1
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McBride CM, Miller EL, Charkoudian LK. An updated catalogue of diverse type II polyketide synthase biosynthetic gene clusters captured from large-scale nucleotide databases. Microb Genom 2023; 9. [PMID: 36951894 PMCID: PMC10132072 DOI: 10.1099/mgen.0.000965] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Nature serves as a rich source of molecules with immense chemical diversity. Aptly named, these 'natural products' boast a wide variety of environmental, medicinal and industrial applications. Type II polyketides, in particular, confer substantial medicinal benefits, including antibacterial, antifungal, anticancer and anti-inflammatory properties. These molecules are produced by enzyme assemblies known as type II polyketide synthases (PKSs), which use domains such as the ketosynthase chain-length factor and acyl carrier protein to produce polyketides with varying lengths, cyclization patterns and oxidation states. In this work, we use a novel bioinformatic workflow to identify biosynthetic gene clusters (BGCs) that code for the core type II PKS enzymes. This method does not rely on annotation and thus was able to unearth previously 'hidden' type II PKS BGCs. This work led us to identify over 6000 putative type II PKS BGCs spanning a diverse set of microbial phyla, nearly double those found in most recent studies. Notably, many of these newly identified BGCs were found in non-actinobacteria, which are relatively underexplored as sources of type II polyketides. Results from this work lay an important foundation for future bioprospecting and engineering efforts that will enable sustainable access to diverse and structurally complex molecules with medicinally relevant properties.
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Affiliation(s)
| | - Eric L Miller
- Department of Biology, Haverford College, Haverford, PA, USA
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2
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Romei M, von Krusenstiern EV, Ridings ST, King RN, Fortier JC, McKeon CA, Nichols KM, Charkoudian LK, Londergan CH. Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments. J Phys Chem B 2023; 127:85-94. [PMID: 36538691 PMCID: PMC9841980 DOI: 10.1021/acs.jpcb.2c06176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/29/2022] [Revised: 11/19/2022] [Indexed: 12/24/2022]
Abstract
The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.
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Affiliation(s)
- Matthew
G. Romei
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Eliana V. von Krusenstiern
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Stephen T. Ridings
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Renee N. King
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Julia C. Fortier
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Caroline A. McKeon
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Krysta M. Nichols
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
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3
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Feeney MA, Newitt JT, Addington E, Algora-Gallardo L, Allan C, Balis L, Birke AS, Castaño-Espriu L, Charkoudian LK, Devine R, Gayrard D, Hamilton J, Hennrich O, Hoskisson PA, Keith-Baker M, Klein JG, Kruasuwan W, Mark DR, Mast Y, McHugh RE, McLean TC, Mohit E, Munnoch JT, Murray J, Noble K, Otani H, Parra J, Pereira CF, Perry L, Pintor-Escobar L, Pritchard L, Prudence SMM, Russell AH, Schniete JK, Seipke RF, Sélem-Mojica N, Undabarrena A, Vind K, van Wezel GP, Wilkinson B, Worsley SF, Duncan KR, Fernández-Martínez LT, Hutchings MI. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria. Microb Genom 2022; 8. [PMID: 35775972 PMCID: PMC9455695 DOI: 10.1099/mgen.0.000824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Indexed: 11/18/2022] Open
Abstract
Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.
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Affiliation(s)
- Morgan Anne Feeney
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jake Terry Newitt
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Emily Addington
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Lis Algora-Gallardo
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Craig Allan
- Swansea University Institute of Life Science, College of Medicine, Swansea, Wales, UK
| | - Lucas Balis
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anna S Birke
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Laia Castaño-Espriu
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jacob Hamilton
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Oliver Hennrich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Paul A Hoskisson
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Molly Keith-Baker
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Worarat Kruasuwan
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David R Mark
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rebecca E McHugh
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Thomas C McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Elmira Mohit
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - John T Munnoch
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jordan Murray
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA 94720, USA
| | - Jonathan Parra
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Camila F Pereira
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Louisa Perry
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Leighton Pritchard
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Samuel M M Prudence
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | | | - Jana K Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nelly Sélem-Mojica
- Universidad Nacional Autónoma de México, Centro de Ciencias Matemáticas, en Morelia, Michoacán, Mexico
| | - Agustina Undabarrena
- Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Valparaíso, 2340000, Chile
| | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Rapenburg, The Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
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4
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Greule A, Izoré T, Machell D, Hansen MH, Schoppet M, De Voss JJ, Charkoudian LK, Schittenhelm RB, Harmer JR, Cryle MJ. The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage. Front Chem 2022; 10:868240. [PMID: 35464232 PMCID: PMC9023744 DOI: 10.3389/fchem.2022.868240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenases that utilize a cysteine thiolate–ligated heme moiety to perform a wide range of demanding oxidative transformations. Given the oxidative power of the active intermediate formed within P450s during their active cycle, it is remarkable that these enzymes can avoid auto-oxidation and retain the axial cysteine ligand in the deprotonated—and thus highly acidic—thiolate form. While little is known about the process of heme incorporation during P450 folding, there is an overwhelming preference for one heme orientation within the P450 active site. Indeed, very few structures to date contain an alternate heme orientation, of which two are OxyA homologs from glycopeptide antibiotic (GPA) biosynthesis. Given the apparent preference for the unusual heme orientation shown by OxyA enzymes, we investigated the OxyA homolog from kistamicin biosynthesis (OxyAkis), which is an atypical GPA. We determined that OxyAkis is highly sensitive to oxidative damage by peroxide, with both UV and EPR measurements showing rapid bleaching of the heme signal. We determined the structure of OxyAkis and found a mixed population of heme orientations present in this enzyme. Our analysis further revealed the possible modification of the heme moiety, which was only present in samples where the alternate heme orientation was present in the protein. These results suggest that the typical heme orientation in cytochrome P450s can help prevent potential damage to the heme—and hence deactivation of the enzyme—during P450 catalysis. It also suggests that some P450 enzymes involved in GPA biosynthesis may be especially prone to oxidative damage due to the heme orientation found in their active sites.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - Daniel Machell
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Mathias H. Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - James J. De Voss
- Department of Chemistry, The University of Queensland, St Lucia, QLD, Australia
| | | | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Jeffrey R. Harmer
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- *Correspondence: Max J. Cryle,
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5
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Cho YI, Armstrong CL, Sulpizio A, Acheampong KK, Banks KN, Bardhan O, Churchill SJ, Connolly-Sporing AE, Crawford CE, Cruz Parrilla PL, Curtis SM, De La Ossa LM, Epstein SC, Farrehi CJ, Hamrick GS, Hillegas WJ, Kang A, Laxton OC, Ling J, Matsumura SM, Merino VM, Mukhtar SH, Shah NJ, Londergan CH, Daly CA, Kokona B, Charkoudian LK. Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins. Biochemistry 2022; 61:217-227. [PMID: 35073057 PMCID: PMC9357449 DOI: 10.1021/acs.biochem.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/23/2022]
Abstract
The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.
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Affiliation(s)
- Yae In Cho
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | - Oishi Bardhan
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | - Sarah M. Curtis
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | | | - Austin Kang
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Joie Ling
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | - Neel J. Shah
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Clyde A. Daly
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA 19041
- Spark Therapeutics, Philadelphia PA 19041
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6
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Hamrick GS, Londergan CH, Charkoudian LK. Heterologous Expression, Purification, and Characterization of Type II Polyketide Synthase Acyl Carrier Proteins. Methods Mol Biol 2022; 2489:239-267. [PMID: 35524054 PMCID: PMC9373356 DOI: 10.1007/978-1-0716-2273-5_13] [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] [Indexed: 06/14/2023]
Abstract
The enzymes that comprise type II polyketide synthases (PKSs) are powerful biocatalysts that, once well-understood and strategically applied, could enable cost-effective and sustainable access to a range of pharmaceutically relevant molecules. Progress toward this goal hinges on gaining ample access to materials for in vitro characterizations and structural analysis of the components of these synthases. A central component of PKSs is the acyl carrier protein (ACP), which serves as a hub during the biosynthesis of type II polyketides. Herein, we share methods for accessing type II PKS ACPs via heterologous expression in E. coli . We also share how the installation of reactive and site-specific spectroscopic probes can be leveraged to study the conformational dynamics and interactions of type II PKS ACPs.
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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8
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Klein JG, Wu Y, Kokona B, Charkoudian LK. Widening the bottleneck: Heterologous expression, purification, and characterization of the Ktedonobacter racemifer minimal type II polyketide synthase in Escherichia coli. Bioorg Med Chem 2020; 28:115686. [PMID: 33069071 DOI: 10.1016/j.bmc.2020.115686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/18/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Enzyme assemblies such as type II polyketide synthases (PKSs) produce a wide array of bioactive secondary metabolites. While the molecules produced by type II PKSs have found remarkable clinical success, the biosynthetic prowess of these enzymes has been stymied by 1) the inability to reconstitute the bioactivity of the minimal PKS enzymes in vitro and 2) limited exploration of type II PKSs from diverse phyla. To begin filling this unmet need, we expressed, purified, and characterized the ketosynthase chain length factor (KS-CLF) and acyl carrier protein (ACP) from Ktedonobacter racemifer (Kr). Using E. coli as a heterologous host, we obtained soluble proteins in titers signifying improvements over previous KS-CLF heterologous expression efforts. Characterization of these enzymes reveals that KrACP has self-malonylating activity. Sedimentation velocity analytical ultracentrifugation (SV-AUC) analysis of holo-KrACP and KrKS-CLF indicates that these enzymes do not interact in vitro, suggesting that the acylated state of these proteins might play an important role in facilitating biosynthetically relevant interactions. These results lay important groundwork for optimizing the interaction between KrKS-CLF and KrACP and exploring the biosynthetic potential of other non-actinomycete type II PKSs.
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Affiliation(s)
- Joshua G Klein
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States
| | - Yang Wu
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States
| | - Bashkim Kokona
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States.
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9
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Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, Selem-Mojica N, Alanjary M, Robinson SL, Lund G, Epstein SC, Sisto AC, Charkoudian LK, Collemare J, Linington RG, Weber T, Medema MH. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res 2020; 48:D454-D458. [PMID: 31612915 PMCID: PMC7145714 DOI: 10.1093/nar/gkz882] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022] Open
Abstract
Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.
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Affiliation(s)
- Satria A Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Simon Shaw
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Jorge C Navarro-Muñoz
- Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, Utrecht, NL, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | | | | | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | | | | | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, MX, Mexico
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | - Serina L Robinson
- BioTechnology Institute, University of Minnesota-Twin Cities, MN, USA
| | - George Lund
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | | | - Ashley C Sisto
- Department of Chemistry, Haverford College, Haverford, PA, USA
| | | | - Jérôme Collemare
- Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, Utrecht, NL, The Netherlands
| | | | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
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10
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Klein JG, Kokona B, Charkoudian LK. Heterologous Expression and Characterization of Ancient Orphaned Type II Polyketide Synthase Enzymes. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03798] [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: 11/11/2022]
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11
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Armstrong C, Kokona B, Charkoudian LK. Constructing Combinatorial Synthases Using Acyl Carrier Protein Chimeras. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03784] [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: 11/11/2022]
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12
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Hamrick GS, Hoang J, Kokona B, Charkoudian LK. Bioprospecting for Novel Natural Products in Ancient Non‐Actinobacteria. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04372] [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: 11/11/2022]
Affiliation(s)
| | - June Hoang
- Department of Chemistry Haverford College
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13
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Acheampong KK, Kokona B, Braun GA, Jacobsen DR, Johnson KA, Charkoudian LK. Colorimetric Assay Reports on Acyl Carrier Protein Interactions. Sci Rep 2019; 9:15589. [PMID: 31666546 PMCID: PMC6821831 DOI: 10.1038/s41598-019-51554-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 06/16/2019] [Accepted: 09/25/2019] [Indexed: 01/15/2023] Open
Abstract
The ability to produce new molecules of potential pharmaceutical relevance via combinatorial biosynthesis hinges on improving our understanding of acyl-carrier protein (ACP)-protein interactions. However, the weak and transient nature of these interactions makes them difficult to study using traditional spectroscopic approaches. Herein we report that converting the terminal thiol of the E. coli ACP 4'-phosphopantetheine arm into a mixed disulfide with 2-nitro-5-thiobenzoate ion (TNB-) activates this site to form a selective covalent cross-link with the active site cysteine of a cognate ketoacyl synthase (KS). The concomitant release of TNB2-, which absorbs at 412 nm, provides a visual and quantitative measure of mechanistically relevant ACP-KS interactions. The colorimetric assay can propel the engineering of biosynthetic routes to novel chemical diversity by providing a high-throughput screen for functional hybrid ACP-KS partnerships as well as the discovery of novel antimicrobial agents by enabling the rapid identification of small molecule inhibitors of ACP-KS interactions.
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Affiliation(s)
- Kofi K Acheampong
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | | | - Karl A Johnson
- Department of Biology, Haverford College, Haverford, PA, 19041-1391, USA.
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14
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Abstract
Engineering microbial biosynthetic pathways represents a compelling route to gain access to expanded chemical diversity. Carrier proteins (CPs) play a central role in biosynthesis, but the fast motions of CPs make their conformational dynamics difficult to capture using traditional spectroscopic approaches. Here we present a low-resource method to directly reveal carrier protein-substrate interactions. Chemoenzymatic loading of commercially available, alkyne-containing substrates onto CPs enables rapid visualization of the molecular cargo's local environment using Raman spectroscopy. This method could clarify the foundations of the chain sequestration mechanism, facilitate the rapid characterization of CPs, and enable visualization of the vectoral processing of natural products both in vitro and in vivo.
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Affiliation(s)
- Samuel C Epstein
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Adam R Huff
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Emily S Winesett
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Casey H Londergan
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA.
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15
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Greule A, Charkoudian LK, Cryle MJ. Studying trans-acting enzymes that target carrier protein-bound amino acids during nonribosomal peptide synthesis. Methods Enzymol 2019; 617:113-154. [PMID: 30784400 DOI: 10.1016/bs.mie.2018.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/10/2023]
Abstract
Nonribosomal peptide biosynthesis is a complex enzymatic assembly responsible for producing a great diversity of bioactive peptide natural products. Due to the recurring arrangement of catalytic domains within these machineries, great interest has been shown in reengineering these pathways to produce novel, designer peptide products. However, in order to realize such ambitions, it is first necessary to develop a comprehensive understanding of the selectivity, mechanisms, and structure of these complex enzymes, which in turn requires significant in vitro experiments. Within nonribosomal biosynthesis, some modifications are performed by enzymatic domains that are not linked to the main nonribosomal peptide synthetase but rather act in trans: these systems offer great potential for redesign, but in turn require detailed study. In this chapter, we present an overview of in vitro experiments that can be used to characterize examples of such trans-interacting enzymes from nonribosomal peptide biosynthesis: Cytochrome P450 monooxygenases and flavin-dependent halogenases.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia
| | | | - Max J Cryle
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia.
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16
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Rivas MA, Courouble VC, Baker MC, Cookmeyer DL, Fiore KE, Frost AJ, Godbe KN, Jordan MR, Krasnow EN, Mollo A, Ridings ST, Sawada K, Shroff KD, Studnitzer B, Thiele GAR, Sisto AC, Nawal S, Huff AR, Fairman R, Johnson KA, Beld J, Kokona B, Charkoudian LK. The Effect of Divalent Cations on the Thermostability of Type II Polyketide Synthase Acyl Carrier Proteins. AIChE J 2018; 64:4308-4318. [PMID: 31527922 DOI: 10.1002/aic.16402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The successful engineering of biosynthetic pathways hinges on understanding the factors that influence acyl carrier protein (ACP) stability and function. The stability and structure of ACPs can be influenced by the presence of divalent cations, but how this relates to primary sequence remains poorly understood. As part of a course-based undergraduate research experience, we investigated the thermostability of type II polyketide synthase (PKS) ACPs. We observed an approximate 40 °C range in the thermostability amongst the 14 ACPs studied, as well as an increase in stability (5 - 26 °C) of the ACPs in the presence of divalent cations. Distribution of charges in the helix II-loop-helix III region was found to impact the enthalpy of denaturation. Taken together, our results reveal clues as to how the sequence of type II PKS ACPs relates to their structural stability, information that can be used to study how ACP sequence relates to function.
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Affiliation(s)
| | - Valentine C. Courouble
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Miranda C. Baker
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Kristen E. Fiore
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Alexander J. Frost
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Michael R. Jordan
- Dept. of Physics Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Emily N. Krasnow
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Aurelio Mollo
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Stephen T. Ridings
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Keisuke Sawada
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Kavita D. Shroff
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Bradley Studnitzer
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Grace A. R. Thiele
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Saadia Nawal
- Dept. of Chemistry Haverford College Haverford PA 19041
| | - Adam R. Huff
- Dept. of Chemistry Haverford College Haverford PA 19041
| | | | | | - Joris Beld
- Dept. of Microbiology and Immunology Drexel University College of Medicine Philadelphia PA 19102
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17
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Lopes LE, Waldis SJ, Terrell SM, Lindgren KA, Charkoudian LK. Vibrant symbiosis: Achieving reciprocal science outreach through biological art. PLoS Biol 2018; 16:e3000061. [PMID: 30500814 PMCID: PMC6291146 DOI: 10.1371/journal.pbio.3000061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/12/2018] [Indexed: 11/18/2022] Open
Abstract
Scientific outreach efforts traditionally involve formally trained scientists teaching the general public about the methods, significance, and excitement of science. We recently experimented with an alternative “symbiotic outreach” model that prioritizes building a reciprocal relationship between formally trained and “outsider” scientists to facilitate active two-way communication. Herein, we present the results of our outreach effort involving college students and adults with intellectual and developmental disabilities working together to make biological and multimedia art. By discussing the steps others can take to cultivate reciprocal outreach within their local communities, we hope to lower the barrier for widespread adoption of similar approaches and ultimately to decrease the gap between formally trained scientists and the general public. This Community Page article presents an alternative outreach model that prioritizes building a reciprocal relationship between scientists and outsiders, describes an example involving college students and adult artists with intellectual and developmental disabilities working together to create BioArt, and discusses how others can cultivate similar opportunities within their local communities.
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Affiliation(s)
- Lindsey E. Lopes
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Sarah J. Waldis
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Stephanie M. Terrell
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Kristin A. Lindgren
- Health Studies Program, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail: (KL); (LC)
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail: (KL); (LC)
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18
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Epstein SC, Charkoudian LK, Medema MH. A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 2018; 13:16. [PMID: 30008988 PMCID: PMC6042397 DOI: 10.1186/s40793-018-0318-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
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Affiliation(s)
- Samuel C. Epstein
- Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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19
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Terrell SM, Wu Y, Klein JG, Charkoudian LK. Accessing new chemical diversity from ancient non‐actinobacterial strains. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.656.21] [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: 11/11/2022]
Affiliation(s)
| | - Yang Wu
- Haverford CollegeHaverfordPA
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20
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Epstein SC, Medema MH, Charkoudian LK. The Minimum Information About A Biosynthetic Gene Cluster Standard as a Means of Organizing Bioinformatic Data. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.547.2] [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: 11/11/2022]
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21
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Chioti VT, Londergan CH, Charkoudian LK. Studying protein‐protein interactions in fatty acid and polyketide biosynthetic pathways via site‐specific vibrational spectroscopy. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.792.8] [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: 11/11/2022]
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22
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Rivas M, Courouble V, Sisto A, Beld J, Kokona B, Charkoudian LK. Thermal Stability of Type II Polyketide Acyl Carrier Proteins. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.792.14] [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: 11/11/2022]
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23
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Abstract
Course-based undergraduate research experiences (CUREs) have gained traction as effective ways to expand the impact of undergraduate research while fulfilling pedagogical goals. In this Perspective, we present innovative ways to incorporate fundamental benefits and principles of CUREs into a classroom environment through information/technology-based research projects that lead to student-generated contributions to digital community resources (CoRes). These projects represent an attractive class of CUREs because they are less resource-intensive than laboratory-based CUREs, and the projects align with the expectations of today's students to create rapid and publicly accessible contributions to society. We provide a detailed discussion of two example types of CoRe projects that can be implemented in courses to impact research and education at the chemistry-biology interface: bioinformatics annotations and development of educational tools. Finally, we present current resources available for faculty interested in incorporating CUREs or CoRe projects into their pedagogical practices. In sharing these stories and resources, we hope to lower the barrier for widespread adoption of CURE and CoRe approaches and generate discussions about how to utilize the classroom experience to make a positive impact on our students and the future of the field of biochemistry.
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Affiliation(s)
- Kathryn L Haas
- Department of Chemistry & Physics, Saint Mary's College , Notre Dame, Indiana 46556, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University , Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Louise K Charkoudian
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
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24
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Cookmeyer DL, Winesett ES, Kokona B, Huff AR, Aliev S, Bloch NB, Bulos JA, Evans IL, Fagre CR, Godbe KN, Khromava M, Konstantinovsky DM, Lafrance AE, Lamacki AJ, Parry RC, Quinn JM, Thurston AM, Tsai KJS, Mollo A, Cryle MJ, Fairman R, Charkoudian LK. Uncovering protein-protein interactions through a team-based undergraduate biochemistry course. PLoS Biol 2017; 15:e2003145. [PMID: 29091712 PMCID: PMC5683658 DOI: 10.1371/journal.pbio.2003145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/13/2017] [Indexed: 11/30/2022] Open
Abstract
How can we provide fertile ground for students to simultaneously explore a breadth of foundational knowledge, develop cross-disciplinary problem-solving skills, gain resiliency, and learn to work as a member of a team? One way is to integrate original research in the context of an undergraduate biochemistry course. In this Community Page, we discuss the development and execution of an interdisciplinary and cross-departmental undergraduate biochemistry laboratory course. We present a template for how a similar course can be replicated at other institutions and provide pedagogical and research results from a sample module in which we challenged our students to study the binding interface between 2 important biosynthetic proteins. Finally, we address the community and invite others to join us in making a larger impact on undergraduate education and the field of biochemistry by coordinating efforts to integrate research and teaching across campuses.
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Affiliation(s)
- David L. Cookmeyer
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Emily S. Winesett
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Adam R. Huff
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Sabina Aliev
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Noah B. Bloch
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Joshua A. Bulos
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Irene L. Evans
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Christian R. Fagre
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Kerilyn N. Godbe
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Maryna Khromava
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | | | - Alexander E. Lafrance
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Alexandra J. Lamacki
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Robert C. Parry
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Jeanne M. Quinn
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Alana M. Thurston
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Kathleen J. S. Tsai
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Aurelio Mollo
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Max J. Cryle
- The Monash Biomedical Discovery Institute, EMBL Australia, Monash University, Clayton, Victoria, Australia
- The Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail: (LKC); (RF)
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail: (LKC); (RF)
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25
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Thiele GAR, Friedman CP, Tsai KJS, Beld J, Londergan CH, Charkoudian LK. Acyl Carrier Protein Cyanylation Delivers a Ketoacyl Synthase-Carrier Protein Cross-Link. Biochemistry 2017; 56:2533-2536. [PMID: 28448715 DOI: 10.1021/acs.biochem.7b00219] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Acyl carrier proteins (ACPs) are central hubs in polyketide and fatty acid biosynthetic pathways, but the fast motions of the ACP's phosphopantetheine (Ppant) arm make its conformational dynamics difficult to capture using traditional spectroscopic approaches. Here we report that converting the terminal thiol of Escherichia coli ACP's Ppant arm into a thiocyanate activates this site to form a selective cross-link with the active site cysteine of its partner ketoacyl synthase (FabF). The reaction releases a cyanide anion, which can be detected by infrared spectroscopy. This represents a practical and generalizable method for obtaining and visualizing ACP-protein complexes relevant to biocatalysis and will be valuable in future structural and engineering studies.
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Affiliation(s)
- Grace A R Thiele
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
| | - Connie P Friedman
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
| | - Kathleen J S Tsai
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102, United States
| | - Casey H Londergan
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
| | - Louise K Charkoudian
- Department of Chemistry, Haverford College , Haverford, Pennsylvania 19041-1392, United States
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26
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Finzel K, Beld J, Burkart MD, Charkoudian LK. Utilizing Mechanistic Cross-Linking Technology to Study Protein-Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab. J Chem Educ 2017; 94:375-379. [PMID: 29255327 PMCID: PMC5731787 DOI: 10.1021/acs.jchemed.6b00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Over the past decade, mechanistic crosslinking probes have been used to study protein-protein interactions in natural product biosynthetic pathways. This approach is highly interdisciplinary, combining elements of protein biochemistry, organic chemistry, and computational docking. The development of an experiment to engage undergraduate students in multidisciplinary research is described that leverages mechanistic crosslinking probes to study protein conformations and protein-protein interactions. This experiment provides students with a platform to learn chemoenzymatic synthesis, polyacrylamide gel electrophoresis, biochemical assays, and computational docking all while exploring a contemporary biochemical topic.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, 19041, United States
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27
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Mollo A, von Krusenstiern AN, Bulos JA, Ulrich V, Åkerfeldt KS, Cryle MJ, Charkoudian LK. P450 monooxygenase ComJ catalyses side chain phenolic cross-coupling during complestatin biosynthesis. RSC Adv 2017. [DOI: 10.1039/c7ra06518c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
P450 monooxygenase enzyme ComJ catalyzed biaryl ether bond formation with high efficiency and low stereoselectivity on selected complestatin-like peptide substrates.
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Affiliation(s)
- Aurelio Mollo
- Department of Chemistry
- Haverford College
- Haverford
- USA
| | | | | | - Veronika Ulrich
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
| | | | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
- EMBL Australia
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. New Structural Data Reveal the Motion of Carrier Proteins in Nonribosomal Peptide Synthesis. Angew Chem Int Ed Engl 2016; 55:9834-40. [PMID: 27435901 PMCID: PMC5113783 DOI: 10.1002/anie.201602614] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 03/15/2016] [Indexed: 12/28/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are one of the most promising resources for the production of new bioactive molecules. The mechanism of NRPS catalysis is based around sequential catalytic domains: these are organized into modules, where each module selects, modifies, and incorporates an amino acid into the growing peptide. The intermediates formed during NRPS catalysis are delivered between enzyme centers by peptidyl carrier protein (PCP) domains, which makes PCP interactions and movements crucial to NRPS mechanism. PCP movement has been linked to the domain alternation cycle of adenylation (A) domains, and recent complete NRPS module structures provide support for this hypothesis. However, it appears as though the A domain alternation alone is insufficient to account for the complete NRPS catalytic cycle and that the loaded state of the PCP must also play a role in choreographing catalysis in these complex and fascinating molecular machines.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Aurelio Mollo
- Department of Chemistry, Haverford College, Haverford, PA, 19041, USA
| | | | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. .,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia. .,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. Neue Strukturdaten geben Einblick in die Bewegungen von Transportproteinen in der nicht-ribosomalen Peptidsynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Tiia Kittilä
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | - Aurelio Mollo
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | | | - Max J. Cryle
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
- EMBL Australia; Monash University; Clayton Victoria 3800 Australien
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging; Monash University; Clayton VIC 3800 Australien
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Kokona B, Winesett ES, Nikolai von Krusenstiern A, Cryle MJ, Fairman R, Charkoudian LK. Probing the selectivity of β-hydroxylation reactions in non-ribosomal peptide synthesis using analytical ultracentrifugation. Anal Biochem 2016; 495:42-51. [DOI: 10.1016/j.ab.2015.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/17/2022]
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Li YF, Tsai KJS, Harvey CJB, Li JJ, Ary BE, Berlew EE, Boehman BL, Findley DM, Friant AG, Gardner CA, Gould MP, Ha JH, Lilley BK, McKinstry EL, Nawal S, Parry RC, Rothchild KW, Silbert SD, Tentilucci MD, Thurston AM, Wai RB, Yoon Y, Aiyar RS, Medema MH, Hillenmeyer ME, Charkoudian LK. Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. Fungal Genet Biol 2016; 89:18-28. [PMID: 26808821 DOI: 10.1016/j.fgb.2016.01.012] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [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: 09/15/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
Microorganisms produce a wide range of natural products (NPs) with clinically and agriculturally relevant biological activities. In bacteria and fungi, genes encoding successive steps in a biosynthetic pathway tend to be clustered on the chromosome as biosynthetic gene clusters (BGCs). Historically, "activity-guided" approaches to NP discovery have focused on bioactivity screening of NPs produced by culturable microbes. In contrast, recent "genome mining" approaches first identify candidate BGCs, express these biosynthetic genes using synthetic biology methods, and finally test for the production of NPs. Fungal genome mining efforts and the exploration of novel sequence and NP space are limited, however, by the lack of a comprehensive catalog of BGCs encoding experimentally-validated products. In this study, we generated a comprehensive reference set of fungal NPs whose biosynthetic gene clusters are described in the published literature. To generate this dataset, we first identified NCBI records that included both a peer-reviewed article and an associated nucleotide record. We filtered these records by text and homology criteria to identify putative NP-related articles and BGCs. Next, we manually curated the resulting articles, chemical structures, and protein sequences. The resulting catalog contains 197 unique NP compounds covering several major classes of fungal NPs, including polyketides, non-ribosomal peptides, terpenoids, and alkaloids. The distribution of articles published per compound shows a bias toward the study of certain popular compounds, such as the aflatoxins. Phylogenetic analysis of biosynthetic genes suggests that much chemical and enzymatic diversity remains to be discovered in fungi. Our catalog was incorporated into the recently launched Minimum Information about Biosynthetic Gene cluster (MIBiG) repository to create the largest known set of fungal BGCs and associated NPs, a resource that we anticipate will guide future genome mining and synthetic biology efforts toward discovering novel fungal enzymes and metabolites.
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Affiliation(s)
- Yong Fuga Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States; Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Kathleen J S Tsai
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Colin J B Harvey
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - James Jian Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - Beatrice E Ary
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | - Erin E Berlew
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Brenna L Boehman
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - David M Findley
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Alexandra G Friant
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | | | - Michael P Gould
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Jae H Ha
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | - Brenna K Lilley
- Department of Biology, Haverford College, Haverford, PA, United States
| | - Emily L McKinstry
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Saadia Nawal
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Robert C Parry
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | | | - Samantha D Silbert
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | | | - Alana M Thurston
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Rebecca B Wai
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Yongjin Yoon
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Raeka S Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, The Netherlands
| | - Maureen E Hillenmeyer
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States.
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Morlon H, O'Connor TK, Bryant JA, Charkoudian LK, Docherty KM, Jones E, Kembel SW, Green JL, Bohannan BJM. The Biogeography of Putative Microbial Antibiotic Production. PLoS One 2015; 10:e0130659. [PMID: 26102275 PMCID: PMC4478008 DOI: 10.1371/journal.pone.0130659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 05/25/2015] [Indexed: 01/28/2023] Open
Abstract
Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.
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Affiliation(s)
- Hélène Morlon
- Institut de Biologie, UMR CNRS 8197, Ecole Normale Supérieure, Paris, France
- * E-mail:
| | - Timothy K. O'Connor
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Jessica A. Bryant
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
| | - Kathryn M. Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, United States of America
| | - Evan Jones
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Steven W. Kembel
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Jessica L. Green
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Brendan J. M. Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Johnson MNR, Londergan CH, Charkoudian LK. Correction to “Probing the Phosphopantetheine Arm Conformations of Acyl Carrier Proteins Using Vibrational Spectroscopy”. J Am Chem Soc 2014. [PMCID: PMC4183641 DOI: 10.1021/ja508661x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Johnson MR, Londergan CH, Charkoudian LK. Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy. J Am Chem Soc 2014; 136:11240-3. [PMID: 25080832 PMCID: PMC4140477 DOI: 10.1021/ja505442h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 12/23/2022]
Abstract
Acyl carrier proteins (ACPs) are universal and highly conserved domains central to both fatty acid and polyketide biosynthesis. These proteins tether reactive acyl intermediates with a swinging 4'-phosphopantetheine (Ppant) arm and interact with a suite of catalytic partners during chain transport and elongation while stabilizing the growing chain throughout the biosynthetic pathway. The flexible nature of the Ppant arm and the transient nature of ACP-enzyme interactions impose a major obstacle to obtaining structural information relevant to understanding polyketide and fatty acid biosynthesis. To overcome this challenge, we installed a thiocyanate vibrational spectroscopic probe on the terminal thiol of the ACP Ppant arm. This site-specific probe successfully reported on the local environment of the Ppant arm of two ACPs previously characterized by solution NMR, and was used to determine the solution exposure of the Ppant arm of an ACP from 6-deoxyerythronolide B synthase (DEBS). Given the sensitivity of the probe's CN stretching band to conformational distributions resolved on the picosecond time scale, this work lays a foundation for observing the dynamic action-related structural changes of ACPs using vibrational spectroscopy.
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Affiliation(s)
- Matthew
N. R. Johnson
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
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Walker MC, Thuronyi BW, Charkoudian LK, Lowry B, Khosla C, Chang MCY. Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science 2013; 341:1089-94. [PMID: 24009388 DOI: 10.1126/science.1242345] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.
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Affiliation(s)
- Mark C Walker
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA
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Abstract
A-74528 is a C30 polyketide natural product that functions as an inhibitor of 2',5'-oligoadenylate phosphodiesterase (2'-PDE), a key regulatory enzyme of the interferon pathway. Modulation of 2'-PDE represents a unique therapeutic approach for regulating viral infections. The gene cluster responsible for biosynthesis of A-74528 yields minute amounts of this natural product together with considerably larger quantities of a structurally dissimilar C30 cytotoxic agent, fredericamycin. Through construction and analysis of a series of knockout mutants, we identified the genes necessary for A-74528 biosynthesis. Remarkably, the formation of six stereocenters and the regiospecific formation of six rings in A-74528 appear to be catalyzed by only two tailoring enzymes, a cyclase and an oxygenase, in addition to the core polyketide synthase. The inferred pathway was genetically refactored in a heterologous host, Streptomyces coelicolor CH999, to produce 3 mg/L A-74528 in the absence of fredericamycin.
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Affiliation(s)
- Jay T Fitzgerald
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Charkoudian LK, Liu CW, Capone S, Kapur S, Cane DE, Togni A, Seebach D, Khosla C. Probing the interactions of an acyl carrier protein domain from the 6-deoxyerythronolide B synthase. Protein Sci 2011; 20:1244-55. [PMID: 21563224 DOI: 10.1002/pro.652] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The assembly-line architecture of polyketide synthases (PKSs) provides an opportunity to rationally reprogram polyketide biosynthetic pathways to produce novel antibiotics. A fundamental challenge toward this goal is to identify the factors that control the unidirectional channeling of reactive biosynthetic intermediates through these enzymatic assembly lines. Within the catalytic cycle of every PKS module, the acyl carrier protein (ACP) first collaborates with the ketosynthase (KS) domain of the paired subunit in its own homodimeric module so as to elongate the growing polyketide chain and then with the KS domain of the next module to translocate the newly elongated polyketide chain. Using NMR spectroscopy, we investigated the features of a structurally characterized ACP domain of the 6-deoxyerythronolide B synthase that contribute to its association with its KS translocation partner. Not only were we able to visualize selective protein-protein interactions between the two partners, but also we detected a significant influence of the acyl chain substrate on this interaction. A novel reagent, CF₃-S-ACP, was developed as a ¹⁹F NMR spectroscopic probe of protein-protein interactions. The implications of our findings for understanding intermodular chain translocation are discussed.
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Zaleta-Rivera K, Charkoudian LK, Ridley CP, Khosla C. Cloning, sequencing, heterologous expression, and mechanistic analysis of A-74528 biosynthesis. J Am Chem Soc 2010; 132:9122-8. [PMID: 20550125 DOI: 10.1021/ja102519v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [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
A-74528 is a recently discovered natural product of Streptomyces sp. SANK 61196 that inhibits 2',5'-oligoadenylate phosphodiesterase (2'-PDE), a key regulatory enzyme of the interferon pathway. Inhibition of 2'-PDE by A-74528 reduces viral replication, and therefore shows promise as a new type of antiviral drug. The complete A-74528 gene cluster, comprising 29 open reading frames, was cloned and sequenced, and shown to possess a type II polyketide synthase (PKS) at its core. Its identity was confirmed by analysis of a mutant generated by targeted disruption of a PKS gene, and by functional expression in a heterologous Streptomyces host. Remarkably, it showed exceptional end-to-end sequence identity to the gene cluster responsible for biosynthesis of fredericamycin A, a structurally unrelated antitumor antibiotic with a distinct mode of action. Whereas the fredericamycin producing strain, Streptomyces griseus, produced undetectable quantities of A-74528, the A-74528 gene cluster was capable of producing both antibiotics. The biosynthetic roles of three genes, including one that represents the only qualitative difference between the two gene clusters, were investigated by targeted gene disruption. The implications for the evolution of antibiotics with different biological activities from the same gene cluster are discussed.
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Charkoudian LK, Dentchev T, Lukinova N, Wolkow N, Dunaief JL, Franz KJ. Iron prochelator BSIH protects retinal pigment epithelial cells against cell death induced by hydrogen peroxide. J Inorg Biochem 2008; 102:2130-5. [PMID: 18835041 DOI: 10.1016/j.jinorgbio.2008.08.001] [Citation(s) in RCA: 40] [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: 05/29/2008] [Revised: 08/04/2008] [Accepted: 08/13/2008] [Indexed: 10/21/2022]
Abstract
Dysregulation of localized iron homeostasis is implicated in several degenerative diseases, including Parkinson's, Alzheimer's, and age-related macular degeneration, wherein iron-mediated oxidative stress is hypothesized to contribute to cell death. Inhibiting toxic iron without altering normal metal-dependent processes presents significant challenges for standard small molecule chelating agents. We previously introduced BSIH (isonicotinic acid [2-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-benzylidene]-hydrazide) prochelators that are converted by hydrogen peroxide into SIH (salicylaldehyde isonicotinoyl hydrazone) chelating agents that inhibit iron-catalyzed hydroxyl radical generation. Here, we show that BSIH protects a cultured cell model for retinal pigment epithelium against cell death induced by hydrogen peroxide. BSIH is more stable than SIH in cell culture medium and is more protective during long-term experiments. Repetitive exposure of cells to BSIH is nontoxic, whereas SIH and desferrioxamine induce cell death after repeated exposure. Combined, our results indicate that cell protection by BSIH involves iron sequestration that occurs only when the cells are stressed by hydrogen peroxide. These findings suggest that prochelators discriminate toxic iron from healthy iron and are promising candidates for neuro- and retinal protection.
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Charkoudian LK, Pham DM, Kwon AM, Vangeloff AD, Franz KJ. Modifications of boronic ester pro-chelators triggered by hydrogen peroxide tune reactivity to inhibit metal-promoted oxidative stress. Dalton Trans 2007:5031-42. [DOI: 10.1039/b705199a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Abstract
The synthesis and structural characterization of a new pro-chelating agent, isonicotinic acid [2-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-benzylidene]-hydrazide (BSIH), are presented. BSIH only weakly interacts with iron unless hydrogen peroxide (H2O2) is present to remove the boronic ester protecting group to reveal a phenol that is a key metal-binding group of tridentate salicylaldehyde isonicotinoyl hydrazone (SIH). BSIH prevents deoxyribose degradation caused by hydroxyl radicals that are generated from H2O2 and redox-active iron by sequestering Fe3+ and preventing iron-promoted hydroxyl radical formation. The rate-determining step for iron sequestration is conversion of BSIH to SIH, followed by rapid Fe3+ complexation. The pro-chelate approach of BSIH represents a promising strategy for chelating a specific pool of detrimental metal ions without disturbing healthy metal ion distribution.
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Affiliation(s)
- Louise K Charkoudian
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, North Carolina 27708, USA
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Charkoudian LK, Franz KJ. Fe(III)-Coordination Properties of Neuromelanin Components: 5,6-Dihydroxyindole and 5,6-Dihydroxyindole-2-carboxylic Acid. Inorg Chem 2006; 45:3657-64. [PMID: 16634598 DOI: 10.1021/ic060014r] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fe(III)-coordination chemistry of neuromelanin building-block compounds, 5,6-dihydroxyindole (DHI), 5,6-dihydroxyindole-2-carboxylic acid (DHICA), and 5,6-dihydroxy-N-methyl-indole (Me-DHI), and the neurotransmitter dopamine were explored in aqueous solution by anaerobic pH-dependent spectrophotometric titrations. The Fe(III)-binding constants and pH-dependent speciation parallel those of catechol in that mono, bis, and tris FeLx species are present at concentrations dependent on the pH. The bis FeL2 dihydroxyindole species are favorable for L = DHI and DHICA under neutral to mildly acidic conditions. DHI and DHICA are stronger Fe(III) chelates than catechol, dopamine, and Me-DHI at pH values from 3 to 10. Oxidation studies reveal that iron accelerates the air oxidation of DHI and DHICA.
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Affiliation(s)
- Louise K Charkoudian
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, North Carolina 27708, USA
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