1
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McCauley M, Huston M, Condren AR, Pereira F, Cline J, Yaple-Maresh M, Painter MM, Zimmerman GE, Robertson AW, Carney N, Goodall C, Terry V, Müller R, Sherman DH, Collins KL. Structure-Activity Relationships of Natural and Semisynthetic Plecomacrolides Suggest Distinct Pathways for HIV-1 Immune Evasion and Vacuolar ATPase-Dependent Lysosomal Acidification. J Med Chem 2024. [PMID: 38452116 DOI: 10.1021/acs.jmedchem.3c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The human immunodeficiency virus (HIV)-encoded accessory protein Nef enhances pathogenicity by reducing major histocompatibility complex I (MHC-I) cell surface expression, protecting HIV-infected cells from immune recognition. Nef-dependent downmodulation of MHC-I can be reversed by subnanomolar concentrations of concanamycin A (1), a well-known inhibitor of vacuolar ATPase, at concentrations below those that interfere with lysosomal acidification or degradation. We conducted a structure-activity relationship study that assessed 76 compounds for Nef inhibition, 24 and 72 h viability, and lysosomal neutralization in Nef-expressing primary T cells. This analysis demonstrated that the most potent compounds were natural concanamycins and their derivatives. Comparison against a set of new, semisynthetic concanamycins revealed that substituents at C-8 and acylation of C-9 significantly affected Nef potency, target cell viability, and lysosomal neutralization. These findings provide important progress toward understanding the mechanism of action of these compounds and the identification of an advanced lead anti-HIV Nef inhibitory compound.
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Affiliation(s)
- Morgan McCauley
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Matthew Huston
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Alanna R Condren
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Filipa Pereira
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Joel Cline
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Marianne Yaple-Maresh
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Mark M Painter
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
| | - Gretchen E Zimmerman
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Andrew W Robertson
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan Natural Products Discovery Core, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Nolan Carney
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Christopher Goodall
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Valeri Terry
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken 66123, Germany
| | - David H Sherman
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Medicinal Chemistry, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Kathleen L Collins
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
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2
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McCullough TM, Dhar A, Akey DL, Konwerski JR, Sherman DH, Smith JL. Structure of a modular polyketide synthase reducing region. Structure 2023; 31:1109-1120.e3. [PMID: 37348494 PMCID: PMC10527585 DOI: 10.1016/j.str.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The chemical scaffolds of numerous therapeutics are polyketide natural products, many formed by bacterial modular polyketide synthases (PKS). The large and flexible dimeric PKS modules have distinct extension and reducing regions. Structures are known for all individual enzyme domains and several extension regions. Here, we report the structure of the full reducing region from a modular PKS, the ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) domains of module 5 of the juvenimicin PKS. The modular PKS-reducing region has a different architecture than the homologous fatty acid synthase (FAS) and iterative PKS systems in its arrangement of domains and dimer interface. The structure reveals a critical role for linker peptides in the domain interfaces, leading to discovery of key differences in KR domains dependent on module composition. Finally, our studies provide insight into the mechanism underlying modular PKS intermediate shuttling by carrier protein (ACP) domains.
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Affiliation(s)
- Tyler M McCullough
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anya Dhar
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David L Akey
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie R Konwerski
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David H Sherman
- Life Sciences Institute, 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; Department of Chemistry, 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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3
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Yancey CE, Yu F, Tripathi A, Sherman DH, Dick GJ. Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie. Appl Environ Microbiol 2023; 89:e0209222. [PMID: 37070981 PMCID: PMC10231183 DOI: 10.1128/aem.02092-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/19/2023] Open
Abstract
Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
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Affiliation(s)
- Colleen E. Yancey
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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4
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Shende VV, Harris NR, Sanders JN, Newmister SA, Khatri Y, Movassaghi M, Houk KN, Sherman DH. Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases. Angew Chem Int Ed Engl 2023; 62:e202210254. [PMID: 36610039 PMCID: PMC10159983 DOI: 10.1002/anie.202210254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp2 -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.
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Affiliation(s)
- Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Natalia R Harris
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
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5
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Liu Z, Rivera S, Newmister SA, Sanders JN, Nie Q, Liu S, Zhao F, Ferrara JD, Shih HW, Patil S, Xu W, Miller MD, Phillips GN, Houk KN, Sherman DH, Gao X. An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity. Nat Chem 2023; 15:526-534. [PMID: 36635598 PMCID: PMC10073347 DOI: 10.1038/s41557-022-01117-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 01/14/2023]
Abstract
The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.
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Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Sebastian Rivera
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Qiuyue Nie
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Shuai Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Hao-Wei Shih
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Siddhant Patil
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, TX, USA
| | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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6
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Shende VV, Harris NR, Sanders JN, Newmister SA, Khatri Y, Movassaghi M, Houk KN, Sherman DH. Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202210254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vikram Vijay Shende
- University of California San Diego Scripps Institution of Oceanography Center for Marine Biotechnology and Biomedicine 8655 Discovery WayScholander Hall 92037 LA JOLLA UNITED STATES
| | - Natalia R Harris
- University of Michigan Life Sciences Institute 210 Washtenaw AveLife Sciences Institute 48109 Ann Arbor UNITED STATES
| | - Jacob N Sanders
- University of California Los Angeles Department of Chemistry and Biochemistry UNITED STATES
| | | | - Yogan Khatri
- University of Michigan Life Sciences Institute UNITED STATES
| | - Mohammad Movassaghi
- MIT: Massachusetts Institute of Technology Department of Chemistry UNITED STATES
| | - Kendall N Houk
- University of California Los Angeles Department of Chemistry and Biochemistry UNITED STATES
| | - David H. Sherman
- University of Michigan Life Sciences Institute 210 Washtenaw Avenue 48109-2216 Ann Arbor UNITED STATES
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7
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Kelly SP, Shende VV, Flynn AR, Dan Q, Ye Y, Smith JL, Tsukamoto S, Sigman MS, Sherman DH. Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A. J Am Chem Soc 2022; 144:19326-19336. [PMID: 36223664 PMCID: PMC9831672 DOI: 10.1021/jacs.2c06631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.
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Affiliation(s)
- Samantha P. Kelly
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,These authors contributed equally: Samantha P. Kelly, Vikram V. Shende
| | - Vikram V. Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,These authors contributed equally: Samantha P. Kelly, Vikram V. Shende
| | - Autumn R. Flynn
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Ye
- Life Sciences Institute, 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
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - David H. Sherman
- Life Sciences Institute, 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
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8
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Yancey CE, Smith DJ, Den Uyl PA, Mohamed OG, Yu F, Ruberg SA, Chaffin JD, Goodwin KD, Tripathi A, Sherman DH, Dick GJ. Metagenomic and Metatranscriptomic Insights into Population Diversity of Microcystis Blooms: Spatial and Temporal Dynamics of mcy Genotypes, Including a Partial Operon That Can Be Abundant and Expressed. Appl Environ Microbiol 2022; 88:e0246421. [PMID: 35438519 PMCID: PMC9088275 DOI: 10.1128/aem.02464-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) degrade freshwater ecosystems globally. Microcystis aeruginosa often dominates cyanoHABs and produces microcystin (MC), a class of hepatotoxins that poses threats to human and animal health. Microcystin toxicity is influenced by distinct structural elements across a diversity of related molecules encoded by variant mcy operons. However, the composition and distribution of mcy operon variants in natural blooms remain poorly understood. Here, we characterized the variant composition of mcy genes in western Lake Erie Microcystis blooms from 2014 and 2018. Sampling was conducted across several spatial and temporal scales, including different bloom phases within 2014, extensive spatial coverage on the same day (2018), and frequent, autonomous sampling over a 2-week period (2018). Mapping of metagenomic and metatranscriptomic sequences to reference sequences revealed three Microcystis mcy genotypes: complete (all genes present [mcyA-J]), partial (truncated mcyA, complete mcyBC, and missing mcyD-J), and absent (no mcy genes). We also detected two different variants of mcyB that may influence the production of microcystin congeners. The relative abundance of these genotypes was correlated with pH and nitrate concentrations. Metatranscriptomic analysis revealed that partial operons were, at times, the most abundant genotype and expressed in situ, suggesting the potential biosynthesis of truncated products. Quantification of genetic divergence between genotypes suggests that the observed strains are the result of preexisting heterogeneity rather than de novo mutation during the sampling period. Overall, our results show that natural Microcystis populations contain several cooccurring mcy genotypes that dynamically shift in abundance spatiotemporally via strain succession and likely influence the observed diversity of the produced congeners. IMPORTANCE Cyanobacteria are responsible for producing microcystins (MCs), a class of potent and structurally diverse toxins, in freshwater systems around the world. While microcystins have been studied for over 50 years, the diversity of their chemical forms and how this variation is encoded at the genetic level remain poorly understood, especially within natural populations of cyanobacterial harmful algal blooms (cyanoHABs). Here, we leverage community DNA and RNA sequences to track shifts in mcy genes responsible for producing microcystin, uncovering the relative abundance, expression, and variation of these genes. We studied this phenomenon in western Lake Erie, which suffers annually from cyanoHAB events, with impacts on drinking water, recreation, tourism, and commercial fishing.
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Affiliation(s)
- Colleen E. Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Derek J. Smith
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul A. Den Uyl
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
| | - Osama G. Mohamed
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Fengan Yu
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A. Ruberg
- National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory, Ann Arbor, Michigan, USA
| | - Justin D. Chaffin
- F. T. Stone Laboratory, The Ohio State University, Put-In-Bay, Ohio, USA
- Ohio Sea Grant, The Ohio State University, Put-In-Bay, Ohio, USA
| | - Kelly D. Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory (AOML), NOAA, Miami, Florida, USA
- Southwest Fisheries Science Center, NOAA, La Jolla, California, USA
| | - Ashootosh Tripathi
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Science Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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9
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Espinoza RV, Maskeri MA, Turlik A, Nangia A, Khatri Y, Montgomery J, Houk KN, Sherman DH. Epoxidation and Late-Stage C–H Functionalization by P450 TamI Are Mediated by Variant Heme-Iron Oxidizing Species. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mark A. Maskeri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Anjanay Nangia
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | | | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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10
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Iizaka Y, Arai R, Takahashi A, Ito M, Sakai M, Fukumoto A, Sherman DH, Anzai Y. Engineering Sequence and Selectivity of Late-Stage C-H Oxidation in the MycG Iterative Cytochrome P450. J Ind Microbiol Biotechnol 2021; 49:6372909. [PMID: 34543433 PMCID: PMC9113108 DOI: 10.1093/jimb/kuab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]
Abstract
MycG is a multifunctional P450 monooxygenase that catalyzes sequential hydroxylation and epoxidation or a single epoxidation in mycinamicin biosynthesis. In the mycinamicin-producing strain Micromonospora griseorubida A11725, very low-level accumulation of mycinamicin V generated by the initial C-14 allylic hydroxylation of MycG is observed due to its subsequent epoxidation to generate mycinamicin II, the terminal metabolite in this pathway. Herein, we investigated whether MycG can be engineered for production of the mycinamicin II intermediate as the predominant metabolite. Thus, mycG was subject to random mutagenesis and screening was conducted in Escherichia coli whole-cell assays. This enabled efficient identification of amino acid residues involved in reaction profile alterations, which included MycG R111Q/V358L, W44R, and V135G/E355K with enhanced monohydroxylation to accumulate mycinamicin V. The MycG V135G/E355K mutant generated 40-fold higher levels of mycinamicin V compared to wild-type M. griseorubida A11725. In addition, the E355K mutation showed improved ability to catalyze sequential hydroxylation and epoxidation with minimal mono-epoxidation product mycinamicin I compared to the wild-type enzyme. These approaches demonstrate the ability to selectively coordinate the catalytic activity of multifunctional P450s and efficiently produce the desired compounds.
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Affiliation(s)
- Yohei Iizaka
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Ryusei Arai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Akari Takahashi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Mikino Ito
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Miho Sakai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - Atsushi Fukumoto
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, Japan
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11
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Espinoza RV, Haatveit KC, Grossman SW, Tan JY, McGlade CA, Khatri Y, Newmister SA, Schmidt JJ, Garcia-Borràs M, Montgomery J, Houk KN, Sherman DH. Engineering P450 TamI as an Iterative Biocatalyst for Selective Late-Stage C-H Functionalization and Epoxidation of Tirandamycin Antibiotics. ACS Catal 2021; 11:8304-8316. [PMID: 35003829 DOI: 10.1021/acscatal.1c01460] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Iterative P450 enzymes are powerful biocatalysts for selective late-stage C-H oxidation of complex natural product scaffolds. These enzymes represent useful tools for selectivity and cascade reactions, facilitating direct access to core structure diversification. Recently, we reported the structure of the multifunctional bacterial P450 TamI and elucidated the molecular basis of its substrate binding and strict reaction sequence at distinct carbon atoms of the substrate. Here, we report the design and characterization of a toolbox of TamI biocatalysts, generated by mutations at Leu101, Leu244, and/or Leu295, that alter the native selectivity, step sequence, and number of reactions catalyzed, including the engineering of a variant capable of catalyzing a four-step oxidative cascade without the assistance of the flavoprotein and oxidative partner TamL. The tuned enzymes override inherent substrate reactivity, enabling catalyst-controlled C-H functionalization and alkene epoxidation of the tetramic acid-containing natural product tirandamycin. Five bioactive tirandamycin derivatives (6-10) were generated through TamI-mediated enzymatic synthesis. Quantum mechanics calculations and MD simulations provide important insights into the basis of altered selectivity and underlying biocatalytic mechanisms for enhanced continuous oxidation of the iterative P450 TamI.
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Affiliation(s)
- Rosa V Espinoza
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kersti Caddell Haatveit
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - S Wald Grossman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jin Yi Tan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Caylie A McGlade
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - John Montgomery
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States; Department of Medicinal Chemistry, Department of Chemistry, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Hohlman RM, Sherman DH. Recent advances in hapalindole-type cyanobacterial alkaloids: biosynthesis, synthesis, and biological activity. Nat Prod Rep 2021; 38:1567-1588. [PMID: 34032254 DOI: 10.1039/d1np00007a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 1984 up to the end of 2020Hapalindoles, fischerindoles, ambiguines and welwitindolinones are all members of a class of indole alkaloid natural products that have been isolated from the Stigonematales order of cyanobacteria. These compounds possess a polycyclic ring system, unique functional groups and various stereo- and regiochemical isomers. Since their initial isolation in 1984, they have been explored as potential therapeutics due to their wide variety of biological activities. Although numerous groups have pursued total syntheses of these densely functionalized structures, hapalindole biosynthesis has only recently been unveiled. Several groups have uncovered a wide range of novel enzymes that catalyze formation and tailoring of the hapalindole-type metabolites. In this article, we provide an overview of these natural products, their biological activities, highlight general synthetic routes, and provide an extensive review on the surprising biosynthetic processes leading to these structurally diverse metabolites.
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Affiliation(s)
- Robert M Hohlman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA. and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA. and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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13
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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14
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Hohlman RM, Newmister SA, Sanders JN, Khatri Y, Li S, Keramati NR, Lowell AN, Houk KN, Sherman DH. Structural diversification of hapalindole and fischerindole natural products via cascade biocatalysis. ACS Catal 2021; 11:4670-4681. [PMID: 34354850 DOI: 10.1021/acscatal.0c05656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hapalindoles and related compounds (ambiguines, fischerindoles, welwitindolinones) are a diverse class of indole alkaloid natural products. They are typically isolated from the Stigonemataceae order of cyanobacteria and possess a broad scope of biological activities. Recently the biosynthetic pathway for assembly of these metabolites has been elucidated. In order to generate the core ring system, L-tryptophan is converted into the cis-indole isonitrile subunit before being prenylated with geranyl pyrophosphate at the C-3 position. A class of cyclases (Stig) catalyzes a three-step process including a Cope rearrangement, 6-exo-trig cyclization and electrophilic aromatic substitution to create a polycyclic core. Formation of the initial alkaloid is followed by diverse late-stage tailoring reactions mediated by additional biosynthetic enzymes to give rise to the wide array of structural variations observed in this compound class. Herein, we demonstrate the versatility and utility of the Fam prenyltransferase and Stig cyclases toward core structural diversification of this family of indole alkaloids. Through synthesis of cis-indole isonitrile subunit derivatives, and aided by protein engineering and computational analysis, we have employed cascade biocatalysis to generate a range of derivatives, and gained insights into the basis for substrate flexibility in this system.
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Affiliation(s)
| | | | - Jacob N. Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | | | | | | | | | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - David H. Sherman
- Department of Microbiology & Immunology, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
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15
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Iizaka Y, Sherman DH, Anzai Y. An overview of the cytochrome P450 enzymes that catalyze the same-site multistep oxidation reactions in biotechnologically relevant selected actinomycete strains. Appl Microbiol Biotechnol 2021; 105:2647-2661. [PMID: 33710358 DOI: 10.1007/s00253-021-11216-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/17/2021] [Accepted: 02/28/2021] [Indexed: 12/18/2022]
Abstract
Cytochrome P450 enzymes (P450s) are one of the major factors responsible for the diversity of metabolites produced through many biosynthetic and biodegradative processes in actinomycetes. P450s typically catalyze a single oxidative modification; however, several P450s have been identified with the unique ability to iteratively oxidize the same-site of the substrate. These P450s are capable of forming diverse compounds that affect biological processes, including alcohols, ketones, aldehydes, and carboxylic acids. Although further structural and functional studies are needed to elucidate the mechanisms that allow multistep oxidative modification, recent studies have revealed the enzymatic properties and reaction mechanisms of these P450s. This mini-review covers the current knowledge of P450s that catalyze the multistep oxidation reactions and contribute to the production of a wide variety of metabolites by selected actinomycete strains, along with insights into their application and utility. Understanding the characteristics of these remarkable enzymes will facilitate their utilization in biotechnological applications to create biologically active and other high-value compounds. KEY POINTS: • The multistep oxidation by P450s plays a key role in the diversity of metabolites. • The mechanisms that enable P450s to catalyze iterative oxidation remains unknown. • The effective use of P450s that iteratively oxidize the same-site is discussed.
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Affiliation(s)
- Yohei Iizaka
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
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16
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Tan JY, Wang S, Dick GJ, Young VB, Sherman DH, Burns MA, Lin XN. Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. Integr Biol (Camb) 2020; 12:263-274. [PMID: 33089329 PMCID: PMC7671993 DOI: 10.1093/intbio/zyaa021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/05/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.
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Affiliation(s)
- James Y Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sida Wang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Deparment of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Infectious Diseases Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Deparment of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Mark A Burns
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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17
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Yang S, DeMars MD, Grandner JM, Olson NM, Anzai Y, Sherman DH, Houk KN. Computational-Based Mechanistic Study and Engineering of Cytochrome P450 MycG for Selective Oxidation of 16-Membered Macrolide Antibiotics. J Am Chem Soc 2020; 142:17981-17988. [PMID: 33030347 PMCID: PMC7720209 DOI: 10.1021/jacs.0c04388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MycG is a cytochrome P450 that performs two sequential oxidation reactions on the 16-membered ring macrolide M-IV. The enzyme evolved to oxidize M-IV preferentially over M-III and M-VI, which differ only by the presence of methoxy vs free hydroxyl groups on one of the macrolide sugar moieties. We utilized a two-pronged computational approach to study both the chemoselective reactivity and substrate specificity of MycG. Density functional theory computations determined that epoxidation of the substrate hampers its ability to undergo C-H abstraction, primarily due to a loss of hyperconjugation in the transition state. Metadynamics and molecular dynamics simulations revealed a hydrophobic sugar-binding pocket that is responsible for substrate recognition/specificity and was not apparent in crystal structures of the enzyme/substrate complex. Computational results also led to the identification of other interactions between the enzyme and its substrates that had not previously been observed in the cocrystal structures. Site-directed mutagenesis was then employed to test the effects of mutations hypothesized to broaden the substrate scope and alter the product profile of MycG. The results of these experiments validated this complementary effort to engineer MycG variants with improved catalytic activity toward earlier stage mycinamicin substrates.
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Affiliation(s)
- Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Matthew D DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jessica M Grandner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Noelle M Olson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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18
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Shende VV, Khatri Y, Newmister SA, Sanders JN, Lindovska P, Yu F, Doyon TJ, Kim J, Houk KN, Movassaghi M, Sherman DH. Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase. J Am Chem Soc 2020; 142:17413-17424. [PMID: 32786740 DOI: 10.1021/jacs.0c06312] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses. Genome mining enabled identification of the cytochrome P450, NzeB (Streptomyces sp. NRRL F-5053), which catalyzes both intermolecular carbon-carbon (C-C) and carbon-nitrogen (C-N) bond formation. To identify the molecular basis for the flexible site-selectivity, stereoselectivity, and chemoselectivity of NzeB, we obtained high-resolution crystal structures (1.5 Å) of the protein in complex with native and non-native substrates. This, to our knowledge, represents the first crystal structure of an oxidase catalyzing direct, intermolecular C-H amination. Site-directed mutagenesis was utilized to assess the role individual active-site residues play in guiding selective DKP dimerization. Finally, computational approaches were employed to evaluate plausible mechanisms regarding NzeB function and its ability to catalyze both C-C and C-N bond formation. These results provide a structural and computational rationale for the catalytic versatility of NzeB, as well as new insights into variables that control selectivity of CYP450 diketopiperazine dimerases.
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Affiliation(s)
| | | | | | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Petra Lindovska
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | | | - Justin Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 2020; 117:23835-23846. [PMID: 32900948 PMCID: PMC7519347 DOI: 10.1073/pnas.2008615117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
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Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | | | - Madeline S Merlino
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew W Robertson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Megan R McLeod
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Lyanne Gomez-Rodriguez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kirsten A Garcia
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jolie A Leonard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kay E Leopold
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Eli Olson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109
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20
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Fraley AE, Tran HT, Kelly SP, Newmister SA, Tripathi A, Kato H, Tsukamoto S, Du L, Li S, Williams RM, Sherman DH. Flavin-Dependent Monooxygenases NotI and NotI' Mediate Spiro-Oxindole Formation in Biosynthesis of the Notoamides. Chembiochem 2020; 21:2449-2454. [PMID: 32246875 PMCID: PMC7483341 DOI: 10.1002/cbic.202000004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/04/2020] [Indexed: 11/08/2022]
Abstract
The fungal indole alkaloids are a unique class of complex molecules that have a characteristic bicyclo[2.2.2]diazaoctane ring and frequently contain a spiro-oxindole moiety. While various strains produce these compounds, an intriguing case involves the formation of individual antipodes by two unique species of fungi in the generation of the potent anticancer agents (+)- and (-)-notoamide A. NotI and NotI' have been characterized as flavin-dependent monooxygenases that catalyze epoxidation and semi-pinacol rearrangement to form the spiro-oxindole center within these molecules. This work elucidates a key step in the biosynthesis of the notoamides and provides an evolutionary hypothesis regarding a common ancestor for production of enantiopure notoamides.
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Affiliation(s)
- Amy E Fraley
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
| | - Hong T Tran
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
| | - Samantha P Kelly
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
| | - Hikaru Kato
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto, 862-0973, Japan
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto, 862-0973, Japan
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Robert M Williams
- Department of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, CO 80523, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150W. Medical Center Drive, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, 930N. University Ave., Ann Arbor, MI 48109, USA
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21
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Fraley AE, Tran HT, Kelly SP, Newmister SA, Tripathi A, Kato H, Tsukamoto S, Du L, Li S, Williams RM, Sherman DH. Cover Feature: Flavin‐Dependent Monooxygenases NotI and NotI′ Mediate Spiro‐Oxindole Formation in Biosynthesis of the Notoamides (ChemBioChem 17/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy E. Fraley
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
- Department of Medicinal ChemistryUniversity of Michigan 428 Church St. Ann Arbor MI 48109 USA
| | - Hong T. Tran
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
- Program in Chemical BiologyUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 48109 USA
| | - Samantha P. Kelly
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
- Program in Chemical BiologyUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 48109 USA
| | - Sean A. Newmister
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
| | - Ashootosh Tripathi
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
- Department of Medicinal ChemistryUniversity of Michigan 428 Church St. Ann Arbor MI 48109 USA
| | - Hikaru Kato
- Graduate School of Pharmaceutical SciencesKumamoto University 5-1 Oe-honmachi Kumamoto 862-0973 Japan
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical SciencesKumamoto University 5-1 Oe-honmachi Kumamoto 862-0973 Japan
| | - Lei Du
- State Key Laboratory of Microbial TechnologyShandong University Qingdao Shandong 266237 China
| | - Shengying Li
- State Key Laboratory of Microbial TechnologyShandong University Qingdao Shandong 266237 China
| | - Robert M. Williams
- Department of ChemistryColorado State University 1301 Center Ave. Fort Collins CO 80523 USA
| | - David H. Sherman
- Life Sciences InstituteUniversity of Michigan 210 Washtenaw Ave. Ann Arbor MI 28104 USA
- Department of Medicinal ChemistryUniversity of Michigan 428 Church St. Ann Arbor MI 48109 USA
- Department of Microbiology and ImmunologyUniversity of Michigan Medical School 1150W. Medical Center Drive Ann Arbor MI 48109
- Department of ChemistryUniversity of Michigan 930N. University Ave. Ann Arbor MI 48109 USA
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22
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Koch AA, Schmidt JJ, Lowell AN, Hansen DA, Coburn KM, Chemler JA, Sherman DH. Probing Selectivity and Creating Structural Diversity Through Hybrid Polyketide Synthases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Aaron A. Koch
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Jennifer J. Schmidt
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Andrew N. Lowell
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Current address: Department of Chemistry Virginia Tech Blacksburg VA 24061 USA
| | - Douglas A. Hansen
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Katherine M. Coburn
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Joseph A. Chemler
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - David H. Sherman
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology The University of Michigan USA
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23
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Khatri Y, Hohlman RM, Mendoza J, Li S, Lowell AN, Asahara H, Sherman DH. Multicomponent Microscale Biosynthesis of Unnatural Cyanobacterial Indole Alkaloids. ACS Synth Biol 2020; 9:1349-1360. [PMID: 32302487 PMCID: PMC7323787 DOI: 10.1021/acssynbio.0c00038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome sequencing and bioinformatics tools have facilitated the identification and expression of an increasing number of cryptic biosynthetic gene clusters (BGCs). However, functional analysis of all components of a metabolic pathway to precisely determine biocatalytic properties remains time-consuming and labor intensive. One way to speed this process involves microscale cell-free protein synthesis (CFPS) for direct gene to biochemical function analysis, which has rarely been applied to study multicomponent enzymatic systems in specialized metabolism. We sought to establish an in vitro transcription/translation (TT)-assay to assess assembly of cyanobacterial-derived hapalindole-type natural products (cNPs) because of their diverse bioactivity profiles and complex structural diversity. Using a CFPS system including a plasmid bearing famD2 prenyltransferase from Fischerella ambigua UTEX 1903, we showed production of the central prenylated intermediate (3GC) in the presence of exogenous geranyl-pyrophosphate (GPP) and cis-indole isonitrile. Further addition of a plasmid bearing the famC1 Stig cyclase resulted in synthesis of both FamD2 and FamC1 enzymes, which was confirmed by proteomics analysis, and catalyzed assembly of 12-epi-hapalindole U. Further combinations of Stig cyclases (FamC1-C4) produced hapalindole U and hapalindole H, while FisC identified from Fischerella sp. SAG46.79 generated 12-epi-fischerindole U. The CFPS system was further employed to screen six unnatural halogenated cis-indole isonitrile substrates using FamC1 and FisC, and the reactions were scaled-up using chemoenzymatic synthesis and identified as 5- and 6-fluoro-12-epi-hapalindole U, and 5- and 6-fluoro-12-epi-fischerindole U, respectively. This approach represents an effective, high throughput strategy to determine the functional role of biosynthetic enzymes from diverse natural product BGCs.
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Affiliation(s)
| | | | | | | | | | - Haruichi Asahara
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
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24
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Koch AA, Schmidt JJ, Lowell AN, Hansen DA, Coburn KM, Chemler JA, Sherman DH. Probing Selectivity and Creating Structural Diversity Through Hybrid Polyketide Synthases. Angew Chem Int Ed Engl 2020; 59:13575-13580. [PMID: 32357274 DOI: 10.1002/anie.202004991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 11/09/2022]
Abstract
Engineering polyketide synthases (PKS) to produce new metabolites requires an understanding of catalytic points of failure during substrate processing. Growing evidence indicates the thioesterase (TE) domain as a significant bottleneck within engineered PKS systems. We created a series of hybrid PKS modules bearing exchanged TE domains from heterologous pathways and challenged them with both native and non-native polyketide substrates. Reactions pairing wildtype PKS modules with non-native substrates primarily resulted in poor conversions to anticipated macrolactones. Likewise, product formation with native substrates and hybrid PKS modules bearing non-cognate TE domains was severely reduced. In contrast, non-native substrates were converted by most hybrid modules containing a substrate compatible TE, directly implicating this domain as the major catalytic gatekeeper and highlighting its value as a target for protein engineering to improve analog production in PKS pathways.
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Affiliation(s)
- Aaron A Koch
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Jennifer J Schmidt
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Andrew N Lowell
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.,Current address: Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Douglas A Hansen
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Katherine M Coburn
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Joseph A Chemler
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - David H Sherman
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.,Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, The University of Michigan, USA
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25
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Affiliation(s)
- Rosa V. Espinoza
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, 48109, United States
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26
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Li S, Newmister SA, Lowell AN, Zi J, Chappell CR, Yu F, Hohlman RM, Orjala J, Williams RM, Sherman DH. Control of Stereoselectivity in Diverse Hapalindole Metabolites is Mediated by Cofactor‐Induced Combinatorial Pairing of Stig Cyclases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shasha Li
- Life Sciences InstituteDepartment of Medicinal ChemistryThe University of Michigan USA
| | | | - Andrew N. Lowell
- Life Science InstituteThe University of Michigan USA
- Department of ChemistryVirginia Tech Blacksburg VA 24061 USA
| | - Jiachen Zi
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Illinois at Chicago Chicago IL 60612 USA
| | - Callie R. Chappell
- Department of Molecular, Cellular & Developmental BiologyThe University of Michigan USA
| | - Fengan Yu
- Life Science InstituteThe University of Michigan USA
| | - Robert M. Hohlman
- Life Sciences InstituteDepartment of Medicinal ChemistryThe University of Michigan USA
| | - Jimmy Orjala
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Illinois at Chicago Chicago IL 60612 USA
| | - Robert M. Williams
- Department of ChemistryColorado State University Fort Collins CO 80523 USA
- University of Colorado Cancer Center Aurora CO 80045 USA
| | - David H. Sherman
- Life Sciences InstituteDepartments of Medicinal Chemistry, Chemistry, Microbiology & ImmunologyThe University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109-2216n USA
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27
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Li S, Newmister SA, Lowell AN, Zi J, Chappell CR, Yu F, Hohlman RM, Orjala J, Williams RM, Sherman DH. Control of Stereoselectivity in Diverse Hapalindole Metabolites is Mediated by Cofactor-Induced Combinatorial Pairing of Stig Cyclases. Angew Chem Int Ed Engl 2020; 59:8166-8172. [PMID: 32052896 PMCID: PMC7274885 DOI: 10.1002/anie.201913686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Indexed: 11/07/2022]
Abstract
Stereospecific polycyclic core formation of hapalindoles and fischerindoles is controlled by Stig cyclases through a three-step cascade involving Cope rearrangement, 6-exo-trig cyclization, and a final electrophilic aromatic substitution. Reported here is a comprehensive study of all currently annotated Stig cyclases, revealing that these proteins can assemble into heteromeric complexes, induced by Ca2+ , to cooperatively control the stereochemistry of hapalindole natural products.
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Affiliation(s)
- Shasha Li
- Life Sciences Institute, Department of Medicinal Chemistry, The University of Michigan, USA
| | | | - Andrew N Lowell
- Life Science Institute, The University of Michigan, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jiachen Zi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Callie R Chappell
- Department of Molecular, Cellular & Developmental Biology, The University of Michigan, USA
| | - Fengan Yu
- Life Science Institute, The University of Michigan, USA
| | - Robert M Hohlman
- Life Sciences Institute, Department of Medicinal Chemistry, The University of Michigan, USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
- University of Colorado Cancer Center, Aurora, CO, 80045, USA
| | - David H Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, The University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216n, USA
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28
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Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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29
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Abstract
New structural classes of antibiotics are rare, structurally novel broad-spectrum antibiotics exceptionally so. The recently discovered baulamycins constitute a remarkable example of these highly prized compounds and, as such, have attracted considerable attention in the form of both synthetic efforts and biological studies. For the first time, we report a gram-scale preparation of the common carbon framework of the baulamycin family, as well as the total synthesis of its most potent member, baulamycin A. Our approach employs highly stereoselective, catalyst-controlled asymmetric conjugate additions to thioesters to set key stereocenters, as well as the first reported use of "dry ozonolysis" to reveal a masked carboxylic acid in the total synthesis of a natural product.
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Affiliation(s)
- Jonathan R Thielman
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States.,University of Colorado Cancer Center, Aurora, Colorado 80045, USA
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30
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Schmidt JJ, Khatri Y, Brody SI, Zhu C, Pietraszkiewicz H, Valeriote FA, Sherman DH. A Versatile Chemoenzymatic Synthesis for the Discovery of Potent Cryptophycin Analogs. ACS Chem Biol 2020; 15:524-532. [PMID: 31961651 DOI: 10.1021/acschembio.9b00998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cryptophycins are a family of macrocyclic depsipeptide natural products that display exceptionally potent antiproliferative activity against drug-resistant cancers. Unique challenges facing the synthesis and derivatization of this complex group of molecules motivated us to investigate a chemoenzymatic synthesis designed to access new analogs for biological evaluation. The cryptophycin thioesterase (CrpTE) and the cryptophycin epoxidase (CrpE) are a versatile set of enzymes that catalyze macrocyclization and epoxidation of over 20 natural cryptophycin metabolites. Thus, we envisioned a drug development strategy involving their use as standalone biocatalysts for production of unnatural derivatives. Herein, we developed a scalable synthesis of 12 new unit A-B-C-D linear chain elongation intermediates containing heterocyclic aromatic groups as alternatives to the native unit A benzyl group. N-Acetyl cysteamine activated forms of each intermediate were assessed for conversion to macrocyclic products using wild type CrpTE, which demonstrated the exceptional flexibility of this enzyme. Semipreparative scale reactions were conducted for isolation and structural characterization of new cryptophycins. Each was then evaluated as a substrate for CrpE P450 and its ability to generate the epoxidized products from these substrates that possess altered electronics at the unit A styrenyl double bond position. Finally, biological evaluation of the new cryptophycins revealed a des-β-epoxy analog with low picomolar potency, previously limited to cryptophycins bearing epoxide functionality.
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Affiliation(s)
| | | | | | | | - Halina Pietraszkiewicz
- Department of Internal Medicine, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan 48202, United States
| | - Frederick A. Valeriote
- Department of Internal Medicine, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan 48202, United States
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31
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Fraley AE, Caddell Haatveit K, Ye Y, Kelly SP, Newmister SA, Yu F, Williams RM, Smith JL, Houk KN, Sherman DH. Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway. J Am Chem Soc 2020; 142:2244-2252. [PMID: 31904957 DOI: 10.1021/jacs.9b09070] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a ΔphqK strain of Penicillium simplicissimum, and subsequent enzymatic reactions with these compounds generated two additional metabolites, paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L is the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents.
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Affiliation(s)
| | - Kersti Caddell Haatveit
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | | | | | | | | | - Robert M Williams
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,University of Colorado Cancer Center , Aurora , Colorado 80045 , United States
| | | | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Gómez-Rodríguez L, Schultz PJ, Tamayo-Castillo G, Dotson GD, Sherman DH, Tripathi A. Adipostatins E-J, New Potent Antimicrobials Identified as Inhibitors of Coenzyme-A Biosynthesis. Tetrahedron Lett 2019; 61. [PMID: 32863451 DOI: 10.1016/j.tetlet.2019.151469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Phosphopantetheine is a key structural element in biological acyl transfer reactions found embedded within coenzyme A (CoA). Phosphopantothenoylcysteine synthetase (PPCS) is responsible for installing a cysteamine group within phosphopantetheine. Therefore, it holds considerable potential as a drug target for developing new antimicrobials. In this study, we adapted a biochemical assay specific for bacterial PPCS to screen for inhibitors of CoA biosynthesis against a library of marine microbial derived natural product extracts (NPEs). Analysis of the NPE derived from Streptomyces blancoensis led to the isolation of novel antibiotics (10-12, and 14) from the adipostatin class of molecules. The most potent molecule (10) displayed in vitro activity with IC50= 0.93 μM, against S. pneumoniae PPCS. The whole cell antimicrobial assay against isolated molecules demonstrated their ability to penetrate bacterial cells and inhibit clinically relevant pathogenic strains. This establishes the validity of PPCS as a pertinent drug target, and the value of NPEs to provide new antibiotics.
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Affiliation(s)
- Lyanne Gómez-Rodríguez
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Pamela J Schultz
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Giselle Tamayo-Castillo
- Escuela de Química & CIPRONA, Universidad de Costa Rica, 2060 San Pedro de Costa Rica & INBio, Santo Domingo de Heredia, Heredia, Costa Rica
| | - Garry D Dotson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - David H Sherman
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ashootosh Tripathi
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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Dan Q, Newmister SA, Klas KR, Fraley AE, McAfoos TJ, Somoza AD, Sunderhaus JD, Ye Y, Shende VV, Yu F, Sanders JN, Brown WC, Zhao L, Paton RS, Houk KN, Smith JL, Sherman DH, Williams RM. Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase. Nat Chem 2019; 11:972-980. [PMID: 31548667 PMCID: PMC6815239 DOI: 10.1038/s41557-019-0326-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022]
Abstract
Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide. Reductive cleavage of an L-Pro-L-Trp dipeptide from the MalG non-ribosomal peptide synthetase (NRPS) followed by reverse prenylation and a cascade of post-NRPS reactions culminates in an intramolecular [4+2] hetero-Diels-Alder (IMDA) cyclization to furnish the bicyclo[2.2.2]diazaoctane scaffold. Enzymatic assembly of optically pure (+)-premalbrancheamide involves an unexpected zwitterionic intermediate where MalC catalyses enantioselective cycloaddition as a bifunctional NADPH-dependent reductase/Diels-Alderase. The crystal structures of substrate and product complexes together with site-directed mutagenesis and molecular dynamics simulations demonstrate how MalC and PhqE (its homologue from the paraherquamide pathway) catalyse diastereo- and enantioselective cyclization in the construction of this important class of secondary metabolites.
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Affiliation(s)
- Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kimberly R Klas
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amy E Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Timothy J McAfoos
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Amber D Somoza
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - James D Sunderhaus
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Ying Ye
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - W Clay Brown
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Le Zhao
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- University of Colorado Cancer Center, Aurora, CO, USA.
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35
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DeMars MD, Samora NL, Yang S, Garcia-Borràs M, Sanders JN, Houk KN, Podust LM, Sherman DH. Exploring the molecular basis for substrate specificity in homologous macrolide biosynthetic cytochromes P450. J Biol Chem 2019; 294:15947-15961. [PMID: 31488542 PMCID: PMC6827315 DOI: 10.1074/jbc.ra119.010352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochromes P450 (P450s) are nature's catalysts of choice for performing demanding and physiologically vital oxidation reactions. Biochemical characterization of these enzymes over the past decades has provided detailed mechanistic insight and highlighted the diversity of substrates P450s accommodate and the spectrum of oxidative transformations they catalyze. Previously, we discovered that the bacterial P450 MycCI from the mycinamicin biosynthetic pathway in Micromonospora griseorubida possesses an unusually broad substrate scope, whereas the homologous P450 from tylosin-producing Streptomyces fradiae (TylHI) exhibits a high degree of specificity for its native substrate. Here, using biochemical, structural, and computational approaches, we aimed to understand the molecular basis for the disparate reactivity profiles of these two P450s. Turnover and equilibrium binding experiments with substrate analogs revealed that TylHI strictly prefers 16-membered ring macrolides bearing the deoxyamino sugar mycaminose. To help rationalize these results, we solved the X-ray crystal structure of TylHI in complex with its native substrate at 1.99-Å resolution and assayed several site-directed mutants. We also conducted molecular dynamics simulations of TylHI and MycCI and biochemically characterized a third P450 homolog from the chalcomycin biosynthetic pathway in Streptomyces bikiniensis These studies provided a basis for constructing P450 chimeras to gain further insight into the features dictating the differences in reaction profile among these structurally and functionally related enzymes, ultimately unveiling the central roles of key loop regions in influencing substrate binding and turnover. Our work highlights the complex nature of P450/substrate interactions and raises interesting questions regarding the evolution of functional diversity among biosynthetic enzymes.
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Affiliation(s)
- Matthew D DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Nathan L Samora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109
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36
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Li T, Tripathi A, Yu F, Sherman DH, Rao A. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases. Bioinformatics 2019; 36:942-944. [PMID: 31504190 PMCID: PMC8215927 DOI: 10.1093/bioinformatics/btz677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/25/2019] [Accepted: 08/30/2019] [Indexed: 01/31/2023] Open
Abstract
SUMMARY DDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing dataset reached 0.88 as measured by the area under the receiver operating characteristic (ROC) curve (AUC); the Mean Reciprocal Ranking (MRR) of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0-1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. DDAP is so far the first machine learning based algorithm for type I PKS DD affinity and pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways. AVAILABILITY AND IMPLEMENTATION The DDAP database is available at https://tylii.github.io/ddap. The prediction algorithm DDAP is freely available on GitHub (https://github.com/tylii/ddap) and released under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tingyang Li
- Department of Computational Medicine and Bioinformatics, MI, USA
| | - Ashootosh Tripathi
- Natural Products Discovery Core, Life Sciences Institute, MI, USA,Department of Medicinal Chemistry, MI, USA
| | - Fengan Yu
- Natural Products Discovery Core, Life Sciences Institute, MI, USA
| | - David H Sherman
- Natural Products Discovery Core, Life Sciences Institute, MI, USA,Department of Medicinal Chemistry, MI, USA,Department of Chemistry, Department of Microbiology and Immunology, MI, USA
| | - Arvind Rao
- To whom correspondence should be addressed.
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Knoot CJ, Khatri Y, Hohlman RM, Sherman DH, Pakrasi HB. Engineered Production of Hapalindole Alkaloids in the Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol 2019; 8:1941-1951. [PMID: 31284716 DOI: 10.1021/acssynbio.9b00229] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria produce numerous valuable bioactive secondary metabolites (natural products) including alkaloids, isoprenoids, nonribosomal peptides, and polyketides. However, the genomic organization of the biosynthetic gene clusters, complex gene expression patterns, and low compound yields synthesized by the native producers currently limits access to the vast majority of these valuable molecules for detailed studies. Molecular cloning and expression of such clusters in heterotrophic hosts is often precarious owing to genetic and biochemical incompatibilities. Production of such biomolecules in photoautotrophic hosts analogous to the native producers is an attractive alternative that has been under-explored. Here, we describe engineering of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce key compounds of the hapalindole family of indole-isonitrile alkaloids. Engineering of the 42-kbp "fam" hapalindole pathway from the cyanobacterium Fischerella ambigua UTEX 1903 into S2973 was accomplished by rationally reconstructing six to seven core biosynthetic genes into synthetic operons. The resulting Synechococcus strains afforded controllable production of indole-isonitrile biosynthetic intermediates and hapalindoles H and 12-epi-hapalindole U at a titer of 0.75-3 mg/L. Exchanging genes encoding fam cyclase enzymes in the synthetic operons was employed to control the stereochemistry of the resulting product. Establishing a robust expression system provides a facile route to scalable levels of similar natural and new forms of bioactive hapalindole derivatives and its structural relatives (e.g., fischerindoles, welwitindolinones). Moreover, this versatile expression system represents a promising tool for exploring other functional characteristics of orphan gene products that mediate the remarkable biosynthesis of this important family of natural products.
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Affiliation(s)
- Cory J. Knoot
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert M. Hohlman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Himadri B. Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
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38
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Dan Q, Newmister SA, Klas KR, Fraley AE, Paton RS, Houk KN, Williams RM, Sherman DH, Smith JL. Evolution of a bifunctional reductase/Diels–Alderase for fungal indole alkaloid biosynthesis. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319097599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Klas KR, Kato H, Frisvad JC, Yu F, Newmister SA, Fraley AE, Sherman DH, Tsukamoto S, Williams RM. Structural and stereochemical diversity in prenylated indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring system from marine and terrestrial fungi. Nat Prod Rep 2019; 35:532-558. [PMID: 29632911 DOI: 10.1039/c7np00042a] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Covering: up to February 2017 Various fungi of the genera Aspergillus, Penicillium, and Malbranchea produce prenylated indole alkaloids possessing a bicyclo[2.2.2]diazaoctane ring system. After the discovery of distinct enantiomers of the natural alkaloids stephacidin A and notoamide B, from A. protuberus MF297-2 and A. amoenus NRRL 35660, another fungi, A. taichungensis, was found to produce their diastereomers, 6-epi-stephacidin A and versicolamide B, as major metabolites. Distinct enantiomers of stephacidin A and 6-epi-stephacidin A may be derived from a common precursor, notoamide S, by enzymes that form a bicyclo[2.2.2]diazaoctane core via a putative intramolecular hetero-Diels-Alder cycloaddition. This review provides our current understanding of the structural and stereochemical homologies and disparities of these alkaloids. Through the deployment of biomimetic syntheses, whole-genome sequencing, and biochemical studies, a unified biogenesis of both the dioxopiperazine and the monooxopiperazine families of prenylated indole alkaloids constituted of bicyclo[2.2.2]diazaoctane ring systems is presented.
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Affiliation(s)
- Kimberly R Klas
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO 80523, USA.
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40
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Newmister SA, Romminger S, Schmidt JJ, Williams RM, Smith JL, Berlinck RGS, Sherman DH. Unveiling sequential late-stage methyltransferase reactions in the meleagrin/oxaline biosynthetic pathway. Org Biomol Chem 2019; 16:6450-6459. [PMID: 30141817 DOI: 10.1039/c8ob01565a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antimicrobial and anti-proliferative meleagrin and oxaline are roquefortine C-derived alkaloids produced by fungi of the genus Penicillium. Tandem O-methylations complete the biosynthesis of oxaline from glandicoline B through meleagrin. Currently, little is known about the role of these methylation patterns in the bioactivity profile of meleagrin and oxaline. To establish the structural and mechanistic basis of methylation in these pathways, crystal structures were determined for two late-stage methyltransferases in the oxaline and meleagrin gene clusters from Penicillium oxalicum and Penicillium chrysogenum. The homologous enzymes OxaG and RoqN were shown to catalyze penultimate hydroxylamine O-methylation to generate meleagrin in vitro. Crystal structures of these enzymes in the presence of methyl donor S-adenosylmethionine revealed an open active site, which lacks an apparent base indicating that catalysis is driven by proximity effects. OxaC was shown to methylate meleagrin to form oxaline in vitro, the terminal pathway product. Crystal structures of OxaC in a pseudo-Michaelis complex containing sinefungin and meleagrin, and in a product complex containing S-adenosyl-homocysteine and oxaline, reveal key active site residues with His313 serving as a base that is activated by Glu369. These data provide structural insights into the enzymatic methylation of these alkaloids that include a rare hydroxylamine oxygen acceptor, and can be used to guide future efforts towards selective derivatization and structural diversification and establishing the role of methylation in bioactivity.
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Affiliation(s)
- Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
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41
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Kalkreuter E, CroweTipton JM, Lowell AN, Sherman DH, Williams GJ. Engineering the Substrate Specificity of a Modular Polyketide Synthase for Installation of Consecutive Non-Natural Extender Units. J Am Chem Soc 2019; 141:1961-1969. [PMID: 30676722 DOI: 10.1021/jacs.8b10521] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is significant interest in diversifying the structures of polyketides to create new analogues of these bioactive molecules. This has traditionally been done by focusing on engineering the acyltransferase (AT) domains of polyketide synthases (PKSs) responsible for the incorporation of malonyl-CoA extender units. Non-natural extender units have been utilized by engineered PKSs previously; however, most of the work to date has been accomplished with ATs that are either naturally promiscuous and/or located in terminal modules lacking downstream bottlenecks. These limitations have prevented the engineering of ATs with low native promiscuity and the study of any potential gatekeeping effects by domains downstream of an engineered AT. In an effort to address this gap in PKS engineering knowledge, the substrate preferences of the final two modules of the pikromycin PKS were compared for several non-natural extender units and through active site mutagenesis. This led to engineering of the methylmalonyl-CoA specificity of both modules and inversion of their selectivity to prefer consecutive non-natural derivatives. Analysis of the product distributions of these bimodular reactions revealed unexpected metabolites resulting from gatekeeping by the downstream ketoreductase and ketosynthase domains. Despite these new bottlenecks, AT engineering provided the first full-length polyketide products incorporating two non-natural extender units. Together, this combination of tandem AT engineering and the identification of previously poorly characterized bottlenecks provides a platform for future advancements in the field.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
| | - Jared M CroweTipton
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Chemistry and Department of Microbiology & Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gavin J Williams
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
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Skiba MA, Bivins MM, Schultz JR, Bernard SM, Fiers WD, Dan Q, Kulkarni S, Wipf P, Gerwick WH, Sherman DH, Aldrich CC, Smitha JL. Structural Basis of Polyketide Synthase O-Methylation. ACS Chem Biol 2018; 13:3221-3228. [PMID: 30489068 PMCID: PMC6470024 DOI: 10.1021/acschembio.8b00687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Modular type I polyketide synthases (PKSs) produce some of the most chemically complex metabolites in nature through a series of multienzyme modules. Each module contains a variety of catalytic domains to selectively tailor the growing molecule. PKS O-methyltransferases ( O-MTs) are predicted to methylate β-hydroxyl or β-keto groups, but their activity and structure have not been reported. We determined the domain boundaries and characterized the catalytic activity and structure of the StiD and StiE O-MTs, which methylate opposite β-hydroxyl stereocenters in the myxobacterial stigmatellin biosynthetic pathway. Substrate stereospecificity was demonstrated for the StiD O-MT. Key catalytic residues were identified in the crystal structures and investigated in StiE O-MT via site-directed mutagenesis and further validated with the cyanobacterial CurL O-MT from the curacin biosynthetic pathway. Initial structural and biochemical analysis of PKS O-MTs supplies a new chemoenzymatic tool, with the unique ability to selectively modify hydroxyl groups during polyketide biosynthesis.
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Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Marissa M. Bivins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - John R. Schultz
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI, 48109, United States
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Sarang Kulkarni
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Janet L. Smitha
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
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43
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Kai A, Kato H, Sherman DH, Williams RM, Tsukamoto S. Isolation of a new indoxyl alkaloid, Amoenamide B, from Aspergillus amoenus NRRL 35600: biosynthetic implications and correction of the structure of Speramide B. Tetrahedron Lett 2018; 50:4236-4240. [PMID: 30765898 DOI: 10.1016/j.tetlet.2018.10.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A new prenylated indoxyl alkaloid, Amoenamide B (1), was isolated from Aspergillus amoenus NRRL 35600 along with Asperochramide A (2). Although many prenylated oxyindole alkaloids, containing bicyclo[2.2.2]diazaoctane cores, have been isolated from the fungus of the genera Aspergillus and Penicillium to date, 1 is the fourth compound with the indoxyl unit containing the cores. During the structure elucidation of 1, we found that the planar structure matched to that of Speramide A (3), isolated from A. ochraceus KM007, but the reported structure of 3 was incorrect and turned out to be that of Taichunamide H (4), recently isolated from A. versicolor HDN11-84.
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Affiliation(s)
- Aika Kai
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe-honmachi 5-1, Kumamoto 862-0973, Kumamoto, Japan
| | - Hikaru Kato
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe-honmachi 5-1, Kumamoto 862-0973, Kumamoto, Japan
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Departments of Medicinal Chemistry, Microbiology & Immunology, and Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert M Williams
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, Colorado 80523, United States.,University of Colorado Cancer Center, Aurora, Colorado 80045, United States
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe-honmachi 5-1, Kumamoto 862-0973, Kumamoto, Japan
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Tripathi A, Park SR, Sikkema AP, Cho HJ, Wu J, Lee B, Xi C, Smith JL, Sherman DH. Cover Feature: A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ (ChemBioChem 15/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ashootosh Tripathi
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Department of Medicinal Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Sung Ryeol Park
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Baruch S. Blumberg Institute; Natural Products Discovery Institute; 3805 Old Easton Road Doylestown PA 18902 USA
| | - Andrew P. Sikkema
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Department of Biological Chemistry; University of Michigan; 1150 W. Medical Center Drive Ann Arbor MI 48109 USA
- Epigenetics and Stem Cell Biology Laboratory; National Institute of Environmental Health Sciences; National Institutes of Health; Research Triangle Park NC 27709 USA
| | - Hyo Je Cho
- Department of Pathology; University of Michigan; Ann Arbor MI 48109 USA
| | - Jianfeng Wu
- Department of Environmental Health Sciences; University of Michigan School of Public Health; Ann Arbor MI 48109 USA
| | - Brian Lee
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Chuanwu Xi
- Department of Environmental Health Sciences; University of Michigan School of Public Health; Ann Arbor MI 48109 USA
| | - Janet L. Smith
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Department of Biological Chemistry; University of Michigan; 1150 W. Medical Center Drive Ann Arbor MI 48109 USA
| | - David H. Sherman
- Life Sciences Institute; University of Michigan; 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Department of Medicinal Chemistry; University of Michigan; Ann Arbor MI 48109 USA
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
- Department of Microbiology and Immunology; University of Michigan; Ann Arbor MI 48109 USA
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Tripathi A, Park SR, Sikkema AP, Cho HJ, Wu J, Lee B, Xi C, Smith JL, Sherman DH. A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ. Chembiochem 2018; 19:1595-1600. [PMID: 29742306 PMCID: PMC6105470 DOI: 10.1002/cbic.201800233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 01/02/2023]
Abstract
Cahuitamycins are biofilm inhibitors assembled by a convergent nonribosomal peptide synthetase pathway. Previous genetic analysis indicated that a discrete enzyme, CahJ, serves as a gatekeeper for cahuitamycin structural diversification. Here, the CahJ protein was probed structurally and functionally to guide the formation of new analogues by mutasynthetic studies. This analysis enabled the in vivo production of a new cahuitamycin congener through targeted precursor incorporation.
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Affiliation(s)
- Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Baruch S. Blumberg Institute, Natural Products Discovery Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Andrew P Sikkema
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianfeng Wu
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Brian Lee
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Chuanwu Xi
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
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Sugimoto K, Sadahiro Y, Kagiyama I, Kato H, Sherman DH, Williams RM, Tsukamoto S. Corrigendum to “Isolation of amoenamide A and five antipodal prenylated alkaloids from Aspergillus amoenus NRRL 35600” [Tetrahedron Lett. 58 (2017) 2797–2800]. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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McDonnell KJ, Chemler JA, Bartels PL, O'Brien E, Marvin ML, Ortega J, Stern RH, Raskin L, Li GM, Sherman DH, Barton JK, Gruber SB. A human MUTYH variant linking colonic polyposis to redox degradation of the [4Fe4S] 2+ cluster. Nat Chem 2018; 10:873-880. [PMID: 29915346 DOI: 10.1038/s41557-018-0068-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 04/20/2018] [Indexed: 12/26/2022]
Abstract
The human DNA repair enzyme MUTYH excises mispaired adenine residues in oxidized DNA. Homozygous MUTYH mutations underlie the autosomal, recessive cancer syndrome MUTYH-associated polyposis. We report a MUTYH variant, p.C306W (c.918C>G), with a tryptophan residue in place of native cysteine, that ligates the [4Fe4S] cluster in a patient with colonic polyposis and family history of early age colon cancer. In bacterial MutY, the [4Fe4S] cluster is redox active, allowing rapid localization to target lesions by long-range, DNA-mediated signalling. In the current study, using DNA electrochemistry, we determine that wild-type MUTYH is similarly redox-active, but MUTYH C306W undergoes rapid oxidative degradation of its cluster to [3Fe4S]+, with loss of redox signalling. In MUTYH C306W, oxidative cluster degradation leads to decreased DNA binding and enzyme function. This study confirms redox activity in eukaryotic DNA repair proteins and establishes MUTYH C306W as a pathogenic variant, highlighting the essential role of redox signalling by the [4Fe4S] cluster.
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Affiliation(s)
- Kevin J McDonnell
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Joseph A Chemler
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Phillip L Bartels
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elizabeth O'Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Monica L Marvin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph H Stern
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA. .,Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Stephen B Gruber
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Fraley AE, Sherman DH. Halogenase engineering and its utility in medicinal chemistry. Bioorg Med Chem Lett 2018; 28:1992-1999. [PMID: 29731363 DOI: 10.1016/j.bmcl.2018.04.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 10/17/2022]
Abstract
Halogenation is commonly used in medicinal chemistry to improve the potency of pharmaceutical leads. While synthetic methods for halogenation present selectivity and reactivity challenges, halogenases have evolved over time to perform selective reactions under benign conditions. The optimization of halogenation biocatalysts has utilized enzyme evolution and structure-based engineering alongside biotransformation in a variety of systems to generate stable site-selective variants. The recent improvements in halogenase-catalyzed reactions has demonstrated the utility of these biocatalysts for industrial purposes, and their ability to achieve a broad substrate scope implies a synthetic tractability with increasing relevance in medicinal chemistry.
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Affiliation(s)
- Amy E Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States.
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Abstract
β-Branching is an expansion upon canonical polyketide synthase extension that allows for the installation of diverse chemical moieties in several natural products. Several of these moieties are unique among natural products, including the two vinyl methylesters found in the core structure of bryostatins. This family of molecules is derived from an obligate bacterial symbiont of a sessile marine bryozoan, Bugula neritina. Within this family, bryostatin 1 has been investigated as an anticancer, neuroprotective, and immunomodulatory compound. We have turned to the biosynthetic gene cluster within the bacterial symbiont to investigate the biosynthesis of bryostatins. Recent sequencing efforts resulted in the annotation of two missing genes: bryT and bryU. Using novel chemoenzymatic techniques, we have validated these as the missing enoyl-CoA hydratase and donor acyl carrier protein, essential components of the β-branching cassette of the bryostatin pathway. Together, this cassette installs the vinyl methylester moieties essential to the activity of bryostatins.
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Affiliation(s)
- Samuel T Slocum
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States.
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