1
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Zhang Y, Zhong J, Munawar A, Cai Y, He W, Zhang Y, Guo H, Gao Y, Zhu Z, Zhou W. Knocking down a DNA demethylase gene affects potato plant defense against a specialist insect herbivore. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:483-499. [PMID: 37781866 DOI: 10.1093/jxb/erad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023]
Abstract
DNA demethylase (DML) is involved in plant development and responses to biotic and abiotic stresses; however, its role in plant-herbivore interaction remains elusive. Here, we found that herbivory by the potato tuber moth, Phthorimaea operculella, rapidly induced the genome-wide DNA methylation and accumulation of DML gene transcripts in potato plants. Herbivory induction of DML transcripts was suppressed in jasmonate-deficient plants, whereas exogenous application of methyl jasmonate (MeJA) improved DML transcripts, indicating that the induction of DML transcripts by herbivory is associated with jasmonate signaling. Moreover, P. operculella larvae grew heavier on DML gene (StDML2) knockdown plants than on wild-type plants, and the decreased biosynthesis of jasmonates in the former may be responsible for this difference, since the larvae feeding on these two genotypes supplemented with MeJA showed similar growth. In addition, P. operculella adult moths preferred to oviposit on StDML2 knockdown plants than on wild-type plants, which was associated with the reduced emission of β-caryophyllene in the former. In addition, supplementing β-caryophyllene to these two genotypes further disrupted moths' oviposit choice preference for them. Interestingly, in StDML2 knockdown plants, hypermethylation was found at the promoter regions for the key genes StAOS and StAOC in the jasmonate biosynthetic pathway, as well as for the key gene StTPS12 in β-caryophyllene production. Our findings suggest that knocking down StDML2 can affect herbivore defense via jasmonate signaling and defense compound production in potato plants.
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Affiliation(s)
- Yadong Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Jian Zhong
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Asim Munawar
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yajie Cai
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yixin Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
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2
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Ray R, Halitschke R, Gase K, Leddy SM, Schuman MC, Rodde N, Baldwin IT. A persistent major mutation in canonical jasmonate signaling is embedded in an herbivory-elicited gene network. Proc Natl Acad Sci U S A 2023; 120:e2308500120. [PMID: 37607232 PMCID: PMC10466192 DOI: 10.1073/pnas.2308500120] [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: 05/21/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
When insect herbivores attack plants, elicitors from oral secretions and regurgitants (OS) enter wounds during feeding, eliciting defense responses. These generally require plant jasmonate (JA) signaling, specifically, a jasmonoyl-L-isoleucine (JA-Ile) burst, for their activation and are well studied in the native tobacco Nicotiana attenuata. We used intraspecific diversity captured in a 26-parent MAGIC population planted in nature and an updated genome assembly to impute natural variation in the OS-elicited JA-Ile burst linked to a mutation in the JA-Ile biosynthetic gene NaJAR4. Experiments revealed that NaJAR4 variants were associated with higher fitness in the absence of herbivores but compromised foliar defenses, with two NaJAR homologues (4 and 6) complementing each other spatially and temporally. From decade-long seed collections of natural populations, we uncovered enzymatically inactive variants occurring at variable frequencies, consistent with a balancing selection regime maintaining variants. Integrative analyses of OS-induced transcriptomes and metabolomes of natural accessions revealed that NaJAR4 is embedded in a nonlinear complex gene coexpression network orchestrating responses to OS, which we tested by silencing four hub genes in two connected coexpressed networks and examining their OS-elicited metabolic responses. Lines silenced in two hub genes (NaGLR and NaFB67) co-occurring in the NaJAR4/6 module showed responses proportional to JA-Ile accumulations; two from an adjacent module (NaERF and NaFB61) had constitutively expressed defenses with high resistance. We infer that mutations with large fitness consequences can persist in natural populations due to compensatory responses from gene networks, which allow for diversification in conserved signaling pathways and are generally consistent with predictions of an omnigene model.
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Affiliation(s)
- Rishav Ray
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Klaus Gase
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Sabrina M. Leddy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14850
| | - Meredith C. Schuman
- Department of Geography, University of Zurich, 8006Zurich, Switzerland
- Department of Chemistry, University of Zurich, 8006Zurich, Switzerland
| | - Nathalie Rodde
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Centre National de Resources Génomiques Végétales, French Plant Genomic Resource Center, Castanet TolosanF-31326, France
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
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3
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Elser D, Pflieger D, Villette C, Moegle B, Miesch L, Gaquerel E. Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations. SCIENCE ADVANCES 2023; 9:eade8984. [PMID: 37624884 PMCID: PMC10456844 DOI: 10.1126/sciadv.ade8984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.
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Affiliation(s)
- David Elser
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Baptiste Moegle
- Institut de Chimie du CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Laurence Miesch
- Institut de Chimie du CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
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4
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Steinbrenner AD, Saldivar E, Hodges N, Guayazán-Palacios N, Chaparro AF, Schmelz EA. Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1255-1270. [PMID: 35315556 DOI: 10.1111/tpj.15732] [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: 09/03/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Chewing herbivores activate plant defense responses through a combination of mechanical wounding and elicitation by herbivore-associated molecular patterns (HAMPs). HAMPs are wound response amplifiers; however, specific defense outputs may also exist that strictly require HAMP-mediated defense signaling. To investigate HAMP-mediated signaling and defense responses, we characterized cowpea (Vigna unguiculata) transcriptome changes following elicitation by inceptin, a peptide HAMP common in Lepidoptera larvae oral secretions. Following inceptin treatment, we observed large-scale reprogramming of the transcriptome consistent with three different response categories: (i) amplification of mechanical wound responses, (ii) temporal extension through accelerated or prolonged responses, and (iii) examples of inceptin-specific elicitation and suppression. At both early and late timepoints, namely 1 and 6 h, large sets of transcripts specifically accumulated following inceptin elicitation. Further early inceptin-regulated transcripts were classified as reversing changes induced by wounding alone. Within key signaling- and defense-related gene families, inceptin-elicited responses included target subsets of wound-induced transcripts. Transcripts displaying the largest inceptin-elicited fold changes included transcripts encoding terpene synthases (TPSs) and peroxidases (POXs) that correspond with induced volatile production and increased POX activity in cowpea. Characterization of inceptin-elicited cowpea defenses via heterologous expression in Nicotiana benthamiana demonstrated that specific cowpea TPSs and POXs were able to confer terpene emission and the reduced growth of beet armyworm (Spodoptera exigua) herbivores, respectively. Collectively, our present findings in cowpea support a model where HAMP elicitation both amplifies concurrent wound responses and specifically contributes to the activation of selective outputs associated with direct and indirect antiherbivore defenses.
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Affiliation(s)
- Adam D Steinbrenner
- Department of Biology, University of Washington, Seattle, WA, USA
- Washington Research Foundation, Seattle, WA, USA
| | - Evan Saldivar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Nile Hodges
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Eric A Schmelz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
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5
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Mao Z, Ge Y, Zhang Y, Zhong J, Munawar A, Zhu Z, Zhou W. Disentangling the Potato Tuber Moth-Induced Early-Defense Response by Simulated Herbivory in Potato Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:902342. [PMID: 35693154 PMCID: PMC9178332 DOI: 10.3389/fpls.2022.902342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 06/02/2023]
Abstract
Plants rely on the perception of a multitude of herbivory-associated cues (HACs) to activate their defense response to insect herbivores. These stimuli are mainly derived from three functional components, namely, mechanical damage, insect-associated microbe, and insect's chemical cues. While simulated herbivory integrating these stimuli is widely exploited for complementing actual herbivory in clarifying the details of plant-herbivore interaction, breaking down these stimuli and identifying the mechanisms of plant responses associated with them have been less explored. In this study, the components of potato tuber moth (Phthorimaea operculella, PTM) herbivory were reorganized in a cumulative way and their impacts on the early defense responses of potato leaf were characterized. We found that simulated and actual herbivory of PTM triggered similar patterns of phytohormonal and transcriptomic responses in potato leaf. Moreover, the microbe in the PTM herbivory stimuli is associated with the regulation of the phytohormones jasmonic acid (JA) and abscisic acid (ABA) since reducing the microbe in HAC could reduce JA while increasing ABA. In addition, seven robust gene modules were identified to illustrate how potato plants respond to different PTM herbivory stimuli when herbivory components increased. Significantly, we found that mechanical damage mainly activated JA-mediated signaling; PTM-derived HACs contributed much more to potato early-defense response and induced signaling molecules such as multiple protein kinases; orally secreted bacteria stimuli could antagonize PTM-derived HACs and modulate plant defense, including repressing phenylpropanoid biosynthesis. Our study broadened the understanding of how potato plants integrate the responses to a multitude of stimuli upon PTM herbivory and evidenced that insect-associated microbes greatly modulated the plants response to insect herbivory.
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Affiliation(s)
- Zhiyao Mao
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Ge
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yadong Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jian Zhong
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Asim Munawar
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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6
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Snoeck S, Guayazán-Palacios N, Steinbrenner AD. Molecular tug-of-war: Plant immune recognition of herbivory. THE PLANT CELL 2022; 34:1497-1513. [PMID: 35026025 PMCID: PMC9048929 DOI: 10.1093/plcell/koac009] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/07/2022] [Indexed: 05/22/2023]
Abstract
Plant defense responses against insect herbivores are induced through wound-induced signaling and the specific perception of herbivore-associated molecular patterns (HAMPs). In addition, herbivores can deliver effectors that suppress plant immunity. Here we review plant immune recognition of HAMPs and effectors, and argue that these initial molecular interactions upon a plant-herbivore encounter mediate and structure effective resistance. While the number of distinct HAMPs and effectors from both chewing and piercing-sucking herbivores has expanded rapidly with omics-enabled approaches, paired receptors and targets in the host are still not well characterized. Herbivore-derived effectors may also be recognized as HAMPs depending on the host plant species, potentially through the evolution of novel immune receptor functions. We compile examples of HAMPs and effectors where natural variation between species may inform evolutionary patterns and mechanisms of plant-herbivore interactions. Finally, we discuss the combined effects of wounding and HAMP recognition, and review potential signaling hubs, which may integrate both sensing functions. Understanding the precise mechanisms for plant sensing of herbivores will be critical for engineering resistance in agriculture.
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Affiliation(s)
- Simon Snoeck
- Department of Biology, University of Washington, Seattle, Washington, USA
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7
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Li J, Halitschke R, Li D, Paetz C, Su H, Heiling S, Xu S, Baldwin IT. Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity. Science 2021; 371:255-260. [PMID: 33446550 DOI: 10.1126/science.abe4713] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2023]
Abstract
Many plant specialized metabolites function in herbivore defense, and abrogating particular steps in their biosynthetic pathways frequently causes autotoxicity. However, the molecular mechanisms underlying their defense and autotoxicity remain unclear. Here, we show that silencing two cytochrome P450s involved in diterpene biosynthesis in the wild tobacco Nicotiana attenuata causes severe autotoxicity symptoms that result from the inhibition of sphingolipid biosynthesis by noncontrolled hydroxylated diterpene derivatives. Moreover, the diterpenes' defensive function is achieved by inhibiting herbivore sphingolipid biosynthesis through postingestive backbone hydroxylation products. Thus, by regulating metabolic modifications, tobacco plants avoid autotoxicity and gain herbivore defense. The postdigestive duet that occurs between plants and their insect herbivores can reflect the plant's solutions to the "toxic waste dump" problem of using potent chemical defenses.
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Affiliation(s)
- Jiancai Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Dapeng Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Christian Paetz
- Department of Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Haichao Su
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Sven Heiling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48161 Münster, Germany.
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany.
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8
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Li D, Halitschke R, Baldwin IT, Gaquerel E. Information theory tests critical predictions of plant defense theory for specialized metabolism. SCIENCE ADVANCES 2020; 6:eaaz0381. [PMID: 32577508 PMCID: PMC7286674 DOI: 10.1126/sciadv.aaz0381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/14/2020] [Indexed: 05/15/2023]
Abstract
Different plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes of Nicotiana attenuata, from single plants to populations, as well as of closely related species, using unbiased tandem mass spectrometry (MS/MS) analyses and processed the abundances of compound spectrum-based MS features within an information theory framework to test critical predictions of optimal defense (OD) and moving target (MT) theories. Information components of plant metabolomes were consistent with the OD theory but contradicted the main prediction of the MT theory for herbivory-induced dynamics of metabolome compositions. From micro- to macroevolutionary scales, jasmonate signaling was confirmed as the master determinant of OD, while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.
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Affiliation(s)
- Dapeng Li
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Rayko Halitschke
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
- Corresponding author. (E.G.); (I.T.B)
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- Corresponding author. (E.G.); (I.T.B)
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9
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Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
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10
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Grissett L, Ali A, Coble AM, Logan K, Washington B, Mateson A, McGee K, Nkrumah Y, Jacobus L, Abraham E, Hann C, Bequette CJ, Hind SR, Schmelz EA, Stratmann JW. Survey of Sensitivity to Fatty Acid-Amino Acid Conjugates in the Solanaceae. J Chem Ecol 2020; 46:330-343. [PMID: 31989490 DOI: 10.1007/s10886-020-01152-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/07/2020] [Accepted: 01/17/2020] [Indexed: 12/17/2022]
Abstract
Plants perceive insect herbivores via a sophisticated surveillance system that detects a range of alarm signals, including herbivore-associated molecular patterns (HAMPs). Fatty acid-amino acid conjugates (FACs) are HAMPs present in oral secretions (OS) of lepidopteran larvae that induce defense responses in many plant species. In contrast to eggplant (Solanum melongena), tomato (S. lycopersicum) does not respond to FACs present in OS from Manduca sexta (Lepidoptera). Since both plants are found in the same genus, we tested whether loss of sensitivity to FACs in tomato may be a domestication effect. Using highly sensitive MAP kinase (MAPK) phosphorylation assays, we demonstrate that four wild tomato species and the closely related potato (S. tuberosum) do not respond to the FACs N-linolenoyl-L-glutamine and N-linolenoyl-L-glutamic acid, excluding a domestication effect. Among other genera within the Solanaceae, we found that bell pepper (Capsicum annuum) is responsive to FACs, while there is a differential responsiveness to FACs among tobacco (Nicotiana) species, ranging from strong responsiveness in N. benthamiana to no responsiveness in N. knightiana. The Petunia lineage is one of the oldest lineages within the Solanaceae and P. hybrida was responsive to FACs. Collectively, we demonstrate that plant responsiveness to FACs does not follow simple phylogenetic relationships in the family Solanaceae. Instead, sensitivity to FACs is a dynamic ancestral trait present in monocots and eudicots that was repeatedly lost during the evolution of Solanaceae species. Although tomato is insensitive to FACs, we found that other unidentified factors in M. sexta OS induce defenses in tomato.
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Affiliation(s)
- Laquita Grissett
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,Fred Hutchinson Cancer Research Center, University of Washington School of Dentistry, Seattle, WA, USA
| | - Azka Ali
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Anne-Marie Coble
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Khalilah Logan
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Brandon Washington
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Abigail Mateson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Kelsey McGee
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Yaw Nkrumah
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Leighton Jacobus
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Evelyn Abraham
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,Department of Plant Biology, Pennsylvania State University, University Park, PA, USA
| | - Claire Hann
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Carlton J Bequette
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,R.J. Reynolds Tobacco, Winston-Salem, NC, USA
| | - Sarah R Hind
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Johannes W Stratmann
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
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Ray R, Li D, Halitschke R, Baldwin IT. Using natural variation to achieve a whole-plant functional understanding of the responses mediated by jasmonate signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:414-425. [PMID: 30927293 DOI: 10.1111/tpj.14331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
The dramatic advances in our understanding of the molecular biology and biochemistry of jasmonate (JA) signaling have been the subject of several excellent recent reviews that have highlighted the phytohormonal function of this signaling pathway. Here, we focus on the responses mediated by JA signaling which have consequences for a plant's Darwinian fitness, i.e. the organism-level function of JA signaling. The most diverse module in the signaling cascade, the JAZ proteins, and their interactions with other proteins and transcription factors, allow this canonical signaling cascade to mediate a bewildering array of traits in different tissues at different times; the functional coherence of these diverse responses are best appreciated in an organismal/ecological context. From published work, it appears that jasmonates can function as the 'Swiss Army knife' of plant signaling, mediating many different biotic and abiotic stress and developmental responses that allow plants to contextualize their responses to their frequently changing local environments and optimize their fitness. We propose that a deeper analysis of the natural variation in both within-plant and within-population JA signaling components is a profitable means of attaining a coherent whole-plant functional perspective of this signaling cascade, and provide examples of this approach from the Nicotiana attenuata system.
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Affiliation(s)
- Rishav Ray
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Dapeng Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
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12
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Guo Q, Major IT, Howe GA. Resolution of growth-defense conflict: mechanistic insights from jasmonate signaling. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:72-81. [PMID: 29555489 DOI: 10.1016/j.pbi.2018.02.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/20/2023]
Abstract
Induced plant resistance depends on the production of specialized metabolites that repel attack by biotic aggressors and is often associated with reduced growth of vegetative tissues. Despite progress in understanding the signal transduction networks that control growth-defense tradeoffs, much remains to be learned about how growth rate is coordinated with changes in metabolism during growth-to-defense transitions. Here, we highlight recent advances in jasmonate research to suggest how a major branch of plant immunity is dynamically regulated to calibrate growth-defense balance with shifts in carbon availability. We review evidence that diminished growth, as an integral facet of induced resistance, may optimize the temporal and spatial expression of defense compounds without compromising other critical roles of central metabolism. New insights into the evolution of jasmonate signaling further suggest that opposing selective pressures associated with too much or too little defense may have shaped the emergence of a modular jasmonate pathway that integrates primary and specialized metabolism through the control of repressor-transcription factor complexes. A better understanding of the mechanistic basis of growth-defense balance has important implications for boosting plant productivity, including insights into how these tradeoffs may be uncoupled for agricultural improvement.
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Affiliation(s)
- Qiang Guo
- Department of Energy-Plant Research Laboratory, Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Ian T Major
- Department of Energy-Plant Research Laboratory, Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Gregg A Howe
- Department of Energy-Plant Research Laboratory, Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA.
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13
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Canales J, Henriquez-Valencia C, Brauchi S. The Integration of Electrical Signals Originating in the Root of Vascular Plants. FRONTIERS IN PLANT SCIENCE 2018; 8:2173. [PMID: 29375591 PMCID: PMC5767606 DOI: 10.3389/fpls.2017.02173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/12/2017] [Indexed: 05/07/2023]
Abstract
Plants have developed different signaling systems allowing for the integration of environmental cues to coordinate molecular processes associated to both early development and the physiology of the adult plant. Research on systemic signaling in plants has traditionally focused on the role of phytohormones as long-distance signaling molecules, and more recently the importance of peptides and miRNAs in building up this communication process has also been described. However, it is well-known that plants have the ability to generate different types of long-range electrical signals in response to different stimuli such as light, temperature variations, wounding, salt stress, or gravitropic stimulation. Presently, it is unclear whether short or long-distance electrical communication in plants is linked to nutrient uptake. This review deals with aspects of sensory input in plant roots and the propagation of discrete signals to the plant body. We discuss the physiological role of electrical signaling in nutrient uptake and how nutrient variations may become an electrical signal propagating along the plant.
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Affiliation(s)
- Javier Canales
- Facultad de Ciencias, Instituto de Bioquimica y Microbiologia, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology, Santiago, Chile
| | - Carlos Henriquez-Valencia
- Facultad de Ciencias, Instituto de Bioquimica y Microbiologia, Universidad Austral de Chile, Valdivia, Chile
| | - Sebastian Brauchi
- Facultad de Medicina, Instituto de Fisiologia, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases, Valdivia, Chile
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14
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De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y. Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana. THE PLANT CELL 2017; 29:2786-2800. [PMID: 29070508 PMCID: PMC5728133 DOI: 10.1105/tpc.17.00531] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/10/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub- or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress.
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Affiliation(s)
- Riet De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Ehsan Sabaghian
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Yvan Saeys
- Center for Inflammation Research, VIB, B-9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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15
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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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16
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Li R, Wang M, Wang Y, Schuman MC, Weinhold A, Schäfer M, Jiménez-Alemán GH, Barthel A, Baldwin IT. Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco. Proc Natl Acad Sci U S A 2017; 114:E7205-E7214. [PMID: 28784761 PMCID: PMC5576791 DOI: 10.1073/pnas.1703463114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Optimal defense (OD) theory predicts that within a plant, tissues are defended in proportion to their fitness value and risk of predation. The fitness value of leaves varies greatly and leaves are protected by jasmonate (JA)-inducible defenses. Flowers are vehicles of Darwinian fitness in flowering plants and are attacked by herbivores and pathogens, but how they are defended is rarely investigated. We used Nicotiana attenuata, an ecological model plant with well-characterized herbivore interactions to characterize defense responses in flowers. Early floral stages constitutively accumulate greater amounts of two well-characterized defensive compounds, the volatile (E)-α-bergamotene and trypsin proteinase inhibitors (TPIs), which are also found in herbivore-induced leaves. Plants rendered deficient in JA biosynthesis or perception by RNA interference had significantly attenuated floral accumulations of defensive compounds known to be regulated by JA in leaves. By RNA-seq, we found a JAZ gene, NaJAZi, specifically expressed in early-stage floral tissues. Gene silencing revealed that NaJAZi functions as a flower-specific jasmonate repressor that regulates JAs, (E)-α-bergamotene, TPIs, and a defensin. Flowers silenced in NaJAZi are more resistant to tobacco budworm attack, a florivore. When the defensin was ectopically expressed in leaves, performance of Manduca sexta larvae, a folivore, decreased. NaJAZi physically interacts with a newly identified NINJA-like protein, but not the canonical NINJA. This NINJA-like recruits the corepressor TOPLESS that contributes to the suppressive function of NaJAZi on floral defenses. This study uncovers the defensive function of JA signaling in flowers, which includes components that tailor JA signaling to provide flower-specific defense.
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Affiliation(s)
- Ran Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Ming Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Yang Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Arne Weinhold
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Martin Schäfer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | | | - Andrea Barthel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany;
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17
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Durrant M, Boyer J, Zhou W, Baldwin IT, Xu S. Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses. THE NEW PHYTOLOGIST 2017; 215:1264-1273. [PMID: 28618009 DOI: 10.1111/nph.14644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes. Highly conserved and evolutionarily ancient genes of primary metabolism were activated at intermediate time points (2-6 h) after elicitation, while less constrained and young genes associated with defense signaling and biosynthesis of specialized metabolites were activated at early (before 2 h) and late (after 6 h) stages of the induced response, respectively - a pattern resembling the evolutionary hourglass pattern observed during embryogenesis in animals and the developmental process in plants and fungi. The hourglass patterns found in herbivory-induced defense responses and developmental process are both likely to be a result of signaling modularization and differential evolutionary constraints on the modules involved in the signaling cascade.
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Affiliation(s)
- Matthew Durrant
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
- Department of Plant and Wildlife Sciences, Brigham Young University, 4105A, LSB, Provo, UT 84602, USA
| | - Justin Boyer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
- Department of Plant and Wildlife Sciences, Brigham Young University, 4105A, LSB, Provo, UT 84602, USA
| | - Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
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18
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Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT. Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proc Natl Acad Sci U S A 2017; 114:6133-6138. [PMID: 28536194 PMCID: PMC5468653 DOI: 10.1073/pnas.1700073114] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways. In contrast to the duplication of the polyamine pathway that is shared among several solanaceous genera producing polyamine-derived tropane alkaloids, we found that lineage-specific duplications within the NAD pathway and the evolution of root-specific expression of the duplicated Solanaceae-specific ethylene response factor that activates the expression of all nicotine biosynthetic genes resulted in the innovative and efficient production of nicotine in the genus Nicotiana Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.
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Affiliation(s)
- Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Thomas Brockmöller
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Aura Navarro-Quezada
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Klaus Gase
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Christoph Kreitzer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Mario Stanke
- Institute for Mathematics and Computer Science, Universität Greifswald, 17489 Greifswald, Germany
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Eric Lyons
- School of Plant Sciences, BIO5 Institute, CyVerse, University of Arizona, Tucson, AZ 85721
| | - Priyanka Pandey
- National Institute of Biomedical Genomics, Kalyani, 741251 West Bengal, India
| | - Shree P Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, 700064 West Bengal, India
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
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19
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Abstract
Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.
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