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Zakaria MM, Kruse LH, Engelhardt A, Ober D. Seeing double: two different homospermidine oxidases are involved in pyrrolizidine alkaloid biosynthesis in different organs of comfrey (Symphytum officinale). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38815125 DOI: 10.1111/tpj.16847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
Pyrrolizidine alkaloids (PAs) are toxic specialized metabolites produced in several plant species and frequently contaminate herbal teas or livestock feed. In comfrey (Symphytum officinale, Boraginaceae), they are produced in two different organs of the plant, the root and young leaves. In this study, we demonstrate that homospermidine oxidase (HSO), a copper-containing amine oxidase (CuAO) responsible for catalyzing the formation of the distinctive pyrrolizidine ring in PAs, is encoded by two individual genes. Specifically, SoCuAO1 is expressed in young leaves, while SoCuAO5 is expressed in roots. CRISPR/Cas9-mediated knockout of socuao5 resulted in hairy roots (HRs) unable to produce PAs, supporting its function as HSO in roots. Plants regenerated from socuao5 knockout HRs remained completely PA-free until the plants began to develop inflorescences, indicating the presence of another HSO that is expressed only during flower development. Stable expression of SoCuAO1 in socuao5 knockout HRs rescued the ability to produce PAs. In vitro assays of both enzymes transiently expressed in Nicotiana benthamiana confirmed their HSO activity and revealed the ability of HSO to control the stereospecific cyclization of the pyrrolizidine backbone. The observation that the first specific step of PA biosynthesis catalyzed by homospermidine synthase requires only one gene copy, while two independent paralogs are recruited for the subsequent homospermidine oxidation in different tissues of the plant, suggests a complex regulation of the pathway. This adds a new level of complexity to PA biosynthesis, a system already characterized by species-specific, tight spatio-temporal regulation, and independent evolutionary origins in multiple plant lineages.
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Affiliation(s)
- Mahmoud M Zakaria
- Botanical Institute and Botanic Gardens, Kiel University, Kiel, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, 44519, Zagazig, Egypt
| | - Lars H Kruse
- Botanical Institute and Botanic Gardens, Kiel University, Kiel, Germany
| | - Annika Engelhardt
- Botanical Institute and Botanic Gardens, Kiel University, Kiel, Germany
| | - Dietrich Ober
- Botanical Institute and Botanic Gardens, Kiel University, Kiel, Germany
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2
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Takano K, Ikeda H, Takanashi K. Pyrrolizidine alkaloids are synthesized and accumulated in flower of Myosotis scorpioides. JOURNAL OF PLANT RESEARCH 2024; 137:455-462. [PMID: 38368590 DOI: 10.1007/s10265-024-01525-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
Pyrrolizidine alkaloids (PAs) are specialized metabolites that are produced by various plant families that act as defense compounds against herbivores. On the other hand, certain lepidopteran insects uptake and utilize these PAs as defense compounds against their predators and as precursors of their sex pheromones. Adult males of Parantica sita, a danaine butterfly, convert PAs into their sex pheromones. In early summer, P. sita swarms over the flowers of Myosotis scorpioides, which belongs to the family Boraginaceae. M. scorpioides produces PAs, but the organs in which PAs are produced and whether P. sita utilizes PAs in M. scorpioides are largely unknown. In the present study, we clarified that M. scorpioides accumulates retronecine-core PAs in N-oxide form in all organs, including flowers. We also identified two M. scorpioides genes encoding homospermidine synthase (HSS), a key enzyme in the PA biosynthetic pathway, and clarified that these genes are expressed in all organs where PAs accumulate. Phylogenetic analysis suggested that these two HSS genes were originated from gene duplication of deoxyhypusine synthase gene like other HSS genes in PA-producing plants. These results suggest that PAs are synthesized and accumulated in the flower of M. scorpioides and provide a possibility for a PA-mediated interaction between P. sita and M. scorpioides.
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Affiliation(s)
- Kyohei Takano
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba Meguro-Ku, Tokyo, 153-8902, Japan
| | - Kojiro Takanashi
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan.
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan.
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3
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Cisneros AF, Nielly-Thibault L, Mallik S, Levy ED, Landry CR. Mutational biases favor complexity increases in protein interaction networks after gene duplication. Mol Syst Biol 2024; 20:549-572. [PMID: 38499674 PMCID: PMC11066126 DOI: 10.1038/s44320-024-00030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Biological systems can gain complexity over time. While some of these transitions are likely driven by natural selection, the extent to which they occur without providing an adaptive benefit is unknown. At the molecular level, one example is heteromeric complexes replacing homomeric ones following gene duplication. Here, we build a biophysical model and simulate the evolution of homodimers and heterodimers following gene duplication using distributions of mutational effects inferred from available protein structures. We keep the specific activity of each dimer identical, so their concentrations drift neutrally without new functions. We show that for more than 60% of tested dimer structures, the relative concentration of the heteromer increases over time due to mutational biases that favor the heterodimer. However, allowing mutational effects on synthesis rates and differences in the specific activity of homo- and heterodimers can limit or reverse the observed bias toward heterodimers. Our results show that the accumulation of more complex protein quaternary structures is likely under neutral evolution, and that natural selection would be needed to reverse this tendency.
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Affiliation(s)
- Angel F Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Lou Nielly-Thibault
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Saurav Mallik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada.
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada.
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada.
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada.
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada.
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4
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Lievens A, Paracchini V, Garlant L, Pietretti D, Maquet A, Ulberth F. Detection and Quantification of Botanical Impurities in Commercial Oregano ( Origanum vulgare) Using Metabarcoding and Digital PCR. Foods 2023; 12:2998. [PMID: 37627997 PMCID: PMC10453138 DOI: 10.3390/foods12162998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
DNA technology for food authentication is already well established, and with the advent of Next Generation Sequencing (NGS) and, more specifically, metabarcoding, compositional analysis of food at the molecular level has rapidly gained popularity. This has led to several reports in the media about the presence of foreign, non-declared species in several food commodities. As herbs and spices are attractive targets for fraudulent manipulation, a combination of digital PCR and metabarcoding by NGS was employed to check the purity of 285 oregano samples taken from the European market. By using novel primers and analytical approaches, it was possible to detect and quantify both adulterants and contaminants in these samples. The results highlight the high potential of NGS for compositional analysis, although its quantitative information (read count percentages) is unreliable, and other techniques are therefore needed to complement the sequencing information for assessing authenticity ('true to the name') of food ingredients.
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Affiliation(s)
- Antoon Lievens
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | | | - Linda Garlant
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Danilo Pietretti
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Alain Maquet
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Franz Ulberth
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
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5
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Nie N, Huo J, Sun S, Zuo Z, Chen Y, Liu Q, He S, Gao S, Zhang H, Zhao N, Zhai H. Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses. Int J Mol Sci 2023; 24:ijms24044092. [PMID: 36835500 PMCID: PMC9965949 DOI: 10.3390/ijms24044092] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H2O2, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.
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Affiliation(s)
- Nan Nie
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jinxi Huo
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sifan Sun
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhidan Zuo
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yanqi Chen
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62732559
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6
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Prakashrao AS, Beuerle T, Simões ARG, Hopf C, Çiçek SS, Stegemann T, Ober D, Kaltenegger E. The long road of functional recruitment-The evolution of a gene duplicate to pyrrolizidine alkaloid biosynthesis in the morning glories (Convolvulaceae). PLANT DIRECT 2022; 6:e420. [PMID: 35865076 PMCID: PMC9295680 DOI: 10.1002/pld3.420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In plants, homospermidine synthase (HSS) is a pathway-specific enzyme initiating the biosynthesis of pyrrolizidine alkaloids (PAs), which function as a chemical defense against herbivores. In PA-producing Convolvulaceae ("morning glories"), HSS originated from deoxyhypusine synthase at least >50 to 75 million years ago via a gene duplication event and subsequent functional diversification. To study the recruitment of this ancient gene duplicate to PA biosynthesis, the presence of putative hss gene copies in 11 Convolvulaceae species was analyzed. Additionally, various plant parts from seven of these species were screened for the presence of PAs. Although all of these species possess a putative hss copy, PAs could only be detected in roots of Ipomoea neei (Spreng.) O'Donell and Distimake quinquefolius (L.) A.R.Simões & Staples in this study. A precursor of PAs was detected in roots of Ipomoea alba L. Thus, despite sharing high sequence identities, the presence of an hss gene copy does not correlate with PA accumulation in particular species of Convolvulaceae. In vitro activity assays of the encoded enzymes revealed a broad spectrum of enzyme activity, further emphasizing a functional diversity of the hss gene copies. A recently identified HSS specific amino acid motif seems to be important for the loss of the ancestral protein function-the activation of the eukaryotic initiation factor 5A (eIF5A). Thus, the motif might be indicative for a change of function but allows not to predict the new function. This emphasizes the challenges in annotating functions for duplicates, even for duplicates from closely related species.
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Affiliation(s)
- Arunraj Saranya Prakashrao
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
- Present address:
Heart Research Center GöttingenUniversity Medical Center GöttingenGöttingenGermany.
| | - Till Beuerle
- Institute of Pharmaceutical BiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Ana Rita G. Simões
- Royal Botanic Gardens, KewRichmondUK
- Systematic and Evolutionary Botany LabGhent UniversityGhentBelgium
| | - Christina Hopf
- Department of Structural Biology, Zoological InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Serhat Sezai Çiçek
- Department of Pharmaceutical Biology, Pharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Thomas Stegemann
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Elisabeth Kaltenegger
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
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7
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Zakaria MM, Stegemann T, Sievert C, Kruse LH, Kaltenegger E, Girreser U, Çiçek SS, Nimtz M, Ober D. Insights into polyamine metabolism: homospermidine is double-oxidized in two discrete steps by a single copper-containing amine oxidase in pyrrolizidine alkaloid biosynthesis. THE PLANT CELL 2022; 34:2364-2382. [PMID: 35212762 PMCID: PMC9134089 DOI: 10.1093/plcell/koac068] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Polyamines are important metabolites in plant development and abiotic and biotic stress responses. Copper-containing amine oxidases (CuAOs) are involved in the regulation of polyamine levels in the cell. CuAOs oxidize primary amines to their respective aldehydes and hydrogen peroxide. In plants, aldehydes are intermediates in various biosynthetic pathways of alkaloids. CuAOs are thought to oxidize polyamines at only one of the primary amino groups, a process frequently resulting in monocyclic structures. These oxidases have been postulated to be involved in pyrrolizidine alkaloid (PA) biosynthesis. Here, we describe the identification and characterization of homospermidine oxidase (HSO), a CuAO of Heliotropium indicum (Indian heliotrope), involved in PA biosynthesis. Virus-induced gene silencing of HSO in H. indicum leads to significantly reduced PA levels. By in vitro enzyme assays after transient in planta expression, we show that this enzyme prefers Hspd over other amines. Nuclear magnetic resonance spectroscopy and mass spectrometry analyses of the reaction products demonstrate that HSO oxidizes both primary amino groups of homospermidine (Hspd) to form a bicyclic structure, 1-formylpyrrolizidine. Using tracer feeding, we have further revealed that 1-formylpyrrolizidine is an intermediate in the biosynthesis of PAs. Our study therefore establishes that HSO, a canonical CuAO, catalyzes the second step of PA biosynthesis and provides evidence for an undescribed and unusual mechanism involving two discrete steps of oxidation that might also be involved in the biosynthesis of complex structures in other alkaloidal pathways.
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Affiliation(s)
| | | | | | | | | | - Ulrich Girreser
- Department of Pharmaceutical and Medicinal Chemistry, Kiel University, Kiel, Germany
| | - Serhat S Çiçek
- Department of Pharmaceutical Biology, Kiel University, Kiel, Germany
| | - Manfred Nimtz
- Cellular Proteome Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
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8
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Lou YR, Pichersky E, Last RL. Deep roots and many branches: Origins of plant-specialized metabolic enzymes in general metabolism. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102192. [PMID: 35217473 DOI: 10.1016/j.pbi.2022.102192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Collectively, plants produce hundreds of thousands of specialized metabolites from simple building blocks such as amino acids, fatty acids, and isoprenoids. As additional specialized metabolic enzymes are described, there is increasing recognition of the importance of cooption of general metabolic enzymes to specialized metabolism by gene duplication, narrowing of expression, and alteration of enzymatic activities. Here, we examine how several classes of enzymes were each coopted multiple times. We demonstrate the simplicity of achieving the synthesis of analogous chemicals by coopting existing enzymes and summarize emerging insights that could inform rational metabolic engineering of both general and specialized metabolic enzymes.
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Affiliation(s)
- Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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9
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Dubs NM, Davis BR, de Brito V, Colebrook KC, Tiefel IJ, Nakayama MB, Huang R, Ledvina AE, Hack SJ, Inkelaar B, Martins TR, Aartila SM, Albritton KS, Almuhanna S, Arnoldi RJ, Austin CK, Battle AC, Begeman GR, Bickings CM, Bradfield JT, Branch EC, Conti EP, Cooley B, Dotson NM, Evans CJ, Fries AS, Gilbert IG, Hillier WD, Huang P, Hyde KW, Jevtovic F, Johnson MC, Keeler JL, Lam A, Leach KM, Livsey JD, Lo JT, Loney KR, Martin NW, Mazahem AS, Mokris AN, Nichols DM, Ojha R, Okorafor NN, Paris JR, Reboucas TF, Sant'Anna PB, Seitz MR, Seymour NR, Slaski LK, Stemaly SO, Ulrich BR, Van Meter EN, Young ML, Barkman TJ. A collaborative classroom investigation of the evolution of SABATH methyltransferase substrate preference shifts over 120 million years of flowering plant history. Mol Biol Evol 2022; 39:6503504. [PMID: 35021222 PMCID: PMC8890502 DOI: 10.1093/molbev/msac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the “tip of the iceberg” since thousands of sequences remain uncharacterized in this enzyme family alone.
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Affiliation(s)
- Nicole M Dubs
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Breck R Davis
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Victor de Brito
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kate C Colebrook
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ian J Tiefel
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Madison B Nakayama
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ruiqi Huang
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Audrey E Ledvina
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Samantha J Hack
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Brent Inkelaar
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Talline R Martins
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Sarah M Aartila
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kelli S Albritton
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Sarah Almuhanna
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ryan J Arnoldi
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Clara K Austin
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber C Battle
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Gregory R Begeman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Caitlin M Bickings
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jonathon T Bradfield
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Eric C Branch
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Eric P Conti
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Breana Cooley
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nicole M Dotson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Cheyone J Evans
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber S Fries
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ivan G Gilbert
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weston D Hillier
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Pornkamol Huang
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kaitlin W Hyde
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Filip Jevtovic
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Mark C Johnson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Julie L Keeler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Albert Lam
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kyle M Leach
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jeremy D Livsey
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jonathan T Lo
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kevin R Loney
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nich W Martin
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber S Mazahem
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Aurora N Mokris
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Destiny M Nichols
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ruchi Ojha
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nnanna N Okorafor
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Joshua R Paris
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | | | | | - Mathew R Seitz
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nathan R Seymour
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Lila K Slaski
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Stephen O Stemaly
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Benjamin R Ulrich
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Emile N Van Meter
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Meghan L Young
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
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10
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Barny LA, Tasca JA, Sanchez HA, Smith CR, Koptur S, Livshultz T, Minbiole KPC. Chemotaxonomic investigation of Apocynaceae for retronecine-type pyrrolizidine alkaloids using HPLC-MS/MS. PHYTOCHEMISTRY 2021; 185:112662. [PMID: 33774572 DOI: 10.1016/j.phytochem.2021.112662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 01/03/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Apocynaceae are well known for diverse specialized metabolites that are distributed in a phylogenetically informative manner. Pyrrolizidine alkaloids (PAs) have been reported sporadically in one lineage in the family, the APSA clade, but few species have been studied to date. We conducted the first systematic survey of Apocynaceae for retronecine-type PAs, sampling leaves from 231 species from 13 of 16 major lineages within the APSA clade using HPLC-MS/MS. We also followed up preliminary evidence for infra-specific variation of PA detectability in Echites umbellatus Jacq. Four precursor ion scans (PREC) were developed for a high-throughput survey for chemicals containing a structural moiety common to many PAs, the retronecine core. We identified with high confidence PAs in 7 of 8 sampled genera of tribe Echiteae, but not in samples from the closely related Odontadenieae and Mesechiteae, confirming the utility of PAs as a taxonomic character in tribal delimitation. Occurrence of PAs in Malouetieae is reported with moderate confidence in Galactophora schomburgkiana Woodson and Eucorymbia alba Stapf, but currently we have low confidence of their presence in Holarrena pubescens Wall. ex G. Don (the one Malouetieae species where they were previously reported), as well as in Holarrena curtisii King & Gamble and in Kibatalia macrophylla (Pierre ex Hua) Woodson. Candidate PAs in some species of Wrightia R. Br. (Wrightieae) and Marsdenia R. Br. (Marsdenieae) are proposed with moderate confidence, but a subset of the compounds in these taxa presenting with a PA-like fragmentation pattern are more likely to be aminobenzoyl glycosides. Candidate PAs are reported in species with predicted (VXXXD) and unexpected (IXXXN) amino acid motifs in their homospermidine synthase-like genes. Detectability of PAs varies among samples of Echites umbellatus and intra-individual plasticity contributes to this variation. Of toxicological importance, novel potential sources of human exposure to pro-toxic PAs were identified in the medicinal plant, Wrightia tinctoria R.Br., and the food plants, Marsdenia glabra Cost. and Echites panduratus A. DC., warranting immediate further research to elucidate the structures of the candidate PAs identified. Method development and limitations are discussed.
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Affiliation(s)
- Lea A Barny
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
| | - Julia A Tasca
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Hugo A Sanchez
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
| | - Chelsea R Smith
- Department of Biodiversity Earth and Environmental Sciences, Drexel University, PA, 19104, USA.
| | - Suzanne Koptur
- Department of Biology, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA.
| | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences, Drexel University, PA, 19104, USA; Department of Botany, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA.
| | - Kevin P C Minbiole
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
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11
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Zakaria MM, Schemmerling B, Ober D. CRISPR/Cas9-Mediated Genome Editing in Comfrey ( Symphytum officinale) Hairy Roots Results in the Complete Eradication of Pyrrolizidine Alkaloids. Molecules 2021; 26:1498. [PMID: 33801907 PMCID: PMC7998174 DOI: 10.3390/molecules26061498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
Comfrey (Symphytum officinale) is a medicinal plant with anti-inflammatory, analgesic, and proliferative properties. However, its pharmaceutical application is hampered by the co-occurrence of toxic pyrrolizidine alkaloids (PAs) in its tissues. Using a CRISPR/Cas9-based approach, we introduced detrimental mutations into the hss gene encoding homospermidine synthase (HSS), the first pathway-specific enzyme of PA biosynthesis. The resulting hairy root (HR) lines were analyzed for the type of gene-editing effect that they exhibited and for their homospermidine and PA content. Inactivation of only one of the two hss alleles resulted in HRs with significantly reduced levels of homospermidine and PAs, whereas no alkaloids were detectable in HRs with two inactivated hss alleles. PAs were detectable once again after the HSS-deficient HRs were fed homospermidine confirming that the inability of these roots to produce PAs was only attributable to the inactivated HSS and not to any unidentified off-target effect of the CRISPR/Cas9 approach. Further analyses showed that PA-free HRs possessed, at least in traces, detectable amounts of homospermidine, and that the PA patterns of manipulated HRs were different from those of control lines. These observations are discussed with regard to the potential use of such a CRISPR/Cas9-mediated approach for the economical exploitation of in vitro systems in a medicinal plant and for further studies of PA biosynthesis in non-model plants.
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Affiliation(s)
- Mahmoud M. Zakaria
- Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany; (M.M.Z.); (B.S.)
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, 44519 Zagazig, Egypt
| | - Brigitte Schemmerling
- Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany; (M.M.Z.); (B.S.)
| | - Dietrich Ober
- Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany; (M.M.Z.); (B.S.)
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12
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Kaltenegger E, Prakashrao AS, Çiçek SS, Ober D. Development of an activity assay for characterizing deoxyhypusine synthase and its diverse reaction products. FEBS Open Bio 2021; 11:10-25. [PMID: 33247548 PMCID: PMC7780104 DOI: 10.1002/2211-5463.13046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/04/2020] [Accepted: 11/24/2020] [Indexed: 02/02/2023] Open
Abstract
Deoxyhypusine synthase transfers an aminobutyl moiety from spermidine to the eukaryotic translation initiation factor 5A (eIF5A) in the first step of eIF5A activation. This exclusive post-translational modification is conserved in all eukaryotes. Activated eIF5A has been shown to be essential for cell proliferation and viability. Recent reports have linked the activation of eIF5A to several human diseases. Deoxyhypusine synthase, which is encoded by a single gene copy in most eukaryotes, was duplicated in several plant lineages during evolution, the copies being repeatedly recruited to pyrrolizidine alkaloid biosynthesis. However, the function of many of these duplicates is unknown. Notably, deoxyhypusine synthase is highly promiscuous and can catalyze various reactions, often of unknown biological relevance. To facilitate in-depth biochemical studies of this enzyme, we report here the development of a simple and robust in vitro enzyme assay. It involves precolumn derivatization of the polyamines taking part in the reaction and avoids the need for the previously used radioactively labeled tracers. The derivatized polyamines are quantified after high-performance liquid chromatography coupled to diode array and fluorescence detectors. By performing kinetic analyses of deoxyhypusine synthase and its paralog from the pyrrolizidine alkaloid-producing plant Senecio vernalis, we demonstrate that the assay unequivocally differentiates the paralogous enzymes. Furthermore, it detects and quantifies, in a single assay, the side reactions that occur in parallel to the main reaction. The presented assay thus provides a detailed biochemical characterization of deoxyhypusine synthase and its paralogs.
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Affiliation(s)
- Elisabeth Kaltenegger
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
| | - Arunraj S. Prakashrao
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
| | - Serhat S. Çiçek
- Pharmacognosy GroupPharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
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13
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Lichman BR. The scaffold-forming steps of plant alkaloid biosynthesis. Nat Prod Rep 2020; 38:103-129. [PMID: 32745157 DOI: 10.1039/d0np00031k] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alkaloids from plants are characterised by structural diversity and bioactivity, and maintain a privileged position in both modern and traditional medicines. In recent years, there have been significant advances in elucidating the biosynthetic origins of plant alkaloids. In this review, I will describe the progress made in determining the metabolic origins of the so-called true alkaloids, specialised metabolites derived from amino acids containing a nitrogen heterocycle. By identifying key biosynthetic steps that feature in the majority of pathways, I highlight the key roles played by modifications to primary metabolism, iminium reactivity and spontaneous reactions in the molecular and evolutionary origins of these pathways.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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14
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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15
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Shimizu Y, Rai A, Okawa Y, Tomatsu H, Sato M, Kera K, Suzuki H, Saito K, Yamazaki M. Metabolic diversification of nitrogen-containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:505-521. [PMID: 31364191 PMCID: PMC6899585 DOI: 10.1111/tpj.14454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 05/04/2023]
Abstract
Lysine decarboxylase converts l-lysine to cadaverine as a branching point for the biosynthesis of plant Lys-derived alkaloids. Although cadaverine contributes towards the biosynthesis of Lys-derived alkaloids, its catabolism, including metabolic intermediates and the enzymes involved, is not known. Here, we generated transgenic Arabidopsis lines by expressing an exogenous lysine/ornithine decarboxylase gene from Lupinus angustifolius (La-L/ODC) and identified cadaverine-derived metabolites as the products of the emerged biosynthetic pathway. Through untargeted metabolic profiling, we observed the upregulation of polyamine metabolism, phenylpropanoid biosynthesis and the biosynthesis of several Lys-derived alkaloids in the transgenic lines. Moreover, we found several cadaverine-derived metabolites specifically detected in the transgenic lines compared with the non-transformed control. Among these, three specific metabolites were identified and confirmed as 5-aminopentanal, 5-aminopentanoate and δ-valerolactam. Cadaverine catabolism in a representative transgenic line (DC29) was traced by feeding stable isotope-labeled [α-15 N]- or [ε-15 N]-l-lysine. Our results show similar 15 N incorporation ratios from both isotopomers for the specific metabolite features identified, indicating that these metabolites were synthesized via the symmetric structure of cadaverine. We propose biosynthetic pathways for the metabolites on the basis of metabolite chemistry and enzymes known or identified through catalyzing specific biochemical reactions in this study. Our study shows that this pool of enzymes with promiscuous activities is the driving force for metabolite diversification in plants. Thus, this study not only provides valuable information for understanding the catabolic mechanism of cadaverine but also demonstrates that cadaverine accumulation is one of the factors to expand plant chemodiversity, which may lead to the emergence of Lys-derived alkaloid biosynthesis.
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Affiliation(s)
- Yohei Shimizu
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- RIKEN Center for Sustainable Resource Science1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohama230‐0045Japan
| | - Amit Rai
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
| | - Yuko Okawa
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
| | - Hajime Tomatsu
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- Present address:
Human Metabolome Technologies, Inc.246‐2 Mizukami, KakuganjiTsuruokaYamagata997‐0052Japan
| | - Masaru Sato
- Kazusa DNA Research Institute2‐6‐7 Kazusa‐KamatariKisarazuChiba292‐0818Japan
| | - Kota Kera
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- Present address:
Department of Biomolecular EngineeringGraduate School of EngineeringTohoku UniversityAobayama 6‐6‐07Sendai980‐8579Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute2‐6‐7 Kazusa‐KamatariKisarazuChiba292‐0818Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- RIKEN Center for Sustainable Resource Science1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohama230‐0045Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
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16
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Specific Distribution of Pyrrolizidine Alkaloids in Floral Parts of Comfrey (Symphytum officinale) and its Implications for Flower Ecology. J Chem Ecol 2018; 45:128-135. [PMID: 30054770 DOI: 10.1007/s10886-018-0990-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/17/2018] [Accepted: 07/06/2018] [Indexed: 02/08/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are a typical class of plant secondary metabolites that are constitutively produced as part of the plant's chemical defense. While roots are a well-established site of pyrrolizidine alkaloid biosynthesis, comfrey plants (Symphytum officinale; Boraginaceae) have been shown to additionally activate alkaloid production in specialized leaves and accumulate PAs in flowers during a short developmental stage in inflorescence development. To gain a better understanding of the accumulation and role of PAs in comfrey flowers and fruits, we have dissected and analyzed their tissues for PA content and patterns. PAs are almost exclusively accumulated in the ovaries, while petals, sepals, and pollen hardly contain PAs. High levels of PAs are detectable in the fruit, but the elaiosome was shown to be PA free. The absence of 7-acetyllycopsamine in floral parts while present in leaves and roots suggests that the additional site of PA biosynthesis provides the pool of PAs for translocation to floral structures. Our data suggest that PA accumulation has to be understood as a highly dynamic system resulting from a combination of efficient transport and additional sites of synthesis that are only temporarily active. Our findings are further discussed in the context of the ecological roles of PAs in comfrey flowers.
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17
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Gill GP, Bryant CJ, Fokin M, Huege J, Fraser K, Jones C, Cao M, Faville MJ. Low pyrrolizidine alkaloid levels in perennial ryegrass is associated with the absence of a homospermidine synthase gene. BMC PLANT BIOLOGY 2018; 18:56. [PMID: 29625552 PMCID: PMC5889531 DOI: 10.1186/s12870-018-1269-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Pyrrolizidine alkaloids (PAs) are a class of secondary metabolites that function as feeding deterrents in a range of different plant species. In perennial ryegrass (Lolium perenne L.) the only PAs that have been identified are the thesinine-rhamnoside group, which displays significant genetic variation. Homospermidine synthase (HSS) has evolved from deoxyhypusine synthase (DHS) and catalyses the first step in the PA pathway, making it a key candidate for the investigation of genes influencing observed PA trait variation. RESULTS During PCR amplification and sequence analysis of DHS we identified two putative HSS genes in perennial ryegrass. One of the genes (LpHSS1) was absent in some perennial ryegrass plants. Thesinine-rhamnoside levels were measured using liquid chromatography coupled with mass spectrometry in a diverse association mapping population, consisting of 693 plants free of fungal endophytic symbionts. Association tests that accounted for population structure identified a significant association of absence of the LpHSS1 gene with lower levels of thesinine-rhamnoside PAs. HSS-like gene sequences were identified for other grass species of the Poaceae, including tall fescue, wheat, maize and sorghum. CONCLUSION HSS is situated at the crucial first step in the PA pathway making it an important candidate gene for investigation of involvement in PA phenotypic variation. In this study, PA level in perennial ryegrass was strongly associated with the presence or absence of the LpHSS1 gene. A genetic marker, developed for the presence/absence of LpHSS1, may be used for marker-assisted breeding to either lower or increase PAs in breeding populations of perennial or Italian ryegrass to investigate a potential role in the deterrence of herbivore pests. The presence of HSS-like genes in several other Poaceae species suggests that PA biosynthesis may occur in plant family members beyond perennial ryegrass and tall fescue and identifies a potential route for manipulating PA levels.
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Affiliation(s)
- Geoffrey P. Gill
- Pastoral Genomics, c/o AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Catherine J. Bryant
- Pastoral Genomics, c/o AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Mikhail Fokin
- Pastoral Genomics, c/o AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Jan Huege
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Karl Fraser
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Chris Jones
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Mingshu Cao
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Marty J. Faville
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442 New Zealand
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18
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Livshultz T, Kaltenegger E, Straub SCK, Weitemier K, Hirsch E, Koval K, Mema L, Liston A. Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de-escalation hypothesis. THE NEW PHYTOLOGIST 2018; 218:762-773. [PMID: 29479722 PMCID: PMC5873419 DOI: 10.1111/nph.15061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/10/2018] [Indexed: 05/23/2023]
Abstract
Plants produce specialized metabolites for their defence. However, specialist herbivores adapt to these compounds and use them for their own benefit. Plants attacked predominantly by specialists may be under selection to reduce or eliminate production of co-opted chemicals: the defence de-escalation hypothesis. We studied the evolution of pyrrolizidine alkaloids (PAs) in Apocynaceae, larval host plants for PA-adapted butterflies (Danainae, milkweed and clearwing butterflies), to test if the evolutionary pattern is consistent with de-escalation. We used the first PA biosynthesis specific enzyme (homospermidine synthase, HSS) as tool for reconstructing PA evolution. We found hss orthologues in diverse Apocynaceae species, not all of them known to produce PAs. The phylogenetic analysis showed a monophyletic origin of the putative hss sequences early in the evolution of one Apocynaceae lineage (the APSA clade). We found an hss pseudogene in Asclepias syriaca, a species known to produce cardiac glycosides but no PAs, and four losses of an HSS amino acid motif. APSA clade species are significantly more likely to be Danainae larval host plants than expected if all Apocynaceae species were equally likely to be exploited. Our findings are consistent with PA de-escalation as an adaptive response to specialist attack.
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Affiliation(s)
- Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Elisabeth Kaltenegger
- Biochemical Ecology and Molecular EvolutionBotanical InstituteChristian‐Albrechts University KielOlshausenstrasse 4024098KielGermany
| | | | - Kevin Weitemier
- Department of Botany & Plant PathologyOregon State University2082 Cordley HallCorvallisOR97331USA
| | - Elliot Hirsch
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Khrystyna Koval
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Lumi Mema
- Department of Biodiversity, Earth, and Environmental SciencesAcademy of Natural Sciences of Drexel University1900 Benjamin Franklin ParkwayPhiladelphiaPA19103USA
| | - Aaron Liston
- Department of Botany & Plant PathologyOregon State University2082 Cordley HallCorvallisOR97331USA
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19
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Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway. eLife 2017; 6:28468. [PMID: 28853706 PMCID: PMC5595436 DOI: 10.7554/elife.28468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022] Open
Abstract
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored. There are about 300,000 species of plant on Earth, which together produce over a million different small molecules called metabolites. Plants use many of these molecules to grow, to communicate with each other or to defend themselves against pests and disease. Humans have co-opted many of the same molecules as well; for example, some are important nutrients while others are active ingredients in medicines. Many plant metabolites are found in almost all plants, but hundreds of thousands of them are more specialized and only found in small groups of related plant species. These specialized metabolites have a wide variety of structures, and are made by different enzymes working together to carry out a series of biochemical reactions. Acylsugars are an example of a group of specialized metabolites with particularly diverse structures. These small molecules are restricted to plants in the Solanaceae family, which includes tomato and tobacco plants. Moghe et al. have now focused on acylsugars to better understand how plants produce the large diversity of chemical structures found in specialized metabolites, and how these processes have evolved over time. An analysis of over 35 plant species from across the Solanaceae family revealed hundreds of acylsugars, with some plants accumulating 300 or more different types of these specialized metabolites. Moghe et al. then looked at the enzymes that make acylsugars from a poorly studied flowering plant called Salpiglossis sinuata, partly because it produces a large diversity of these small molecules and partly because it sits in a unique position in the Solanaceae family tree. The activities of the enzymes were confirmed both in test tubes and in plants. This suggested that many of the enzymes were “promiscuous”, meaning that they could likely use a variety of molecules as starting points for their chemical reactions. This finding could help to explain how this plant species can make such a wide variety of acylsugars. Moghe et al. also discovered that many of the enzymes that make acylsugars are encoded by genes that were originally copies of other genes and that have subsequently evolved new activities. Plant scientists and plant breeders value tomato plants that produce acylsugars because these natural chemicals protect against pests like whiteflies and spider mites. A clearer understanding of the diversity of acylsugars in the Solanaceae family, as well as the enzymes that make these specialized metabolites, could help efforts to breed crops that are more resistant to pests. Some of the enzymes related to those involved in acylsugar production could also help to make chemicals with pharmaceutical value. These new findings might also eventually lead to innovative ways to produce these chemicals on a large scale.
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Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Bryan J Leong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Steven M Hurney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
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Kruse LH, Stegemann T, Sievert C, Ober D. Identification of a Second Site of Pyrrolizidine Alkaloid Biosynthesis in Comfrey to Boost Plant Defense in Floral Stage . PLANT PHYSIOLOGY 2017; 174:47-55. [PMID: 28275146 PMCID: PMC5411159 DOI: 10.1104/pp.17.00265] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/05/2017] [Indexed: 05/09/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are toxic secondary metabolites that are found in several distantly related families of the angiosperms. The first specific step in PA biosynthesis is catalyzed by homospermidine synthase (HSS), which has been recruited several times independently by duplication of the gene encoding deoxyhypusine synthase, an enzyme involved in the posttranslational activation of the eukaryotic initiation factor 5A. HSS shows highly diverse spatiotemporal gene expression in various PA-producing species. In comfrey (Symphytum officinale; Boraginaceae), PAs are reported to be synthesized in the roots, with HSS being localized in cells of the root endodermis. Here, we show that comfrey plants activate a second site of HSS expression when inflorescences start to develop. HSS has been localized in the bundle sheath cells of specific leaves. Tracer feeding experiments have confirmed that these young leaves express not only HSS but the whole PA biosynthetic route. This second site of PA biosynthesis results in drastically increased PA levels within the inflorescences. The boost of PA biosynthesis is proposed to guarantee optimal protection especially of the reproductive structures.
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Affiliation(s)
- Lars H Kruse
- Botanisches Institut und Botanischer Garten, Universität Kiel, D-24098 Kiel, Germany
| | - Thomas Stegemann
- Botanisches Institut und Botanischer Garten, Universität Kiel, D-24098 Kiel, Germany
| | - Christian Sievert
- Botanisches Institut und Botanischer Garten, Universität Kiel, D-24098 Kiel, Germany
| | - Dietrich Ober
- Botanisches Institut und Botanischer Garten, Universität Kiel, D-24098 Kiel, Germany
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21
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Bunsupa S, Hanada K, Maruyama A, Aoyagi K, Komatsu K, Ueno H, Yamashita M, Sasaki R, Oikawa A, Saito K, Yamazaki M. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis. PLANT PHYSIOLOGY 2016; 171:2432-44. [PMID: 27303024 PMCID: PMC4972286 DOI: 10.1104/pp.16.00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/09/2016] [Indexed: 05/03/2023]
Abstract
Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer's disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase.
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Affiliation(s)
- Somnuk Bunsupa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kousuke Hanada
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Maruyama
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kaori Aoyagi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kana Komatsu
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Hideki Ueno
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Madoka Yamashita
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Ryosuke Sasaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Oikawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
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Kaltenegger E, Ober D. Paralogue Interference Affects the Dynamics after Gene Duplication. TRENDS IN PLANT SCIENCE 2015; 20:814-821. [PMID: 26638775 DOI: 10.1016/j.tplants.2015.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
Proteins tend to form homomeric complexes of identical subunits, which act as functional units. By definition, the subunits are encoded from a single genetic locus. When such a gene is duplicated, the gene products are suggested initially to cross-interact when coexpressed, thus resulting in the phenomenon of paralogue interference. In this opinion article, we explore how paralogue interference can shape the fate of a duplicated gene. One important outcome is a prolonged time window in which both copies remain under selection increasing the chance to accumulate mutations and to develop new properties. Thereby, paralogue interference can mediate the coevolution of duplicates and here we illustrate the potential of this phenomenon in light of recent new studies.
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Affiliation(s)
- Elisabeth Kaltenegger
- Department of Biochemical Ecology and Molecular Evolution, Botanical Institute, Christian-Albrechts-University, 24098 Kiel, Germany.
| | - Dietrich Ober
- Department of Biochemical Ecology and Molecular Evolution, Botanical Institute, Christian-Albrechts-University, 24098 Kiel, Germany
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23
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Moghe GD, Last RL. Something Old, Something New: Conserved Enzymes and the Evolution of Novelty in Plant Specialized Metabolism. PLANT PHYSIOLOGY 2015; 169:1512-23. [PMID: 26276843 PMCID: PMC4634076 DOI: 10.1104/pp.15.00994] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/13/2015] [Indexed: 05/18/2023]
Abstract
Plants produce hundreds of thousands of small molecules known as specialized metabolites, many of which are of economic and ecological importance. This remarkable variety is a consequence of the diversity and rapid evolution of specialized metabolic pathways. These novel biosynthetic pathways originate via gene duplication or by functional divergence of existing genes, and they subsequently evolve through selection and/or drift. Studies over the past two decades revealed that diverse specialized metabolic pathways have resulted from the incorporation of primary metabolic enzymes. We discuss examples of enzyme recruitment from primary metabolism and the variety of paths taken by duplicated primary metabolic enzymes toward integration into specialized metabolism. These examples provide insight into processes by which plant specialized metabolic pathways evolve and suggest approaches to discover enzymes of previously uncharacterized metabolic networks.
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Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology (G.D.M., R.L.L.) and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Biochemistry and Molecular Biology (G.D.M., R.L.L.) and Department of Plant Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
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24
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Sievert C, Beuerle T, Hollmann J, Ober D. Single cell subtractive transcriptomics for identification of cell-specifically expressed candidate genes of pyrrolizidine alkaloid biosynthesis. PHYTOCHEMISTRY 2015; 117:17-24. [PMID: 26057225 DOI: 10.1016/j.phytochem.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
Progress has recently been made in the elucidation of pathways of secondary metabolism. However, because of its diversity, genetic information concerning biosynthetic details is still missing for many natural products. This is also the case for the biosynthesis of pyrrolizidine alkaloids. To close this gap, we tested strategies using tissues that express this pathway in comparison to tissues in which this pathway is not expressed. As many pathways of secondary metabolism are known to be induced by jasmonates, the pyrrolizidine alkaloid-producing species Heliotropium indicum, Symphytum officinale, and Cynoglossum officinale of the Boraginales order were treated with methyl jasmonate. An effect on pyrrolizidine alkaloid levels and on transcript levels of homospermidine synthase, the first specific enzyme of pyrrolizidine alkaloid biosynthesis, was not detectable. Therefore, a method was developed by making use of the often observed cell-specific production of secondary compounds. H. indicum produces pyrrolizidine alkaloids exclusively in the shoot. Homospermidine synthase is expressed only in the cells of the lower leaf epidermis and the epidermis of the stem. Suggesting that the whole pathway of pyrrolizidine alkaloid biosynthesis might be localized in these cells, we have isolated single cells of the upper and lower epidermis by laser-capture microdissection. The resulting cDNA preparations have been used in a subtractive transcriptomic approach. Quantitative real-time polymerase chain reaction has shown that the resulting library is significantly enriched for homospermidine-synthase-coding transcripts providing a valuable source for the identification of further genes involved in pyrrolizidine alkaloid biosynthesis.
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Affiliation(s)
- Christian Sievert
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany
| | - Till Beuerle
- Institute for Pharmaceutical Biology, TU Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany
| | - Julien Hollmann
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany
| | - Dietrich Ober
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany.
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25
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New sources of lycopsamine-type pyrrolizidine alkaloids and their distribution in Apocynaceae. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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New aspect of plant-rhizobia interaction: alkaloid biosynthesis in Crotalaria depends on nodulation. Proc Natl Acad Sci U S A 2015; 112:4164-9. [PMID: 25775562 DOI: 10.1073/pnas.1423457112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Infection of legume hosts by rhizobial bacteria results in the formation of a specialized organ, the nodule, in which atmospheric nitrogen is reduced to ammonia. Nodulation requires the reprogramming of the plant cell, allowing the microsymbiont to enter the plant tissue in a highly controlled manner. We have found that, in Crotalaria (Fabaceae), this reprogramming is associated with the biosynthesis of pyrrolizidine alkaloids (PAs). These compounds are part of the plant's chemical defense against herbivores and cannot be regarded as being functionally involved in the symbiosis. PAs in Crotalaria are detectable only when the plants form nodules after infection with their rhizobial partner. The identification of a plant-derived sequence encoding homospermidine synthase (HSS), the first pathway-specific enzyme of PA biosynthesis, suggests that the plant and not the microbiont is the producer of PAs. Transcripts of HSS are detectable exclusively in the nodules, the tissue with the highest concentration of PAs, indicating that PA biosynthesis is restricted to the nodules and that the nodules are the source from which the alkaloids are transported to the above ground parts of the plant. The link between nodulation and the biosynthesis of nitrogen-containing alkaloids in Crotalaria highlights a further facet of the effect of symbiosis with rhizobia on the ecologically important trait of the plant's chemical defense.
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Geilfus CM, Ober D, Eichacker LA, Mühling KH, Zörb C. Down-regulation of ZmEXPB6 (Zea mays β-expansin 6) protein is correlated with salt-mediated growth reduction in the leaves of Z. mays L. J Biol Chem 2015; 290:11235-45. [PMID: 25750129 DOI: 10.1074/jbc.m114.619718] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 11/06/2022] Open
Abstract
The salt-sensitive crop Zea mays L. shows a rapid leaf growth reduction upon NaCl stress. There is increasing evidence that salinity impairs the ability of the cell walls to expand, ultimately inhibiting growth. Wall-loosening is a prerequisite for cell wall expansion, a process that is under the control of cell wall-located expansin proteins. In this study the abundance of those proteins was analyzed against salt stress using gel-based two-dimensional proteomics and two-dimensional Western blotting. Results show that ZmEXPB6 (Z. mays β-expansin 6) protein is lacking in growth-inhibited leaves of salt-stressed maize. Of note, the exogenous application of heterologously expressed and metal-chelate-affinity chromatography-purified ZmEXPB6 on growth-reduced leaves that lack native ZmEXPB6 under NaCl stress partially restored leaf growth. In vitro assays on frozen-thawed leaf sections revealed that recombinant ZmEXPB6 acts on the capacity of the walls to extend. Our results identify expansins as a factor that partially restores leaf growth of maize in saline environments.
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Affiliation(s)
- Christoph-Martin Geilfus
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany,
| | - Dietrich Ober
- Botanical Institute and Botanical Gardens, Biochemical Ecology and Molecular Evolution, Christian-Albrechts-University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Lutz A Eichacker
- Universitetet i Stavanger, Center for Organelle Research (CORE), Richard Johnsensgt. 4, N-4021, Norway, and
| | - Karl Hermann Mühling
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany
| | - Christian Zörb
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany, Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof West, 118, 70593 Stuttgart, Germany
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Chen H, Li G, Köllner TG, Jia Q, Gershenzon J, Chen F. Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza. BMC PLANT BIOLOGY 2014; 14:239. [PMID: 25224158 PMCID: PMC4172859 DOI: 10.1186/s12870-014-0239-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/03/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Terpenoids constitute the largest class of secondary metabolites made by plants and display vast chemical diversity among and within species. Terpene synthases (TPSs) are the pivotal enzymes for terpenoid biosynthesis that create the basic carbon skeletons of this class. Functional divergence of paralogous and orthologous TPS genes is a major mechanism for the diversification of terpenoid biosynthesis. However, little is known about the evolutionary forces that have shaped the evolution of plant TPS genes leading to terpenoid diversity. RESULTS The orthologs of Oryza Terpene Synthase 1 (OryzaTPS1), a rice terpene synthase gene involved in indirect defense against insects in Oryza sativa, were cloned from six additional Oryza species. In vitro biochemical analysis showed that the enzymes encoded by these OryzaTPS1 genes functioned either as (E)-β-caryophyllene synthases (ECS), or (E)-β-caryophyllene & germacrene A synthases (EGS), or germacrene D & germacrene A synthases (DAS). Because the orthologs of OryzaTPS1 in maize and sorghum function as ECS, the ECS activity was inferred to be ancestral. Molecular evolutionary detected the signature of positive Darwinian selection in five codon substitutions in the evolution from ECS to DAS. Homology-based structure modeling and the biochemical analysis of laboratory-generated protein variants validated the contribution of the five positively selected sites to functional divergence of OryzaTPS1. The changes in the in vitro product spectra of OryzaTPS1 proteins also correlated closely to the changes in in vivo blends of volatile terpenes released from insect-damaged rice plants. CONCLUSIONS In this study, we found that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. This finding suggests that the diverged sesquiterpene blend produced by the Oryza species containing DAS may be adaptive, likely in the attraction of the natural enemies of insect herbivores.
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Affiliation(s)
- Hao Chen
- />Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- />Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Guanglin Li
- />Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- />College of Life Sciences, Shaanxi Normal University, Xi’an, 710062 China
| | - Tobias G Köllner
- />Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Qidong Jia
- />Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Jonathan Gershenzon
- />Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Feng Chen
- />Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- />Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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Bedewitz MA, Góngora-Castillo E, Uebler JB, Gonzales-Vigil E, Wiegert-Rininger KE, Childs KL, Hamilton JP, Vaillancourt B, Yeo YS, Chappell J, DellaPenna D, Jones AD, Buell CR, Barry CS. A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. THE PLANT CELL 2014; 26:3745-62. [PMID: 25228340 PMCID: PMC4213168 DOI: 10.1105/tpc.114.130534] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The tropane alkaloids, hyoscyamine and scopolamine, are medicinal compounds that are the active components of several therapeutics. Hyoscyamine and scopolamine are synthesized in the roots of specific genera of the Solanaceae in a multistep pathway that is only partially elucidated. To facilitate greater understanding of tropane alkaloid biosynthesis, a de novo transcriptome assembly was developed for Deadly Nightshade (Atropa belladonna). Littorine is a key intermediate in hyoscyamine and scopolamine biosynthesis that is produced by the condensation of tropine and phenyllactic acid. Phenyllactic acid is derived from phenylalanine via its transamination to phenylpyruvate, and mining of the transcriptome identified a phylogenetically distinct aromatic amino acid aminotransferase (ArAT), designated Ab-ArAT4, that is coexpressed with known tropane alkaloid biosynthesis genes in the roots of A. belladonna. Silencing of Ab-ArAT4 disrupted synthesis of hyoscyamine and scopolamine through reduction of phenyllactic acid levels. Recombinant Ab-ArAT4 preferentially catalyzes the first step in phenyllactic acid synthesis, the transamination of phenylalanine to phenylpyruvate. However, rather than utilizing the typical keto-acid cosubstrates, 2-oxoglutarate, pyruvate, and oxaloacetate, Ab-ArAT4 possesses strong substrate preference and highest activity with the aromatic keto-acid, 4-hydroxyphenylpyruvate. Thus, Ab-ArAT4 operates at the interface between primary and specialized metabolism, contributing to both tropane alkaloid biosynthesis and the direct conversion of phenylalanine to tyrosine.
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Affiliation(s)
- Matthew A Bedewitz
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Elsa Góngora-Castillo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Joseph B Uebler
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | | | | | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yun-Soo Yeo
- Plant Biology Program and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40546
| | - Joseph Chappell
- Plant Biology Program and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40546
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
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30
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Does HIV evolve towards a more adaptive state similar to that of simian immunodeficiency virus? AIDS 2013; 27:2965-7. [PMID: 24963705 DOI: 10.1097/qad.0000000000000017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Bartlett ME, Whipple CJ. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity. FRONTIERS IN PLANT SCIENCE 2013; 4:382. [PMID: 24124420 PMCID: PMC3794426 DOI: 10.3389/fpls.2013.00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 09/06/2013] [Indexed: 05/29/2023]
Abstract
Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.
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Affiliation(s)
| | - Clinton J. Whipple
- *Correspondence: Clinton J. Whipple, Biology Department, Brigham Young University, 401 WIDB, Provo, UT 84602, USA e-mail:
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