific inhibitors that may be useful as novel therapeutics against M. tuberculosis and to metabolically engineer bacteria to produce steroid pharmaceuticals with desired steroid rings and side chain structures.
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14
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Goldsmith M, Barad S, Knafo M, Savidor A, Ben-Dor S, Brandis A, Mehlman T, Peleg Y, Albeck S, Dym O, Ben-Zeev E, Barbole RS, Aharoni A, Reich Z. Identification and characterization of the key enzyme in the biosynthesis of the neurotoxin β-ODAP in grass pea. J Biol Chem 2022; 298:101806. [PMID: 35271851 PMCID: PMC9061259 DOI: 10.1016/j.jbc.2022.101806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
Grass pea (Lathyrus sativus L.) is a grain legume commonly grown in Asia and Africa for food and forage. It is a highly nutritious and robust crop, capable of surviving both droughts and floods. However, it produces a neurotoxic compound, β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a severe neurological disorder when consumed as a primary diet component. While the catalytic activity associated with β-ODAP formation was demonstrated more than 50 years ago, the enzyme responsible for this activity has not been identified. Here, we report on the identity, activity, 3D structure, and phylogenesis of this enzyme—β-ODAP synthase (BOS). We show that BOS belongs to the benzylalcohol O-acetyltransferase, anthocyanin O-hydroxycinnamoyltransferase, anthranilate N-hydroxycinnamoyl/benzoyltransferase, deacetylvindoline 4-O-acetyltransferase superfamily of acyltransferases and is structurally similar to hydroxycinnamoyl transferase. Using molecular docking, we propose a mechanism for its catalytic activity, and using heterologous expression in tobacco leaves (Nicotiana benthamiana), we demonstrate that expression of BOS in the presence of its substrates is sufficient for β-ODAP production in vivo. The identification of BOS may pave the way toward engineering β-ODAP–free grass pea cultivars, which are safe for human and animal consumption.
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Affiliation(s)
- Moshe Goldsmith
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Shiri Barad
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maor Knafo
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alon Savidor
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shifra Ben-Dor
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alexander Brandis
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tevie Mehlman
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yoav Peleg
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shira Albeck
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Orly Dym
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Ben-Zeev
- Medicinal Chemistry Unit, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ranjit S Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel; Plant Molecular Biology Unit, Division of Biochemical Sciences, Council of Scientific and Industrial Research-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Reich
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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15
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Phan HT, Hosoe Y, Guex M, Tomoi M, Tomita H, Zinn M, Matsumoto K. Directed Evolution of Sequence-Regulating Polyhydroxyalkanoate Synthase to Synthesize a Medium-Chain-Length-Short-Chain-Length (MCL-SCL) Block Copolymer. Biomacromolecules 2022; 23:1221-1231. [PMID: 34991313 DOI: 10.1021/acs.biomac.1c01480] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Sequence-regulating polyhydroxyalkanoate synthase PhaCAR is a chimeric enzyme comprising PhaCs from Aeromonas caviae and Ralstonia eutropha (Cupriavidus necator). It spontaneously synthesizes a short-chain-length (SCL, ≤C5) block copolymer poly(2-hydroxybutyrate)-b-poly(3-hydroxybutyrate) [P(2HB)-b-P(3HB)] from a mixture of monomer substrates. In this study, directed evolution of PhaCAR was performed to increase its activity toward a medium-chain-length (MCL, C6-12) monomer, 3-hydroxyhexanoyl (3HHx)-coenzyme A (CoA). Random mutagenesis and selection based on P(3HB-co-3HHx) production in Escherichia coli found that beneficial mutations N149D and F314L increase the 3HHx fraction. The site-directed saturation mutagenesis at position 314, which is adjacent to the catalytic center C315, demonstrated that F314H synthesizes the P(3HHx) homopolymer. The F314H mutant exhibited increased activity toward 3HHx-CoA compared with the parent enzyme, whereas the activity toward 3HB-CoA decreased. The predicted tertiary structure of PhaCAR by AlphaFold2 provided insight into the mechanism of the beneficial mutations. In addition, this finding enabled the synthesis of a new PHA block copolymer, P(3HHx)-b-P(2HB). Solvent fractionation indicated the presence of a covalent linkage between the polymer segments. This novel MCL-SCL block copolymer considerably expands the range of the molecular design of PHA block copolymers.
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Affiliation(s)
- Hien Thi Phan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yumi Hosoe
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Maureen Guex
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), 1950 Sion, Switzerland
| | - Masayoshi Tomoi
- Course of Applied Chemistry, Department of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hiroya Tomita
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), 1950 Sion, Switzerland
| | - Ken'ichiro Matsumoto
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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16
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Stunkard LM, Benjamin AB, Bower JB, Huth TJ, Lohman JR. Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*. Chembiochem 2021; 23:e202100487. [PMID: 34856049 DOI: 10.1002/cbic.202100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/02/2021] [Indexed: 11/05/2022]
Abstract
Methylmalonyl-CoA epimerase (MMCE) is proposed to use general acid-base catalysis, but the proposed catalytic glutamic acids are highly asymmetrical in the active site unlike many other racemases. To gain insight into the puzzling relationships between catalytic mechanism, structure, and substrate preference, we solved Streptomyces coelicolor MMCE structures with substrate or 2-nitropropionyl-CoA, an intermediate/transition state analogue. Both ligand bound structures have a planar methylmalonate/2-nitropropionyl moiety indicating a deprotonated C2 with ≥4 Å distances to either catalytic acid. Both glutamates interact with the carboxylate/nitro group, either directly or through other residues. This suggests the proposed catalytic acids sequentially catalyze proton shifts between C2 and carboxylate of the substrate with an enolate intermediate. In addition, our structures provide a platform to design mutations for expanding substrate scope to support combinatorial biosynthesis.
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Affiliation(s)
- Lee M Stunkard
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA
| | - Aaron B Benjamin
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA
| | - James B Bower
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA
| | - Tyler J Huth
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA
| | - Jeremy R Lohman
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA
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17
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Dewulf JP, Paquay S, Marbaix E, Achouri Y, Van Schaftingen E, Bommer GT. ECHDC1 knockout mice accumulate ethyl-branched lipids and excrete abnormal intermediates of branched-chain fatty acid metabolism. J Biol Chem 2021; 297:101083. [PMID: 34419447 PMCID: PMC8473548 DOI: 10.1016/j.jbc.2021.101083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022] Open
Abstract
The cytosolic enzyme ethylmalonyl-CoA decarboxylase (ECHDC1) decarboxylates ethyl- or methyl-malonyl-CoA, two side products of acetyl-CoA carboxylase. These CoA derivatives can be used to synthesize a subset of branched-chain fatty acids (FAs). We previously found that ECHDC1 limits the synthesis of these abnormal FAs in cell lines, but its effects in vivo are unknown. To further evaluate the effects of ECHDC1 deficiency, we generated knockout mice. These mice were viable, fertile, showed normal postnatal growth, and lacked obvious macroscopic and histologic changes. Surprisingly, tissues from wild-type mice already contained methyl-branched FAs due to methylmalonyl-CoA incorporation, but these FAs were only increased in the intraorbital glands of ECHDC1 knockout mice. In contrast, ECHDC1 knockout mice accumulated 16–20-carbon FAs carrying ethyl-branches in all tissues, which were undetectable in wild-type mice. Ethyl-branched FAs were incorporated into different lipids, including acylcarnitines, phosphatidylcholines, plasmanylcholines, and triglycerides. Interestingly, we found a variety of unusual glycine-conjugates in the urine of knockout mice, which included adducts of ethyl-branched compounds in different stages of oxidation. This suggests that the excretion of potentially toxic intermediates of branched-chain FA metabolism might prevent a more dramatic phenotype in these mice. Curiously, ECHDC1 knockout mice also accumulated 2,2-dimethylmalonyl-CoA. This indicates that the broad specificity of ECHDC1 might help eliminate a variety of potentially dangerous branched-chain dicarboxylyl-CoAs. We conclude that ECHDC1 prevents the formation of ethyl-branched FAs and that urinary excretion of glycine-conjugates allows mice to eliminate potentially deleterious intermediates of branched-chain FA metabolism.
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Affiliation(s)
- Joseph P Dewulf
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium; Department of Laboratory Medicine, University Hospital St Luc, UCLouvain, Bruxelles, Belgium.
| | - Stéphanie Paquay
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium; Department of Neuropediatrics, University Hospital St Luc, UCLouvain, Bruxelles, Belgium
| | - Etienne Marbaix
- Department of Anatomical Pathology, University Hospital St Luc, UCLouvain, Bruxelles, Belgium; Department of Cell Biology, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Younès Achouri
- Transgenesis Platform, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Emile Van Schaftingen
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.
| | - Guido T Bommer
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.
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18
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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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19
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Smith MD, Tassoulas LJ, Biernath TA, Richman JE, Aukema KG, Wackett LP. p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA. Comput Struct Biotechnol J 2021; 19:3087-3096. [PMID: 34141132 PMCID: PMC8180931 DOI: 10.1016/j.csbj.2021.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/21/2022] Open
Abstract
The OleA enzyme is distinct amongst thiolase enzymes in binding two long (≥C8) acyl chains into structurally-opposed hydrophobic channels, denoted A and B, to carry out a non-decarboxylative Claisen condensation reaction and initiate the biosynthesis of membrane hydrocarbons and β-lactone natural products. OleA has now been identified in hundreds of diverse bacteria via bioinformatics and high-throughput screening using p-nitrophenyl alkanoate esters as surrogate substrates. In the present study, p-nitrophenyl esters were used to probe the reaction mechanism of OleA and shown to be incorporated into Claisen condensation products for the first time. p-Nitrophenyl alkanoate substrates alone were shown not to undergo Claisen condensation, but co-incubation of p-nitrophenyl esters and CoA thioesters produced mixed Claisen products. Mixed product reactions were shown to initiate via acyl group transfer from a p-nitrophenyl carrier to the enzyme active site cysteine, C143. Acyl chains esterified to p-nitrophenol were synthesized and shown to undergo Claisen condensation with an acyl-CoA substrate, showing potential to greatly expand the range of possible Claisen products. Using p-nitrophenyl 1-13C-decanoate, the Channel A bound thioester chain was shown to act as the Claisen nucleophile, representing the first direct evidence for the directionality of the Claisen reaction in any OleA enzyme. These results both provide new insights into OleA catalysis and open a path for making unnatural hydrocarbon and β-lactone natural products for biotechnological applications using cheap and easily synthesized p-nitrophenyl esters.
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Affiliation(s)
- Megan D. Smith
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
| | - Lambros J. Tassoulas
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Troy A. Biernath
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
| | - Jack E. Richman
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Kelly G. Aukema
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Lawrence P. Wackett
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
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20
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Cakić N, Kopke B, Rabus R, Wilkes H. Suspect screening and targeted analysis of acyl coenzyme A thioesters in bacterial cultures using a high-resolution tribrid mass spectrometer. Anal Bioanal Chem 2021; 413:3599-3610. [PMID: 33881564 PMCID: PMC8141488 DOI: 10.1007/s00216-021-03318-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/14/2021] [Accepted: 03/30/2021] [Indexed: 11/20/2022]
Abstract
Analysis of acyl coenzyme A thioesters (acyl-CoAs) is crucial in the investigation of a wide range of biochemical reactions and paves the way to fully understand the concerned metabolic pathways and their superimposed networks. We developed two methods for suspect screening of acyl-CoAs in bacterial cultures using a high-resolution Orbitrap Fusion tribrid mass spectrometer. The methods rely on specific fragmentation patterns of the target compounds, which originate from the coenzyme A moiety. They make use of the formation of the adenosine 3′,5′-diphosphate key fragment (m/z 428.0365) and the neutral loss of the adenosine 3′-phosphate-5′-diphosphate moiety (506.9952) as preselection criteria for the detection of acyl-CoAs. These characteristic ions are generated either by an optimised in-source fragmentation in a full scan Orbitrap measurement or by optimised HCD fragmentation. Additionally, five different filters are included in the design of method. Finally, data-dependent MS/MS experiments on specifically preselected precursor ions are performed. The utility of the methods is demonstrated by analysing cultures of the denitrifying betaproteobacterium “Aromatoleum” sp. strain HxN1 anaerobically grown with hexanoate. We detected 35 acyl-CoAs in total and identified 24 of them by comparison with reference standards, including all 9 acyl-CoA intermediates expected to occur in the degradation pathway of hexanoate. The identification of additional acyl-CoAs provides insight into further metabolic processes occurring in this bacterium. The sensitivity of the method described allows detecting acyl-CoAs present in biological samples in highly variable abundances. Graphical abstract ![]()
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Affiliation(s)
- Nevenka Cakić
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany.
| | - Bernd Kopke
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Ralf Rabus
- General & Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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21
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Wang W, Qi X, Wu X. Palladium‐Catalyzed Thiocarbonylation of Benzyl Chlorides with Sulfonyl Chlorides for the Synthesis of Arylacetyl Thioesters. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Wei Wang
- Department of Chemistry Zhejiang Sci-Tech University Hangzhou Zhejiang 310018 People's Republic of China
| | - Xinxin Qi
- Department of Chemistry Zhejiang Sci-Tech University Hangzhou Zhejiang 310018 People's Republic of China
| | - Xiao‐Feng Wu
- Dalian National Laboratory for Clean Energy Dalian Institute of Chemical Physics Chinese Academy of Sciences 116023 Dalian Liaoning People's Republic of China
- Leibniz-Institut für Katalyse e.V. an der Institution Universität Rostock Albert-Einstein-Straße 29a Rostock 18059 Germany
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22
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Stunkard LM, Kick BJ, Lohman JR. Structures of LnmK, a Bifunctional Acyltransferase/Decarboxylase, with Substrate Analogues Reveal the Basis for Selectivity and Stereospecificity. Biochemistry 2021; 60:365-372. [PMID: 33482062 DOI: 10.1021/acs.biochem.0c00893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LnmK stereospecifically accepts (2R)-methylmalonyl-CoA, generating propionyl-S-acyl carrier protein to support polyketide biosynthesis. LnmK and its homologues are the only known enzymes that carry out a decarboxylation (DC) and acyl transfer (AT) reaction in the same active site as revealed by structure-function studies. Substrate-assisted catalysis powers LnmK, as decarboxylation of (2R)-methylmalonyl-CoA generates an enolate capable of deprotonating active site Tyr62, and the Tyr62 phenolate subsequently attacks propionyl-CoA leading to a propionyl-O-LnmK acyl-enzyme intermediate. Due to the inherent reactivity of LnmK and methylmalonyl-CoA, a substrate-bound structure could not be obtained. To gain insight into substrate specificity, stereospecificity, and catalytic mechanism, we determined the structures of LnmK with bound substrate analogues that bear malonyl-thioester isosteres where the carboxylate is represented by a nitro or sulfonate group. The nitro-bearing malonyl-thioester isosteres bind in the nitronate form, with specific hydrogen bonds that allow modeling of the (2R)-methylmalonyl-CoA substrate and rationalization of stereospecificity. The sulfonate isosteres bind in multiple conformations, suggesting the large active site of LnmK allows multiple binding modes. Considering the smaller malonyl group has more conformational freedom than the methylmalonyl group, we hypothesized the active site can entropically screen against catalysis with the smaller malonyl-CoA substrate. Indeed, our kinetic analysis reveals malonyl-CoA is accepted at 1% of the rate of methylmalonyl-CoA. This study represents another example of how our nitro- and sulfonate-bearing methylmalonyl-thioester isosteres are of use for elucidating enzyme-substrate binding interactions and revealing insights into catalytic mechanism. Synthesis of a larger panel of analogues presents an opportunity to study enzymes with complicated structure-function relationships such as acyl-CoA carboxylases, trans-carboxytransferases, malonyltransferases, and β-ketoacylsynthases.
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Affiliation(s)
- Lee M Stunkard
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Benjamin J Kick
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jeremy R Lohman
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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23
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Special Issue "Metabolic Engineering and Synthetic Biology Volume 2". Metabolites 2021; 11:metabo11010035. [PMID: 33418903 PMCID: PMC7825028 DOI: 10.3390/metabo11010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022] Open
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24
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Cotton CAR, Bernhardsgrütter I, He H, Burgener S, Schulz L, Paczia N, Dronsella B, Erban A, Toman S, Dempfle M, De Maria A, Kopka J, Lindner SN, Erb TJ, Bar-Even A. Underground isoleucine biosynthesis pathways in E. coli. eLife 2020; 9:e54207. [PMID: 32831171 PMCID: PMC7476758 DOI: 10.7554/elife.54207] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 08/22/2020] [Indexed: 12/26/2022] Open
Abstract
The promiscuous activities of enzymes provide fertile ground for the evolution of new metabolic pathways. Here, we systematically explore the ability of E. coli to harness underground metabolism to compensate for the deletion of an essential biosynthetic pathway. By deleting all threonine deaminases, we generated a strain in which isoleucine biosynthesis was interrupted at the level of 2-ketobutyrate. Incubation of this strain under aerobic conditions resulted in the emergence of a novel 2-ketobutyrate biosynthesis pathway based upon the promiscuous cleavage of O-succinyl-L-homoserine by cystathionine γ-synthase (MetB). Under anaerobic conditions, pyruvate formate-lyase enabled 2-ketobutyrate biosynthesis from propionyl-CoA and formate. Surprisingly, we found this anaerobic route to provide a substantial fraction of isoleucine in a wild-type strain when propionate is available in the medium. This study demonstrates the selective advantage underground metabolism offers, providing metabolic redundancy and flexibility which allow for the best use of environmental carbon sources.
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Affiliation(s)
| | | | - Hai He
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Simon Burgener
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Luca Schulz
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Stepan Toman
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Marian Dempfle
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Alberto De Maria
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | | | - Tobias J Erb
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
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25
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Gläser L, Kuhl M, Jovanovic S, Fritz M, Vögeli B, Erb TJ, Becker J, Wittmann C. A common approach for absolute quantification of short chain CoA thioesters in prokaryotic and eukaryotic microbes. Microb Cell Fact 2020; 19:160. [PMID: 32778124 PMCID: PMC7418318 DOI: 10.1186/s12934-020-01413-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thioesters of coenzyme A participate in 5% of all enzymatic reactions. In microbial cell factories, they function as building blocks for products of recognized commercial value, including natural products such as polyketides, polyunsaturated fatty acids, biofuels, and biopolymers. A core spectrum of approximately 5-10 short chain thioesters is present in many microbes, as inferred from their genomic repertoire. The relevance of these metabolites explains the high interest to trace and quantify them in microbial cells. RESULTS Here, we describe a common workflow for extraction and absolute quantification of short chain CoA thioesters in different gram-positive and gram-negative bacteria and eukaryotic yeast, i.e. Corynebacterium glutamicum, Streptomyces albus, Pseudomonas putida, and Yarrowia lipolytica. The approach assessed intracellular CoA thioesters down to the picomolar level and exhibited high precision and reproducibility for all microbes, as shown by principal component analysis. Furthermore, it provided interesting insights into microbial CoA metabolism. A succinyl-CoA synthase defective mutant of C. glutamicum exhibited an unaffected level of succinyl-CoA that indicated a complete compensation by the L-lysine pathway to bypass the disrupted TCA cycle. Methylmalonyl-CoA, an important building block of high-value polyketides, was identified as dominant CoA thioester in the actinomycete S. albus. The microbe revealed a more than 10,000-fold difference in the abundance of intracellular CoA thioesters. A recombinant strain of S. albus, which produced different derivatives of the antituberculosis polyketide pamamycin, revealed a significant depletion of CoA thioesters of the ethylmalonyl CoA pathway, influencing product level and spectrum. CONCLUSIONS The high relevance of short chain CoA thioesters to synthetize industrial products and the interesting insights gained from the examples shown in this work, suggest analyzing these metabolites in microbial cell factories more routinely than done so far. Due to its broad application range, the developed approach appears useful to be applied this purpose. Hereby, the possibility to use one single protocol promises to facilitate automatized efforts, which rely on standardized workflows.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Sofija Jovanovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michel Fritz
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J. Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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26
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Miller TE, Beneyton T, Schwander T, Diehl C, Girault M, McLean R, Chotel T, Claus P, Cortina NS, Baret JC, Erb TJ. Light-powered CO 2 fixation in a chloroplast mimic with natural and synthetic parts. Science 2020; 368:649-654. [PMID: 32381722 DOI: 10.1126/science.aaz6802] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.
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Affiliation(s)
- Tarryn E Miller
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Thomas Beneyton
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Thomas Schwander
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | | | - Richard McLean
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tanguy Chotel
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Peter Claus
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France. .,Institut Universitaire de France, Paris 75005, France
| | - 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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27
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Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ. The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. J Biol Chem 2020; 295:2822-2838. [PMID: 31969391 DOI: 10.1074/jbc.ra119.011277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-l-2,4-diaminobutyrate (N-γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ-ADABA but not the ectoine catabolic intermediate N-α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
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Affiliation(s)
- Alexandra A Richter
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany; Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany; Institute of Biochemistry, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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28
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Spieker M, Saleem-Batcha R, Teufel R. Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. ACS Chem Biol 2019; 14:2876-2886. [PMID: 31689071 DOI: 10.1021/acschembio.9b00742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous aromatic compounds are aerobically degraded in bacteria via the central intermediate phenylacetic acid (paa). In one of the key steps of this widespread catabolic pathway, 1,2-epoxyphenylacetyl-CoA is converted by PaaG into the heterocyclic oxepin-CoA. PaaG thereby elegantly generates an α,β-unsaturated CoA ester that is predisposed to undergo β-oxidation subsequent to hydrolytic ring-cleavage. Moreover, oxepin-CoA serves as a precursor for secondary metabolites (e.g., tropodithietic acid) that act as antibiotics and quorum-sensing signals. Here we verify that PaaG adopts a second role in aromatic catabolism by converting cis-3,4-didehydroadipoyl-CoA into trans-2,3-didehydroadipoyl-CoA and corroborate a Δ3,Δ2-enoyl-CoA isomerase-like proton shuttling mechanism for both distinct substrates. Biochemical and structural investigations of PaaG reveal active site adaptations to the structurally different substrates and provide detailed insight into catalysis and control of stereospecificity. This work elucidates the mechanism of action of unusual isomerase PaaG and sheds new light on the ubiquitous enoyl-CoA isomerases of the crotonase superfamily.
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Affiliation(s)
- Melanie Spieker
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Raspudin Saleem-Batcha
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Robin Teufel
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
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29
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Reiter S, Cahn JKB, Wiebach V, Ueoka R, Piel J. Characterization of an Orphan Type III Polyketide Synthase Conserved in Uncultivated "Entotheonella" Sponge Symbionts. Chembiochem 2019; 21:564-571. [PMID: 31430416 PMCID: PMC7064976 DOI: 10.1002/cbic.201900352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/19/2019] [Indexed: 02/06/2023]
Abstract
Uncultivated bacterial symbionts from the candidate genus "Entotheonella" have been shown to produce diverse natural products previously attributed to their sponge hosts. In addition to these known compounds, "Entotheonella" genomes contain rich sets of biosynthetic gene clusters that lack identified natural products. Among these is a small type III polyketide synthase (PKS) cluster, one of only three clusters present in all known "Entotheonella" genomes. This conserved "Entotheonella" PKS (cep) cluster encodes the type III PKS CepA and the putative methyltransferase CepB. Herein, the characterization of CepA as an enzyme involved in phenolic lipid biosynthesis is reported. In vitro analysis showed a specificity for alkyl starter substrates and the production of tri- and tetraketide pyrones and tetraketide resorcinols. The conserved distribution of the cep cluster suggests an important role for the phenolic lipid polyketides produced in "Entotheonella" variants.
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Affiliation(s)
- Silke Reiter
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jackson K B Cahn
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Vincent Wiebach
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Reiko Ueoka
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jörn Piel
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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30
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The synthesis of branched-chain fatty acids is limited by enzymatic decarboxylation of ethyl- and methylmalonyl-CoA. Biochem J 2019; 476:2427-2447. [PMID: 31416829 PMCID: PMC6717113 DOI: 10.1042/bcj20190500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022]
Abstract
Most fatty acids (FAs) are straight chains and are synthesized by fatty acid synthase (FASN) using acetyl-CoA and malonyl-CoA units. Yet, FASN is known to be promiscuous as it may use methylmalonyl-CoA instead of malonyl-CoA and thereby introduce methyl-branches. We have recently found that the cytosolic enzyme ECHDC1 degrades ethylmalonyl-CoA and methylmalonyl-CoA, which presumably result from promiscuous reactions catalyzed by acetyl-CoA carboxylase on butyryl- and propionyl-CoA. Here, we tested the hypothesis that ECHDC1 is a metabolite repair enzyme that serves to prevent the formation of methyl- or ethyl-branched FAs by FASN. Using the purified enzyme, we found that FASN can incorporate not only methylmalonyl-CoA but also ethylmalonyl-CoA, producing methyl- or ethyl-branched FAs. Using a combination of gas-chromatography and liquid chromatography coupled to mass spectrometry, we observed that inactivation of ECHDC1 in adipocytes led to an increase in several methyl-branched FAs (present in different lipid classes), while its overexpression reduced them below wild-type levels. In contrast, the formation of ethyl-branched FAs was observed almost exclusively in ECHDC1 knockout cells, indicating that ECHDC1 and the low activity of FASN toward ethylmalonyl-CoA efficiently prevent their formation. We conclude that ECHDC1 performs a typical metabolite repair function by destroying methyl- and ethylmalonyl-CoA. This reduces the formation of methyl-branched FAs and prevents the formation of ethyl-branched FAs by FASN. The identification of ECHDC1 as a key modulator of the abundance of methyl-branched FAs opens the way to investigate their function.
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31
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Kremer K, van Teeseling MCF, Schada von Borzyskowski L, Bernhardsgrütter I, van Spanning RJM, Gates AJ, Remus-Emsermann MNP, Thanbichler M, Erb TJ. Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. mBio 2019; 10:e00805-19. [PMID: 31289174 PMCID: PMC6747724 DOI: 10.1128/mbio.00805-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/21/2022] Open
Abstract
During growth, microorganisms have to balance metabolic flux between energy and biosynthesis. One of the key intermediates in central carbon metabolism is acetyl coenzyme A (acetyl-CoA), which can be either oxidized in the citric acid cycle or assimilated into biomass through dedicated pathways. Two acetyl-CoA assimilation strategies in bacteria have been described so far, the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). Here, we show that Paracoccus denitrificans uses both strategies for acetyl-CoA assimilation during different growth stages, revealing an unexpected metabolic complexity in the organism's central carbon metabolism. The EMCP is constitutively expressed on various substrates and leads to high biomass yields on substrates requiring acetyl-CoA assimilation, such as acetate, while the GC is specifically induced on these substrates, enabling high growth rates. Even though each acetyl-CoA assimilation strategy alone confers a distinct growth advantage, P. denitrificans recruits both to adapt to changing environmental conditions, such as a switch from succinate to acetate. Time-resolved single-cell experiments show that during this switch, expression of the EMCP and GC is highly coordinated, indicating fine-tuned genetic programming. The dynamic metabolic rewiring of acetyl-CoA assimilation is an evolutionary innovation by P. denitrificans that allows this organism to respond in a highly flexible manner to changes in the nature and availability of the carbon source to meet the physiological needs of the cell, representing a new phenomenon in central carbon metabolism.IMPORTANCE Central carbon metabolism provides organisms with energy and cellular building blocks during growth and is considered the invariable "operating system" of the cell. Here, we describe a new phenomenon in bacterial central carbon metabolism. In contrast to many other bacteria that employ only one pathway for the conversion of the central metabolite acetyl-CoA, Paracoccus denitrificans possesses two different acetyl-CoA assimilation pathways. These two pathways are dynamically recruited during different stages of growth, which allows P. denitrificans to achieve both high biomass yield and high growth rates under changing environmental conditions. Overall, this dynamic rewiring of central carbon metabolism in P. denitrificans represents a new strategy compared to those of other organisms employing only one acetyl-CoA assimilation pathway.
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Affiliation(s)
- Katharina Kremer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | | | | | - Rob J M van Spanning
- Department of Molecular Cell Biology, Vrije Universiteit, HV, Amsterdam, The Netherlands
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Martin Thanbichler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
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32
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Four amino acids define the CO 2 binding pocket of enoyl-CoA carboxylases/reductases. Proc Natl Acad Sci U S A 2019; 116:13964-13969. [PMID: 31243147 PMCID: PMC6628652 DOI: 10.1073/pnas.1901471116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carboxylases capture and convert CO2, which makes them key enzymes in photosynthesis and the global carbon cycle. However, the question how enzymes bind atmospheric CO2 is still unsolved. We studied enoyl-CoA carboxylases/reductases (Ecrs), the fastest CO2-fixing enzymes in nature, using structural biology, biochemistry, and advanced computational methods. Ecrs create a highly specific CO2-binding pocket with 4 amino acids at the active site. The pocket controls the fate of the gaseous molecule during catalysis and shields the catalytic center from oxygen and water. This exquisite control makes Ecrs highly efficient carboxylases outcompeting RuBisCO, the key enzyme of photosynthesis, by an order of magnitude. Our findings define the atomic framework for the future development of CO2-converting catalysts in biology and chemistry. Carboxylases are biocatalysts that capture and convert carbon dioxide (CO2) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO2 molecule during catalysis is only poorly understood. One of the most efficient classes of carboxylating enzymes are enoyl-CoA carboxylases/reductases (Ecrs), which outcompete the plant enzyme RuBisCO in catalytic efficiency and fidelity by more than an order of magnitude. Here we investigated the interactions of CO2 within the active site of Ecr from Kitasatospora setae. Combining experimental biochemistry, protein crystallography, and advanced computer simulations we show that 4 amino acids, N81, F170, E171, and H365, are required to create a highly efficient CO2-fixing enzyme. Together, these 4 residues anchor and position the CO2 molecule for the attack by a reactive enolate created during the catalytic cycle. Notably, a highly ordered water molecule plays an important role in an active site that is otherwise carefully shielded from water, which is detrimental to CO2 fixation. Altogether, our study reveals unprecedented molecular details of selective CO2 binding and C–C-bond formation during the catalytic cycle of nature’s most efficient CO2-fixing enzyme. This knowledge provides the basis for the future development of catalytic frameworks for the capture and conversion of CO2 in biology and chemistry.
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33
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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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34
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The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat Chem Biol 2018; 14:1127-1132. [PMID: 30374166 DOI: 10.1038/s41589-018-0153-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022]
Abstract
Cells must cope with toxic or reactive intermediates formed during metabolism. One coping strategy is to sequester reactions that produce such intermediates within specialized compartments or tunnels connecting different active sites. Here, we show that propionyl-CoA synthase (PCS), an ∼ 400-kDa homodimer, three-domain fusion protein and the key enzyme of the 3-hydroxypropionate bi-cycle for CO2 fixation, sequesters its reactive intermediate acrylyl-CoA. Structural analysis showed that PCS forms a multicatalytic reaction chamber. Kinetic analysis suggested that access to the reaction chamber and catalysis are synchronized by interdomain communication. The reaction chamber of PCS features three active sites and has a volume of only 33 nm3. As one of the smallest multireaction chambers described in biology, PCS may inspire the engineering of a new class of dynamically regulated nanoreactors.
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35
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Himmelberg AM, Brüls T, Farmani Z, Weyrauch P, Barthel G, Schrader W, Meckenstock RU. Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture. Environ Microbiol 2018; 20:3589-3600. [DOI: 10.1111/1462-2920.14335] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Anne M. Himmelberg
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope; Evry France
- CNRS-UMR8030; Université Paris-Saclay; Evry France
| | - Zahra Farmani
- Biofilm Centre; University of Duisburg-Essen; Essen Germany
- Max-Planck-Institut für Kohlenforschung; Mülheim Germany
| | | | - Gabriele Barthel
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
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36
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Vögeli B, Rosenthal RG, Stoffel GMM, Wagner T, Kiefer P, Cortina NS, Shima S, Erb TJ. InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis. J Biol Chem 2018; 293:17200-17207. [PMID: 30217823 PMCID: PMC6222099 DOI: 10.1074/jbc.ra118.005405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/09/2018] [Indexed: 11/06/2022] Open
Abstract
The enoyl-thioester reductase InhA catalyzes an essential step in fatty acid biosynthesis of Mycobacterium tuberculosis and is a key target of antituberculosis drugs to combat multidrug-resistant M. tuberculosis strains. This has prompted intense interest in the mechanism and intermediates of the InhA reaction. Here, using enzyme mutagenesis, NMR, stopped-flow spectroscopy, and LC-MS, we found that the NADH cofactor and the CoA thioester substrate form a covalent adduct during the InhA catalytic cycle. We used the isolated adduct as a molecular probe to directly access the second half-reaction of the catalytic cycle of InhA (i.e. the proton transfer), independently of the first half-reaction (i.e. the initial hydride transfer) and to assign functions to two conserved active-site residues, Tyr-158 and Thr-196. We found that Tyr-158 is required for the stereospecificity of protonation and that Thr-196 is partially involved in hydride transfer and protonation. The natural tendency of InhA to form a covalent C2-ene adduct calls for a careful reconsideration of the enzyme's reaction mechanism. It also provides the basis for the development of effective tools to study, manipulate, and inhibit the catalytic cycle of InhA and related enzymes of the short-chain dehydrogenase/reductase (SDR) superfamily. In summary, our work has uncovered the formation of a covalent adduct during the InhA catalytic cycle and identified critical residues required for catalysis, providing further insights into the InhA reaction mechanism important for the development of antituberculosis drugs.
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Affiliation(s)
- Bastian Vögeli
- From the Departments of Biochemistry and Synthetic Metabolism and
| | | | | | - Tristan Wagner
- Microbial Protein Structure, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany and
| | - Patrick Kiefer
- the Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Seigo Shima
- Microbial Protein Structure, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany and
| | - Tobias J Erb
- From the Departments of Biochemistry and Synthetic Metabolism and
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37
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Vögeli B, Geyer K, Gerlinger PD, Benkstein S, Cortina NS, Erb TJ. Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. Cell Chem Biol 2018; 25:833-839.e4. [PMID: 29731424 DOI: 10.1016/j.chembiol.2018.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
The incorporation of different extender units generates structural diversity in polyketides. There is significant interest in engineering substrate specificity of polyketide synthases (PKSs) to change their chemical structure. Efforts to change extender unit selectivity are hindered by the lack of simple screening methods and easily available atypical extender units. Here, we present a chemo-biosynthetic strategy that employs biocatalytic proofreading and allows access to a large variety of extender units. First, saturated acids are chemically coupled to free coenzyme A (CoA). The corresponding acyl-CoAs are then converted to alkylmalonyl-CoAs in a "one-pot" reaction through the combined action of an acyl-CoA oxidase and enoyl-CoA carboxylase/reductase. We synthesized six different extender units and used them in in vitro competition screens to investigate active site residues conferring extender unit selectivity. Our results show the importance of an uncharacterized glutamine in extender unit selectivity and open the possibility for comprehensive studies on extender incorporation in PKSs.
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Affiliation(s)
- Bastian Vögeli
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Kyra Geyer
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Patrick D Gerlinger
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Sarah Benkstein
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
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38
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Krink-Koutsoubelis N, Loechner AC, Lechner A, Link H, Denby CM, Vögeli B, Erb TJ, Yuzawa S, Jakociunas T, Katz L, Jensen MK, Sourjik V, Keasling JD. Engineered Production of Short-Chain Acyl-Coenzyme A Esters in Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:1105-1115. [PMID: 29498824 DOI: 10.1021/acssynbio.7b00466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Short-chain acyl-coenzyme A esters serve as intermediate compounds in fatty acid biosynthesis, and the production of polyketides, biopolymers and other value-added chemicals. S. cerevisiae is a model organism that has been utilized for the biosynthesis of such biologically and economically valuable compounds. However, its limited repertoire of short-chain acyl-CoAs effectively prevents its application as a production host for a plethora of natural products. Therefore, we introduced biosynthetic metabolic pathways to five different acyl-CoA esters into S. cerevisiae. Our engineered strains provide the following acyl-CoAs: propionyl-CoA, methylmalonyl-CoA, n-butyryl-CoA, isovaleryl-CoA and n-hexanoyl-CoA. We established a yeast-specific metabolite extraction protocol to determine the intracellular acyl-CoA concentrations in the engineered strains. Propionyl-CoA was produced at 4-9 μM; methylmalonyl-CoA at 0.5 μM; and isovaleryl-CoA, n-butyryl-CoA, and n-hexanoyl-CoA at 6 μM each. The acyl-CoAs produced in this study are common building blocks of secondary metabolites and will enable the engineered production of a variety of natural products in S. cerevisiae. By providing this toolbox of acyl-CoA producing strains, we have laid the foundation to explore S. cerevisiae as a heterologous production host for novel secondary metabolites.
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Affiliation(s)
- Nicolas Krink-Koutsoubelis
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Anne C. Loechner
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Anna Lechner
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Charles M. Denby
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Tobias J. Erb
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tadas Jakociunas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Leonard Katz
- Synthetic Biology Engineering Research Center, Emeryville, California 94608, United States
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Synthetic Biology Engineering Research Center, Emeryville, California 94608, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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39
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Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates. Methods Enzymol 2018; 604:333-366. [PMID: 29779658 DOI: 10.1016/bs.mie.2018.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Flavin-adenine dinucleotide (FAD)-dependent halogenases are widespread in natural product biosynthetic gene clusters and have been demonstrated to employ small organic molecules as substrates for halogenation, as well as substrates that are tethered to carrier proteins (CPs). Despite numerous reports of FAD-dependent halogenases utilizing CP-tethered substrates, only a few have been biochemically characterized due to limited accessibility to the physiological substrates. Here, we describe a method for the preparation of acyl-S-CP substrates and their use in biochemical assays to query the activity of FAD-dependent halogenases. Furthermore, we describe a mass spectrometry-based method for the characterization of acyl-S-CP substrates and the corresponding halogenated products generated by the halogenases. Finally, we test the substrate specificity of a physiological chlorinase and a physiological brominase from marine bacteria, and, for the first time, demonstrate the distinct halide specificity of halogenases. The methodology described here will enable characterization of new halogenases employing CP-tethered substrates.
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40
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Becher E, Heese A, Claußen L, Eisen S, Jehmlich N, Rohwerder T, Purswani J. Active site alanine preceding catalytic cysteine determines unique substrate specificity in bacterial CoA-acylating prenal dehydrogenase. FEBS Lett 2018; 592:1150-1160. [PMID: 29485713 DOI: 10.1002/1873-3468.13019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/08/2018] [Accepted: 02/19/2018] [Indexed: 11/06/2022]
Abstract
In detoxification and fermentation processes, acylating dehydrogenases catalyze the reversible oxidation of aldehydes to their corresponding acyl-CoA esters. Here, we characterize an enzyme from Aquincola tertiaricarbonis L108 responsible for prenal (3-methyl-2-butenal) to 3-methylcrotonyl-CoA oxidation. Enzyme kinetics demonstrate a preference for C5 substrates not yet observed in aldehyde dehydrogenases. Compared to acetaldehyde and acetyl-CoA, conversion of valeraldehyde and valeryl-CoA is > 100- and 8-fold more efficient, respectively. Enzyme variants with A254I, A254P, and A254G mutations indicate that active site Ala preceding the catalytic C255 is crucial for this unique specificity. These results shed new light on evolutionary adaptation of aldehyde dehydrogenases toward xenobiotics and structure-guided design of highly specific enzymes for production of biofuels, such as linear or iso-branched butanols and pentanols.
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Affiliation(s)
- Ellen Becher
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Alexander Heese
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Laura Claußen
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sebastian Eisen
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jessica Purswani
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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41
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Molecular Basis for Converting (2S)-Methylsuccinyl-CoA Dehydrogenase into an Oxidase. Molecules 2017; 23:molecules23010068. [PMID: 29283425 PMCID: PMC6017585 DOI: 10.3390/molecules23010068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 11/17/2022] Open
Abstract
Although flavoenzymes have been studied in detail, the molecular basis of their dioxygen reactivity is only partially understood. The members of the flavin adenosine dinucleotide (FAD)-dependent acyl-CoA dehydrogenase and acyl-CoA oxidase families catalyze similar reactions and share common structural features. However, both enzyme families feature opposing reaction specificities in respect to dioxygen. Dehydrogenases react with electron transfer flavoproteins as terminal electron acceptors and do not show a considerable reactivity with dioxygen, whereas dioxygen serves as a bona fide substrate for oxidases. We recently engineered (2S)-methylsuccinyl-CoA dehydrogenase towards oxidase activity by rational mutagenesis. Here we characterized the (2S)-methylsuccinyl-CoA dehydrogenase wild-type, as well as the engineered (2S)-methylsuccinyl-CoA oxidase, in detail. Using stopped-flow UV-spectroscopy and liquid chromatography-mass spectrometry (LC-MS) based assays, we explain the molecular base for dioxygen reactivity in the engineered oxidase and show that the increased oxidase function of the engineered enzyme comes at a decreased dehydrogenase activity. Our findings add to the common notion that an increased activity for a specific substrate is achieved at the expense of reaction promiscuity and provide guidelines for rational engineering efforts of acyl-CoA dehydrogenases and oxidases.
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42
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Schwander T, McLean R, Zarzycki J, Erb TJ. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J Biol Chem 2017; 293:1702-1712. [PMID: 29275330 PMCID: PMC5798300 DOI: 10.1074/jbc.ra117.000764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to α,β-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 Å. The enzyme forms a homodimer of two 60-kDa subunits. Compared with other ACDs, MCD contains an ∼170-residue-long N-terminal extension that structurally mimics a dimer–dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an α-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homolog of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD toward succinyl-CoA through active-site mutagenesis.
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Affiliation(s)
- Thomas Schwander
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Richard McLean
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Jan Zarzycki
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Tobias J Erb
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and .,the LOEWE Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
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43
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Chou YL, Jhong Y, Swain SP, Hou DR. Microwave-Assisted Direct Thioesterification of Carboxylic Acids. J Org Chem 2017; 82:10201-10208. [PMID: 28875699 DOI: 10.1021/acs.joc.7b01705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A one-pot synthesis of thioesters directly from carboxylic acids, N,N'-diphenylthiourea, triethylamine, and primary alkyl halides is described. Microwave-assisted heating and a catalytic amount of 4-(dimethylamino)pyridine (DMAP) further improved the yields. Both aromatic and aliphatic carboxylic acids were converted to the corresponding thioesters, and many functional groups were compatible with this reaction. Several possible reaction intermediates were investigated, and the quaternary ammonium salts, derived from alkyl halides and tertiary amines, were the intermediates to yield thioesters. A new reaction mechanism for this thioesterification is proposed.
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Affiliation(s)
- Yen-Lin Chou
- Department of Chemistry, National Central University , No. 300 Jhong-Da Road, Jhong-li, Taoyuan, Taiwan 32001
| | - Yi Jhong
- Department of Chemistry, National Central University , No. 300 Jhong-Da Road, Jhong-li, Taoyuan, Taiwan 32001
| | - Sharada Prasanna Swain
- Department of Chemistry, National Central University , No. 300 Jhong-Da Road, Jhong-li, Taoyuan, Taiwan 32001
| | - Duen-Ren Hou
- Department of Chemistry, National Central University , No. 300 Jhong-Da Road, Jhong-li, Taoyuan, Taiwan 32001
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44
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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45
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Sanichar R, Vederas JC. One-Step Transformation of Coenzyme A into Analogues by Transamidation. Org Lett 2017; 19:1950-1953. [PMID: 28393528 DOI: 10.1021/acs.orglett.7b00291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several coenzyme A (CoA) analogues are made in a single step under mild conditions via transamidation reactions catalyzed by boric acid in water. This approach offers rapid access to compounds useful for the study of a wide spectrum of enzyme catalyzed reactions, especially processes involving acyl carrier proteins (ACP) of polyketide synthases (PKS), fatty acid synthases (FAS), and nonribosomal peptide synthetases (NRPS). The CoA analogues presented are readily elaborated or extended by precedented reactions for specific applications that may be required.
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Affiliation(s)
- Randy Sanichar
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - John C Vederas
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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46
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Zarzycki J, Sutter M, Cortina NS, Erb TJ, Kerfeld CA. In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment. Sci Rep 2017; 7:42757. [PMID: 28202954 PMCID: PMC5311937 DOI: 10.1038/srep42757] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/13/2017] [Indexed: 11/09/2022] Open
Abstract
Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO2-fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B12-dependent enzymes. Genes required to form BMCs are typically organized in gene clusters, which promoted their distribution across phyla by horizontal gene transfer. Recently, BMCs associated with glycyl radical enzymes (GREs) were discovered; these are widespread and comprise at least three functionally distinct types. Previously, we predicted one type of these GRE-associated microcompartments (GRMs) represents a B12-independent propanediol-utilizing BMC. Here we functionally and structurally characterize enzymes of the GRM of Rhodopseudomonas palustris BisB18 and demonstrate their concerted function in vitro. The GRM signature enzyme, the GRE, is a dedicated 1,2-propanediol dehydratase with a new type of intramolecular encapsulation peptide. It forms a complex with its activating enzyme and, in conjunction with an aldehyde dehydrogenase, converts 1,2-propanediol to propionyl-CoA. Notably, homologous GRMs are also encoded in pathogenic Escherichia coli strains. Our high-resolution crystal structures of the aldehyde dehydrogenase lead to a revised reaction mechanism. The successful in vitro reconstitution of a part of the GRM metabolism provides insights into the metabolic function and steps in the assembly of this BMC.
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Affiliation(s)
- Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Niña Socorro Cortina
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Tobias J Erb
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Biochemistry &Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Berkeley Synthetic Biology Institute, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
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47
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Becker T, Pasteels J, Weigel C, Dahse HM, Voigt K, Boland W. A tale of four kingdoms – isoxazolin-5-one- and 3-nitropropanoic acid-derived natural products. Nat Prod Rep 2017; 34:343-360. [DOI: 10.1039/c6np00122j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The occurrence, structural diversity, (bio-)synthesis, properties and detoxification mechanisms of isoxazolinone- and 3-nitropropanoic acid-derived natural compounds are reviewed.
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Affiliation(s)
- Tobias Becker
- Department of Bioorganic Chemistry
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
| | - Jacques Pasteels
- Department of Biology
- Université Libre de Bruxelles
- Brussels
- Belgium
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
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48
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Schwander T, Schada von Borzyskowski L, Burgener S, Cortina NS, Erb TJ. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 2016; 354:900-904. [PMID: 27856910 PMCID: PMC5892708 DOI: 10.1126/science.aah5237] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/05/2016] [Indexed: 01/20/2023]
Abstract
Carbon dioxide (CO2) is an important carbon feedstock for a future green economy. This requires the development of efficient strategies for its conversion into multicarbon compounds. We describe a synthetic cycle for the continuous fixation of CO2 in vitro. The crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle is a reaction network of 17 enzymes that converts CO2 into organic molecules at a rate of 5 nanomoles of CO2 per minute per milligram of protein. The CETCH cycle was drafted by metabolic retrosynthesis, established with enzymes originating from nine different organisms of all three domains of life, and optimized in several rounds by enzyme engineering and metabolic proofreading. The CETCH cycle adds a seventh, synthetic alternative to the six naturally evolved CO2 fixation pathways, thereby opening the way for in vitro and in vivo applications.
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Affiliation(s)
- Thomas Schwander
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Lennart Schada von Borzyskowski
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Simon Burgener
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany.
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
- LOEWE Center for Synthetic Microbiology, Universität Marburg, D-35037 Marburg, Germany
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