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Daniel-Ivad P, Ryan KS. Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine. J Biol Chem 2024; 300:105520. [PMID: 38042494 PMCID: PMC10784701 DOI: 10.1016/j.jbc.2023.105520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Bisindoles are biologically active natural products that arise from the oxidative dimerization of two molecules of l-tryptophan. In bacterial bisindole pathways, a core set of transformations is followed by the action of diverse tailoring enzymes that catalyze reactions that lead to diverse bisindole products. Among bisindoles, reductasporine is distinct due to its dimethylpyrrolinium structure. Its previously reported biosynthetic gene cluster encodes two unique tailoring enzymes, the imine reductase RedE and the dimethyltransferase RedM, which were shown to produce reductasporine from a common bisindole intermediate in recombinant E. coli. To gain more insight into the unique tailoring enzymes in reductasporine assembly, we reconstituted the biosynthetic pathway to reductasporine in vitro and then solved the 1.7 Å resolution structure of RedM. Our work reveals RedM adopts a variety of conformational changes with distinct open and closed conformations, and site-directed mutagenesis alongside sequence analysis identifies important active site residues. Finally, our work sets the stage for understanding how RedM evolved to react with a pyrrolinium scaffold and may enable the development of new dimethyltransferase catalysts.
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Affiliation(s)
- Phillip Daniel-Ivad
- Department of Chemistry, The University of British Columbia, Vancouver, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, Canada.
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2
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Ueoka R, Sondermann P, Leopold-Messer S, Liu Y, Suo R, Bhushan A, Vadakumchery L, Greczmiel U, Yashiroda Y, Kimura H, Nishimura S, Hoshikawa Y, Yoshida M, Oxenius A, Matsunaga S, Williamson RT, Carreira EM, Piel J. Genome-based discovery and total synthesis of janustatins, potent cytotoxins from a plant-associated bacterium. Nat Chem 2022; 14:1193-1201. [PMID: 36064972 PMCID: PMC7613652 DOI: 10.1038/s41557-022-01020-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Host-associated bacteria are increasingly being recognized as underexplored sources of bioactive natural products with unprecedented chemical scaffolds. A recently identified example is the plant-root-associated marine bacterium Gynuella sunshinyii of the chemically underexplored order Oceanospirillales. Its genome contains at least 22 biosynthetic gene clusters, suggesting a rich and mostly uncharacterized specialized metabolism. Here, in silico chemical prediction of a non-canonical polyketide synthase cluster has led to the discovery of janustatins, structurally unprecedented polyketide alkaloids with potent cytotoxicity that are produced in minute quantities. A combination of MS and two-dimensional NMR experiments, density functional theory calculations of 13C chemical shifts and semiquantitative interpretation of transverse rotating-frame Overhauser effect spectroscopy data were conducted to determine the relative configuration, which enabled the total synthesis of both enantiomers and assignment of the absolute configuration. Janustatins feature a previously unknown pyridodihydropyranone heterocycle and an unusual biological activity consisting of delayed, synchronized cell death at subnanomolar concentrations.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Philipp Sondermann
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yizhou Liu
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Rei Suo
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Lida Vadakumchery
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yoko Yashiroda
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiromi Kimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shinichi Nishimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yojiro Hoshikawa
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Annette Oxenius
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - R. Thomas Williamson
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Erick M. Carreira
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland,Correspondence and requests for materials should be addressed to J.P. or E.M.C.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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3
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Lao Y, Skiba MA, Chun SW, Narayan ARH, Smith JL. Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C-Methyltransferases. ACS Chem Biol 2022; 17:2088-2098. [PMID: 35594521 PMCID: PMC9462956 DOI: 10.1021/acschembio.2c00085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Installation of methyl groups can significantly improve the binding of small-molecule drugs to protein targets; however, site-selective methylation often presents a significant synthetic challenge. Metal- and S-adenosyl-methionine (SAM)-dependent methyltransferases (MTs) in natural-product biosynthetic pathways are powerful enzymatic tools for selective or chemically challenging C-methylation reactions. Each of these MTs selectively catalyzes one or two methyl transfer reactions. Crystal structures and biochemical assays of the Mn2+-dependent monomethyltransferase from the saxitoxin biosynthetic pathway (SxtA MT) revealed the structural basis for control of methylation extent. The SxtA monomethyltransferase was converted to a dimethyltransferase by modification of the metal binding site, addition of an active site base, and an amino acid substitution to provide space in the substrate pocket for two methyl substituents. A reciprocal change converted a related dimethyltransferase into a monomethyltransferase, supporting our hypothesis that steric hindrance can prevent a second methylation event. A novel understanding of MTs will accelerate the development of MT-based catalysts and MT engineering for use in small-molecule synthesis.
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Affiliation(s)
- Yongtong Lao
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Meredith A Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephanie W Chun
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L Smith
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Structure and mechanism for iterative amide N-methylation in the biosynthesis of channel-forming peptide cytotoxins. Proc Natl Acad Sci U S A 2022; 119:e2116578119. [PMID: 35316135 PMCID: PMC9060474 DOI: 10.1073/pnas.2116578119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The channel-forming proteusins are bacterial helical peptides that allow permeation of positively charged ions to influence membrane potential and cellular physiology. We biochemically characterize the effect of two critical posttranslational modifications on the secondary structure of the peptide substrate. We determine how a methyl group can be added to the side chains of D-Asn residues in a peptide substrate and show how flanking residues influence selectivity. These studies should foster the development of small-molecule peptide ion channels as therapeutics. The polytheonamides are highly modified and potent, cytotoxic peptides with a unique β-helical structure (helical diameter ∼4 Å) that affords selective membrane permeation of monovalent cations. Toxicity has been linked to promiscuous ion-channel behavior in studies of the prototypical polytheonamide B. Specific structural features of the β-helical toxins include, among other modifications, Cα-epimerizations and Nγ-methylations, which have been highlighted as the early-stage modifications most critical for β-helix formation. Here, we interrogate Cα-epimerization and Nγ-methylation to understand the importance of these modifications for secondary structure. We characterize the mechanism of Nγ-methylations on the amide side chains of D-Asn, an enzymatic modification with little biochemical precedent. Crystal structures of the AerE methyltransferase in complex with its epimerized peptide substrate and S-adenosyl-homocysteine reveal features of substrate recognition and an unexpected metal-ion that may mediate methyl transfer to the poorly nucleophilic amide. These studies provide a framework for the engineering of novel β-helical peptides with ion and membrane selectivity.
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5
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Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021; 38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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6
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Andler O, Kazmaier U. Total synthesis of apratoxin A and B using Matteson's homologation approach. Org Biomol Chem 2021; 19:4866-4870. [PMID: 33998628 DOI: 10.1039/d1ob00713k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Apratoxin A and B, two members of an interesting class of marine cyclodepsipeptides are synthesized in a straightforward manner via Matteson homologation. Starting from a chiral boronic ester, the polyketide fragment of the apratoxins was obtained via five successive homologation steps in an overall yield of 27% and very good diastereoselectivity. This approach is highly flexible and should allow modification also of this part of the natural products, while previous modifications have been carried out mainly in the peptide fragment.
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Affiliation(s)
- Oliver Andler
- Organic Chemistry, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany.
| | - Uli Kazmaier
- Organic Chemistry, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany.
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7
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Abt K, Castelo-Branco R, Leão PN. Biosynthesis of Chlorinated Lactylates in Sphaerospermopsis sp. LEGE 00249. JOURNAL OF NATURAL PRODUCTS 2021; 84:278-286. [PMID: 33444023 PMCID: PMC7923214 DOI: 10.1021/acs.jnatprod.0c00950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 05/14/2023]
Abstract
Lactylates are an important group of molecules in the food and cosmetic industries. A series of natural halogenated 1-lactylates, chlorosphaerolactylates (1-4), were recently reported from Sphaerospermopsis sp. LEGE 00249. Here, we identify the cly biosynthetic gene cluster, containing all the necessary functionalities for the biosynthesis of the natural lactylates, based on in silico analyses. Using a combination of stable isotope incorporation experiments and bioinformatic analysis, we propose that dodecanoic acid and pyruvate are the key building blocks in the biosynthesis of 1-4. We additionally report minor analogues of these molecules with varying alkyl chains. This work paves the way to accessing industrially relevant lactylates through pathway engineering.
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Affiliation(s)
- Kathleen Abt
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Institute
of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Raquel Castelo-Branco
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
| | - Pedro N. Leão
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
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8
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Skiba MA, Tran CL, Dan Q, Sikkema AP, Klaver Z, Gerwick WH, Sherman DH, Smith JL. Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis. Structure 2020; 28:63-74.e4. [PMID: 31785925 PMCID: PMC6949403 DOI: 10.1016/j.str.2019.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/06/2019] [Accepted: 11/08/2019] [Indexed: 12/19/2022]
Abstract
Natural product biosynthetic pathways are replete with enzymes repurposed for new catalytic functions. In some modular polyketide synthase (PKS) pathways, a GCN5-related N-acetyltransferase (GNAT)-like enzyme with an additional decarboxylation function initiates biosynthesis. Here, we probe two PKS GNAT-like domains for the dual activities of S-acyl transfer from coenzyme A (CoA) to an acyl carrier protein (ACP) and decarboxylation. The GphF and CurA GNAT-like domains selectively decarboxylate substrates that yield the anticipated pathway starter units. The GphF enzyme lacks detectable acyl transfer activity, and a crystal structure with an isobutyryl-CoA product analog reveals a partially occluded acyltransfer acceptor site. Further analysis indicates that the CurA GNAT-like domain also catalyzes only decarboxylation, and the initial acyl transfer is catalyzed by an unidentified enzyme. Thus, PKS GNAT-like domains are re-classified as GNAT-like decarboxylases. Two other decarboxylases, malonyl-CoA decarboxylase and EryM, reside on distant nodes of the superfamily, illustrating the adaptability of the GNAT fold.
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Affiliation(s)
- Meredith A Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Collin L Tran
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew P Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zachary Klaver
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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9
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Kishimoto S, Tsunematsu Y, Matsushita T, Hara K, Hashimoto H, Tang Y, Watanabe K. Functional and Structural Analyses of trans C-Methyltransferase in Fungal Polyketide Biosynthesis. Biochemistry 2019; 58:3933-3937. [DOI: 10.1021/acs.biochem.9b00702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Takuma Matsushita
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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10
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Liao J, Pang K, Sun G, Pai T, Hsu P, Lin J, Sun K, Hsieh C, Tang S. Chimeric 6-methylsalicylic acid synthase with domains of acyl carrier protein and methyltransferase from Pseudallescheria boydii shows novel biosynthetic activity. Microb Biotechnol 2019; 12:920-931. [PMID: 31199579 PMCID: PMC6681407 DOI: 10.1111/1751-7915.13445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 01/09/2023] Open
Abstract
Polyketides are important secondary metabolites, many of which exhibit potent pharmacological applications. Biosynthesis of polyketides is carried out by a single polyketide synthase (PKS) or multiple PKSs in successive elongations of enzyme-bound intermediates related to fatty acid biosynthesis. The polyketide gene PKS306 from Pseudallescheria boydii NTOU2362 containing domains of ketosynthase (KS), acyltransferase (AT), dehydratase (DH), acyl carrier protein (ACP) and methyltransferase (MT) was cloned in an attempt to produce novel chemical compounds, and this PKS harbouring green fluorescent protein (GFP) was expressed in Saccharomyces cerevisiae. Although fluorescence of GFP and fusion protein analysed by anti-GFP antibody were observed, no novel compound was detected. 6-methylsalicylic acid synthase (6MSAS) was then used as a template and engineered with PKS306 by combinatorial fusion. The chimeric PKS containing domains of KS, AT, DH and ketoreductase (KR) from 6MSAS with ACP and MT from PKS306 demonstrated biosynthesis of a novel compound. The compound was identified with a deduced chemical formula of C7 H10 O3 , and the chemical structure was named as 2-hydroxy-2-(propan-2-yl) cyclobutane-1,3-dione. The novel compound synthesized by the chimeric PKS in this study demonstrates the feasibility of combinatorial fusion of PKS genes to produce novel polyketides.
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Affiliation(s)
- Ji‐Long Liao
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Ka‐Lai Pang
- Department of Marine BiologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Guang‐Huan Sun
- Division of UrologyDepartment of SurgeryNational Defense Medical CenterTri‐Service General HospitalNo. 325, Sec. 2, Cheng‐gong Rd.TaipeiTaiwan
| | - Tun‐Wen Pai
- Department of Computer Science and EngineeringNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Pang‐Hung Hsu
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Jyuan‐Siou Lin
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Kuang‐Hui Sun
- Department of Biotechnology and Laboratory Science in MedicineNational Yang‐Ming UniversityNo. 155, Sec. 2, Linong StreetTaipeiTaiwan
- Department of Education and ResearchTaipei City HospitalTaipeiTaiwan
| | | | - Shye‐Jye Tang
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
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Abstract
Stereospecific generation of α-amino ketones from common α-amino acids is difficult to achieve, often employing superstoichiometric alkylating reagents and requiring multiple protecting group manipulations. In contrast, the α-oxoamine synthase protein family performs this transformation stereospecifically in a single step without the need for protecting groups. Herein, we detail the characterization of the 8-amino-7-oxononanoate synthase (AONS) domain of the four-domain polyketide-like synthase SxtA, which natively mediates the formation of the ethyl ketone derivative of arginine. The function of each of the four domains is elucidated, leading to a revised proposal for the initiation of saxitoxin biosynthesis, a potent neurotoxin. We also demonstrate the synthetic potential of SxtA AONS, which is applied to the synthesis of a panel of novel α-amino ketones.
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Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA.,Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA.,Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
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12
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Via CW, Glukhov E, Costa S, Zimba PV, Moeller PDR, Gerwick WH, Bertin MJ. The Metabolome of a Cyanobacterial Bloom Visualized by MS/MS-Based Molecular Networking Reveals New Neurotoxic Smenamide Analogs (C, D, and E). Front Chem 2018; 6:316. [PMID: 30094232 PMCID: PMC6071517 DOI: 10.3389/fchem.2018.00316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 11/29/2022] Open
Abstract
Members of the cyanobacterial genus Trichodesmium are well known for their substantial impact on nitrogen influx in ocean ecosystems and the enormous surface blooms they form in tropical and subtropical locations. However, the secondary metabolite composition of these complex environmental bloom events is not well known, nor the possibility of the production of potent toxins that have been observed in other bloom-forming marine and freshwater cyanobacteria species. In the present work, we aimed to characterize the metabolome of a Trichodesmium bloom utilizing MS/MS-based molecular networking. Furthermore, we integrated cytotoxicity assays in order to identify and ultimately isolate potential cyanotoxins from the bloom. These efforts led to the isolation and identification of several members of the smenamide family, including three new smenamide analogs (1-3) as well as the previously reported smenothiazole A-hybrid polyketide-peptide compounds. Two of these new smenamides possessed cytotoxicity to neuro-2A cells (1 and 3) and their presence elicits further questions as to their potential ecological roles. HPLC profiling and molecular networking of chromatography fractions from the bloom revealed an elaborate secondary metabolome, generating hypotheses with respect to the environmental role of these metabolites and the consistency of this chemical composition across genera, space and time.
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Affiliation(s)
- Christopher W. Via
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Samuel Costa
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Paul V. Zimba
- Center for Coastal Studies and Department of Life Sciences, Texas A&M Corpus Christi, Corpus Christi, TX, United States
| | - Peter D. R. Moeller
- Emerging Toxins Program, Hollings Marine Laboratory, National Ocean Service/NOAA, Charleston, SC, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Matthew J. Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
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Skiba MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. ACS Chem Biol 2018; 13:1640-1650. [PMID: 29701944 PMCID: PMC6003868 DOI: 10.1021/acschembio.8b00252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.
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Affiliation(s)
- Meredith A Skiba
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Andrew P Sikkema
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew N Lowell
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Rebecca M Sturgis
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - David H Sherman
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Microbiology and Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Janet L Smith
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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Chun SW, Hinze ME, Skiba MA, Narayan ARH. Chemistry of a Unique Polyketide-like Synthase. J Am Chem Soc 2018; 140:2430-2433. [PMID: 29390180 DOI: 10.1021/jacs.7b13297] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Like many complex natural products, the intricate architecture of saxitoxin (STX) has hindered full exploration of this scaffold's utility as a tool for studying voltage-gated sodium ion channels and as a pharmaceutical agent. Established chemical strategies can provide access to the natural product; however, a chemoenzymatic route to saxitoxin that could provide expedited access to related compounds has not been devised. The first step toward realizing a chemoenzymatic approach toward this class of molecules is the elucidation of the saxitoxin biosynthetic pathway. To date, a biochemical link between STX and its putative biosynthetic enzymes has not been demonstrated. Herein, we report the first biochemical characterization of any enzyme involved in STX biosynthesis. Specifically, the chemical functions of a polyketide-like synthase, SxtA, from the cyanobacteria Cylindrospermopsis raciborskii T3 are elucidated. This unique megasynthase is comprised of four domains: methyltransferase (MT), GCN5-related N-acetyltransferase (GNAT), acyl carrier protein (ACP), and the first example of an 8-amino-7-oxononanoate synthase (AONS) associated with a multidomain synthase. We have established that this single polypeptide carries out the formation of two carbon-carbon bonds, two decarboxylation events and a stereospecific protonation to afford the linear biosynthetic precursor to STX (4). The synthetic utility of the SxtA AONS is demonstrated by the synthesis of a suite of α-amino ketones from the corresponding α-amino acid in a single step.
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Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Meagan E Hinze
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Meredith A Skiba
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Alison R H Narayan
- Department of Chemistry, ‡Life Sciences Institute, §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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