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Decker RL, Schray D, Pfeffer HI, Grond S, Wagner JP. Conformations and Rearrangements of Collinolactone - Experiments and Theory on a Dynamic Cyclodecatriene. Chemistry 2024; 30:e202303435. [PMID: 38051282 DOI: 10.1002/chem.202303435] [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: 10/18/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Collinolactone A is a microbial specialized metabolite with a unique 6-10-7 tricyclic bislactone skeleton which was isolated from Streptomyces bacteria. The unusual cyclodecatriene motif features dynamic interconversions of two rotamers. Given the biological profiling of collinolactone A as neuroprotective agent, semisynthetic modifications represent an invaluable strategy to enhance its efficacy. Since understanding conformations and reactions of bioactive substances is crucial for rational structure-based design and synthesis of derivatives, we conducted computational studies on conformational behavior as well as experiments on thermal and acid induced rearrangements of the cyclodecatriene. Experimental conformer ratios of collinolactone A and its biosynthetic ketolactone precursor are well reproduced by computations at the PW6B95-D3/def2-QZVPP//r2 SCAN-3c level. Upon heating collinolactone A in anhydrous dioxane at 100 °C, three collinolactone B stereoisomers exhibiting enollactone structures form via Cope rearrangements. Our computations predict the energetic preference for a boat-like transition state in agreement with the stereochemical outcome of the main reaction pathway. Constriction of the ten-membered ring forms collinolactone C with four annulated rings and an exocyclic double bond. Computations and semisynthetic experiments demonstrate strong preference for an acid-catalyzed reaction pathway over an alternative Alder-ene route to collinolactone C with a prohibitive reaction barrier, again in line with stereochemical observations.
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Affiliation(s)
- Rhena L Decker
- Organic and Biomolecular Chemistry, Institut für Organische Chemie, Eberhard Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - David Schray
- Organic and Computational Chemistry, Institut für Organische Chemie, Eberhard Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Heiko I Pfeffer
- Organic and Computational Chemistry, Institut für Organische Chemie, Eberhard Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Stephanie Grond
- Organic and Biomolecular Chemistry, Institut für Organische Chemie, Eberhard Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - J Philipp Wagner
- Organic and Computational Chemistry, Institut für Organische Chemie, Eberhard Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
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Zhang Y, Kashkooli AB, Blom S, Zhao T, Bouwmeester HJ, Kappers IF. The Capsicum terpenoid biosynthetic module is affected by spider-mite herbivory. PLANT MOLECULAR BIOLOGY 2023; 113:303-321. [PMID: 37995005 PMCID: PMC10721696 DOI: 10.1007/s11103-023-01390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
In response to herbivory, Capsicum annuum leaves adapt their specialized metabolome that may protect the plant against herbivore feeding either directly or indirectly through volatile metabolites acting as cues for natural enemies of the herbivore. The volatile blend of spider-mite infested leaves differs from non-challenged leaves predominantly by a higher contribution of mono- and sesquiterpenes. In addition to these terpenoids released into the headspace, the terpenoid composition of the leaves alters upon herbivory. All this suggests an important role for terpenoids and their biosynthetic machinery in the defence against herbivory. Here, we show that the C. annuum genome contains a terpene synthase (TPS) gene family of 103 putative members of which structural analysis revealed that 27 encode functional enzymes. Transcriptome analysis showed that several TPS loci were differentially expressed upon herbivory in leaves of two C. annuum genotypes, that differ in susceptibility towards spider mites. The relative expression of upstream biosynthetic genes from the mevalonate and the methylerythritol phosphate pathway also altered upon herbivory, revealing a shift in the metabolic flux through the terpene biosynthetic module. The expression of multiple genes potentially acting downstream of the TPSs, including cytochrome P450 monooxygenases, UDP-glucosyl transferases, and transcription factors strongly correlated with the herbivory-induced TPS genes. A selection of herbivory-induced TPS genes was functionally characterized through heterologous expression and the products that these enzymes catalysed matched with the volatile and non-volatile terpenoids induced in response to herbivory.
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Affiliation(s)
- Yuanyuan Zhang
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Arman B Kashkooli
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Tarbiat Modares University, Tehran, Iran
| | - Suze Blom
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics, Wageningen University, Wageningen, The Netherlands
- Northwest Agriculture and Forestry University, Xi'an, China
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iris F Kappers
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands.
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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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Xu H, Lauterbach L, Goldfuss B, Schnakenburg G, Dickschat JS. Fragmentation and [4 + 3] cycloaddition in sodorifen biosynthesis. Nat Chem 2023:10.1038/s41557-023-01223-z. [PMID: 37248344 DOI: 10.1038/s41557-023-01223-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Terpenes constitute the largest class of natural products. Their skeletons are formed by terpene cyclases (TCs) from acyclic oligoprenyl diphosphates through sophisticated enzymatic conversions. These enzyme reactions start with substrate ionization through diphosphate abstraction, followed by a cascade reaction via cationic intermediates. Based on isotopic-labelling experiments in combination with a computational study, the cyclization mechanism for sodorifen, a highly methylated sesquiterpene from the soil bacterium Serratia plymuthica, was resolved. A peculiar problem in its biosynthesis lies in the formation of several methyl groups from chain methylene carbons. The underlying mechanism involves a methyltransferase-mediated cyclization and unprecedented ring contraction with carbon extrusion from the chain to form a methyl group. A terpene cyclase subsequently catalyses a fragmentation into two reactive intermediates, followed by hydrogen transfers between them and recombination of the fragments by [4 + 3] cycloaddition. This study solves the intricate mechanistic problem of extra methyl group formation in sodorifen biosynthesis.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lukas Lauterbach
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Bernd Goldfuss
- Institut für Organische Chemie, Universität zu Köln, Köln, Germany
| | - Gregor Schnakenburg
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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Amariei DA, Pozhydaieva N, David B, Schneider P, Classen T, Gohlke H, Weiergräber OH, Pietruszka J. Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD─Crystal Structure, Catalytic Mechanism, and Preparative Applications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Diana A. Amariei
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Nadiia Pozhydaieva
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Benoit David
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
| | - Pascal Schneider
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
- Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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Piechulla B, Zhang C, Eisenschmidt-Bönn D, Chen F, Magnus N. Non-canonical substrates for terpene synthases in bacteria are synthesized by a new family of methyltransferases. FEMS Microbiol Rev 2021; 45:6232159. [PMID: 33864462 DOI: 10.1093/femsre/fuab024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/15/2021] [Indexed: 01/01/2023] Open
Abstract
The 'biogenetic isoprene rule', formulated in the mid 20th century, predicted that terpenoids are biosynthesized via polymerization of C5 isoprene units. The polymerizing enzymes have been identified to be isoprenyl diphosphate synthases, products of which are catalyzed by terpene synthases (TPSs) to achieve vast structural diversity of terpene skeletons. Irregular terpenes (e.g, C11, C12, C16, C17) are also frequently observed, and they have presumed to be synthesized by the modification of terpene skeletons. This review highlights the exciting discovery of an additional route to the biosynthesis of irregular terpenes which involves the action of a newly discovered enzyme family of isoprenyl diphosphate methyltransferases (IDMTs). These enzymes methylate, and sometimes cyclize, the classical isoprenyl diphosphate substrates to produce modified, non-canonical substrates for specifically evolved TPSs. So far, this new pathway has been found only in bacteria. Structure and sequence comparisons of the IDMTs strongly indicate a conservation of their active pockets and overall topologies. Some bacterial IDMTs and TPSs appear in small gene clusters, which may facilitate future mining of bacterial genomes for identification of irregular terpene-producing enzymes. The IDMT-TPS route for terpenoid biosynthesis presents another example of nature's ingenuity in creating chemical diversity, particularly terpenoids, for organismal fitness. IDMT isoprenyl diphosphate methyltransferases IDPMT isopentenyl diphosphate methyltransferase GDPMT geranyl diphosphate methyltransferase FDPMT farnesyl diphosphate methyltransferases BGC biosynthetic gene cluster TPS terpene synthase MIBS 2-methylisoborneol synthase MBS 2-methylenebornane synthase DMADP Dimethylallyl diphosphate SAM S-adenosyl-L-methionine.
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Affiliation(s)
- Birgit Piechulla
- University of Rostock, Institute for Biological Sciences, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Chi Zhang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniela Eisenschmidt-Bönn
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Nancy Magnus
- University of Rostock, Institute for Biological Sciences, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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