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Rebholz Z, Shewade L, Kaler K, Larose H, Schubot F, Tholl D, Morozov AV, O'Maille PE. Emergence of terpene chemical communication in insects: Evolutionary recruitment of isoprenoid metabolism. Protein Sci 2023; 32:e4634. [PMID: 36974623 PMCID: PMC10108439 DOI: 10.1002/pro.4634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Insects have evolved a chemical communication system using terpenoids, a structurally diverse class of specialized metabolites, previously thought to be exclusively produced by plants and microbes. Gene discovery, bioinformatics, and biochemical characterization of multiple insect terpene synthases (TPSs) revealed that isoprenyl diphosphate synthases (IDS), enzymes from primary isoprenoid metabolism, are their likely evolutionary progenitors. However, the mutations underlying the emergence of the TPS function remain a mystery. To address this gap, we present the first structural and mechanistic model for the evolutionary emergence of TPS function in insects. Through identifying key mechanistic differences between IDS and TPS enzymes, we hypothesize that the loss of isopentenyl diphosphate (IPP) binding motifs strongly correlates with the gain of the TPS function. Based on this premise, we have elaborated the first explicit structural definition of isopentenyl diphosphate-binding motifs (IBMs) and used the IBM definitions to examine previously characterized insect IDSs and TPSs and to predict the functions of as yet uncharacterized insect IDSs. Consistent with our hypothesis, we observed a clear pattern of disruptive substitutions to IBMs in characterized insect TPSs. In contrast, insect IDSs maintain essential consensus residues for binding IPP. Extending our analysis, we constructed the most comprehensive phylogeny of insect IDS sequences (430 full length sequences from eight insect orders) and used IBMs to predict the function of TPSs. Based on our analysis, we infer multiple, independent TPS emergence events across the class of insects, paving the way for future gene discovery efforts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zarley Rebholz
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Leena Shewade
- SRI International, Biosciences Division, Menlo Park, CA, 92122
| | - Kylie Kaler
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Hailey Larose
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Florian Schubot
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, 136 Frelinghuysen Rd., Piscataway, NJ, 08854, USA
| | - Paul E O'Maille
- SRI International, Biosciences Division, Menlo Park, CA, 92122
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Tholl D, Rebholz Z, Morozov AV, O'Maille PE. Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals. Nat Prod Rep 2023; 40:766-793. [PMID: 36880348 DOI: 10.1039/d2np00076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Covering: up to the beginning of 2023Many animals release volatile or semi-volatile terpenes as semiochemicals in intra- and inter-specific interactions. Terpenes are important constituents of pheromones and serve as chemical defenses to ward off predators. Despite the occurrence of terpene specialized metabolites from soft corals to mammals, the biosynthetic origin of these compounds has largely remained obscure. An increasing number of animal genome and transcriptome resources is facilitating the identification of enzymes and pathways that allow animals to produce terpenes independent of their food sources or microbial endosymbionts. Substantial evidence has emerged for the presence of terpene biosynthetic pathways such as in the formation of the iridoid sex pheromone nepetalactone in aphids. In addition, terpene synthase (TPS) enzymes have been discovered that are evolutionary unrelated to canonical plant and microbial TPSs and instead resemble precursor enzymes called isoprenyl diphosphate synthases (IDSs) in central terpene metabolism. Structural modifications of substrate binding motifs in canonical IDS proteins presumably facilitated the transition to TPS function at an early state in insect evolution. Other arthropods such as mites appear to have adopted their TPS genes from microbial sources via horizontal gene transfer. A similar scenario likely occurred in soft corals, where TPS families with closer resemblance to microbial TPSs have been discovered recently. Together, these findings will spur the identification of similar or still unknown enzymes in terpene biosynthesis in other lineages of animals. They will also help develop biotechnological applications for animal derived terpenes of pharmaceutical value or advance sustainable agricultural practices in pest management.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
| | - Zarley Rebholz
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
| | - Alexandre V Morozov
- Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
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Ballal A, Laurendon C, Salmon M, Vardakou M, Cheema J, Defernez M, O'Maille PE, Morozov AV. Sparse Epistatic Patterns in the Evolution of Terpene Synthases. Mol Biol Evol 2020; 37:1907-1924. [PMID: 32119077 DOI: 10.1093/molbev/msaa052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes-complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-β-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data were used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in nonlinear fitness landscapes that are considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of microevolutionary exploration of sequence space around naturally occurring enzymes.
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Affiliation(s)
- Aditya Ballal
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
| | - Caroline Laurendon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Department of Computational and Systems Biology, Norwich Research Park, Norwich, United Kingdom
| | - Marianne Defernez
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,SRI International, Menlo Park, CA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
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Hraber P, O'Maille PE, Silberfarb A, Davis-Anderson K, Generous N, McMahon BH, Fair JM. Resources to Discover and Use Short Linear Motifs in Viral Proteins. Trends Biotechnol 2020; 38:113-127. [PMID: 31427097 PMCID: PMC7114124 DOI: 10.1016/j.tibtech.2019.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022]
Abstract
Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.
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Affiliation(s)
- Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Paul E O'Maille
- Biosciences Division, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Andrew Silberfarb
- Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Katie Davis-Anderson
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nicholas Generous
- Global Security Directorate, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeanne M Fair
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Cheema J, Faraldos JA, O'Maille PE. REVIEW: Epistasis and dominance in the emergence of catalytic function as exemplified by the evolution of plant terpene synthases. Plant Sci 2017; 255:29-38. [PMID: 28131339 DOI: 10.1016/j.plantsci.2016.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/17/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes. Using the emergence of terpene cyclization in specialized metabolism as an excellent example, this review describes the process of discovery and interpretation of dominance and epistasis in relation to current efforts. Specifically, we outline experimental approaches to isolating epistatic networks of mutations in protein structure, formally quantifying epistatic interactions, then building biochemical models with chemical mechanisms in efforts to achieve an understanding of the physical basis for epistasis. From these models we describe informed conjectures about past evolutionary events that underlie the emergence, divergence and specialization of terpene synthases to illustrate key principles of the constraining forces of epistasis in enzyme function.
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Affiliation(s)
- Jitender Cheema
- John Innes Centre, Computational and Systems Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Juan A Faraldos
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Food Research, Food & Health Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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Abstract
Background Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions? Results We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and an Escherichia coli metabolic model. Conclusions Pathway collages enable facile construction of personalized multi-pathway diagrams.
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Affiliation(s)
- Suzanne Paley
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, and the Institute of Food Research, Food & Health Programme, Norwich Research Park, Norfolk, NR4 7UH, UK.,Current address: Biosciences Division, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA
| | - Daniel Weaver
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA
| | - Peter D Karp
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA.
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Nguyen TD, Faraldos JA, Vardakou M, Salmon M, O'Maille PE, Ro DK. Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae. Biochem Biophys Res Commun 2016; 479:622-627. [PMID: 27697527 DOI: 10.1016/j.bbrc.2016.09.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 12/21/2022]
Abstract
The Andes-endemic Barnadesioideae lineage is the oldest surviving and phylogenetically basal subfamily of the Asteraceae (Compositae), a prolific group of flowering plants with world-wide distribution (∼24,000 species) marked by a rich diversity of sesquiterpene lactones (STLs). Intriguingly, there is no evidence that members of the Barnadesioideae produce STLs, specialized metabolites thought to have contributed to the adaptive success of the Asteraceae family outside South America. The biosynthesis of STLs requires the intimate expression and functional integration of germacrene A synthase (GAS) and germacrene A oxidase (GAO) to sequentially cyclize and oxidize farnesyl diphosphate into the advanced intermediate germacrene A acid leading to diverse STLs. Our previous discovery of GAO activity conserved across all major subfamilies of Asteraceae, including the phylogenetically basal lineage of Barnadesioideae, prompted further investigation of the presence of the gateway GAS in Barnadesioideae. Herein we isolated two terpene synthases (BsGAS1/BsGAS2) from the basal Barnadesia spinosa (Barnadesioideae) that displayed robust GAS activity when reconstituted in yeast and characterized in vitro. Despite the apparent lack of STLs in the Barnadesioideae, this work unambiguously confirms the presence of GAS in the basal genera of the Asteraceae. Phylogenetic analysis reveals that the two BsGASs fall into two distinct clades of the Asteraceae's GASs, and BsGAS1 clade is only retained in the evolutionary closer Cichorioideae subfamily, implicating BsGAS2 is likely the ancestral base of most GASs found in the lineages outside the Barnadesioideae. Taken together, these results show the enzymatic capacities of GAS and GAO emerged prior to the subsequent radiation of STL-producing Asteraceae subfamilies.
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Affiliation(s)
- Trinh-Don Nguyen
- University of Calgary, Department of Biological Sciences, Calgary, T2N 1N4, Canada
| | - Juan A Faraldos
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich, NR4 7UH, United Kingdom; Institute of Food Research, Food and Health Programme, Norwich, NR4 7UA, United Kingdom.
| | - Dae-Kyun Ro
- University of Calgary, Department of Biological Sciences, Calgary, T2N 1N4, Canada.
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Salmon M, Laurendon C, Vardakou M, Cheema J, Defernez M, Green S, Faraldos JA, O'Maille PE. Emergence of terpene cyclization in Artemisia annua. Nat Commun 2015; 6:6143. [PMID: 25644758 PMCID: PMC4327562 DOI: 10.1038/ncomms7143] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 08/13/2014] [Accepted: 12/17/2014] [Indexed: 01/14/2023] Open
Abstract
The emergence of terpene cyclization was critical to the evolutionary expansion of chemical diversity yet remains unexplored. Here we report the first discovery of an epistatic network of residues that controls the onset of terpene cyclization in Artemisia annua. We begin with amorpha-4,11-diene synthase (ADS) and (E)-β-farnesene synthase (BFS), a pair of terpene synthases that produce cyclic or linear terpenes, respectively. A library of ~27,000 enzymes is generated by breeding combinations of natural amino-acid substitutions from the cyclic into the linear producer. We discover one dominant mutation is sufficient to activate cyclization, and together with two additional residues comprise a network of strongly epistatic interactions that activate, suppress or reactivate cyclization. Remarkably, this epistatic network of equivalent residues also controls cyclization in a BFS homologue from Citrus junos. Fitness landscape analysis of mutational trajectories provides quantitative insights into a major epoch in specialized metabolism. Terpene cyclases are ring-forming enzymes found in many biosynthetic pathways, but the evolutionary origins of the cyclization mechanism is not well understood. Here, the authors use structure-guided breeding to identify an epistatic network that controls the onset of cyclization activity in Artemisia annua.
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Affiliation(s)
- Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Laurendon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jitender Cheema
- John Innes Centre, Computational and Systems Biology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marianne Defernez
- Institute of Food Research, Analytical Sciences Unit, Norwich Research Park, Norwich NR4 7UA, UK
| | - Sol Green
- Plant and Food Research, 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
| | - Juan A Faraldos
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Paul E O'Maille
- 1] John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK [2] Institute of Food Research, Food &Health Programme, Norwich Research Park, Norwich NR4 7UA, UK
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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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Affiliation(s)
- Anne E Osbourn
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul E O'Maille
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan J Rosser
- Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow, G12 8QQ, UK
| | - Keith Lindsey
- School of Biological Sciences, University of Durham, Durham, DH1 3UP, UK
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Abstract
Sesquiterpene synthases produce a wide variety of structurally diverse hydrocarbon products from a single substrate: farnesyl pyrophosphate. Each enzyme will often produce a multitude of products for which the kinetic efficiency is traditionally measured using a radioactivity assay. Here, we introduce a gas chromatography-mass spectroscopy-based assay to measure the formation of a single abundant product from which the kinetic parameters of the enzyme in question can be elucidated. We present an accounting of experimental components and considerations, such as solution conditions and instrument parameters, necessary to perform a standardized vial assay experiment. Further, we outline pilot experiments to establish analyte quantification and the linear range of enzyme concentration versus reaction velocity. Finally, we describe a protocol for a steady-state kinetics experiment, and the processing of experimental data to produce a Michaelis-Menten plot enabling one to derive kinetic parameters.
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Affiliation(s)
- Steven R Garrett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Ikezawa N, Göpfert JC, Nguyen DT, Kim SU, O'Maille PE, Spring O, Ro DK. Lettuce costunolide synthase (CYP71BL2) and its homolog (CYP71BL1) from sunflower catalyze distinct regio- and stereoselective hydroxylations in sesquiterpene lactone metabolism. J Biol Chem 2011; 286:21601-11. [PMID: 21515683 DOI: 10.1074/jbc.m110.216804] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sesquiterpene lactones (STLs) are terpenoid natural products possessing the γ-lactone, well known for their diverse biological and medicinal activities. The occurrence of STLs is sporadic in nature, but most STLs have been isolated from plants in the Asteraceae family. Despite the implication of the γ-lactone group in many reported bioactivities of STLs, the biosynthetic origins of the γ-lactone ring remains elusive. Germacrene A acid (GAA) has been suggested as a central precursor of diverse STLs. The regioselective (C6 or C8) and stereoselective (α or β) hydroxylation on a carbon of GAA adjacent to its carboxylic acid at C12 is responsible for the γ-lactone formation. Here, we report two cytochrome P450 monooxygenases (P450s) capable of catalyzing 6α- and 8β-hydroxylation of GAA from lettuce and sunflower, respectively. To identify these P450s, sunflower trichomes were isolated to generate a trichome-specific transcript library, from which 10 P450 clones were retrieved. Expression of these clones in a yeast strain metabolically engineered to synthesize substrate GAA identified a P450 catalyzing 8β-hydroxylation of GAA, but the STL was not formed by spontaneous lactonization. Subsequently, we identified the closest homolog of the GAA 8β-hydroxylase from lettuce and discovered 6α-hydroxylation of GAA by the recombinant enzyme. The resulting 6α-hydroxy-GAA spontaneously undergoes a lactonization to yield the simplest form of STL, costunolide. Furthermore, we demonstrate the milligram per liter scale de novo synthesis of costunolide using the lettuce P450 in an engineered yeast strain, an important advance that will enable exploitation of STLs. Evolution and homology models of these two P450s are discussed.
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Affiliation(s)
- Nobuhiro Ikezawa
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
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Faraldos JA, O'Maille PE, Dellas N, Noel JP, Coates RM. Bisabolyl-derived sesquiterpenes from tobacco 5-epi-aristolochene synthase-catalyzed cyclization of (2Z,6E)-farnesyl diphosphate. J Am Chem Soc 2010; 132:4281-9. [PMID: 20201526 DOI: 10.1021/ja909886q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the structures and stereochemistry of seven bisabolyl-derived sesquiterpenes arising from an unprecedented 1,6-cyclization (cisoid pathway) efficiently catalyzed by tobacco 5-epi-aristolochene synthase (TEAS). The use of (2Z,6E)-farnesyl diphosphate as an alternate substrate for recombinant TEAS resulted in a robust enzymatic cyclization to an array of products derived exclusively (>/=99.5%) from the cisoid pathway, whereas these same products account for ca. 2.5% of the total hydrocarbons obtained using (2E,6E)-farnesyl diphosphate. Chromatographic fractionations of extracts from preparative incubations with the 2Z,6E substrate afforded, in addition to the acyclic allylic alcohols (2Z,6E)-farnesol (6.7%) and nerolidol (3.6%), five cyclic sesquiterpene hydrocarbons and two cyclic sesquiterpene alcohols: (+)-2-epi-prezizaene (44%), (-)-alpha-cedrene (21.5%), (R)-(-)-beta-curcumene (15.5%), alpha-acoradiene (3.9%), 4-epi-alpha-acoradiene (1.3%), and equal amounts of alpha-bisabolol (1.8%) and epi-alpha-bisalolol (1.8%). The structures, stereochemistry, and enantiopurities were established by comprehensive spectroscopic analyses, optical rotations, chemical correlations with known sesquiterpenes, comparisons with literature data, and GC analyses. The major product, (+)-2-epi-prezizaene, is structurally related to the naturally occurring tricyclic alcohol, jinkohol (2-epi-prezizaan-7beta-ol). Cisoid cyclization pathways are proposed by which all five sesquiterpene hydrocarbons are derived from a common (7R)-beta-bisabolyl(+)/pyrophosphate(-) ion pair intermediate. The implications of the "cisoid" catalytic activity of TEAS are discussed.
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Affiliation(s)
- Juan A Faraldos
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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O'Maille PE, Malone A, Dellas N, Andes Hess B, Smentek L, Sheehan I, Greenhagen BT, Chappell J, Manning G, Noel JP. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol 2008; 4:617-23. [PMID: 18776889 PMCID: PMC2664519 DOI: 10.1038/nchembio.113] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [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: 08/08/2008] [Accepted: 08/18/2008] [Indexed: 11/10/2022]
Abstract
Throughout molecular evolution, organisms create assorted chemicals in response to varying ecological niches. Catalytic landscapes underlie metabolic evolution, wherein mutational steps alter the biosynthetic properties of enzymes. Here we report the first systematic quantitative characterization of the catalytic landscape underlying the evolution of sesquiterpene chemical diversity. On the basis of our previous discovery of a set of nine naturally occurring amino acid substitutions that functionally interconverted orthologous sesquiterpene synthases from Nicotiana tabacum and Hyoscyamus muticus, we created a library of all possible residue combinations (2(9) = 512) in the N. tabacum enzyme. The product spectra of 418 active enzymes revealed a rugged landscape where several minimal combinations of the nine mutations encode convergent solutions to the interconversions of parental activities. Quantitative comparisons indicated context dependence for mutational effects--epistasis--in product specificity and promiscuity. These results provide a measure of the mutational accessibility of phenotypic variability in a diverging lineage of terpene synthases.
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Affiliation(s)
- Paul E O'Maille
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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Faraldos JA, Zhao Y, O'Maille PE, Noel JP, Coates RM. Interception of the enzymatic conversion of farnesyl diphosphate to 5-epi-aristolochene by using a fluoro substrate analogue: 1-fluorogermacrene A from (2E,6Z)-6-fluorofarnesyl diphosphate. Chembiochem 2007; 8:1826-33. [PMID: 17886322 PMCID: PMC2735885 DOI: 10.1002/cbic.200700398] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [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] [Received: 07/20/2007] [Indexed: 11/11/2022]
Abstract
Tobacco 5-epi-aristolochene synthase (TEAS) catalyzes the Mg(II)-dependent cyclizations and rearrangements of (E,E)-farnesyl diphosphate (PP) to the bicyclic sesquiterpene hydrocarbon via a tightly bound (+)-germacrene A as a deprotonated intermediate. With the native enzyme, only a few percent of the putative germacrene A intermediate is released from the active site during the catalytic cycle. 6-Fluorofarnesyl PP was designed and synthesized with the aim of arresting the cyclization-rearrangement mechanism en route to 5-epi-aristolochene. Indeed, incubation of (2E,6Z)-6-fluorofarnesyl PP with recombinant TEAS afforded (-)-1-fluorogermacrene A as the sole product in 58% yield. Steady-state kinetic experiments with farnesyl PP and the 6-fluoro analogue showed that the overall catalytic efficiencies (k(cat)/K(m)) are essentially the same for both substrates. 1-Fluorogermacrene A was characterized by chromatographic properties (TLC, GC), MS, optical rotation, UV, IR and (1)H NMR data, and by heat-induced Cope rearrangement to (+)-1-fluoro-beta-elemene. (1)H NMR spectra at room temperature revealed that this (E,E)-configured fluorocyclodecadiene exists in solution as a 7:3 mixture of UU and UD conformers. 1-Fluorogermacrene A underwent trifluoroacetic acid-catalyzed cyclization to give three 1alpha-fluoroselinene isomers at a rate estimated to be about 1000 times slower than that of the similar cyclization of (+)-germacrene A to the parent selinenes.
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Affiliation(s)
- Juan A. Faraldos
- Department of Chemistry, University of Illinois 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Yuxin Zhao
- Department of Chemistry, University of Illinois 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Paul E. O'Maille
- Howard Hughes Medical Institute Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92307 (USA)
| | - Joseph P. Noel
- Howard Hughes Medical Institute Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 N. Torrey Pines Road, La Jolla, CA 92307 (USA)
| | - Robert M. Coates
- Department of Chemistry, University of Illinois 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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Köllner TG, O'Maille PE, Gatto N, Boland W, Gershenzon J, Degenhardt J. Two pockets in the active site of maize sesquiterpene synthase TPS4 carry out sequential parts of the reaction scheme resulting in multiple products. Arch Biochem Biophys 2005; 448:83-92. [PMID: 16297849 DOI: 10.1016/j.abb.2005.10.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 10/12/2005] [Accepted: 10/13/2005] [Indexed: 11/19/2022]
Abstract
One of the most interesting features of terpene synthases is their ability to form multiple products with different carbon skeletons from a single prenyl diphosphate substrate. The maize sesquiterpene synthase TPS4, for example, produces a mixture of 14 different olefinic sesquiterpenes. To understand the complex TPS4 reaction mechanism, we modeled the active site cavity and conducted docking simulations with the substrate farnesyl diphosphate, several predicted carbocation intermediates, and the final reaction products. The model suggests that discrete steps of the reaction sequence are controlled by two different active site pockets, with the conformational change of the bisabolyl cation intermediate causing a shift from one pocket to the other. Site-directed mutagenesis and measurements of mutant activity in the presence of (E,E)- and (Z,E)-farnesyl diphosphate as substrates were employed to test this model. Amino acid alterations in pocket I indicated that early steps of the catalytic process up to the formation of the monocyclic bisabolyl cation are probably localized in this compartment. Mutations in pocket II primarily inhibited the formation of bicylic compounds, suggesting that secondary cyclizations of the bisabolyl cation are catalyzed in pocket II.
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Affiliation(s)
- Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, D-07745 Jena, Germany
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O'Maille PE, Chappell J, Noel JP. A single-vial analytical and quantitative gas chromatography-mass spectrometry assay for terpene synthases. Anal Biochem 2004; 335:210-7. [PMID: 15556559 DOI: 10.1016/j.ab.2004.09.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Indexed: 11/18/2022]
Abstract
A quantitative assay for the analysis of sesquiterpene synthases, wherein each reaction mixture is formulated in glass gas chromatography vials, overlaid with organic solvent such as ethyl acetate, and subsequently vortexed to extract hydrocarbon reaction products into the organic phase after a suitable incubation period, was developed. The product-enriched organic phase is then sampled in an automated fashion and injected directly into a gas chromatograph-mass spectrometer without further workup for analysis and quantification of hydrocarbon products. Application of the vial assay to the analysis of amorpha-4,11-diene synthase (ADS), a sesquiterpene synthase, demonstrated the sensitivity of the assay for detection of major and minor reaction products and most notably for the identification of several sesquiterpene products that had escaped previous detection. A steady-state kinetic analysis of tobacco 5-epi-aristolochene synthase (TEAS), another sesquiterpene synthase, validated the quantitative nature of the assay, providing an alternative means to the established method of using radiolabeled substrate, extraction, and scintillation counting. This simplified assay provides a standardized method to facilitate analysis of terpene synthases and diverse mutant enzyme libraries by supplanting the common practice of using larger scale reactions, multiple extractions, and evaporative concentration of the organic phase prior to gas chromatography-mass spectrometry (GC-MS) analysis.
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Affiliation(s)
- Paul E O'Maille
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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Affiliation(s)
- Paul E O'Maille
- Structural Biology Laboratory, The Stalk Institute for Biological Studies, La Jolla, California 92037, USA
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Abstract
Presented here is the development a semi-rational protein engineering approach that uses information from protein structure coupled with established DNA manipulation techniques to design and create multiple crossover libraries from non-homologous genes. The utility of structure-based combinatorial protein engineering (SCOPE) was demonstrated by its application to two distantly related members of the X-family of DNA polymerases: rat DNA polymerase beta (Pol beta) and African swine fever virus DNA polymerase X (Pol X). These proteins share similar folds but have low sequence identity, and differ greatly in both size and activity. "Equivalent" subdomain elements of structure were designed on the basis of the tertiary structure of Pol beta and the corresponding regions of Pol X were inferred from homology modeling and sequence alignment analysis. Libraries of chimeric genes with up to five crossovers were synthesized in a series of PCR reactions by employing hybrid oligonucleotides that code for variable connections between structural elements. Genetic complementation in Escherichia coli enabled identification of several novel DNA polymerases with enhanced phenotypes. Both the composition of structural elements and the manner in which they were linked were shown to be essential for this property, indicating the importance of these aspects of design.
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Affiliation(s)
- Paul E O'Maille
- Ohio State Biochemistry Program, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1173, USA
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