51
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Su P, Guan H, Zhang Y, Wang X, Gao L, Zhao Y, Hu T, Zhou J, Ma B, Tu L, Tong Y, Huang L, Gao W. Probing the Single Key Amino Acid Responsible for the Novel Catalytic Function of ent-Kaurene Oxidase Supported by NADPH-Cytochrome P450 Reductases in Tripterygium wilfordii. FRONTIERS IN PLANT SCIENCE 2017; 8:1756. [PMID: 29081786 PMCID: PMC5645531 DOI: 10.3389/fpls.2017.01756] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/25/2017] [Indexed: 05/07/2023]
Abstract
Tripterygium wilfordii produces not only ent-kaurene, which is an intermediate of gibberellin (GA) biosynthesis in flowering plants, but also 16α-hydroxy-ent-kaurane, whose physiological role has not been characterized. The two compounds are biosynthesized from the universal diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate (GGPP) by diterpene synthases, which have been discovered and functionally characterized in T. wilfordii. Here, we described the functional characterization of four cytochrome P450 reductases (TwCPR) and one ent-kaurene oxidase (TwKO). Four TwCPRs were found to have relatively ubiquitous expression in T. wilfordii root, stem, leaf, and flower tissues. Co-expression of both a TwCPR and TwKO in yeast showed that TwCPR3 has a slightly better activity for providing the electrons required for these reactions, indicating that TwCPR3 is more suitable for use in the functional analysis of other cytochrome P450 monooxygenases. TwKO catalyzed the three-step oxidation of the C4α methyl of the tetracyclic diterpene intermediate ent-kaurene to form ent-kaurenoic acid as an early step in GA biosynthesis. Notably, TwKO could also convert 16α-hydroxy-ent-kaurane to 16α-hydroxy-ent-kaurenoic acid, indicating an important function of 16α-hydroxy-ent-kaurane in the anti-HIV principle tripterifordin biosynthetic pathway in planta. Homology modeling and molecular docking were used to investigate the unknown crucial active amino acid residue involved in the catalytic reaction of TwKO, and one key residue (Leu387) contributed to the formation of 16α-hydroxy-ent-kaurenoic acid, most likely by forming hydrogen bonds with the hydroxyl group (-OH) of 16α-hydroxy-ent-kaurane, which laid the basis for further investigation of the multifunctional nature of KO catalysis. Also, our findings paved the way for the complete biosynthesis of the anti-HIV principle tripterifordin.
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Affiliation(s)
- Ping Su
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hongyu Guan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Yifeng Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Lab of TCM Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Linhui Gao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yujun Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Baowei Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Luqi Huang, Wei Gao,
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Lab of TCM Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- *Correspondence: Luqi Huang, Wei Gao,
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52
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Hammer SC, Syrén PO, Hauer B. Substrate Pre-Folding and Water Molecule Organization Matters for Terpene Cyclase Catalyzed Conversion of Unnatural Substrates. ChemistrySelect 2016. [DOI: 10.1002/slct.201600572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stephan C. Hammer
- Division of Chemistry; Chemical Engineering; California Institute of Technology; Pasadena, CA 91125 USA
| | - Per-Olof Syrén
- School of Chemical Science and Engineering; Division of Applied Physical Chemistry; KTH Royal Institute of Technology; 100 44 Stockholm Sweden
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 D-70569 Stuttgart Germany
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53
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Rudolf JD, Dong LB, Cao H, Hatzos-Skintges C, Osipiuk J, Endres M, Chang CY, Ma M, Babnigg G, Joachimiak A, Phillips GN, Shen B. Structure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase. J Am Chem Soc 2016; 138:10905-15. [PMID: 27490479 PMCID: PMC5013971 DOI: 10.1021/jacs.6b04317] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Terpenoids are the largest and most structurally diverse family of natural products found in nature, yet their presence in bacteria is underappreciated. The carbon skeletons of terpenoids are generated through carbocation-dependent cyclization cascades catalyzed by terpene synthases (TSs). Type I and type II TSs initiate cyclization via diphosphate ionization and protonation, respectively, and protein structures of both types are known. Most plant diterpene synthases (DTSs) possess three α-helical domains (αβγ), which are thought to have arisen from the fusion of discrete, ancestral bacterial type I TSs (α) and type II TSs (βγ). Type II DTSs of bacterial origin, of which there are no structurally characterized members, are a missing piece in the structural evolution of TSs. Here, we report the first crystal structure of a type II DTS from bacteria. PtmT2 from Streptomyces platensis CB00739 was verified as an ent-copalyl diphosphate synthase involved in the biosynthesis of platensimycin and platencin. The crystal structure of PtmT2 was solved at a resolution of 1.80 Å, and docking studies suggest the catalytically active conformation of geranylgeranyl diphosphate (GGPP). Site-directed mutagenesis confirmed residues involved in binding the diphosphate moiety of GGPP and identified DxxxxE as a potential Mg(2+)-binding motif for type II DTSs of bacterial origin. Finally, both the shape and physicochemical properties of the active sites are responsible for determining specific catalytic outcomes of TSs. The structure of PtmT2 fundamentally advances the knowledge of bacterial TSs, their mechanisms, and their role in the evolution of TSs.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Liao-Bin Dong
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hongnan Cao
- Department of Biosciences, Rice University , Houston, Texas 77005, United States
| | - Catherine Hatzos-Skintges
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Michael Endres
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - George N Phillips
- Department of Biosciences, Rice University , Houston, Texas 77005, United States
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.,Department of Molecular Therapeutics, The Scripps Research Institute , Jupiter, Florida 33458, United States.,Natural Products Library Initiative, The Scripps Research Institute , Jupiter, Florida 33458, United States
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54
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Chen M, Harris GG, Pemberton TA, Christianson DW. Multi-domain terpenoid cyclase architecture and prospects for proximity in bifunctional catalysis. Curr Opin Struct Biol 2016; 41:27-37. [PMID: 27285057 DOI: 10.1016/j.sbi.2016.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/22/2016] [Indexed: 10/21/2022]
Abstract
Crystal structures of terpenoid cyclases reveal assemblies of three basic domains designated α, β, and γ. While the biosynthesis of cyclic monoterpenes (C10) and sesquiterpenes (C15) most often involves enzymes with α or αβ domain architecture, the biosynthesis of cyclic diterpenes (C20), sesterterpenes (C25), and triterpenes (C30) can involve enzymes with α, αα, βγ, or αβγ domain architecture. Indeed, some enzymes of terpenoid biosynthesis are bifunctional, with distinct active sites that catalyze sequential reactions. Interestingly, some of these enzymes oligomerize to form dimers, tetramers, and hexamers. Not only can such assemblies enable enzyme regulation by allostery, but they can also provide a modest enhancement of terpenoid product flux through proximity channeling or cluster channeling. The mixing and matching of functional terpenoid cyclase domains through tertiary and/or quaternary structure may also comprise an evolutionary strategy for facile product diversification.
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Affiliation(s)
- Mengbin Chen
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - Golda G Harris
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States.
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55
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Geisler K, Jensen NB, Yuen MMS, Madilao L, Bohlmann J. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products. PLANT PHYSIOLOGY 2016; 171:152-64. [PMID: 26936895 PMCID: PMC4854711 DOI: 10.1104/pp.16.00180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 05/06/2023]
Abstract
Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.
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Affiliation(s)
- Katrin Geisler
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Niels Berg Jensen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Lina Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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56
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Chen M, Chou WKW, Toyomasu T, Cane DE, Christianson DW. Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase. ACS Chem Biol 2016; 11:889-99. [PMID: 26734760 PMCID: PMC4833508 DOI: 10.1021/acschembio.5b00960] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fusicoccin A is a diterpene glucoside phytotoxin generated by the fungal pathogen Phomopsis amygdali that causes the plant disease constriction canker, first discovered in New Jersey peach orchards in the 1930s. Fusicoccin A is also an emerging new lead in cancer chemotherapy. The hydrocarbon precursor of fusicoccin A is the tricyclic diterpene fusicoccadiene, which is generated by a bifunctional terpenoid synthase. Here, we report X-ray crystal structures of the individual catalytic domains of fusicoccadiene synthase: the C-terminal domain is a chain elongation enzyme that generates geranylgeranyl diphosphate, and the N-terminal domain catalyzes the cyclization of geranylgeranyl diphosphate to form fusicoccadiene. Crystal structures of each domain complexed with bisphosphonate substrate analogues suggest that three metal ions and three positively charged amino acid side chains trigger substrate ionization in each active site. While in vitro incubations reveal that the cyclase domain can utilize farnesyl diphosphate and geranyl diphosphate as surrogate substrates, these shorter isoprenoid diphosphates are mainly converted into acyclic alcohol or hydrocarbon products. Gel filtration chromatography and analytical ultracentrifugation experiments indicate that full-length fusicoccadiene synthase adopts hexameric quaternary structure, and small-angle X-ray scattering data yield a well-defined molecular envelope illustrating a plausible model for hexamer assembly.
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Affiliation(s)
- Mengbin Chen
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, United States
| | - Wayne K. W. Chou
- Department of Chemistry, Brown University, Box H, Providence, Rhode Island, 02912, United States
| | - Tomonobu Toyomasu
- Department of Bioresource Engineering, Faculty of Agriculture, Yamagata University, Wakaba-cho 1-23, Tsuruoka, Yamagata, Japan
| | - David E. Cane
- Department of Chemistry, Brown University, Box H, Providence, Rhode Island, 02912, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, United States
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, United States
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57
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Identification of amino acid networks governing catalysis in the closed complex of class I terpene synthases. Proc Natl Acad Sci U S A 2016; 113:E958-67. [PMID: 26842837 DOI: 10.1073/pnas.1519680113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class I terpene synthases generate the structural core of bioactive terpenoids. Deciphering structure-function relationships in the reactive closed complex and targeted engineering is hampered by highly dynamic carbocation rearrangements during catalysis. Available crystal structures, however, represent the open, catalytically inactive form or harbor nonproductive substrate analogs. Here, we present a catalytically relevant, closed conformation of taxadiene synthase (TXS), the model class I terpene synthase, which simulates the initial catalytic time point. In silico modeling of subsequent catalytic steps allowed unprecedented insights into the dynamic reaction cascades and promiscuity mechanisms of class I terpene synthases. This generally applicable methodology enables the active-site localization of carbocations and demonstrates the presence of an active-site base motif and its dominating role during catalysis. It additionally allowed in silico-designed targeted protein engineering that unlocked the path to alternate monocyclic and bicyclic synthons representing the basis of a myriad of bioactive terpenoids.
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58
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Yahyaa M, Matsuba Y, Brandt W, Doron-Faigenboim A, Bar E, McClain A, Davidovich-Rikanati R, Lewinsohn E, Pichersky E, Ibdah M. Identification, Functional Characterization, and Evolution of Terpene Synthases from a Basal Dicot. PLANT PHYSIOLOGY 2015; 169:1683-97. [PMID: 26157114 PMCID: PMC4634067 DOI: 10.1104/pp.15.00930] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 05/06/2023]
Abstract
Bay laurel (Laurus nobilis) is an agriculturally and economically important dioecious tree in the basal dicot family Lauraceae used in food and drugs and in the cosmetics industry. Bay leaves, with their abundant monoterpenes and sesquiterpenes, are used to impart flavor and aroma to food, and have also drawn attention in recent years because of their potential pharmaceutical applications. To identify terpene synthases (TPSs) involved in the production of these volatile terpenes, we performed RNA sequencing to profile the transcriptome of L. nobilis leaves. Bioinformatic analysis led to the identification of eight TPS complementary DNAs. We characterized the enzymes encoded by three of these complementary DNAs: a monoterpene synthase that belongs to the TPS-b clade catalyzes the formation of mostly 1,8-cineole; a sesquiterpene synthase belonging to the TPS-a clade catalyzes the formation of mainly cadinenes; and a diterpene synthase of the TPS-e/f clade catalyzes the formation of geranyllinalool. Comparison of the sequences of these three TPSs indicated that the TPS-a and TPS-b clades of the TPS gene family evolved early in the evolution of the angiosperm lineage, and that geranyllinalool synthase activity is the likely ancestral function in angiosperms of genes belonging to an ancient TPS-e/f subclade that diverged from the kaurene synthase gene lineages before the split of angiosperms and gymnosperms.
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Affiliation(s)
- Mosaab Yahyaa
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Yuki Matsuba
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Wolfgang Brandt
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Adi Doron-Faigenboim
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Einat Bar
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Alan McClain
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Rachel Davidovich-Rikanati
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Efraim Lewinsohn
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Eran Pichersky
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Mwafaq Ibdah
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
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Misra RC, Garg A, Roy S, Chanotiya CS, Vasudev PG, Ghosh S. Involvement of an ent-copalyl diphosphate synthase in tissue-specific accumulation of specialized diterpenes in Andrographis paniculata. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:50-64. [PMID: 26475187 DOI: 10.1016/j.plantsci.2015.08.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 08/13/2015] [Accepted: 08/22/2015] [Indexed: 05/24/2023]
Abstract
Ent-labdane-related diterpene (ent-LRD) specialized (i.e. secondary) metabolites of the medicinal plant kalmegh (Andrographis paniculata) have long been known for several pharmacological activities. However, our understanding of the ent-LRD biosynthetic pathway has remained largely incomplete. Since ent-LRDs accumulate in leaves, we carried out a comparative transcriptional analysis using leaf and root tissues, and identified 389 differentially expressed transcripts, including 223 transcripts that were preferentially expressed in leaf tissue. Analysis of the transcripts revealed various specialized metabolic pathways, including transcripts of the ent-LRD biosynthetic pathway. Two class II diterpene synthases (ApCPS1 and ApCPS2) along with one (ApCPS1') and two (ApCPS2' and ApCPS2″) transcriptional variants that were the outcomes of alternative splicing of the precursor mRNA and alternative transcriptional termination, respectively, were identified. ApCPS1 and ApCPS2 encode for 832- and 817-amino acids proteins, respectively, and are phylogenetically related to the dicotyledons ent-copalyl diphosphate synthases (ent-CPSs). The spatio-temporal patterns of ent-LRD metabolites accumulation and gene expression suggested a likely role for ApCPS1 in general (i.e. primary) metabolism, perhaps by providing precursor for the biosynthesis of phytohormone gibberellin (GA). However, ApCPS2 is potentially involved in tissue-specific accumulation of ent-LRD specialized metabolites. Bacterially expressed recombinant ApCPS2 catalyzed the conversion of (E,E,E)-geranylgeranyl diphosphate (GGPP), the general precursor of diterpenes to ent-copalyl diphosphate (ent-CPP), the precursor of ent-LRDs. Taken together, these results advance our understanding of the tissue-specific accumulation of specialized ent-LRDs of medicinal importance.
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Affiliation(s)
- Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Sudeep Roy
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Chemical Sciences Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Prema G Vasudev
- Metabolic and Structural Biology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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60
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Mafu S, Potter KC, Hillwig ML, Schulte S, Criswell J, Peters RJ. Efficient heterocyclisation by (di)terpene synthases. Chem Commun (Camb) 2015; 51:13485-13487. [PMID: 26214384 PMCID: PMC4543578 DOI: 10.1039/c5cc05754j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While cyclic ether forming terpene synthases are known, the basis for such heterocyclisation is unclear. Here it is reported that numerous (di)terpene synthases, particularly including the ancestral ent-kaurene synthase, efficiently produce isomers of manoyl oxide from the stereochemically appropriate substrate. Accordingly, such heterocyclisation is easily accomplished by terpene synthases. Indeed, the use of single residue changes to induce production of the appropriate substrate in the upstream active site leads to efficient bifunctional enzymes producing isomers of manoyl oxide, representing novel enzymatic activity.
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Affiliation(s)
- S Mafu
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - K C Potter
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - M L Hillwig
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - S Schulte
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - J Criswell
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - R J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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61
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Plant diterpene synthases: exploring modularity and metabolic diversity for bioengineering. Trends Biotechnol 2015; 33:419-28. [DOI: 10.1016/j.tibtech.2015.04.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/22/2022]
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62
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Tholl D. Biosynthesis and biological functions of terpenoids in plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:63-106. [PMID: 25583224 DOI: 10.1007/10_2014_295] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, 409 Latham Hall, 24061, Blacksburg, VA, USA,
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63
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Exploring the interactions between isoprenoid chain and labdenediol diphosphate synthase based on molecular docking and quartz crystal microbalance. J Mol Model 2014; 20:2527. [PMID: 25472483 DOI: 10.1007/s00894-014-2527-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Many natural products and biosynthetic intermediates contain isoprenoid chains. Isoprenoid chains are believed to interact with some proteins in the biological systems, but such interactions remain poorly understood. Here labdenediol diphosphate synthase (LPPS) was used as a model to explore the molecular interactions involving isoprenoid chains. Both homology modeling and docking simulation results indicated that binding form between isoprenoid chain and LPPS is dominated by hydrophobic forces in one binding site. The interactions were also examined via quartz crystal microbalance (QCM) technology using synthetic isoprenoid chain-contained probes. The binding constant (1.51 μM(-1)), binding site number (n = 1) and key amino acid residues (Y196, F262, W266, F301, F308, W398, W439, and Y445) were obtained. Both computational and QCM results suggested that LPPS interacts strongly with farnesyl and geranylgeranyl groups. These interactions are primarily caused by hydrophobic and π-π interaction nature. Together, this study provided insightful information to understand molecular interactions between isoprenoid chains and proteins.
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64
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Kwon M, Cochrane SA, Vederas JC, Ro DK. Molecular cloning and characterization of drimenol synthase from valerian plant (Valeriana officinalis). FEBS Lett 2014; 588:4597-603. [DOI: 10.1016/j.febslet.2014.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/25/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
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Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol 2014; 10:e1003874. [PMID: 25299649 PMCID: PMC4191879 DOI: 10.1371/journal.pcbi.1003874] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications of the current approach, such as enzyme mechanistic studies and enzyme redesign by mutagenesis, are discussed. The rapid growth in the number of protein sequences presents challenges for enzyme function assignment. Computational methods, such as bioinformatics, homology modeling and docking, are becoming increasingly important for predicting of enzyme functions from protein sequences. Terpenoids are one of largest classes of natural products, and many drugs (e.g. taxol) consist of terpenoids or terpenoid derivatives. Understanding the biosynthesis of the terpenoids is of great interest. Terpenoid synthases catalyze the key cyclization steps of the biosynthesis of terpenoids via carbocation rearrangements, generating numerous multiple-ring carbon skeletons. Triterpenoid synthases, as an important class of terpenoid synthases, catalyze the cyclization of either squalene or oxido-squalene into cyclized products such as sterols (e.g. lanosterol). In this work, we propose a computational approach that can be used to predict product specificity of the triterpenoid synthases. Our approach provides insight into the ‘design principles’ of these fascinating enzymes, and may become a practical approach for function prediction and enzyme engineering.
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Affiliation(s)
- Bo-Xue Tian
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - Frank H. Wallrapp
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - Gemma L. Holiday
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeng-Yeong Chow
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Patricia C. Babbitt
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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66
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Structure, function and inhibition of ent-kaurene synthase from Bradyrhizobium japonicum. Sci Rep 2014; 4:6214. [PMID: 25269599 PMCID: PMC4180811 DOI: 10.1038/srep06214] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/07/2014] [Indexed: 11/12/2022] Open
Abstract
We report the first X-ray crystal structure of ent-kaur-16-ene synthase from Bradyrhizobium japonicum, together with the results of a site-directed mutagenesis investigation into catalytic activity. The structure is very similar to that of the α domains of modern plant terpene cyclases, a result that is of interest since it has been proposed that many plant terpene cyclases may have arisen from bacterial diterpene cyclases. The ent-copalyl diphosphate substrate binds to a hydrophobic pocket near a cluster of Asp and Arg residues that are essential for catalysis, with the carbocations formed on ionization being protected by Leu, Tyr and Phe residues. A bisphosphonate inhibitor binds to the same site. In the kaurene synthase from the moss Physcomitrella patens, 16-α-hydroxy-ent-kaurane as well as kaurene are produced since Leu and Tyr in the P. patens kaurene synthase active site are replaced by smaller residues enabling carbocation quenching by water. Overall, the results represent the first structure determination of a bacterial diterpene cyclase, providing insights into catalytic activity, as well as structural comparisons with diverse terpene synthases and cyclases which clearly separate the terpene cyclases from other terpene synthases having highly α-helical structures.
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Abstract
Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids.
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Affiliation(s)
- Maureen B Quin
- University of Minnesota, Dept. of Biochemistry, Molecular Biology and Biophysics, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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68
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel Product Chemistry from Mechanistic Analysis of
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‐Copalyl Diphosphate Synthases from Plant Hormone Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jared Criswell
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jiachen Zi
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Alisha Stubbs
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Reuben J. Peters
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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69
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel product chemistry from mechanistic analysis of ent-copalyl diphosphate synthases from plant hormone biosynthesis. Angew Chem Int Ed Engl 2014; 53:7198-202. [PMID: 24862907 DOI: 10.1002/anie.201402911] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Indexed: 11/08/2022]
Abstract
An active-site water molecule coordinated by conserved histidine and asparagine residues seems to serve as the catalytic base in all ent-copalyl diphosphate synthases (CPSs). When these residues are substituted by alanine, the mutant CPSs produce stereochemically novel ent-8-hydroxy-CPP. Given the requisite presence of CPSs in all land plants for gibberellin phytohormone biosynthesis, such plasticity presumably underlies the observed extensive diversification of the resulting labdane-related diterpenoids.
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Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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70
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Janke R, Görner C, Hirte M, Brück T, Loll B. The first structure of a bacterial diterpene cyclase: CotB2. ACTA ACUST UNITED AC 2014; 70:1528-37. [PMID: 24914964 DOI: 10.1107/s1399004714005513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/11/2014] [Indexed: 02/05/2023]
Abstract
Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Å resolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.
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Affiliation(s)
- Ronja Janke
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Christian Görner
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Max Hirte
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Thomas Brück
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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Brück T, Kourist R, Loll B. Production of Macrocyclic Sesqui- and Diterpenes in Heterologous Microbial Hosts: A Systems Approach to Harness Nature’s Molecular Diversity. ChemCatChem 2014. [DOI: 10.1002/cctc.201300733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Zi J, Mafu S, Peters RJ. To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:259-86. [PMID: 24471837 PMCID: PMC4118669 DOI: 10.1146/annurev-arplant-050213-035705] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The diterpenoids are classically defined by their composition--four isoprenyl units (20 carbons)--and are generally derived from [E,E,E]-geranylgeranyl diphosphate (GGPP). Such metabolism seems to be ancient and has been extensively diversified, with ∼12,000 diterpenoid natural products known. Particularly notable are the gibberellin phytohormones, whose requisite biosynthesis has provided a genetic reservoir that gave rise to not only a large superfamily of ∼7,000 diterpenoids but also, to some degree, all plant terpenoid natural products. This review focuses on the diterpenoids, particularly the defining biosynthetic characteristics of the major superfamilies defined by the cyclization and/or rearrangement of GGPP catalyzed by diterpene synthases/cyclases, although it also includes some discussion of the important subsequent elaboration in the few cases where sufficient molecular genetic information is available. It additionally addresses the array of biological activity providing the selective pressures that drive the observed gene family expansion and diversification, along with biosynthetic gene clustering.
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73
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Schmidt-Dannert C. Biosynthesis of terpenoid natural products in fungi. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 148:19-61. [PMID: 25414054 DOI: 10.1007/10_2014_283] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tens of thousands of terpenoid natural products have been isolated from plants and microbial sources. Higher fungi (Ascomycota and Basidiomycota) are known to produce an array of well-known terpenoid natural products, including mycotoxins, antibiotics, antitumor compounds, and phytohormones. Except for a few well-studied fungal biosynthetic pathways, the majority of genes and biosynthetic pathways responsible for the biosynthesis of a small number of these secondary metabolites have only been discovered and characterized in the past 5-10 years. This chapter provides a comprehensive overview of the current knowledge on fungal terpenoid biosynthesis from biochemical, genetic, and genomic viewpoints. Enzymes involved in synthesizing, transferring, and cyclizing the prenyl chains that form the hydrocarbon scaffolds of fungal terpenoid natural products are systematically discussed. Genomic information and functional evidence suggest differences between the terpenome of the two major fungal phyla--the Ascomycota and Basidiomycota--which will be illustrated for each group of terpenoid natural products.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minneapolis, MN, 55108, USA,
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Köksal M, Potter K, Peters RJ, Christianson DW. 1.55Å-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis. Biochim Biophys Acta Gen Subj 2013; 1840:184-90. [PMID: 24036329 DOI: 10.1016/j.bbagen.2013.09.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained. METHOD Use of crystallization additives yielded CPS crystals diffracting to 1.55Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. RESULTS This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. CONCLUSIONS Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg(2+) required for optimal catalytic activity. GENERAL SIGNIFICANCE This work establishes structure-function relationships for class II terpenoid cyclases.
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Affiliation(s)
- Mustafa Köksal
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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75
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Görner C, Häuslein I, Schrepfer P, Eisenreich W, Brück T. Targeted Engineering of Cyclooctat-9-en-7-ol Synthase: A Stereospecific Access to Two New Non-natural Fusicoccane-Type Diterpenes. ChemCatChem 2013. [DOI: 10.1002/cctc.201300285] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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76
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Hall DE, Zerbe P, Jancsik S, Quesada AL, Dullat H, Madilao LL, Yuen M, Bohlmann J. Evolution of conifer diterpene synthases: diterpene resin acid biosynthesis in lodgepole pine and jack pine involves monofunctional and bifunctional diterpene synthases. PLANT PHYSIOLOGY 2013; 161:600-16. [PMID: 23370714 PMCID: PMC3561007 DOI: 10.1104/pp.112.208546] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diterpene resin acids (DRAs) are major components of pine (Pinus spp.) oleoresin. They play critical roles in conifer defense against insects and pathogens and as a renewable resource for industrial bioproducts. The core structures of DRAs are formed in secondary (i.e. specialized) metabolism via cycloisomerization of geranylgeranyl diphosphate (GGPP) by diterpene synthases (diTPSs). Previously described gymnosperm diTPSs of DRA biosynthesis are bifunctional enzymes that catalyze the initial bicyclization of GGPP followed by rearrangement of a (+)-copalyl diphosphate intermediate at two discrete class II and class I active sites. In contrast, similar diterpenes of gibberellin primary (i.e. general) metabolism are produced by the consecutive activity of two monofunctional class II and class I diTPSs. Using high-throughput transcriptome sequencing, we discovered 11 diTPS from jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta). Three of these were orthologous to known conifer bifunctional levopimaradiene/abietadiene synthases. Surprisingly, two sets of orthologous PbdiTPSs and PcdiTPSs were monofunctional class I enzymes that lacked functional class II active sites and converted (+)-copalyl diphosphate, but not GGPP, into isopimaradiene and pimaradiene as major products. Diterpene profiles and transcriptome sequences of lodgepole pine and jack pine are consistent with roles for these diTPSs in DRA biosynthesis. The monofunctional class I diTPSs of DRA biosynthesis form a new clade within the gymnosperm-specific TPS-d3 subfamily that evolved from bifunctional diTPS rather than monofunctional enzymes (TPS-c and TPS-e) of gibberellin metabolism. Homology modeling suggested alterations in the class I active site that may have contributed to their functional specialization relative to other conifer diTPSs.
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77
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Fischer MJC, Meyer S, Claudel P, Steyer D, Bergdoll M, Hugueney P. Determination of amino-acidic positions important for <i>Ocimum basilicum</i> geraniol synthase activity. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.42033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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78
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Vanommeslaeghe K, MacKerell AD. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J Chem Inf Model 2012; 52:3144-54. [PMID: 23146088 DOI: 10.1021/ci300363c] [Citation(s) in RCA: 1220] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .
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Affiliation(s)
- K Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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79
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Criswell J, Potter K, Shephard F, Beale MH, Peters RJ. A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase. Org Lett 2012; 14:5828-31. [PMID: 23167845 DOI: 10.1021/ol3026022] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Class II diterpene cyclases catalyze bicyclization of geranylgeranyl diphosphate. While this reaction typically is terminated via methyl deprotonation to yield copalyl diphosphate, in rare cases hydroxylated bicycles are produced instead. Abietadiene synthase is a bifunctional diterpene cyclase that usually produces a copalyl diphosphate intermediate. Here it is shown that substitution of aspartate for a conserved histidine in the class II active site of abietadiene synthase leads to selective production of 8α-hydroxy-CPP instead, demonstrating striking plasticity.
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Affiliation(s)
- Jared Criswell
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Gao Y, Honzatko RB, Peters RJ. Terpenoid synthase structures: a so far incomplete view of complex catalysis. Nat Prod Rep 2012; 29:1153-75. [PMID: 22907771 PMCID: PMC3448952 DOI: 10.1039/c2np20059g] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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Caniard A, Zerbe P, Legrand S, Cohade A, Valot N, Magnard JL, Bohlmann J, Legendre L. Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea (L.) and their relevance for perfume manufacture. BMC PLANT BIOLOGY 2012; 12:119. [PMID: 22834731 PMCID: PMC3520730 DOI: 10.1186/1471-2229-12-119] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/26/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sclareol is a diterpene natural product of high value for the fragrance industry. Its labdane carbon skeleton and its two hydroxyl groups also make it a valued starting material for semisynthesis of numerous commercial substances, including production of Ambrox® and related ambergris substitutes used in the formulation of high end perfumes. Most of the commercially-produced sclareol is derived from cultivated clary sage (Salvia sclarea) and extraction of the plant material. In clary sage, sclareol mainly accumulates in essential oil-producing trichomes that densely cover flower calices. Manool also is a minor diterpene of this species and the main diterpene of related Salvia species. RESULTS Based on previous general knowledge of diterpene biosynthesis in angiosperms, and based on mining of our recently published transcriptome database obtained by deep 454-sequencing of cDNA from clary sage calices, we cloned and functionally characterized two new diterpene synthase (diTPS) enzymes for the complete biosynthesis of sclareol in clary sage. A class II diTPS (SsLPPS) produced labda-13-en-8-ol diphosphate as major product from geranylgeranyl diphosphate (GGPP) with some minor quantities of its non-hydroxylated analogue, (9 S, 10 S)-copalyl diphosphate. A class I diTPS (SsSS) then transformed these intermediates into sclareol and manool, respectively. The production of sclareol was reconstructed in vitro by combining the two recombinant diTPS enzymes with the GGPP starting substrate and in vivo by co-expression of the two proteins in yeast (Saccharomyces cerevisiae). Tobacco-based transient expression assays of green fluorescent protein-fusion constructs revealed that both enzymes possess an N-terminal signal sequence that actively targets SsLPPS and SsSS to the chloroplast, a major site of GGPP and diterpene production in plants. CONCLUSIONS SsLPPS and SsSS are two monofunctional diTPSs which, together, produce the diterpenoid specialized metabolite sclareol in a two-step process. They represent two of the first characterized hydroxylating diTPSs in angiosperms and generate the dihydroxylated labdane sclareol without requirement for additional enzymatic oxidation by activities such as cytochrome P450 monoxygenases. Yeast-based production of sclareol by co-expresssion of SsLPPS and SsSS was efficient enough to warrant the development and use of such technology for the biotechnological production of scareol and other oxygenated diterpenes.
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Affiliation(s)
- Anne Caniard
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Philipp Zerbe
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sylvain Legrand
- Université Lille Nord de France, Lille, F-59000, France
- Université Lille1, Villeneuve d’Ascq, F-59655, France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), UMR INRA 1281, Bâtiment SN2, Villeneuve d'Ascq, F-59655, France
| | - Allison Cohade
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Nadine Valot
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Jean-Louis Magnard
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laurent Legendre
- Université de Lyon, Lyon, F-69622, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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