1
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Nartey C, Koo HJ, Laurendon C, Shaik HZ, O’maille P, Noel JP, Morcos F. Coevolutionary Information Captures Catalytic Functions and Reveals Divergent Roles of Terpene Synthase Interdomain Connections. Biochemistry 2024; 63:355-366. [PMID: 38206111 PMCID: PMC10851433 DOI: 10.1021/acs.biochem.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/24/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Inferring the historical and biophysical causes of diversity within protein families is a complex puzzle. A key to unraveling this problem is characterizing the rugged topography of sequence-function adaptive landscapes. Using biochemical data from a 29 = 512 combinatorial library of tobacco 5-epi-aristolochene synthase (TEAS) mutants engineered to make the native major product of Egyptian henbane premnaspirodiene synthase (HPS) and a complementary 512 mutant HPS library, we address the question of how product specificity is controlled. These data sets reveal that HPS is far more robust and resistant to mutations than TEAS, where most mutants are promiscuous. We also combine experimental data with a sequence Potts Hamiltonian model and direct coupling analysis to quantify mutant fitness. Our results demonstrate that the Hamiltonian captures variation in product outputs across both libraries, clusters native family members based on their substrate specificities, and exposes the divergent catalytic roles of couplings between the catalytic and noncatalytic domains of TEAS versus HPS. Specifically, we found that the role of the interdomain connectivities in specifying product output is more important in TEAS than connectivities within the catalytic domain. Despite being 75% identical, this property is not shared by HPS, where connectivities within the catalytic domain are more important for specificity. By solving the X-ray crystal structure of HPS, we assessed structural bases for their interdomain network differences. Last, we calculate the product profile Shannon entropies of the two libraries, which showcases that site-site connectivities also play divergent roles in catalytic accuracy.
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Affiliation(s)
- Charisse
M. Nartey
- Department
of Biological Sciences, The University of
Texas at Dallas, Richardson, Texas 75080, United States
| | - Hyun Jo Koo
- Howard
Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Caroline Laurendon
- John
Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, U.K.
| | - Hana Z. Shaik
- Department
of Bioengineering, The University of Texas
at Dallas, Richardson, Texas 75080, United States
| | - Paul O’maille
- John
Innes Centre, Institute of Food Research, Food & Health Programme, Norwich Research Park, Norwich NR4 7UA, U.K.
| | - Joseph P. Noel
- Howard
Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Faruck Morcos
- Department
of Biological Sciences, The University of
Texas at Dallas, Richardson, Texas 75080, United States
- Department
of Bioengineering, The University of Texas
at Dallas, Richardson, Texas 75080, United States
- Center for
Systems Biology, The University of Texas
at Dallas, Richardson, Texas 75080, United States
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2
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Chen A, Re RN, Davis TD, Tran K, Moriuchi YW, Wu S, La Clair JJ, Louie GV, Bowman ME, Clarke DJ, Mackay CL, Campopiano DJ, Noel JP, Burkart MD. Visualizing the Interface of Biotin and Fatty Acid Biosynthesis through SuFEx Probes. J Am Chem Soc 2024; 146:1388-1395. [PMID: 38176024 DOI: 10.1021/jacs.3c10181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/06/2024]
Abstract
Site-specific covalent conjugation offers a powerful tool to identify and understand protein-protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coli acyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5'-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF-AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Rebecca N Re
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Kelley Tran
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Yuta W Moriuchi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Sitong Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - David J Clarke
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Dominic J Campopiano
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
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3
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Xie L, Bowman ME, Louie GV, Zhang C, Ardejani MS, Huang X, Chu Q, Donaldson CJ, Vaughan JM, Shan H, Powers ET, Kelly JW, Lyumkis D, Noel JP, Saghatelian A. Biochemistry and Protein Interactions of the CYREN Microprotein. Biochemistry 2023; 62:3050-3060. [PMID: 37813856 DOI: 10.1021/acs.biochem.3c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 10/11/2023]
Abstract
Over the past decade, advances in genomics have identified thousands of additional protein-coding small open reading frames (smORFs) missed by traditional gene finding approaches. These smORFs encode peptides and small proteins, commonly termed micropeptides or microproteins. Several of these newly discovered microproteins have biological functions and operate through interactions with proteins and protein complexes within the cell. CYREN1 is a characterized microprotein that regulates double-strand break repair in mammalian cells through interaction with Ku70/80 heterodimer. Ku70/80 binds to and stabilizes double-strand breaks and recruits the machinery needed for nonhomologous end join repair. In this study, we examined the biochemical properties of CYREN1 to better understand and explain its cellular protein interactions. Our findings support that CYREN1 is an intrinsically disordered microprotein and this disordered structure allows it to enriches several proteins, including a newly discovered interaction with SF3B1 via a distinct short linear motif (SLiMs) on CYREN1. Since many microproteins are predicted to be disordered, CYREN1 is an exemplar of how microproteins interact with other proteins and reveals an unknown scaffolding function of this microprotein that may link NHEJ and splicing.
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Affiliation(s)
- Lina Xie
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Cheng Zhang
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maziar S Ardejani
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xuemei Huang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Qian Chu
- Department of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Cynthia J Donaldson
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joan M Vaughan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Huanqi Shan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dimitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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4
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Jiang Z, Chen A, Chen J, Sekhon A, Louie GV, Noel JP, La Clair JJ, Burkart MD. Masked cerulenin enables a dual-site selective protein crosslink. Chem Sci 2023; 14:10925-10933. [PMID: 37829009 PMCID: PMC10566503 DOI: 10.1039/d3sc02864j] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023] Open
Abstract
Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.
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Affiliation(s)
- Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Jeffrey Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Arman Sekhon
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Gordon V Louie
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - Joseph P Noel
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
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5
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Patel A, Mindrebo JT, Misson LE, McCammon JA, Noel JP, Burkart MD. Elucidating the origins of acyltransferase selectivity in primary and secondary metabolism. Biophys J 2023; 122:328a. [PMID: 36783653 DOI: 10.1016/j.bpj.2022.11.1832] [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: 02/12/2023] Open
Affiliation(s)
- Ashay Patel
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey T Mindrebo
- Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Laetitia E Misson
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA
| | - James A McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Joseph P Noel
- Structural Biology Laboratory, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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6
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Chen PYT, Adak S, Chekan JR, Liscombe DK, Miyanaga A, Bernhardt P, Diethelm S, Fielding EN, George JH, Miles ZD, Murray LAM, Steele TS, Winter JM, Noel JP, Moore BS. Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis. Biochemistry 2022; 61:1844-1852. [PMID: 35985031 PMCID: PMC10978243 DOI: 10.1021/acs.biochem.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/28/2022]
Abstract
Vanadium-dependent haloperoxidases (VHPOs) from Streptomyces bacteria differ from their counterparts in fungi, macroalgae, and other bacteria by catalyzing organohalogenating reactions with strict regiochemical and stereochemical control. While this group of enzymes collectively uses hydrogen peroxide to oxidize halides for incorporation into electron-rich organic molecules, the mechanism for the controlled transfer of highly reactive chloronium ions in the biosynthesis of napyradiomycin and merochlorin antibiotics sets the Streptomyces vanadium-dependent chloroperoxidases apart. Here we report high-resolution crystal structures of two homologous VHPO family members associated with napyradiomycin biosynthesis, NapH1 and NapH3, that catalyze distinctive chemical reactions in the construction of meroterpenoid natural products. The structures, combined with site-directed mutagenesis and intact protein mass spectrometry studies, afforded a mechanistic model for the asymmetric alkene and arene chlorination reactions catalyzed by NapH1 and the isomerase activity catalyzed by NapH3. A key lysine residue in NapH1 situated between the coordinated vanadate and the putative substrate binding pocket was shown to be essential for catalysis. This observation suggested the involvement of the ε-NH2, possibly through formation of a transient chloramine, as the chlorinating species much as proposed in structurally distinct flavin-dependent halogenases. Unexpectedly, NapH3 is modified post-translationally by phosphorylation of an active site His (τ-pHis) consistent with its repurposed halogenation-independent, α-hydroxyketone isomerase activity. These structural studies deepen our understanding of the mechanistic underpinnings of VHPO enzymes and their evolution as enantioselective biocatalysts.
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Affiliation(s)
- Percival Yang-Ting Chen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - David K Liscombe
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Peter Bernhardt
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Stefan Diethelm
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Elisha N Fielding
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zachary D Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lauren A M Murray
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Taylor S Steele
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaclyn M Winter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Bradley S Moore
- 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
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7
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Chen A, Mindrebo JT, Davis TD, Kim WE, Katsuyama Y, Jiang Z, Ohnishi Y, Noel JP, Burkart MD. Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states. Acta Crystallogr D Struct Biol 2022; 78:1171-1179. [PMID: 36048156 PMCID: PMC9435599 DOI: 10.1107/s2059798322007434] [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: 04/12/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
Ketosynthases (KSs) catalyse essential carbon-carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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8
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Abstract
Single-particle analysis (SPA) by cryo-electron microscopy (cryo-EM) is now a mainstream technique for high-resolution structural biology. Structure determination by SPA relies upon obtaining multiple distinct views of a macromolecular object vitrified within a thin layer of ice. Ideally, a collection of uniformly distributed random projection orientations would amount to all possible views of the object, giving rise to reconstructions characterized by isotropic directional resolution. However, in reality, many samples suffer from preferentially oriented particles adhering to the air-water interface. This leads to non-uniform angular orientation distributions in the dataset and inhomogeneous Fourier-space sampling in the reconstruction, translating into maps characterized by anisotropic resolution. Tilting the specimen stage provides a generalizable solution to overcoming resolution anisotropy by virtue of improving the uniformity of orientation distributions, and thus the isotropy of Fourier space sampling. The present protocol describes a tilted-stage automated data collection strategy using Leginon, a software for automated image acquisition. The procedure is simple to implement, does not require any additional equipment or software, and is compatible with most standard transmission electron microscopes (TEMs) used for imaging biological macromolecules.
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Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies
| | | | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies; Department of Chemistry and Biochemistry, University of California San Diego
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies; Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego; Department of Integrative Structural and Computational Biology, The Scripps Research Institute;
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9
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Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases. ACS Catal 2021; 11:6787-6799. [DOI: 10.1021/acscatal.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Rebecca N. Re
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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10
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Abstract
This study demonstrates how integration of plants into an artificial carbon cycle is capable of harmoniously operating with Earth's natural cycles as one means to recycle atmospheric CO2 for economically lucrative green materials.
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Affiliation(s)
- Suzanne T. Thomas
- Jack H. Skirball Center for Chemical Biology and Proteomics
- Salk Institute for Biological Studies
- La Jolla
- USA
| | - Yongsoon Shin
- Materials Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - James J. La Clair
- Jack H. Skirball Center for Chemical Biology and Proteomics
- Salk Institute for Biological Studies
- La Jolla
- USA
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics
- Salk Institute for Biological Studies
- La Jolla
- USA
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11
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Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry 2020; 59:3626-3638. [PMID: 32857494 DOI: 10.1021/acs.biochem.0c00605] [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
Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laetitia E Misson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Caitlin Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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12
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Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. Gating mechanism of elongating β-ketoacyl-ACP synthases. Nat Commun 2020; 11:1727. [PMID: 32265440 PMCID: PMC7138838 DOI: 10.1038/s41467-020-15455-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 05/08/2019] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Carbon-carbon bond forming reactions are essential transformations in natural product biosynthesis. During de novo fatty acid and polyketide biosynthesis, β-ketoacyl-acyl carrier protein (ACP) synthases (KS), catalyze this process via a decarboxylative Claisen-like condensation reaction. KSs must recognize multiple chemically distinct ACPs and choreograph a ping-pong mechanism, often in an iterative fashion. Here, we report crystal structures of substrate mimetic bearing ACPs in complex with the elongating KSs from Escherichia coli, FabF and FabB, in order to better understand the stereochemical features governing substrate discrimination by KSs. Complemented by molecular dynamics (MD) simulations and mutagenesis studies, these structures reveal conformational states accessed during KS catalysis. These data taken together support a gating mechanism that regulates acyl-ACP binding and substrate delivery to the KS active site. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features in elongating KSs.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Joseph P Noel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. .,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. .,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
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13
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Mindrebo JT, Misson LE, Patel A, Charov K, Noel JP, Burkart MD. The Complete Characterization of a Trapped ACYL Carrier Protein-Ketosynthase Complex. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1114] [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: 10/25/2022] Open
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14
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Patel A, MIndrebo JT, Kim WE, Chen A, Bartholow TG, Davis TD, La Clair JJ, McCammon JA, Noel JP, Burkart MD. A Computational Perspective on the Gating Mechanism of β-Ketoacyl-ACP Synthases. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2771] [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] Open
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15
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Vickery CR, McCulloch IP, Sonnenschein EC, Beld J, Noel JP, Burkart MD. Dissecting modular synthases through inhibition: A complementary chemical and genetic approach. Bioorg Med Chem Lett 2020; 30:126820. [PMID: 31812466 DOI: 10.1016/j.bmcl.2019.126820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/29/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/23/2023]
Abstract
Modular synthases, such as fatty acid, polyketide, and non-ribosomal peptide synthases (NRPSs), are sophisticated machineries essential in both primary and secondary metabolism. Various techniques have been developed to understand their genetic background and enzymatic abilities. However, uncovering the actual biosynthetic pathways remains challenging. Herein, we demonstrate a pipeline to study an assembly line synthase by interrogating the enzymatic function of each individual enzymatic domain of BpsA, a NRPS that produces the blue 3,3'-bipyridyl pigment indigoidine. Specific inhibitors for each biosynthetic domain of BpsA were obtained or synthesized, and the enzymatic performance of BpsA upon addition of each inhibitor was monitored by pigment development in vitro and in living bacteria. The results were verified using genetic mutants to inactivate each domain. Finally, the results complemented the currently proposed biosynthetic pathway of BpsA.
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Affiliation(s)
- Christopher R Vickery
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian P McCulloch
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Eva C Sonnenschein
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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16
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Thomas ST, Louie GV, Lubin JW, Lundblad V, Noel JP. Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase. ACS Chem Biol 2019; 14:1767-1779. [PMID: 31268677 DOI: 10.1021/acschembio.9b00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A bifurcation of the mevalonate (MVA) pathway was recently discovered in bacteria of the Chloroflexi phylum. In this alternative route for the biosynthesis of isopentenylpyrophosphate (IPP), the penultimate step is the decarboxylation of (R)-mevalonate 5-phosphate ((R)-MVAP) to isopentenyl phosphate (IP), which is followed by the ATP-dependent phosphorylation of IP to IPP catalyzed by isopentenyl phosphate kinase (IPK). Notably, the decarboxylation reaction is catalyzed by mevalonate 5-phosphate decarboxylase (MPD), which shares considerable sequence similarity with mevalonate diphosphate decarboxylase (MDD) of the classical MVA pathway. We show that an enzyme originally annotated as an MDD from the Chloroflexi bacterium Anaerolinea thermophila possesses equal catalytic efficiency for (R)-MVAP and (R)-mevalonate 5-diphosphate ((R)-MVAPP). Further, the molecular basis for this dual specificity is revealed by near atomic-resolution X-ray crystal structures of A. thermophila MPD/MDD bound to (R)-MVAP or (R)-MVAPP. These findings, when combined with sequence and structural comparisons of this bacterial enzyme, functional MDDs, and several putative MPDs, delineate key active-site residues that confer substrate specificity and functionally distinguish MPD and MDD enzyme classes. Extensive sequence analyses identified functional MPDs in the halobacteria class of archaea that had been annotated as MDDs. Finally, no eukaryotic MPD candidates were identified, suggesting the absence of the alternative MVA (altMVA) pathway in all eukaryotes, including, paradoxically, plants, which universally encode a structural and functional homologue of IPK. Additionally, we have developed a viable engineered strain of Saccharomyces cerevisiae as an in vivo metabolic model and a synthetic biology platform for enzyme engineering and terpene biosynthesis in which the classical MVA pathway has been replaced with the altMVA pathway.
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17
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Burke JR, La Clair JJ, Philippe RN, Pabis A, Corbella M, Jez JM, Cortina GA, Kaltenbach M, Bowman ME, Louie GV, Woods KB, Nelson AT, Tawfik DS, Kamerlin SC, Noel JP. Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jason R. Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J. La Clair
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Ryan N. Philippe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph M. Jez
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - George A. Cortina
- Department of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Miriam Kaltenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Gordon V. Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Katherine B. Woods
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Andrew T. Nelson
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shina C.L. Kamerlin
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
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18
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Seto Y, Yasui R, Kameoka H, Tamiru M, Cao M, Terauchi R, Sakurada A, Hirano R, Kisugi T, Hanada A, Umehara M, Seo E, Akiyama K, Burke J, Takeda-Kamiya N, Li W, Hirano Y, Hakoshima T, Mashiguchi K, Noel JP, Kyozuka J, Yamaguchi S. Strigolactone perception and deactivation by a hydrolase receptor DWARF14. Nat Commun 2019; 10:191. [PMID: 30643123 PMCID: PMC6331613 DOI: 10.1038/s41467-018-08124-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [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: 03/27/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
The perception mechanism for the strigolactone (SL) class of plant hormones has been a subject of debate because their receptor, DWARF14 (D14), is an α/β-hydrolase that can cleave SLs. Here we show via time-course analyses of SL binding and hydrolysis by Arabidopsis thaliana D14, that the level of uncleaved SL strongly correlates with the induction of the active signaling state. In addition, we show that an AtD14D218A catalytic mutant that lacks enzymatic activity is still able to complement the atd14 mutant phenotype in an SL-dependent manner. We conclude that the intact SL molecules trigger the D14 active signaling state, and we also describe that D14 deactivates bioactive SLs by the hydrolytic degradation after signal transmission. Together, these results reveal that D14 is a dual-functional receptor, responsible for both the perception and deactivation of bioactive SLs.
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Affiliation(s)
- Yoshiya Seto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. .,RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. .,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. .,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. .,Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
| | - Rei Yasui
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Hiromu Kameoka
- Graduate School of Agricultural and Life Science, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.,Graduates School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Muluneh Tamiru
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan.,Department of Animal, Plant and Soil Sciences AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road Bundoora, Melbourne, VIC, 3086, Australia
| | - Mengmeng Cao
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan.,Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto, 617-0001, Japan
| | - Akane Sakurada
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Rena Hirano
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Takaya Kisugi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Atsushi Hanada
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikihisa Umehara
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.,Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Eunjoo Seo
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kohki Akiyama
- Graduates School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Jason Burke
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Weiqiang Li
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.,Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoshinori Hirano
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takeyama, Ikoma, Nara, 630-0192, Japan
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takeyama, Ikoma, Nara, 630-0192, Japan
| | - Kiyoshi Mashiguchi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Junko Kyozuka
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Agricultural and Life Science, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shinjiro Yamaguchi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. .,RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. .,Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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19
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Seto Y, Yasui R, Kameoka H, Tamiru M, Cao M, Terauchi R, Sakurada A, Hirano R, Kisugi T, Hanada A, Umehara M, Seo E, Akiyama K, Burke J, Takeda-Kamiya N, Li W, Hirano Y, Hakoshima T, Mashiguchi K, Noel JP, Kyozuka J, Yamaguchi S. Strigolactone perception and deactivation by a hydrolase receptor DWARF14. Nat Commun 2019. [PMID: 30643123 DOI: 10.1038/s41467-018-08124-8127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The perception mechanism for the strigolactone (SL) class of plant hormones has been a subject of debate because their receptor, DWARF14 (D14), is an α/β-hydrolase that can cleave SLs. Here we show via time-course analyses of SL binding and hydrolysis by Arabidopsis thaliana D14, that the level of uncleaved SL strongly correlates with the induction of the active signaling state. In addition, we show that an AtD14D218A catalytic mutant that lacks enzymatic activity is still able to complement the atd14 mutant phenotype in an SL-dependent manner. We conclude that the intact SL molecules trigger the D14 active signaling state, and we also describe that D14 deactivates bioactive SLs by the hydrolytic degradation after signal transmission. Together, these results reveal that D14 is a dual-functional receptor, responsible for both the perception and deactivation of bioactive SLs.
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Affiliation(s)
- Yoshiya Seto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
| | - Rei Yasui
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Hiromu Kameoka
- Graduate School of Agricultural and Life Science, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Graduates School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Muluneh Tamiru
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan
- Department of Animal, Plant and Soil Sciences AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road Bundoora, Melbourne, VIC, 3086, Australia
| | - Mengmeng Cao
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto, 617-0001, Japan
| | - Akane Sakurada
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Rena Hirano
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Takaya Kisugi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Atsushi Hanada
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikihisa Umehara
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Eunjoo Seo
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kohki Akiyama
- Graduates School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Jason Burke
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Weiqiang Li
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoshinori Hirano
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takeyama, Ikoma, Nara, 630-0192, Japan
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takeyama, Ikoma, Nara, 630-0192, Japan
| | - Kiyoshi Mashiguchi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Junko Kyozuka
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
- Graduate School of Agricultural and Life Science, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shinjiro Yamaguchi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
- RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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20
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Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N. Contribution of isopentenyl phosphate to plant terpenoid metabolism. Nat Plants 2018; 4:721-729. [PMID: 30127411 DOI: 10.1038/s41477-018-0220-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/13/2018] [Indexed: 05/24/2023]
Abstract
Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and regulatory roles of IP in plant terpenoid metabolism. Here, we provide genetic and biochemical evidence showing that IP forms during specific dephosphorylation of IPP catalysed by a subset of Nudix superfamily hydrolases. Increasing metabolically available IP by overexpression of a bacterial phosphomevalonate decarboxylase (MPD) in Nicotiana tabacum resulted in significant enhancement in both monoterpene and sesquiterpene production. These results indicate that perturbing IP metabolism results in measurable changes in terpene products derived from both the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways. Moreover, the unpredicted peroxisomal localization of bacterial MPD led us to discover that the step catalysed by phosphomevalonate kinase (PMK) imposes a hidden constraint on flux through the classical MVA pathway. These complementary findings fundamentally alter conventional views of metabolic regulation of terpenoid metabolism in plants and provide new metabolic engineering targets for the production of high-value terpenes in plants.
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Affiliation(s)
- Laura K Henry
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Suzanne T Thomas
- Jack H Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Thomas C Davis
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Sharon A Kessler
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Joseph P Noel
- Jack H Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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21
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Kaltenbach M, Burke JR, Dindo M, Pabis A, Munsberg FS, Rabin A, Kamerlin SCL, Noel JP, Tawfik DS. Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor. Nat Chem Biol 2018; 14:988. [PMID: 29760514 DOI: 10.1038/s41589-018-0079-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article originally published, the number for the equal contributions footnote was missing for Miriam Kaltenbach and Jason R. Burke in the author list. The error has been corrected in the PDF and print versions of this article.
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Affiliation(s)
- Miriam Kaltenbach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Jason R Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mirco Dindo
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Verona, Italy
| | - Anna Pabis
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Fabian S Munsberg
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Avigayel Rabin
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Shina C L Kamerlin
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Dan S Tawfik
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
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22
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Kaltenbach M, Burke JR, Dindo M, Pabis A, Munsberg FS, Rabin A, Kamerlin SCL, Noel JP, Tawfik DS. Evolution of chalcone isomerase from a noncatalytic ancestor. Nat Chem Biol 2018; 14:548-555. [PMID: 29686356 DOI: 10.1038/s41589-018-0042-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022]
Abstract
The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI's laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity could readily emerge despite a catalytically inactive starting point. Accordingly, X-ray crystallography, NMR, and molecular dynamics simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.
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Affiliation(s)
- Miriam Kaltenbach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Jason R Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mirco Dindo
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Verona, Italy
| | - Anna Pabis
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Fabian S Munsberg
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Avigayel Rabin
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Shina C L Kamerlin
- Uppsala Biomedicinsk Centrum, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Dan S Tawfik
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
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23
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Vickery CR, Cardenas J, Bowman ME, Burkart MD, Da Silva NA, Noel JP. A coupled in vitro/in vivo approach for engineering a heterologous type III PKS to enhance polyketide biosynthesis in Saccharomyces cerevisiae. Biotechnol Bioeng 2018; 115:1394-1402. [PMID: 29457628 DOI: 10.1002/bit.26564] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 01/01/2023]
Abstract
Polyketides are attractive compounds for uses ranging from biorenewable chemical precursors to high-value therapeutics. In many cases, synthesis in a heterologous host is required to produce these compounds in industrially relevant quantities. The type III polyketide synthase 2-pyrone synthase (2-PS) from Gerbera hybrida was used for the production of triacetic acid lactone (TAL) in Saccharomyces cerevisiae. Initial in vitro characterization of 2-PS led to the identification of active site variants with improved kinetic properties relative to wildtype. Further in vivo evaluation in S. cerevisiae suggested certain 2-PS mutations altered enzyme stability during fermentation. In vivo experiments also revealed beneficial cysteine to serine mutations that were not initially explored due to their distance from the active site of 2-PS, leading to the design of additional 2-PS enzymes. While these variants showed varying catalytic efficiencies in vitro, they exhibited up to 2.5-fold increases in TAL production when expressed in S. cerevisiae. Coupling of the 2-PS variant [C35S,C372S] to an engineered S. cerevisiae strain led to over 10 g/L TAL at 38% of theoretical yield following fed-batch fermentation, the highest reported to date. Our studies demonstrate the success of a coupled in vitro/in vivo approach to engineering enzymes and provide insight on cysteine-rich enzymes and design principles toward their use in non-native microbial hosts.
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Affiliation(s)
- Christopher R Vickery
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Javier Cardenas
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California
| | - Marianne E Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California
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24
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Stewart C, Woods K, Macias G, Allan AC, Hellens RP, Noel JP. Molecular architectures of benzoic acid-specific type III polyketide synthases. Acta Crystallogr D Struct Biol 2017; 73:1007-1019. [PMID: 29199980 PMCID: PMC5713876 DOI: 10.1107/s2059798317016618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 07/11/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022] Open
Abstract
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica. Both biphenyl synthase and benzophenone synthase contain mutations that reshape their active-site cavities to prevent the binding of 4-coumaroyl-CoA and to favor the binding of small hydrophobic substrates. The active-site cavities of biphenyl synthase and benzophenone synthase also contain a novel pocket associated with their chain-elongation and cyclization reactions. Collectively, these results illuminate structural determinants of benzoic acid-specific type III PKSs and expand the understanding of the evolution of specialized metabolic pathways in plants.
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Affiliation(s)
- Charles Stewart
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, 0202 Molecular Biology Building, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Kate Woods
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Greg Macias
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Joseph P. Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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25
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Kersten RD, Lee S, Fujita D, Pluskal T, Kram S, Smith JE, Iwai T, Noel JP, Fujita M, Weng JK. A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis. J Am Chem Soc 2017; 139:16838-16844. [PMID: 29083151 DOI: 10.1021/jacs.7b09452] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products. Here, we report the identification and biochemical characterization of LphTPS-A, a sesquiterpene synthase from the red macroalga Laurencia pacifica. Using the combination of transcriptomics, sesquiterpene synthase expression in yeast, and microgram-scale nuclear magnetic resonance-coupled crystalline sponge X-ray diffraction analysis, we resolved the absolute stereochemistry of prespatane, the major sesquiterpene product of LphTPS-A, and thereby functionally define LphTPS-A as the first bourbonane-producing sesquiterpene synthase and the first biochemically characterized sesquiterpene synthase from red algae. Our study showcases a workflow integrating multiomics approaches, synthetic biology, and the crystalline sponge method, which is generally applicable for uncovering new terpene chemistry and biochemistry from source-limited living organisms.
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Affiliation(s)
- Roland D Kersten
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Shoukou Lee
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Daishi Fujita
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Susan Kram
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Jennifer E Smith
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Takahiro Iwai
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies , La Jolla, California 92037, United States
| | - Makoto Fujita
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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26
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Weng JK, Ye M, Li B, Noel JP. Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity. Cell 2016; 166:881-893. [PMID: 27518563 DOI: 10.1016/j.cell.2016.06.027] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 02/24/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
Abstract
Classically, hormones elicit specific cellular responses by activating dedicated receptors. Nevertheless, the biosynthesis and turnover of many of these hormone molecules also produce chemically related metabolites. These molecules may also possess hormonal activities; therefore, one or more may contribute to the adaptive plasticity of signaling outcomes in host organisms. Here, we show that a catabolite of the plant hormone abscisic acid (ABA), namely phaseic acid (PA), likely emerged in seed plants as a signaling molecule that fine-tunes plant physiology, environmental adaptation, and development. This trait was facilitated by both the emergence-selection of a PA reductase that modulates PA concentrations and by the functional diversification of the ABA receptor family to perceive and respond to PA. Our results suggest that PA serves as a hormone in seed plants through activation of a subset of ABA receptors. This study demonstrates that the co-evolution of hormone metabolism and signaling networks can expand organismal resilience.
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Affiliation(s)
- Jing-Ke Weng
- Howard Hughes Medical Institute and Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mingli Ye
- Howard Hughes Medical Institute and Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, San Diego School of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute and Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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27
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Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol 2016; 41:233-246. [PMID: 27662376 PMCID: PMC5687975 DOI: 10.1016/j.sbi.2016.08.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [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: 08/17/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/13/2022]
Abstract
The alpha/beta hydrolase (ABH) superfamily is a widespread and functionally malleable protein fold recognized for its diverse biochemical activities across all three domains of life. ABH enzymes possess unexpected catalytic activity in the green plant lineage through selective alterations in active site architecture and chemistry. Furthermore, the ABH fold serves as the core structure for phytohormone and ligand receptors in the gibberellin, strigolactone, and karrikin signaling pathways in plants. Despite recent discoveries, the ABH family is sparsely characterized in plants, a sessile kingdom known to evolve complex and specialized chemical adaptations as survival responses to widely varying biotic and abiotic ecologies. This review calls attention to the ABH superfamily in the plant kingdom to highlight the functional adaptability of the ABH fold.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charisse M Nartey
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yoshiya Seto
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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28
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Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Corrigendum to "Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom" [Curr Opin Struct Biol 2016, 41:233-246]. Curr Opin Struct Biol 2016; 41:256-257. [PMID: 27884574 DOI: 10.1016/j.sbi.2016.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charisse M Nartey
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yoshiya Seto
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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29
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Levsh O, Chiang YC, Tung CF, Noel JP, Wang Y, Weng JK. Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase. Biochemistry 2016; 55:6314-6326. [PMID: 27805809 PMCID: PMC6276119 DOI: 10.1021/acs.biochem.6b00887] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 11/28/2022]
Abstract
Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native and non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, permitted by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.
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Affiliation(s)
- Olesya Levsh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ying-Chih Chiang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Fai Tung
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, La Jolla, CA
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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30
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Zheng Z, Guo Y, Novák O, Chen W, Ljung K, Noel JP, Chory J. Local auxin metabolism regulates environment-induced hypocotyl elongation. Nat Plants 2016; 2:16025. [PMID: 27249562 PMCID: PMC4849989 DOI: 10.1038/nplants.2016.25] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/12/2016] [Indexed: 05/18/2023]
Abstract
A hallmark of plants is their adaptability of size and form in response to widely fluctuating environments. The metabolism and redistribution of the phytohormone auxin play pivotal roles in establishing active auxin gradients and resulting cellular differentiation. In Arabidopsis thaliana, cotyledons and leaves synthesize indole-3-acetic acid (IAA) from tryptophan through indole-3-pyruvic acid (3-IPA) in response to vegetational shade. This newly synthesized auxin moves to the hypocotyl where it induces elongation of hypocotyl cells. Here we show that loss of function of VAS2 (IAA-amido synthetase Gretchen Hagen 3 (GH3).17) leads to increases in free IAA at the expense of IAA-Glu (IAA-glutamate) in the hypocotyl epidermis. This active IAA elicits shade- and high temperature-induced hypocotyl elongation largely independently of 3-IPA-mediated IAA biosynthesis in cotyledons. Our results reveal an unexpected capacity of local auxin metabolism to modulate the homeostasis and spatial distribution of free auxin in specialized organs such as hypocotyls in response to shade and high temperature.
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Affiliation(s)
- Zuyu Zheng
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Yongxia Guo
- The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtielů 11, 783 71 Olomouc, Czech Republic
| | - William Chen
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Joseph P. Noel
- Howard Hughes Medical Institute and The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA, Czech Republic
- Correspondence and requests for materials should be addressed to J.P.N. and J.C. ;
| | - Joanne Chory
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Correspondence and requests for materials should be addressed to J.P.N. and J.C. ;
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31
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Kersten R, Diedrich JK, Yates JR, Noel JP. Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases. ACS Chem Biol 2015; 10:2501-11. [PMID: 26378620 PMCID: PMC4655415 DOI: 10.1021/acschembio.5b00539] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 07/13/2015] [Accepted: 08/20/2015] [Indexed: 12/14/2022]
Abstract
Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myriad of chemotypes for organismal fitness. As most terpene biosynthesis mechanistically involves highly reactive carbocationic intermediates, the protein surfaces catalyzing these cascade reactions possess reactive regions possibly prone to premature carbocation capture and potentially enzyme inactivation. Here, we show using proteomic and X-ray crystallographic analyses that cationic intermediates undergo capture by conserved active site residues leading to inhibitory self-alkylation. Moreover, the level of cation-mediated inactivation increases with mutation of the active site, upon changes in the size and structure of isoprenoid diphosphate substrates, and alongside increases in reaction temperatures. TPSs that individually synthesize multiple products are less prone to self-alkylation then TPSs possessing relatively high product specificity. In total, the results presented suggest that mechanism-based alkylation represents an overlooked mechanistic pressure during the evolution of cation-derived terpene biosynthesis.
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Affiliation(s)
- Roland
D. Kersten
- Howard
Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology
& Proteomics, The Salk Institute for
Biological Studies, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department
of Chemical Physiology, The Scripps Research
Institute, La Jolla, California 92037, United States
- Vincent
J. Coates Mass Spectrometry Center, The
Salk Institute of Biological Studies, La Jolla, California 92037, United States
| | - John R. Yates
- Department
of Chemical Physiology, The Scripps Research
Institute, La Jolla, California 92037, United States
- Vincent
J. Coates Mass Spectrometry Center, The
Salk Institute of Biological Studies, La Jolla, California 92037, United States
| | - Joseph P. Noel
- Howard
Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology
& Proteomics, The Salk Institute for
Biological Studies, La Jolla, California 92037, United States
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32
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Henry LK, Gutensohn M, Thomas ST, Noel JP, Dudareva N. Orthologs of the archaeal isopentenyl phosphate kinase regulate terpenoid production in plants. Proc Natl Acad Sci U S A 2015; 112:10050-5. [PMID: 26216978 PMCID: PMC4538610 DOI: 10.1073/pnas.1504798112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [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] [Indexed: 11/18/2022] Open
Abstract
Terpenoids, compounds found in all domains of life, represent the largest class of natural products with essential roles in their hosts. All terpenoids originate from the five-carbon building blocks, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), which can be derived from the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. The absence of two components of the MVA pathway from archaeal genomes led to the discovery of an alternative MVA pathway with isopentenyl phosphate kinase (IPK) catalyzing the final step, the formation of IPP. Despite the fact that plants contain the complete classical MVA pathway, IPK homologs were identified in every sequenced green plant genome. Here, we show that IPK is indeed a member of the plant terpenoid metabolic network. It is localized in the cytosol and is coexpressed with MVA pathway and downstream terpenoid network genes. In planta, IPK acts in parallel with the MVA pathway and plays an important role in regulating the formation of both MVA and MEP pathway-derived terpenoid compounds by controlling the ratio of IP/DMAP to IPP/DMAPP. IP and DMAP can also competitively inhibit farnesyl diphosphate synthase. Moreover, we discovered a metabolically available carbon source for terpenoid formation in plants that is accessible via IPK overexpression. This metabolite reactivation approach offers new strategies for metabolic engineering of terpenoid production.
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Affiliation(s)
- Laura K Henry
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907
| | - Michael Gutensohn
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907
| | - Suzanne T Thomas
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907;
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33
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Rising KA, Crenshaw CM, Koo HJ, Subramanian T, Chehade KAH, Starks C, Allen KD, Andres DA, Spielmann HP, Noel JP, Chappell J. Formation of a Novel Macrocyclic Alkaloid from the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate by 5-Epi-Aristolochene Synthase. ACS Chem Biol 2015; 10:1729-36. [PMID: 25897591 PMCID: PMC4570970 DOI: 10.1021/acschembio.5b00145] [Citation(s) in RCA: 26] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of an effort to identify substrate analogs suitable for helping to resolve structural features important for terpene synthases, the inhibition of 5-epi-aristolochene biosynthesis from farnesyl diphosphate (FPP) by the tobacco 5-epi-aristolochene synthase incubated with anilinogeranyl diphosphate (AGPP) was examined. The apparent noncompetitive nature of the inhibition supported further assessment of how AGPP might be bound to crystallographic forms of the enzyme. Surprisingly, the bound form of the inhibitor appeared to have undergone a cyclization event consistent with the native mechanism associated with FPP catalysis. Biocatalytic formation of a novel 13-membered macrocyclic paracyclophane alkaloid was confirmed by high-resolution GC-MS and NMR analysis. This work provides insights into new biosynthetic means for generating novel, functionally diversified, medium-sized terpene alkaloids.
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Affiliation(s)
- Kathleen A. Rising
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - Charisse M. Crenshaw
- Howard Hughes Medical Institute, Salk Institute, La Jolla, California 92037, United States
| | - Hyun Jo Koo
- Howard Hughes Medical Institute, Salk Institute, La Jolla, California 92037, United States
| | - Thangaiah Subramanian
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - Kareem A. H. Chehade
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - Courtney Starks
- Howard Hughes Medical Institute, Salk Institute, La Jolla, California 92037, United States
| | - Keith D. Allen
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - Douglas A. Andres
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - H. Peter Spielmann
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, Lexington, Kentucky, United States
- Department of Chemistry, University of Kentucky, Lexington, Lexington, Kentucky, United States
- Center for Structural Biology, University of Kentucky, Lexington, Lexington, Kentucky, United States
- Markey Cancer Center, University of Kentucky, Lexington, Lexington, Kentucky, United States
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Salk Institute, La Jolla, California 92037, United States
| | - Joe Chappell
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Lexington, Kentucky, United States
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34
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Vickery CR, Kosa NM, Casavant EP, Duan S, Noel JP, Burkart MD. Structure, biochemistry, and inhibition of essential 4'-phosphopantetheinyl transferases from two species of Mycobacteria. ACS Chem Biol 2014; 9:1939-44. [PMID: 24963544 PMCID: PMC4168790 DOI: 10.1021/cb500263p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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] [Indexed: 01/22/2023]
Abstract
![]()
4′-Phosphopantetheinyl
transferases (PPTase) post-translationally
modify carrier proteins with a phosphopantetheine moiety, an essential
reaction in all three domains of life. In the bacterial genus Mycobacteria, the Sfp-type PPTase activates pathways necessary
for the biosynthesis of cell wall components and small molecule virulence
factors. We solved the X-ray crystal structures and biochemically
characterized the Sfp-type PPTases from two of the most prevalent
Mycobacterial pathogens, PptT of M. tuberculosis and
MuPPT of M. ulcerans. Structural analyses reveal
significant differences in cofactor binding and active site composition
when compared to previously characterized Sfp-type PPTases. Functional
analyses including the efficacy of Sfp-type PPTase-specific inhibitors
also suggest that the Mycobacterial Sfp-type PPTases can serve as
therapeutic targets against Mycobacterial infections.
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Affiliation(s)
- Christopher R. Vickery
- Department
of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack
Skirball Center for Chemical Biology and Proteomics, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Nicolas M. Kosa
- Department
of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Ellen P. Casavant
- Department
of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Shiteng Duan
- Department
of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Howard Hughes Medical Institute, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
- Jack
Skirball Center for Chemical Biology and Proteomics, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department
of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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35
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Pan H, Zhou R, Louie GV, Mühlemann JK, Bomati EK, Bowman ME, Dudareva N, Dixon RA, Noel JP, Wang X. Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis. Plant Cell 2014; 26:3709-27. [PMID: 25217505 PMCID: PMC4213152 DOI: 10.1105/tpc.114.127399] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/27/2014] [Accepted: 08/08/2014] [Indexed: 05/18/2023]
Abstract
The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates.
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Affiliation(s)
- Haiyun Pan
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rui Zhou
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Gordon V Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joëlle K Mühlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Erin K Bomati
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Marianne E Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Richard A Dixon
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Xiaoqiang Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
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36
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Hoppmann C, Lacey VK, Louie GV, Wei J, Noel JP, Wang L. Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells. Angew Chem Int Ed Engl 2014; 53:3932-6. [PMID: 24615769 PMCID: PMC4051619 DOI: 10.1002/anie.201400001] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 12/31/2013] [Revised: 01/27/2014] [Indexed: 01/31/2023]
Abstract
The ability to reversibly control protein structure and function with light would offer high spatiotemporal resolution for investigating biological processes. To confer photoresponsiveness on general proteins, we genetically incorporated a set of photoswitchable click amino acids (PSCaas), which contain both a reversible photoswitch and an additional click functional group for further modifications. Orthogonal tRNA-synthetases were evolved to genetically encode PSCaas bearing azobenzene with an alkene, keto, or benzyl chloride group in E. coli and in mammalian cells. After incorporation into calmodulin, the benzyl chloride PSCaa spontaneously generated a covalent protein bridge by reacting with a nearby cysteine residue through proximity-enabled bioreactivity. The resultant azobenzene bridge isomerized in response to light, thereby changing the conformation of calmodulin. These genetically encodable PSCaas will prove valuable for engineering photoswitchable bridges into proteins for reversible optogenetic regulation.
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Affiliation(s)
- Christian Hoppmann
- Chemical Biology and Proteomics Laboratory The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Vanessa K. Lacey
- Chemical Biology and Proteomics Laboratory The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Gordon V. Louie
- Chemical Biology and Proteomics Laboratory The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Jing Wei
- Jadebio, Inc., La Jolla, CA 92037 (USA)
| | - Joseph P. Noel
- Chemical Biology and Proteomics Laboratory The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
- Howard Hughes Medical Institute
| | - Lei Wang
- Chemical Biology and Proteomics Laboratory The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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37
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Hoppmann C, Lacey VK, Louie GV, Wei J, Noel JP, Wang L. Genetically Encoding Photoswitchable Click Amino Acids inEscherichia coliand Mammalian Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Schorn M, Zettler J, Noel JP, Dorrestein PC, Moore BS, Kaysser L. Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. ACS Chem Biol 2014; 9:301-9. [PMID: 24168704 DOI: 10.1021/cb400699p] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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 epoxyketone proteasome inhibitors are an established class of therapeutic agents for the treatment of cancer. Their unique α',β'-epoxyketone pharmacophore allows binding to the catalytic β-subunits of the proteasome with extraordinary specificity. Here, we report the characterization of the first gene clusters for the biosynthesis of natural peptidyl-epoxyketones. The clusters for epoxomicin, the lead compound for the anticancer drug Kyprolis, and for eponemycin were identified in the actinobacterial producer strains ATCC 53904 and Streptomyces hygroscopicus ATCC 53709, respectively, using a modified protocol for Ion Torrent PGM genome sequencing. Both gene clusters code for a hybrid nonribosomal peptide synthetase/polyketide synthase multifunctional enzyme complex and homologous redox enzymes. Epoxomicin and eponemycin were heterologously produced in Streptomyces albus J1046 via whole pathway expression. Moreover, we employed mass spectral molecular networking for a new comparative metabolomics approach in a heterologous system and discovered a number of putative epoxyketone derivatives. With this study, we have definitively linked epoxyketone proteasome inhibitors and their biosynthesis genes for the first time in any organism, which will now allow for their detailed biochemical investigation.
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Affiliation(s)
- Michelle Schorn
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
| | - Judith Zettler
- Pharmaceutical
Biology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Center
for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Joseph P. Noel
- Jack
H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States of America
| | - Pieter C. Dorrestein
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States of America
| | - Bradley S. Moore
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States of America
| | - Leonard Kaysser
- Scripps
Institution of Oceanography, University of California, San Diego, California 92093, United States of America
- Pharmaceutical
Biology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Center
for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
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39
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [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: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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40
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Abstract
Eukarya, Archaea, and some Bacteria encode all or part of the essential mevalonate (MVA) metabolic pathway clinically modulated using statins. Curiously, two components of the MVA pathway are often absent from archaeal genomes. The search for these missing elements led to the discovery of isopentenyl phosphate kinase (IPK), one of two activities necessary to furnish the universal five-carbon isoprenoid building block, isopentenyl diphosphate (IPP). Unexpectedly, we now report functional IPKs also exist in Bacteria and Eukarya. Furthermore, amongst a subset of species within the bacterial phylum Chloroflexi, we identified a new enzyme catalyzing the missing decarboxylative step of the putative alternative MVA pathway. These results demonstrate, for the first time, a functioning alternative MVA pathway. Key to this pathway is the catalytic actions of a newly uncovered enzyme, mevalonate phosphate decarboxylase (MPD) and IPK. Together, these two discoveries suggest that unforeseen variation in isoprenoid metabolism may be widespread in nature. DOI: http://dx.doi.org/10.7554/eLife.00672.001.
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Affiliation(s)
- Nikki Dellas
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
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41
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Teufel R, Miyanaga A, Michaudel Q, Stull F, Louie G, Noel JP, Baran PS, Palfey B, Moore BS. Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement. Nature 2013; 503:552-556. [PMID: 24162851 PMCID: PMC3844076 DOI: 10.1038/nature12643] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [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: 04/15/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022]
Abstract
Flavoproteins catalyze a diversity of fundamental redox reactions and are one of the most studied enzyme families1,2. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate1,3,4. Here we report that the bacterial flavoenzyme EncM5,6 catalyzes the peroxyflavin-independent oxygenation-dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics coupled with isotope labeling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unanticipated stable flavin oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization.
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Affiliation(s)
- Robin Teufel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - Quentin Michaudel
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Frederick Stull
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Gordon Louie
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, La Jolla, California 92037, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, La Jolla, California 92037, USA
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Bruce Palfey
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
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42
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Lacey VK, Louie GV, Noel JP, Wang L. Expanding the library and substrate diversity of the pyrrolysyl-tRNA synthetase to incorporate unnatural amino acids containing conjugated rings. Chembiochem 2013; 14:2100-5. [PMID: 24019075 DOI: 10.1002/cbic.201300400] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [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: 06/20/2013] [Indexed: 11/08/2022]
Abstract
Unnatural amino acids (UAAs) containing conjugated ring systems are of interest for their optical properties. Until now, such bulky and planar UAAs could not be incorporated into proteins using the pyrrolysyl tRNA/synthetase shuttling system. Using the "small-intelligent" approach to construct a highly diverse library, we evolved novel synthetases specific for two such UAAs and incorporated them into proteins in E. coli and mammalian cells.
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Affiliation(s)
- Vanessa K Lacey
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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43
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Stewart C, Vickery CR, Burkart MD, Noel JP. Confluence of structural and chemical biology: plant polyketide synthases as biocatalysts for a bio-based future. Curr Opin Plant Biol 2013; 16:365-372. [PMID: 23481348 DOI: 10.1016/j.pbi.2013.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 02/07/2013] [Indexed: 06/01/2023]
Abstract
Type III plant polyketide synthases (PKSs) biosynthesize a dazzling array of polyphenolic products that serve important roles in both plant and human health. Recent advances in structural characterization of these enzymes and new tools from the field of chemical biology have facilitated exquisite probing of plant PKS iterative catalysis. These tools have also been used to exploit type III PKSs as biocatalysts to generate new chemicals. Going forward, chemical, structural and biochemical analyses will provide an atomic resolution understanding of plant PKSs and will serve as a springboard for bioengineering and scalable production of valuable molecules in vitro, by fermentation and in planta.
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Affiliation(s)
- Charles Stewart
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
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44
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Crenshaw C, Aljadeff J, Fernandez I, Laurendon C, Defernez M, Koo HJ, O'Maille PE, Sharpee T, Noel JP. Protein Epistasis Revealed from Thermostability Profiles of Nicotiana tabacum 5‐epi‐Aristolochene Synthase. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.561.5] [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)
- Charisse Crenshaw
- Proteomics and Chemical Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA
| | - Johnatan Aljadeff
- Computational Neurobiology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA
- Center for Theoretical Biological Physics and Department of PhysicsUniversity of California at San DiegoLa JollaCA
| | - Irma Fernandez
- Department of Chemistry and BiochemistryUniversity of California at San DiegoLa JollaCA
| | | | | | - Hyun Jo Koo
- Proteomics and Chemical Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA
| | - Paul E. O'Maille
- Department of Metabolic BiologyJohn Innes CentreNorwichUnited Kingdom
- Institute of Food ResearchNorwichUnited Kingdom
| | - Tatyana Sharpee
- Computational Neurobiology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA
- Center for Theoretical Biological Physics and Department of PhysicsUniversity of California at San DiegoLa JollaCA
| | - Joseph P. Noel
- Proteomics and Chemical Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA
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45
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Zheng Z, Guo Y, Novák O, Dai X, Zhao Y, Ljung K, Noel JP, Chory J. Coordination of auxin and ethylene biosynthesis by the aminotransferase VAS1. Nat Chem Biol 2013; 9:244-6. [PMID: 23377040 PMCID: PMC3948326 DOI: 10.1038/nchembio.1178] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 08/23/2012] [Accepted: 01/03/2013] [Indexed: 01/08/2023]
Abstract
We identify an Arabidopsis pyridoxal-phosphate (PLP)-dependent aminotransferase, VAS1, whose loss-of-function simultaneously increases levels of the phytohormone auxin and the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). VAS1 uses the ethylene biosynthetic intermediate Met as an amino donor and the auxin biosynthetic intermediate, indole-3-pyruvic acid (3-IPA) as an amino acceptor to produce L-Trp and 2-oxo-4-methylthiobutyric acid (KMBA). Our data indicate that VAS1 serves key roles in coordinating the levels of these two vital hormones.
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Affiliation(s)
- Zuyu Zheng
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California, USA
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46
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Weng JK, Noel JP. Chemodiversity in Selaginella: a reference system for parallel and convergent metabolic evolution in terrestrial plants. Front Plant Sci 2013; 4:119. [PMID: 23717312 PMCID: PMC3650682 DOI: 10.3389/fpls.2013.00119] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/16/2013] [Indexed: 05/05/2023]
Abstract
Early plants began colonizing the terrestrial earth approximately 450 million years ago. Their success on land has been partially attributed to the evolution of specialized metabolic systems from core metabolic pathways, the former yielding structurally and functionally diverse chemicals to cope with a myriad of biotic and abiotic ecological pressures. Over the past two decades, functional genomics, primarily focused on flowering plants, has begun cataloging the biosynthetic players underpinning assorted classes of plant specialized metabolites. However, the molecular mechanisms enriching specialized metabolic pathways during land plant evolution remain largely unexplored. Selaginella is an extant lycopodiophyte genus representative of an ancient lineage of tracheophytes. Notably, the lycopodiophytes diverged from euphyllophytes over 400 million years ago. The recent completion of the whole-genome sequence of an extant lycopodiophyte, S. moellendorffii, provides new genomic and biochemical resources for studying metabolic evolution in vascular plants. 400 million years of independent evolution of lycopodiophytes and euphyllophytes resulted in numerous metabolic traits confined to each lineage. Surprisingly, a cadre of specialized metabolites, generally accepted to be restricted to seed plants, have been identified in Selaginella. Initial work suggested that Selaginella lacks obvious catalytic homologs known to be involved in the biosynthesis of well-studied specialized metabolites in seed plants. Therefore, these initial functional analyses suggest that the same chemical phenotypes arose independently more commonly than anticipated from our conventional understanding of the evolution of metabolism. Notably, the emergence of analogous and homologous catalytic machineries through convergent and parallel evolution, respectively, seems to have occurred repeatedly in different plant lineages.
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Affiliation(s)
| | - Joseph P. Noel
- *Correspondence: Joseph P. Noel, Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, USA. e-mail:
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47
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Abstract
Metabolic pathways are often considered "perfected" or at least predictable as substrates efficiently rearrange into products through the intervention of an optimized enzyme. Moreover, single catalytic steps link up, forming a myriad of metabolic circuits that are often modeled with a high degree of certainty. However, on closer examination, most enzymes are not precise with respect to their activity, using not just one substrate but often a variety and producing not just one product but a diversity. Hence, the metabolic systems assembled from enzymes possessing varying degrees of what can be termed catalytic promiscuity are not clear-cut and restrictive; rather, they may at times operate stochastically in the intracellular milieu. This "messiness" complicates our understanding of normal and aberrant cellular behavior, while paradoxically sowing the seeds for future advantageous metabolic adaptations for host organisms. Catalytic promiscuity is intrinsically associated with the dynamic nature of enzyme structures and their chemical mechanisms, both key to enzyme and metabolic evolvability. In addition to primary (core) metabolism, which is essential for survival, organisms also possess highly elaborated secondary (specialized) metabolic systems. These specialized enzymes and pathways often provide unique adaptive strategies for a myriad of organisms and their populations in challenging and changing ecosystems. Generally, enzymes of specialized metabolism show attenuated kinetic activities and expanded catalytic promiscuity compared with their phylogenetic relatives rooted in primary metabolism. We propose that evolvability may be a selected trait in many specialized metabolic systems spread across populations of organisms exposed to continually fluctuating biotic and abiotic environmental pressures. As minor metabolites arising from catalytic messiness provided enhanced population fitness, specificity relaxed, and catalytic efficiency was attenuated. This updated view provides a mechanistic basis for reaching a deeper understanding of the evolutionary underpinnings of the explosion of chemodiversity in nature.
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Affiliation(s)
- J-K Weng
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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48
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Elleder D, Baiga TJ, Russell RL, Naughton JA, Hughes SH, Noel JP, Young JAT. Identification of a 3-aminoimidazo[1,2-a]pyridine inhibitor of HIV-1 reverse transcriptase. Virol J 2012; 9:305. [PMID: 23231773 PMCID: PMC3560175 DOI: 10.1186/1743-422x-9-305] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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: 07/11/2012] [Accepted: 11/28/2012] [Indexed: 11/29/2022] Open
Abstract
Background Despite the effectiveness of highly active antiretroviral therapy (HAART), there remains an urgent need to develop new human immunodeficiency virus type 1 (HIV-1) inhibitors with better pharmacokinetic properties that are well tolerated, and that block common drug resistant virus strains. Methods Here we screened an in-house small molecule library for novel inhibitors of HIV-1 replication. Results An active compound containing a 3-aminoimidazo[1,2-a]pyridine scaffold was identified and quantitatively characterized as a non-nucleoside reverse transcriptase inhibitor (NNRTI). Conclusions The potency of this compound coupled with its inexpensive chemical synthesis and tractability for downstream SAR analysis make this inhibitor a suitable lead candidate for further development as an antiviral drug.
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Affiliation(s)
- Daniel Elleder
- The Salk Institute for Biological Studies, Nomis Center for Immunobiology and Microbial Pathogenesis, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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49
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Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y. Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem Biol 2012; 7:1462-70. [PMID: 22670809 DOI: 10.1021/cb3000887] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [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 C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.
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Affiliation(s)
- Mengmeng Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Xiaodong J. Wang
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Xi Chen
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Marianne E. Bowman
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Yonghua Luo
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Joseph P. Noel
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Andrew D. Ellington
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Yan Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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50
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Abstract
The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.
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Affiliation(s)
- David K Liscombe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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