1
|
Oshikiri H, Li H, Manabe M, Yamamoto H, Yazaki K, Takanashi K. Comparative Analysis of Shikonin and Alkannin Acyltransferases Reveals Their Functional Conservation in Boraginaceae. PLANT & CELL PHYSIOLOGY 2024; 65:362-371. [PMID: 38181221 DOI: 10.1093/pcp/pcad158] [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: 02/07/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Shikonin and its enantiomer, alkannin, are bioactive naphthoquinones produced in several plants of the family Boraginaceae. The structures of these acylated derivatives, which have various short-chain acyl moieties, differ among plant species. The acylation of shikonin and alkannin in Lithospermum erythrorhizon was previously reported to be catalyzed by two enantioselective BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1). However, the mechanisms by which various shikonin and alkannin derivatives are produced in Boraginaceae plants remain to be determined. In the present study, evaluation of six Boraginaceae plants identified 23 homologs of LeSAT1 and LeAAT1, with 15 of these enzymes found to catalyze the acylation of shikonin or alkannin, utilizing acetyl-CoA, isobutyryl-CoA or isovaleryl-CoA as an acyl donor. Analyses of substrate specificities of these enzymes for both acyl donors and acyl acceptors and determination of their subcellular localization using Nicotiana benthamiana revealed a distinct functional differentiation of BAHD acyltransferases in Boraginaceae plants. Gene expression of these acyltransferases correlated with the enantiomeric ratio of produced shikonin/alkannin derivatives in L. erythrorhizon and Echium plantagineum. These enzymes showed conserved substrate specificities for acyl donors among plant species, indicating that the diversity in acyl moieties of shikonin/alkannin derivatives involved factors other than the differentiation of acyltransferases. These findings provide insight into the chemical diversification and evolutionary processes of shikonin/alkannin derivatives.
Collapse
Affiliation(s)
- Haruka Oshikiri
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hao Li
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Misaki Manabe
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hirobumi Yamamoto
- Department of Applied Biology, Faculty of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Oru-gun, Gunma, 374-0193 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| |
Collapse
|
2
|
Yuan J, Ma L, Wang Y, Xu X, Zhang R, Wang C, Meng W, Tian Z, Zhou Y, Wang G. A recently evolved BAHD acetyltransferase, responsible for bitter soyasaponin A production, is indispensable for soybean seed germination. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2490-2504. [PMID: 37548097 DOI: 10.1111/jipb.13553] [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: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Soyasaponins are major small molecules that accumulate in soybean (Glycine max) seeds. Among them, type-A soyasaponins, fully acetylated at the terminal sugar of their C22 sugar chain, are responsible for the bitter taste of soybean-derived foods. However, the molecular basis for the acetylation of type-A soyasaponins remains unclear. Here, we identify and characterize GmSSAcT1, encoding a BADH-type soyasaponin acetyltransferase that catalyzes three or four consecutive acetylations on type-A soyasaponins in vitro and in planta. Phylogenetic analysis and biochemical assays suggest that GmSSAcT1 likely evolved from acyltransferases present in leguminous plants involved in isoflavonoid acylation. Loss-of-function mutants of GmSSAcT1 exhibited impaired seed germination, which attribute to the excessive accumulation of null-acetylated type-A soyasaponins. We conclude that GmSSAcT1 not only functions as a detoxification gene for high accumulation of type-A soyasaponins in soybean seeds but is also a promising target for breeding new soybean varieties with lower bitter soyasaponin content.
Collapse
Affiliation(s)
- Jia Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Liya Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Xindan Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Zhang
- State Key Laboratory of Molecular Developmental Biology, the Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengyuan Wang
- The Center for Microbes, Development and Health, Institute of Pasteur of Shanghai, the Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wenxiang Meng
- State Key Laboratory of Molecular Developmental Biology, the Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhixi Tian
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| |
Collapse
|
3
|
Stack GM, Snyder SI, Toth JA, Quade MA, Crawford JL, McKay JK, Jackowetz JN, Wang P, Philippe G, Hansen JL, Moore VM, Rose JKC, Smart LB. Cannabinoids function in defense against chewing herbivores in Cannabis sativa L. HORTICULTURE RESEARCH 2023; 10:uhad207. [PMID: 38023471 PMCID: PMC10681003 DOI: 10.1093/hr/uhad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023]
Abstract
In the decades since the first cannabinoids were identified by scientists, research has focused almost exclusively on the function and capacity of cannabinoids as medicines and intoxicants for humans and other vertebrates. Very little is known about the adaptive value of cannabinoid production, though several hypotheses have been proposed including protection from ultraviolet radiation, pathogens, and herbivores. To test the prediction that genotypes with greater concentrations of cannabinoids will have reduced herbivory, a segregating F2 population of Cannabis sativa was leveraged to conduct lab- and field-based bioassays investigating the function of cannabinoids in mediating interactions with chewing herbivores. In the field, foliar cannabinoid concentration was inversely correlated with chewing herbivore damage. On detached leaves, Trichoplusia ni larvae consumed less leaf area and grew less when feeding on leaves with greater concentrations of cannabinoids. Scanning electron and light microscopy were used to characterize variation in glandular trichome morphology. Cannabinoid-free genotypes had trichomes that appeared collapsed. To isolate cannabinoids from confounding factors, artificial insect diet was amended with cannabinoids in a range of physiologically relevant concentrations. Larvae grew less and had lower rates of survival as cannabinoid concentration increased. These results support the hypothesis that cannabinoids function in defense against chewing herbivores.
Collapse
Affiliation(s)
- George M Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Stephen I Snyder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Jamie L Crawford
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | | - Ping Wang
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Julie L Hansen
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Virginia M Moore
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| |
Collapse
|
4
|
Riahi C, Urbaneja A, Fernández-Muñoz R, Fortes IM, Moriones E, Pérez-Hedo M. Induction of Glandular Trichomes to Control Bemisia tabaci in Tomato Crops: Modulation by the Natural Enemy Nesidiocoris tenuis. PHYTOPATHOLOGY 2023; 113:1677-1685. [PMID: 36998120 DOI: 10.1094/phyto-11-22-0440-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Whitefly-transmitted viruses are one of the biggest threats to tomato (Solanum lycopersicum) growing worldwide. Strategies based on the introgression of resistance traits from wild relatives are promoted to control tomato pests and diseases. Recently, a trichome-based resistance characterizing the wild species Solanum pimpinellifolium was introgressed into a cultivated tomato. An advanced backcross line (BC5S2) exhibiting the presence of acylsugar-associated type IV trichomes, which are lacking in cultivated tomatoes, was effective at controlling whiteflies (Hemiptera: Aleyrodidae) and limiting the spread of whitefly-transmitted viruses. However, at early growth stages, type IV trichome density and acylsugar production are limited; thus, protection against whiteflies and whitefly-transmitted viruses remains irrelevant. In this work, we demonstrate that young BC5S2 tomato plants feeding-punctured by the zoophytophagous predator Nesidiocoris tenuis (Hemiptera: Miridae) displayed an increase (above 50%) in type IV trichome density. Acylsugar production was consistently increased in N. tenuis-punctured BC5S2 plants, which was more likely associated with upregulated expression of the BCKD-E2 gene related to acylsugar biosynthesis. In addition, the infestation of BC5S2 plants with N. tenuis effectively induced the expression of defensive genes involved in the jasmonic acid signaling pathway, resulting in strong repellence to Bemisia tabaci and attractiveness to N. tenuis. Thus, through preplant release of N. tenuis in tomato nurseries carried out in some integrated pest management programs, type IV trichome-expressing plants can be prepared to control whiteflies and whitefly-transmitted viruses at early growth stages. This study emphasizes the advantage of reinforcing constitutive resistance using defense inducers to guarantee robust protection against pests and transmitted viruses.
Collapse
Affiliation(s)
- Chaymaa Riahi
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), 46113 Moncada, Valencia, Spain
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), 46113 Moncada, Valencia, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
| | - Isabel M Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
| | - Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), 46113 Moncada, Valencia, Spain
| |
Collapse
|
5
|
Sonawane PD, Gharat SA, Jozwiak A, Barbole R, Heinicke S, Almekias-Siegl E, Meir S, Rogachev I, Connor SEO, Giri AP, Aharoni A. A BAHD-type acyltransferase concludes the biosynthetic pathway of non-bitter glycoalkaloids in ripe tomato fruit. Nat Commun 2023; 14:4540. [PMID: 37500644 PMCID: PMC10374582 DOI: 10.1038/s41467-023-40092-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
Tomato is the highest value fruit and vegetable crop worldwide, yet produces α-tomatine, a renowned toxic and bitter-tasting anti-nutritional steroidal glycoalkaloid (SGA) involved in plant defense. A suite of modifications during tomato fruit maturation and ripening converts α-tomatine to the non-bitter and less toxic Esculeoside A. This important metabolic shift prevents bitterness and toxicity in ripe tomato fruit. While the enzymes catalyzing glycosylation and hydroxylation reactions in the Esculeoside A pathway have been resolved, the proposed acetylating step remains, to date, elusive. Here, we discovered that GAME36 (GLYCOALKALOID METABOLISM36), a BAHD-type acyltransferase catalyzes SGA-acetylation in cultivated and wild tomatoes. This finding completes the elucidation of the core Esculeoside A biosynthetic pathway in ripe tomato, allowing reconstitution of Esculeoside A production in heterologous microbial and plant hosts. The involvement of GAME36 in bitter SGA detoxification pathway points to a key role in the evolution of sweet-tasting tomato as well as in the domestication and breeding of modern cultivated tomato fruit.
Collapse
Affiliation(s)
- Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany.
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Sachin A Gharat
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adam Jozwiak
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ranjit Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarah Heinicke
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sarah E O' Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ashok P Giri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| |
Collapse
|
6
|
Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP. In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1. Front Microbiol 2023; 14:1140249. [PMID: 37408640 PMCID: PMC10318148 DOI: 10.3389/fmicb.2023.1140249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023] Open
Abstract
A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.
Collapse
Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Vaishnavi Rawat
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Afreen Shadan
- Department of Microbiology, Dr. Shyama Prasad Mukerjee University, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| |
Collapse
|
7
|
Abstract
Environmental factors such as light, water, minerals, temperature, and other organisms affect plant growth and development. Unlike animals, plants can't escape from unfavorable biotic and abiotic stresses. Thus, they evolved the ability to biosynthesize specific chemicals referred to as plant specialized metabolites in order to facilitate successful interactions with the surrounding environment, as well as with other organisms including plants, insects, microorganisms, and animals. While the exact number of plant specialized metabolites, historically called secondary metabolites, is currently unknown, it has been estimated to range from 200,000 to 1,000,000 compounds. In contrast to the species-, organ- and tissue-specific nature of plant specialized metabolites, primary metabolites are shared by all living organisms, are vital for growth, development and reproduction, and comprise only about 8,000 compounds. The biosynthesis and storage of plant specialized metabolites are developmentally and temporally regulated and depend on biotic and abiotic factors. Specific cell types, subcellular organelles, microcompartments, and/or anatomical structures are often devoted to producing and storing these compounds. The functions of many specialized metabolites are still not fully understood but are generally considered to be essential for the fitness and survival of plants, partially by interacting with other organisms in both mutualistic (for example, attraction of pollinators) and antagonistic (such as defense against herbivores and pathogens) ways. In this primer, we will focus on specialized-metabolite functions in plant defense interactions and on the genetic, molecular, and biochemical mechanisms leading to the structural diversity of specialized metabolites. Though less understood, we will also touch on the mode of action of specialized metabolites in plant defense.
Collapse
Affiliation(s)
- Xing-Qi Huang
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
8
|
Moghe G, Irfan M, Sarmah B. Dangerous sugars: Structural diversity and functional significance of acylsugar-like defense compounds in flowering plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 73:102348. [PMID: 36842412 DOI: 10.1016/j.pbi.2023.102348] [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: 10/30/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/10/2023]
Abstract
Acylsugars constitute a diverse class of secondary metabolites found in many flowering plant families. Comprising sugar cores and acyl groups connected by ester and/or ether linkages, acylsugar structures vary considerably at all taxonomic levels - from populations of the same species to across species of the same family and across flowering plants, with some species producing hundreds of acylsugars in a single organ. Acylsugars have been most well-studied in the Solanaceae family, but structurally analogous compounds have also been reported in the Convolvulaceae, Martyniaceae, Geraniaceae, Rubiaceae, Rosaceae and Caryophyllaceae families. Focusing on Solanaceae and Convolvulaceae acylsugars, this review highlights their structural diversity, the potential biosynthetic mechanisms that produce this diversity, and its functional significance. Finally, we also discuss the possibility that some of this diversity is merely "noise", arising out of enzyme promiscuity and/or non-adaptive evolutionary mechanisms.
Collapse
Affiliation(s)
- Gaurav Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Bhaswati Sarmah
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, Assam 785013, India
| |
Collapse
|
9
|
Chen TT, Liu H, Li YP, Yao XH, Qin W, Yan X, Wang XY, Peng BW, Zhang YJ, Shao J, Hu XY, Fu XQ, Li L, Wang YL, Tang KX. AaSEPALLATA1 integrates jasmonate and light-regulated glandular secretory trichome initiation in Artemisia annua. PLANT PHYSIOLOGY 2023; 192:1483-1497. [PMID: 36810650 PMCID: PMC10231397 DOI: 10.1093/plphys/kiad113] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/24/2023] [Accepted: 02/12/2023] [Indexed: 06/01/2023]
Abstract
Glandular secretory trichomes (GSTs) can secrete and store a variety of specific metabolites. By increasing GST density, valuable metabolites can be enhanced in terms of productivity. However, the comprehensive and detailed regulatory network of GST initiation still needs further investigation. By screening a complementary DNA library derived from young leaves of Artemisia annua, we identified a MADS-box transcription factor, AaSEPALLATA1 (AaSEP1), that positively regulates GST initiation. Overexpression of AaSEP1 in A. annua substantially increased GST density and artemisinin content. The HOMEODOMAIN PROTEIN 1 (AaHD1)-AaMYB16 regulatory network regulates GST initiation via the jasmonate (JA) signaling pathway. In this study, AaSEP1 enhanced the function of AaHD1 activation on downstream GST initiation gene GLANDULAR TRICHOME-SPECIFIC WRKY 2 (AaGSW2) through interaction with AaMYB16. Moreover, AaSEP1 interacted with the JA ZIM-domain 8 (AaJAZ8) and served as an important factor in JA-mediated GST initiation. We also found that AaSEP1 interacted with CONSTITUTIVE PHOTOMORPHOGENIC 1 (AaCOP1), a major repressor of light signaling. In this study, we identified a MADS-box transcription factor that is induced by JA and light signaling and that promotes the initiation of GST in A. annua.
Collapse
Affiliation(s)
- Tian-Tian Chen
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hang Liu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong-Peng Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xing-Hao Yao
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Qin
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Yan
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiu-Yun Wang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo-Wen Peng
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yao-Jie Zhang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Shao
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Yi Hu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qing Fu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Liang Wang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ke-Xuan Tang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic & Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & Southwest University, School of Life Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
10
|
Yoo HJ, Chung MY, Lee HA, Lee SB, Grandillo S, Giovannoni JJ, Lee JM. Natural overexpression of CAROTENOID CLEAVAGE DIOXYGENASE 4 in tomato alters carotenoid flux. PLANT PHYSIOLOGY 2023; 192:1289-1306. [PMID: 36715630 PMCID: PMC10231392 DOI: 10.1093/plphys/kiad049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 06/01/2023]
Abstract
Carotenoids and apocarotenoids function as pigments and flavor volatiles in plants that enhance consumer appeal and offer health benefits. Tomato (Solanum lycopersicum.) fruit, especially those of wild species, exhibit a high degree of natural variation in carotenoid and apocarotenoid contents. Using positional cloning and an introgression line (IL) of Solanum habrochaites "LA1777', IL8A, we identified carotenoid cleavage dioxygenase 4 (CCD4) as the factor responsible for controlling the dark orange fruit color. CCD4b expression in ripe fruit of IL8A plants was ∼8,000 times greater than that in the wild type, presumably due to 5' cis-regulatory changes. The ShCCD4b-GFP fusion protein localized in the plastid. Phytoene, ζ-carotene, and neurosporene levels increased in ShCCD4b-overexpressing ripe fruit, whereas trans-lycopene, β-carotene, and lutein levels were reduced, suggestive of feedback regulation in the carotenoid pathway by an unknown apocarotenoid. Solid-phase microextraction-gas chromatography-mass spectrometry analysis showed increased levels of geranylacetone and β-ionone in ShCCD4b-overexpressing ripe fruit coupled with a β-cyclocitral deficiency. In carotenoid-accumulating Escherichia coli strains, ShCCD4b cleaved both ζ-carotene and β-carotene at the C9-C10 (C9'-C10') positions to produce geranylacetone and β-ionone, respectively. Exogenous β-cyclocitral decreased carotenoid synthesis in the ripening fruit of tomato and pepper (Capsicum annuum), suggesting feedback inhibition in the pathway. Our findings will be helpful for enhancing the aesthetic and nutritional value of tomato and for understanding the complex regulatory mechanisms of carotenoid and apocarotenoid biogenesis.
Collapse
Affiliation(s)
- Hee Ju Yoo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, Suncheon 57922, Korea
| | - Hyun-Ah Lee
- Division of Eco-Friendly Horticulture, Yonam College, Cheonan 31005, Korea
| | - Soo-Bin Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Silvana Grandillo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy
| | - James J Giovannoni
- Boyce Thompson Institute and USDA-ARS Robert W. Holley Center, Tower Rd., Cornell University Campus, Ithaca, NY 14853, USA
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
11
|
Mutschler MA, Kennedy GG, Ullman DE. Acylsugar-mediated resistance as part of a multilayered defense against thrips, orthotospoviruses, and beyond. CURRENT OPINION IN INSECT SCIENCE 2023; 56:101021. [PMID: 36925103 DOI: 10.1016/j.cois.2023.101021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 05/03/2023]
Abstract
Resistant varieties are critical tools for crop production, and single-resistance genes providing strong protection against pests or pathogens are deployed in agriculture. Durability of these traits is threatened by emergence of resistance-breaking pests and pathogens. This review focuses on acylsugar-mediated resistance in tomato. Wild tomatoes have type-IV trichomes that exude chemically complex mixtures of acylsugars altering behavior and suppressing multiple pest species, and with thrips and whiteflies (WF), suppressing virus transmission, for example, Tomato spotted wilt orthotospovirus and Tomato yellow leaf curl virus, respectively. Marker-assisted selection and bioassays led to development of advanced cultivated tomato breeding lines rich in acylsugar variations, allowing acylsugar-mediated resistance to be combined with other resistance traits providing a layered defense system that reduces pest populations and virus disease prevalence. This strategy also holds promise for enhancing durability of virus resistance genes by reducing the intensity of selection for resistance-breaking variants.
Collapse
|
12
|
Wang C, Chen T, Li Y, Liu H, Qin W, Wu Z, Peng B, Wang X, Yan X, Fu X, Li L, Tang K. AaWIN1, an AP2/ERF protein, positively regulates glandular secretory trichome initiation in Artemisia annua. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111602. [PMID: 36690278 DOI: 10.1016/j.plantsci.2023.111602] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Exploring the genetic network of glandular trichomes and manipulating genes relevant to secondary metabolite biosynthesis are of great importance and value. Artemisinin, a key antimalarial drug ingredient, is synthesized and stored in glandular secretory trichomes (GSTs) in Artemisia annua. WIN/SHN proteins, a clade of AP2/ERF family, are known as regulators for cuticle biosynthesis. However, their function in glandular trichome development is less unknown. In this study, we identified a WIN/SHN gene from A. annua and named it as AaWIN1. AaWIN1 was predominantly expressed in buds, flowers and trichomes, and encoded a nuclear-localized protein. Overexpressing AaWIN1 in A. annua significantly increased the density of GST as well as the artemisinin content. Furthermore, AaGSW2 was reported to play an important role in promoting GST initiation, and the expression of AaGSW2 was induced in AaWIN1-overexpression lines. AaMIXTA1, a MYB protein positively regulating trichome initiation and cuticle biosynthesis, was confirmed to interact with AaWIN1. In addition, the ectopic expression of AaWIN1 resulted in slender and curled leaves, fewer trichomes, and rising expressions of cuticle biosynthesis genes in Arabidopsis thaliana. Taken together, based on phenotype observations, content measurements and gene expression detections, AaWIN1 was considered as a positive regulator for GST initiation in A. annua.
Collapse
Affiliation(s)
- Chen Wang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Chen
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yongpeng Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hang Liu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Qin
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhangkuanyu Wu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Peng
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuyun Wang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yan
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xueqing Fu
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ling Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kexuan Tang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
13
|
Kerwin RE. Blurred lines: Primary metabolic machinery coopted for specialized metabolism in tomato trichomes. PLANT PHYSIOLOGY 2023; 191:831-833. [PMID: 36454673 PMCID: PMC9922385 DOI: 10.1093/plphys/kiac532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
|
14
|
Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
Collapse
|
15
|
Schenck CA, Anthony TM, Jacobs M, Jones AD, Last RL. Natural variation meets synthetic biology: Promiscuous trichome-expressed acyltransferases from Nicotiana. PLANT PHYSIOLOGY 2022; 190:146-164. [PMID: 35477794 PMCID: PMC9434288 DOI: 10.1093/plphys/kiac192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Acylsugars are defensive, trichome-synthesized sugar esters produced in plants across the Solanaceae (nightshade) family. Although assembled from simple metabolites and synthesized by a relatively short core biosynthetic pathway, tremendous within- and across-species acylsugar structural variation is documented across the family. To advance our understanding of the diversity and the synthesis of acylsugars within the Nicotiana genus, trichome extracts were profiled across the genus coupled with transcriptomics-guided enzyme discovery and in vivo and in vitro analysis. Differences in the types of sugar cores, numbers of acylations, and acyl chain structures contributed to over 300 unique annotated acylsugars throughout Nicotiana. Placement of acyl chain length into a phylogenetic context revealed that an unsaturated acyl chain type was detected in a few closely related species. A comparative transcriptomics approach identified trichome-enriched Nicotiana acuminata acylsugar biosynthetic candidate enzymes. More than 25 acylsugar variants could be produced in a single enzyme assay with four N. acuminata acylsugar acyltransferases (NacASAT1-4) together with structurally diverse acyl-CoAs and sucrose. Liquid chromatography coupled with mass spectrometry screening of in vitro products revealed the ability of these enzymes to make acylsugars not present in Nicotiana plant extracts. In vitro acylsugar production also provided insights into acyltransferase acyl donor promiscuity and acyl acceptor specificity as well as regiospecificity of some ASATs. This study suggests that promiscuous Nicotiana acyltransferases can be used as synthetic biology tools to produce novel and potentially useful metabolites.
Collapse
Affiliation(s)
- Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Thilani M Anthony
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - MacKenzie Jacobs
- Department of Physical Sciences and Mathematics, West Liberty University, West Liberty, West Virginia 26074, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| |
Collapse
|
16
|
Yu J, Tu X, Huang AC. Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions. Nat Prod Rep 2022; 39:1393-1422. [PMID: 35766105 DOI: 10.1039/d2np00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.
Collapse
Affiliation(s)
- Jingwei Yu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xingzhao Tu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| |
Collapse
|
17
|
Akiyama R, Watanabe B, Kato J, Nakayasu M, Lee HJ, Umemoto N, Muranaka T, Saito K, Sugimoto Y, Mizutani M. Tandem Gene Duplication of Dioxygenases Drives the Structural Diversity of Steroidal Glycoalkaloids in the Tomato Clade. PLANT & CELL PHYSIOLOGY 2022; 63:981-990. [PMID: 35560060 DOI: 10.1093/pcp/pcac064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Cultivated tomato (Solanum lycopersicum) contains α-tomatine, a steroidal glycoalkaloid (SGA), which functions as a defense compound to protect against pathogens and herbivores; interestingly, wild species in the tomato clade biosynthesize a variety of SGAs. In cultivated tomato, the metabolic detoxification of α-tomatine during tomato fruit ripening is an important trait that aided in its domestication, and two distinct 2-oxoglutarate-dependent dioxygenases (DOXs), a C-23 hydroxylase of α-tomatine (Sl23DOX) and a C-27 hydroxylase of lycoperoside C (Sl27DOX), are key to this process. There are tandemly duplicated DOX genes on tomato chromosome 1, with high levels of similarity to Sl23DOX. While these DOX genes are rarely expressed in cultivated tomato tissues, the recombinant enzymes of Solyc01g006580 and Solyc01g006610 metabolized α-tomatine to habrochaitoside A and (20R)-20-hydroxytomatine and were therefore named as habrochaitoside A synthase (HAS) and α-tomatine 20-hydroxylase (20DOX), respectively. Furthermore, 20DOX and HAS exist in the genome of wild tomato S. habrochaites accession LA1777, which accumulates habrochaitoside A in its fruits, and their expression patterns were in agreement with the SGA profiles in LA1777. These results indicate that the functional divergence of α-tomatine-metabolizing DOX enzymes results from gene duplication and the neofunctionalization of catalytic activity and gene expression, and this contributes to the structural diversity of SGAs in the tomato clade.
Collapse
Affiliation(s)
- Ryota Akiyama
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| | - Bunta Watanabe
- Institute for Chemical Research, Kyoto University, Gokasyo, Uji, Kyoto, 611-0011 Japan
| | - Junpei Kato
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| | - Masaru Nakayasu
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| | - Hyoung Jae Lee
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| | - Naoyuki Umemoto
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871 Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675 Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501 Japan
| |
Collapse
|
18
|
Schenck CA, Busta L. Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism. PLANT MOLECULAR BIOLOGY 2022; 109:355-367. [PMID: 34816350 DOI: 10.1007/s11103-021-01220-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.
Collapse
Affiliation(s)
- Craig A Schenck
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA
| |
Collapse
|
19
|
Feng H, Acosta-Gamboa L, Kruse LH, Tracy JD, Chung SH, Nava Fereira AR, Shakir S, Xu H, Sunter G, Gore MA, Casteel CL, Moghe GD, Jander G. Acylsugars protect Nicotiana benthamiana against insect herbivory and desiccation. PLANT MOLECULAR BIOLOGY 2022; 109:505-522. [PMID: 34586580 DOI: 10.1007/s11103-021-01191-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Nicotiana benthamiana acylsugar acyltransferase (ASAT) is required for protection against desiccation and insect herbivory. Knockout mutations provide a new resource for investigation of plant-aphid and plant-whitefly interactions. Nicotiana benthamiana is used extensively as a transient expression platform for functional analysis of genes from other species. Acylsugars, which are produced in the trichomes, are a hypothesized cause of the relatively high insect resistance that is observed in N. benthamiana. We characterized the N. benthamiana acylsugar profile, bioinformatically identified two acylsugar acyltransferase genes, ASAT1 and ASAT2, and used CRISPR/Cas9 mutagenesis to produce acylsugar-deficient plants for investigation of insect resistance and foliar water loss. Whereas asat1 mutations reduced accumulation, asat2 mutations caused almost complete depletion of foliar acylsucroses. Three hemipteran and three lepidopteran herbivores survived, gained weight, and/or reproduced significantly better on asat2 mutants than on wildtype N. benthamiana. Both asat1 and asat2 mutations reduced the water content and increased leaf temperature. Our results demonstrate the specific function of two ASAT proteins in N. benthamiana acylsugar biosynthesis, insect resistance, and desiccation tolerance. The improved growth of aphids and whiteflies on asat2 mutants will facilitate the use of N. benthamiana as a transient expression platform for the functional analysis of insect effectors and resistance genes from other plant species. Similarly, the absence of acylsugars in asat2 mutants will enable analysis of acylsugar biosynthesis genes from other Solanaceae by transient expression.
Collapse
Affiliation(s)
- Honglin Feng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Lucia Acosta-Gamboa
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake D Tracy
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Alba Ruth Nava Fereira
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Sara Shakir
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Gembloux Agro-Bio Tech Institute, The University of Liege, Gembloux, Belgium
| | - Hongxing Xu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- College of Life Science, The Shaanxi Normal University, Xi'an, China
| | - Garry Sunter
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Clare L Casteel
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.
| |
Collapse
|
20
|
Chang A, Hu Z, Chen B, Vanderschuren H, Chen M, Qu Y, Yu W, Li Y, Sun H, Cao J, Vasudevan K, Li C, Cao Y, Zhang J, Shen Y, Yang A, Wang Y. Characterization of trichome-specific BAHD acyltransferases involved in acylsugar biosynthesis in Nicotiana tabacum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3913-3928. [PMID: 35262703 DOI: 10.1093/jxb/erac095] [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: 11/08/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Glandular trichomes of tobacco (Nicotiana tabacum) produce blends of acylsucroses that contribute to defence against pathogens and herbivorous insects, but the mechanism of assembly of these acylsugars has not yet been determined. In this study, we isolated and characterized two trichome-specific acylsugar acyltransferases that are localized in the endoplasmic reticulum, NtASAT1 and NtASAT2. They sequentially catalyse two additive steps of acyl donors to sucrose to produce di-acylsucrose. Knocking out of NtASAT1 or NtASAT2 resulted in deficiency of acylsucrose; however, there was no effect on acylsugar accumulation in plants overexpressing NtASAT1 or NtASAT2. Genomic analysis and profiling revealed that NtASATs originated from the T subgenome, which is derived from the acylsugar-producing diploid ancestor N. tomentosiformis. Our identification of NtASAT1 and NtASAT2 as enzymes involved in acylsugar assembly in tobacco potentially provides a new approach and target genes for improving crop resistance against pathogens and insects.
Collapse
Affiliation(s)
- Aixia Chang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Plant Genetics Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Zhongyi Hu
- Jiangxi Food Inspection and Testing Research Institute, Nanchang, 330001, China
| | - Biao Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Herve Vanderschuren
- Plant Genetics Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Tropical Crop Improvement Lab, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Ming Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yafang Qu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Weisong Yu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, 410004, China
| | - Huiqing Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jianmin Cao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Kumar Vasudevan
- Plant Genetics Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Chenying Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yanan Cao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jianye Zhang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Yeming Shen
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yuanying Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| |
Collapse
|
21
|
Pennelliiside D, a New Acyl Glucose from Solanum pennellii and Chemical Synthesis of Pennelliisides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123728. [PMID: 35744854 PMCID: PMC9231340 DOI: 10.3390/molecules27123728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Acyl glucoses are a group of specialized metabolites produced by Solanaceae. Solanum pennellii, a wild-type tomato plant, produces acyl glucoses in its hair-like epidermal structures known as trichomes. These compounds have been found to be herbicides, microbial growth inhibitors, or allelopathic compounds. However, there are a few reports regarding isolation and investigation of biological activities of acyl glucoses in its pure form due to the difficulty of isolation. Here, we report a new acyl glucose, pennelliiside D, isolated and identified from S. pennellii. Its structure was determined by 1D NMR and 2D NMR, together with FD-MS analysis. To clarify the absolute configuration of the acyl moiety of 2-methylbutyryl in the natural compound, two possible isomers were synthesized starting from β-D-glucose pentaacetate. By comparing the spectroscopic data of natural and synthesized compounds of isomers, the structure of pennelliiside D was confirmed to be 3,4-O-diisobutyryl-2-O-((S)-2-methylbutyryl)-D-glucose. Pennelliiside D and its constituent fatty acid moiety, (S)-2-methylbutanoic acid, did not show root growth-inhibitory activity. Additionally, in this study, chemical synthesis pathways toward pennelliisides A and B were adapted to give 1,6-O-dibenzylpennelliisides A and B.
Collapse
|
22
|
Leong BJ, Hurney S, Fiesel P, Anthony TM, Moghe G, Jones AD, Last RL. Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla). PLANT DIRECT 2022; 6:e415. [PMID: 35774622 PMCID: PMC9219006 DOI: 10.1002/pld3.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/26/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes, and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plant Solanum quitoense (lulo or naranjilla). We characterized three additional S. quitoense trichome expressed enzymes and found that virus-induced gene silencing of each caused changes in acylinositol accumulation. pH was shown to influence the stability and rearrangement of the product of ASAT1H and could potentially play a role in acylinositol biosynthesis. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulate in planta. This suggests that additional enzymes are required in acylinositol biosynthesis. These characterized S. quitoense enzymes, nonetheless, provide opportunities to test the biological impact and properties of these triacylinositols in vitro.
Collapse
Affiliation(s)
- Bryan J. Leong
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Steven Hurney
- Department of ChemistryMichigan State UniversityEast LansingMichiganUSA
- Present address:
Michigan Department of Health and Human ServicesLansingMichiganUSA
| | - Paul Fiesel
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Thilani M. Anthony
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Gaurav Moghe
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
Plant Biology Section, School of Integrative Plant SciencesCornell UniversityIthacaNew YorkUSA
| | - Arthur Daniel Jones
- Department of ChemistryMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Robert L. Last
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
23
|
Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H, Nakano M, Dusia A, Meyers BC, Frank MH. The evolutionary history of small RNAs in Solanaceae. PLANT PHYSIOLOGY 2022; 189:644-665. [PMID: 35642548 PMCID: PMC9157080 DOI: 10.1093/plphys/kiac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
Collapse
Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Shuyao Kong
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Suresh Pokhrel
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Sai Guna Ranjan Gurazada
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
- Corteva Agriscience, Wilmington, Delaware 19805, USA
| | - Pallavi Gupta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Hamid Razifard
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ayush Dusia
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| |
Collapse
|
24
|
Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
Collapse
Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| |
Collapse
|
25
|
The Genetic Complexity of Type-IV Trichome Development Reveals the Steps towards an Insect-Resistant Tomato. PLANTS 2022; 11:plants11101309. [PMID: 35631734 PMCID: PMC9148003 DOI: 10.3390/plants11101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022]
Abstract
The leaves of the wild tomato Solanum galapagense harbor type-IV glandular trichomes (GT) that produce high levels of acylsugars (AS), conferring insect resistance. Conversely, domesticated tomatoes (S. lycopersicum) lack type-IV trichomes on the leaves of mature plants, preventing high AS production, thus rendering the plants more vulnerable to insect predation. We hypothesized that cultivated tomatoes engineered to harbor type-IV trichomes on the leaves of adult plants could be insect-resistant. We introgressed the genetic determinants controlling type-IV trichome development from S. galapagense into cv. Micro-Tom (MT) and created a line named “Galapagos-enhanced trichomes” (MT-Get). Mapping-by-sequencing revealed that five chromosomal regions of S. galapagense were present in MT-Get. Further genetic mapping showed that S. galapagense alleles in chromosomes 1, 2, and 3 were sufficient for the presence of type-IV trichomes on adult organs but at lower densities. Metabolic and gene expression analyses demonstrated that type-IV trichome density was not accompanied by the AS production and exudation in MT-Get. Although the plants produce a significant amount of acylsugars, those are still not enough to make them resistant to whiteflies. We demonstrate that type-IV glandular trichome development is insufficient for high AS accumulation. The results from our study provided additional insights into the steps necessary for breeding an insect-resistant tomato.
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior. World J Microbiol Biotechnol 2022; 38:49. [DOI: 10.1007/s11274-022-03238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
|
28
|
Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
Collapse
Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
| |
Collapse
|
29
|
Kruse LH, Bennett AA, Mahood EH, Lazarus E, Park SJ, Schroeder F, Moghe GD. Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics. HORTICULTURE RESEARCH 2022; 9:uhab079. [PMID: 35039851 PMCID: PMC8825387 DOI: 10.1093/hr/uhab079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/24/2021] [Accepted: 11/12/2021] [Indexed: 05/13/2023]
Abstract
Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus - the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
Collapse
Affiliation(s)
- Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Institute of Analytical Chemistry, Universität für Bodenkultur Wien, Vienna, 1090, Austria
| | - Elizabeth H Mahood
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Elena Lazarus
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Present Address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Se Jin Park
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Frank Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
30
|
Lou YR, Anthony TM, Fiesel PD, Arking RE, Christensen EM, Jones AD, Last RL. It happened again: Convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato. SCIENCE ADVANCES 2021; 7:eabj8726. [PMID: 34757799 PMCID: PMC8580325 DOI: 10.1126/sciadv.abj8726] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/20/2021] [Indexed: 05/09/2023]
Abstract
Plants synthesize myriad phylogenetically restricted specialized (aka “secondary”) metabolites with diverse structures. Metabolism of acylated sugar esters in epidermal glandular secreting trichomes across the Solanaceae (nightshade) family is ideal for investigating the mechanisms of evolutionary metabolic diversification. We developed methods to structurally analyze acylhexose mixtures by 2D NMR, which led to the insight that the Old World species black nightshade (Solanum nigrum) accumulates acylglucoses and acylinositols in the same tissue. Detailed in vitro biochemistry, cross-validated by in vivo virus-induced gene silencing, revealed two unique features of the four-step acylglucose biosynthetic pathway: A trichome-expressed, neofunctionalized invertase-like enzyme, SnASFF1, converts BAHD-produced acylsucroses to acylglucoses, which, in turn, are substrates for the acylglucose acyltransferase, SnAGAT1. This biosynthetic pathway evolved independently from that recently described in the wild tomato Solanum pennellii, reinforcing that acylsugar biosynthesis is evolutionarily dynamic with independent examples of primary metabolic enzyme cooption and additional variation in BAHD acyltransferases.
Collapse
Affiliation(s)
- Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Thilani M. Anthony
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | | | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, 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
| |
Collapse
|
31
|
Blanco-Sánchez L, Planelló R, Llorente L, Díaz-Pendón JA, Ferrero V, Fernández-Muñoz R, Herrero Ó, de la Peña E. Characterization of the detrimental effects of type IV glandular trichomes on the aphid Macrosiphum euphorbiae in tomato. PEST MANAGEMENT SCIENCE 2021; 77:4117-4127. [PMID: 33914389 DOI: 10.1002/ps.6437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/04/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Glandular trichomes are essential in plants' defence against pests however, the mechanisms of action are not completely understood. While there is considerable evidence of feeding and movement impairment by trichomes, the effect on other traits is less clear. We combined laboratory and greenhouse experiments with molecular analysis to understand how glandular trichomes affect the behavior, population growth, and the expression of biomarkers involved in detoxification, primary metabolism, and developmental pathways of the aphid Macrosiphum euphorbiae. We used two isogenic tomato lines that differ in the presence of type IV glandular trichomes and production of acylsucroses; i.e.,Solanum lycopersicum cv. 'Moneymaker' and an introgressed line from Solanum pimpinellifolium (with trichomes type IV). RESULTS Type IV glandular trichomes affected host selection and aphid proliferation with aphids avoiding, and showing impaired multiplication on the genotype with trichomes. The exposure to type IV glandular trichomes resulted in the overexpression of detoxication markers (i.e., Hsp70, Hsp17, Hsp10); the repression of the energetic metabolism (GAPDH), and the activation of the ecdysone pathway; all these, underlying the key adaptations and metabolic trade-offs in aphids exposed to glandular trichomes. CONCLUSION Our results demonstrate the detrimental effect of glandular trichomes (type IV) on the aphid and put forward their mode of action. Given the prevalence of glandular trichomes in wild and cultivated Solanaceae; and of the investigated molecular biomarkers in insects in general, our results provide relevant mechanisms to understand the effect of trichomes not only on herbivorous insects but also on other trophic levels.
Collapse
Affiliation(s)
- Lidia Blanco-Sánchez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", Málaga, Spain
| | - Rosario Planelló
- Biology and Environmental Toxicology Group, Faculty of Sciences, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Lola Llorente
- Biology and Environmental Toxicology Group, Faculty of Sciences, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Juan A Díaz-Pendón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", Málaga, Spain
| | - Victoria Ferrero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", Málaga, Spain
- Centro de Ecología Funcional, Departamento de Ciencias de la Vida, Universidade de Coimbra, Coimbra, Portugal
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", Málaga, Spain
| | - Óscar Herrero
- Biology and Environmental Toxicology Group, Faculty of Sciences, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Eduardo de la Peña
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", Málaga, Spain
- Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
32
|
Kortbeek RWJ, Galland MD, Muras A, van der Kloet FM, André B, Heilijgers M, van Hijum SAFT, Haring MA, Schuurink RC, Bleeker PM. Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach. BMC PLANT BIOLOGY 2021; 21:315. [PMID: 34215189 PMCID: PMC8252294 DOI: 10.1186/s12870-021-03070-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/20/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant-produced specialised metabolites are a powerful part of a plant's first line of defence against herbivorous insects, bacteria and fungi. Wild ancestors of present-day cultivated tomato produce a plethora of acylsugars in their type-I/IV trichomes and volatiles in their type-VI trichomes that have a potential role in plant resistance against insects. However, metabolic profiles are often complex mixtures making identification of the functionally interesting metabolites challenging. Here, we aimed to identify specialised metabolites from a wide range of wild tomato genotypes that could explain resistance to vector insects whitefly (Bemisia tabaci) and Western flower thrips (Frankliniella occidentalis). We evaluated plant resistance, determined trichome density and obtained metabolite profiles of the glandular trichomes by LC-MS (acylsugars) and GC-MS (volatiles). Using a customised Random Forest learning algorithm, we determined the contribution of specific specialised metabolites to the resistance phenotypes observed. RESULTS The selected wild tomato accessions showed different levels of resistance to both whiteflies and thrips. Accessions resistant to one insect can be susceptible to another. Glandular trichome density is not necessarily a good predictor for plant resistance although the density of type-I/IV trichomes, related to the production of acylsugars, appears to correlate with whitefly resistance. For type VI-trichomes, however, it seems resistance is determined by the specific content of the glands. There is a strong qualitative and quantitative variation in the metabolite profiles between different accessions, even when they are from the same species. Out of 76 acylsugars found, the random forest algorithm linked two acylsugars (S3:15 and S3:21) to whitefly resistance, but none to thrips resistance. Out of 86 volatiles detected, the sesquiterpene α-humulene was linked to whitefly susceptible accessions instead. The algorithm did not link any specific metabolite to resistance against thrips, but monoterpenes α-phellandrene, α-terpinene and β-phellandrene/D-limonene were significantly associated with susceptible tomato accessions. CONCLUSIONS Whiteflies and thrips are distinctly targeted by certain specialised metabolites found in wild tomatoes. The machine learning approach presented helped to identify features with efficacy toward the insect species studied. These acylsugar metabolites can be targets for breeding efforts towards the selection of insect-resistant cultivars.
Collapse
Affiliation(s)
- Ruy W J Kortbeek
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Marc D Galland
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Aleksandra Muras
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Frans M van der Kloet
- Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Bart André
- Enza Zaden Research & Development B.V, Haling 1E, 1602 DB, Enkhuizen, The Netherlands
| | - Maurice Heilijgers
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Sacha A F T van Hijum
- Radboud University Medical Center, Bacterial Genomics Group, Geert Grooteplein Zuid 26-28, 6525 GA, Nijmegen, The Netherlands
| | - Michel A Haring
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Robert C Schuurink
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Petra M Bleeker
- Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands.
| |
Collapse
|
33
|
Feng Z, Bartholomew ES, Liu Z, Cui Y, Dong Y, Li S, Wu H, Ren H, Liu X. Glandular trichomes: new focus on horticultural crops. HORTICULTURE RESEARCH 2021; 8:158. [PMID: 34193839 PMCID: PMC8245418 DOI: 10.1038/s41438-021-00592-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/07/2021] [Accepted: 05/10/2021] [Indexed: 05/31/2023]
Abstract
Plant glandular trichomes (GTs) are epidermal outgrowths with the capacity to biosynthesize and secrete specialized metabolites, that are of great scientific and practical significance. Our understanding of the developmental process of GTs is limited, and no single plant species serves as a unique model. Here, we review the genetic mechanisms of GT initiation and development and provide a summary of the biosynthetic pathways of GT-specialized metabolites in nonmodel plant species, especially horticultural crops. We discuss the morphology and classification of GT types. Moreover, we highlight technological advancements in methods employed for investigating GTs. Understanding the molecular basis of GT development and specialized metabolites not only offers useful avenues for research in plant breeding that will lead to the improved production of desirable metabolites, but also provides insights for plant epidermal development research.
Collapse
Affiliation(s)
- Zhongxuan Feng
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Ezra S Bartholomew
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Ziyu Liu
- Library of China Agricultural University, China Agricultural University, 100193, Beijing, P. R. China
| | - Yuanyuan Cui
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Yuming Dong
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Sen Li
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Haoying Wu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Huazhong Ren
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China.
| | - Xingwang Liu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
| |
Collapse
|
34
|
Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
Collapse
Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
| |
Collapse
|
35
|
Katz E, Li JJ, Jaegle B, Ashkenazy H, Abrahams SR, Bagaza C, Holden S, Pires CJ, Angelovici R, Kliebenstein DJ. Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe. eLife 2021; 10:67784. [PMID: 33949309 PMCID: PMC8205490 DOI: 10.7554/elife.67784] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/02/2021] [Indexed: 12/03/2022] Open
Abstract
Plants produce diverse metabolites to cope with the challenges presented by complex and ever-changing environments. These challenges drive the diversification of specialized metabolites within and between plant species. However, we are just beginning to understand how frequently new alleles arise controlling specialized metabolite diversity and how the geographic distribution of these alleles may be structured by ecological and demographic pressures. Here, we measure the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions. We show that a combination of geography, environmental parameters, demography and different genetic processes all combine to influence the specific chemotypes and their distribution. This showed that causal loci in specialized metabolism contain frequent independently generated alleles with patterns suggesting potential within-species convergence. This provides a new perspective about the complexity of the selective forces and mechanisms that shape the generation and distribution of allelic variation that may influence local adaptation. Since plants cannot move, they have evolved chemical defenses to help them respond to changes in their surroundings. For example, where animals run from predators, plants may produce toxins to put predators off. This approach is why plants are such a rich source of drugs, poisons, dyes and other useful substances. The chemicals plants produce are known as specialized metabolites, and they can change a lot between, and even within, plant species. The variety of specialized metabolites is a result of genetic changes and evolution over millions of years. Evolution is a slow process, yet plants are able to rapidly develop new specialized metabolites to protect them from new threats. Even different populations of the same species produce many distinct metabolites that help them survive in their surroundings. However, the factors that lead plants to produce new metabolites are not well understood, and it is not known how this affects genetic variation. To gain a better understanding of this process, Katz et al. studied 797 European variants of a common weed species called Arabidopsis thaliana, which is widely studied. The investigation found that many factors affect the range of specialized metabolites in each variant. These included local geography and environment, as well as genetics and population history (demography). Katz et al. revealed a pattern of relationships between the variants that could mirror their evolutionary history as the species spread and adapted to new locations. These results highlight the complex network of factors that affect plant evolution. Rapid diversification is key to plant survival in new and changing environments and has resulted in a wide range of specialized metabolites. As such they are of interest both for studying plant evolution and for understanding their ecology. Expanding similar work to more populations and other species will broaden the scope of our ability to understand how plants adapt to their surroundings.
Collapse
Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Jia-Jie Li
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Benjamin Jaegle
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shawn R Abrahams
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Clement Bagaza
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Samuel Holden
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Chris J Pires
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Ruthie Angelovici
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, United States.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
36
|
Balestrini R, Brunetti C, Cammareri M, Caretto S, Cavallaro V, Cominelli E, De Palma M, Docimo T, Giovinazzo G, Grandillo S, Locatelli F, Lumini E, Paolo D, Patanè C, Sparvoli F, Tucci M, Zampieri E. Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. Int J Mol Sci 2021; 22:ijms22062887. [PMID: 33809189 PMCID: PMC7999214 DOI: 10.3390/ijms22062887] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/21/2022] Open
Abstract
Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.
Collapse
Affiliation(s)
- Raffaella Balestrini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
- Correspondence: ; Tel.: +39-01165-02927
| | - Cecilia Brunetti
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Maria Cammareri
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Sofia Caretto
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Valeria Cavallaro
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Eleonora Cominelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Monica De Palma
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Teresa Docimo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Giovanna Giovinazzo
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Silvana Grandillo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Franca Locatelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Erica Lumini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Dario Paolo
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Cristina Patanè
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Francesca Sparvoli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Marina Tucci
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Elisa Zampieri
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| |
Collapse
|
37
|
The biosynthetic pathway of potato solanidanes diverged from that of spirosolanes due to evolution of a dioxygenase. Nat Commun 2021; 12:1300. [PMID: 33637735 PMCID: PMC7910490 DOI: 10.1038/s41467-021-21546-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/22/2021] [Indexed: 12/16/2022] Open
Abstract
Potato (Solanum tuberosum), a worldwide major food crop, produces the toxic, bitter tasting solanidane glycoalkaloids α-solanine and α-chaconine. Controlling levels of glycoalkaloids is an important focus on potato breeding. Tomato (Solanum lycopersicum) contains a bitter spirosolane glycoalkaloid, α-tomatine. These glycoalkaloids are biosynthesized from cholesterol via a partly common pathway, although the mechanisms giving rise to the structural differences between solanidane and spirosolane remained elusive. Here we identify a 2-oxoglutarate dependent dioxygenase, designated as DPS (Dioxygenase for Potato Solanidane synthesis), that is a key enzyme for solanidane glycoalkaloid biosynthesis in potato. DPS catalyzes the ring-rearrangement from spirosolane to solanidane via C-16 hydroxylation. Evolutionary divergence of spirosolane-metabolizing dioxygenases contributes to the emergence of toxic solanidane glycoalkaloids in potato and the chemical diversity in Solanaceae. One goal of potato breeding is to reduce the accumulation of toxic solanidane glycoalkaloids. Here the authors show that potato DPS, a 2-oxoglutarate dependent dioxygenase, catalyzes ring rearrangement of a biosynthetic precursor to differentiate solanidanes from spirosolanes that are found in other solanaceous plants.
Collapse
|
38
|
Mata-Nicolás E, Montero-Pau J, Gimeno-Paez E, García-Pérez A, Ziarsolo P, Blanca J, van der Knaap E, Díez MJ, Cañizares J. Discovery of a Major QTL Controlling Trichome IV Density in Tomato Using K-Seq Genotyping. Genes (Basel) 2021; 12:243. [PMID: 33567670 PMCID: PMC7915031 DOI: 10.3390/genes12020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 11/23/2022] Open
Abstract
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some natural defense mechanisms, such as those afforded by trichomes, present in certain Solanum species. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. This accession was crossed with a S. lycopersicum var. cerasiforme and a S. lycopersicum var. lycopersicum accessions, and the two resulting F2 populations have been characterized and genotyped using a new genotyping methodology, K-seq. We have been able to build an ultra-dense genetic map with 147,326 SNP markers with an average distance between markers of 0.2 cm that has allowed us to perform a detailed mapping. We have used two different families and two different approaches, QTL mapping and QTL-seq, to identify several QTLs implicated in the control of trichome type IV developed in this accession on the chromosomes 5, 6, 9 and 11. The QTL located on chromosome 9 is a major QTL that has not been previously reported in S. pimpinellifolium. This QTL could be easily introgressed in cultivated tomato due to the close genetic relationship between both species.
Collapse
Affiliation(s)
- Estefanía Mata-Nicolás
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - Javier Montero-Pau
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, 46980 Paterna, Spain;
| | - Esther Gimeno-Paez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - Ana García-Pérez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - Peio Ziarsolo
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - José Blanca
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - María José Díez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| | - Joaquín Cañizares
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, 46022 Valencia, Spain; (E.M.-N.); (E.G.-P.); (A.G.-P.); (P.Z.); (J.B.); (M.J.D.)
| |
Collapse
|
39
|
Oshikiri H, Watanabe B, Yamamoto H, Yazaki K, Takanashi K. Two BAHD Acyltransferases Catalyze the Last Step in the Shikonin/Alkannin Biosynthetic Pathway. PLANT PHYSIOLOGY 2020; 184:753-761. [PMID: 32727911 PMCID: PMC7536692 DOI: 10.1104/pp.20.00207] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/24/2020] [Indexed: 05/28/2023]
Abstract
Several Boraginaceae plants produce biologically active red naphthoquinone pigments, derivatives of the enantiomers shikonin and alkannin, which vary in acyl groups on their side chains. Compositions of shikonin/alkannin derivatives vary in plant species, but the mechanisms generating the diversity of shikonin/alkannin derivatives are largely unknown. This study describes the identification and characterization of two BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1), from Lithospermum erythrorhizon, a medicinal plant in the family Boraginaceae that primarily produces the shikonin/alkannin derivatives acetylshikonin and β-hydroxyisovalerylshikonin. Enzyme assays using Escherichia coli showed that the acylation activity of LeSAT1 was specific to shikonin, whereas the acylation activity of LeAAT1 was specific to alkannin. Both enzymes recognized acetyl-CoA, isobutyryl-CoA, and isovaleryl-CoA as acyl donors to produce their corresponding shikonin/alkannin derivatives, with both enzymes showing the highest activity for acetyl-CoA. These findings were consistent with the composition of shikonin/alkannin derivatives in intact L erythrorhizon plants and cell cultures. Genes encoding both enzymes were preferentially expressed in the roots and cell cultures in the dark in pigment production medium M9, conditions associated with shikonin/alkannin production. These results indicated that LeSAT1 and LeAAT1 are enantiomer-specific acyltransferases that generate various shikonin/alkannin derivatives.
Collapse
Affiliation(s)
- Haruka Oshikiri
- Department of Biology, Faculty of Science, Shinshu University, Nagano 390-8621, Japan
| | - Bunta Watanabe
- Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Hirobumi Yamamoto
- Department of Applied Biology, Faculty of Life Sciences, Toyo University, Gunma 374-0193, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 611-0011, Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Nagano 390-8621, Japan
| |
Collapse
|
40
|
Moore BM, Wang P, Fan P, Lee A, Leong B, Lou YR, Schenck CA, Sugimoto K, Last R, Lehti-Shiu MD, Barry CS, Shiu SH. Within- and cross-species predictions of plant specialized metabolism genes using transfer learning. IN SILICO PLANTS 2020; 2:diaa005. [PMID: 33344884 PMCID: PMC7731531 DOI: 10.1093/insilicoplants/diaa005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/21/2020] [Indexed: 06/12/2023]
Abstract
Plant specialized metabolites mediate interactions between plants and the environment and have significant agronomical/pharmaceutical value. Most genes involved in specialized metabolism (SM) are unknown because of the large number of metabolites and the challenge in differentiating SM genes from general metabolism (GM) genes. Plant models like Arabidopsis thaliana have extensive, experimentally derived annotations, whereas many non-model species do not. Here we employed a machine learning strategy, transfer learning, where knowledge from A. thaliana is transferred to predict gene functions in cultivated tomato with fewer experimentally annotated genes. The first tomato SM/GM prediction model using only tomato data performs well (F-measure = 0.74, compared with 0.5 for random and 1.0 for perfect predictions), but from manually curating 88 SM/GM genes, we found many mis-predicted entries were likely mis-annotated. When the SM/GM prediction models built with A. thaliana data were used to filter out genes where the A. thaliana-based model predictions disagreed with tomato annotations, the new tomato model trained with filtered data improved significantly (F-measure = 0.92). Our study demonstrates that SM/GM genes can be better predicted by leveraging cross-species information. Additionally, our findings provide an example for transfer learning in genomics where knowledge can be transferred from an information-rich species to an information-poor one.
Collapse
Affiliation(s)
- Bethany M Moore
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Aaron Lee
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Bryan Leong
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Koichi Sugimoto
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Science Research Center, Yamaguchi University, Yamaguchi, Japan
| | - Robert Last
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI
| |
Collapse
|
41
|
Chang AX, Chen B, Yang AG, Hu RS, Feng QF, Chen M, Yang XN, Luo CG, Li YY, Wang YY. The trichome-specific acetolactate synthase NtALS1 gene, is involved in acylsugar biosynthesis in tobacco (Nicotiana tabacum L.). PLANTA 2020; 252:13. [PMID: 32621079 DOI: 10.1007/s00425-020-03418-x] [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: 04/08/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
MAIN CONCLUSION NtALS1 is specifically expressed in glandular trichomes, and can improve the content of acylsugars in tobacco. ABTRACT The glandular trichomes of many species in the Solanaceae family play an important role in plant defense. These epidermal outgrowths exhibit specialized secondary metabolism, including the production of structurally diverse acylsugars that function in defense against insects and have substantial developmental potential for commercial uses. However, our current understanding of genes involved in acyl chain biosynthesis of acylsugars remains poor in tobacco. In this study, we identified three acetolactate synthase (ALS) genes in tobacco through homology-based gene prediction using Arabidopsis ALS. Quantitative real-time PCR (qRT-PCR) and tissue distribution analyses suggested that NtALS1 was highly expressed in the tips of glandular trichomes. Subcellular localization analysis showed that the NtALS1 localized to the chloroplast. Moreover, in the wild-type K326 variety background, we generated two ntals1 loss-of-function mutants using the CRISPR-Cas9 system. Acylsugars contents in the two ntals1 mutants were significantly lower than those in the wild type. Through phylogenetic tree analysis, we also identified NtALS1 orthologs that may be involved in acylsugar biosynthesis in other Solanaceae species. Taken together, these findings indicate a functional role for NtALS1 in acylsugar biosynthesis in tobacco.
Collapse
Affiliation(s)
- Ai-Xia Chang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Biao Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ai-Guo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ri-Sheng Hu
- Hunan Tobacco Research Institute, Changsha, China
| | - Quan-Fu Feng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ming Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiao-Ning Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Cheng-Gang Luo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yang-Yang Li
- Hunan Tobacco Research Institute, Changsha, China.
| | - Yuan-Ying Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
| |
Collapse
|
42
|
Fan P, Wang P, Lou YR, Leong BJ, Moore BM, Schenck CA, Combs R, Cao P, Brandizzi F, Shiu SH, Last RL. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife 2020; 9:e56717. [PMID: 32613943 PMCID: PMC7386920 DOI: 10.7554/elife.56717] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.
Collapse
Affiliation(s)
- Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Peipei Wang
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Bryan J Leong
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Bethany M Moore
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- University of WisconsinMadisonUnited States
| | - Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Rachel Combs
- Division of Biological Sciences, University of MissouriColumbusUnited States
| | - Pengfei Cao
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Federica Brandizzi
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- Department of Computational Mathematics, Science, and Engineering, Michigan State UniversityEast LansingUnited States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| |
Collapse
|
43
|
Leong BJ, Hurney SM, Fiesel PD, Moghe GD, Jones AD, Last RL. Specialized Metabolism in a Nonmodel Nightshade: Trichome Acylinositol Biosynthesis. PLANT PHYSIOLOGY 2020; 183:915-924. [PMID: 32354879 PMCID: PMC7333698 DOI: 10.1104/pp.20.00276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 05/13/2023]
Abstract
Plants make many biologically active, specialized metabolites, which vary in structure, biosynthesis, and the processes they influence. An increasing number of these compounds are documented to protect plants from insects, pathogens, or herbivores or to mediate interactions with beneficial organisms, including pollinators and nitrogen-fixing microbes. Acylsugars, one class of protective compounds, are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit crop naranjilla (lulo; Solanum quitoense) produces acylsugars containing a myoinositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in the acylsucrose biosynthetic pathway of tomato (Solanum lycopersicum). Our analysis reveals parallels between S. lycopersicum acylsucrose and S. quitoense acylinositol biosynthesis, suggesting a common evolutionary origin.
Collapse
Affiliation(s)
- Bryan J Leong
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Steven M Hurney
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Paul D Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - A Daniel Jones
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
44
|
Fernie AR, Wen W. Editorial overview: Evolution of metabolic diversity. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:A1-A4. [PMID: 32546303 DOI: 10.1016/j.pbi.2020.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
45
|
Sonawane PD, Jozwiak A, Panda S, Aharoni A. 'Hijacking' core metabolism: a new panache for the evolution of steroidal glycoalkaloids structural diversity. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:118-128. [PMID: 32446857 DOI: 10.1016/j.pbi.2020.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/07/2020] [Accepted: 03/15/2020] [Indexed: 06/11/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are defense specialized metabolites produced by thousands of Solanum species. These metabolites are remarkable in structural diversity formed following modifications in their core scaffold. In recent years, it became clear that a large portion of this chemical repertoire was acquired through various molecular mechanisms involving 'hijacking' of core metabolism enzymes. This was typically accompanied by gene duplication and divergence and further neofunctionalization as well as modified subcellular localization and evolution of new substrate preferences. In this review, we highlight recent findings in the SGAs biosynthetic pathway and elaborate on similar occurrences in other chemical classes that enabled evolution of specialized metabolic pathways and its underlying structural diversity.
Collapse
Affiliation(s)
- Prashant D Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jozwiak
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
46
|
Chalvin C, Drevensek S, Dron M, Bendahmane A, Boualem A. Genetic Control of Glandular Trichome Development. TRENDS IN PLANT SCIENCE 2020; 25:477-487. [PMID: 31983619 DOI: 10.1016/j.tplants.2019.12.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 05/28/2023]
Abstract
Plant glandular trichomes are epidermal secretory structures producing various specialized metabolites. These metabolites are involved in plant adaptation to its environment and many of them have remarkable properties exploited by fragrance, flavor, and pharmaceutical industries. The identification of genes controlling glandular trichome development is of high interest to understand how plants produce specialized metabolites. Our knowledge about this developmental process is still limited, but genes controlling glandular trichome initiation and morphogenesis have recently been identified. In particular, R2R3-MYB and HD-ZIP IV transcription factors appear to play essential roles in glandular trichome initiation in Artemisia annua and tomato. In this review, we focus on the results obtained in these two species and we propose genetic regulation models integrating these data.
Collapse
Affiliation(s)
- Camille Chalvin
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Stéphanie Drevensek
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Michel Dron
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Adnane Boualem
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| |
Collapse
|
47
|
Schuurink R, Tissier A. Glandular trichomes: micro-organs with model status? THE NEW PHYTOLOGIST 2020; 225:2251-2266. [PMID: 31651036 DOI: 10.1111/nph.16283] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/01/2019] [Indexed: 05/19/2023]
Abstract
Glandular trichomes are epidermal outgrowths that are the site of biosynthesis and storage of large quantities of specialized metabolites. Besides their role in the protection of plants against biotic and abiotic stresses, they have attracted interest owing to the importance of the compounds they produce for human use; for example, as pharmaceuticals, flavor and fragrance ingredients, or pesticides. Here, we review what novel concepts investigations on glandular trichomes have brought to the field of specialized metabolism, particularly with respect to chemical and enzymatic diversity. Furthermore, the next challenges in the field are understanding the metabolic network underlying the high productivity of glandular trichomes and the transport and storage of metabolites. Another emerging area is the development of glandular trichomes. Studies in some model species, essentially tomato, tobacco, and Artemisia, are now providing the first molecular clues, but many open questions remain: How is the distribution and density of different trichome types on the leaf surface controlled? When is the decision for an epidermal cell to differentiate into one type of trichome or another taken? Recent advances in gene editing make it now possible to address these questions and promise exciting discoveries in the near future.
Collapse
Affiliation(s)
- Robert Schuurink
- Swammerdam Institute for Life Sciences, Green Life Science Research Cluster, University of Amsterdam, Postbus 1210, 1000 BE, Amsterdam, the Netherlands
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| |
Collapse
|
48
|
Schenck CA, Last RL. Location, location! cellular relocalization primes specialized metabolic diversification. FEBS J 2019; 287:1359-1368. [PMID: 31623016 DOI: 10.1111/febs.15097] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/12/2019] [Accepted: 10/14/2019] [Indexed: 12/31/2022]
Abstract
Specialized metabolites are structurally diverse and cell- or tissue-specific molecules produced in restricted plant lineages. In contrast, primary metabolic pathways are highly conserved in plants and produce metabolites essential for all of life, such as amino acids and nucleotides. Substrate promiscuity - the capacity to accept non-native substrates - is a common characteristic of enzymes, and its impact is especially apparent in generating specialized metabolite variation. However, promiscuity only leads to metabolic diversity when alternative substrates are available; thus, enzyme cellular and subcellular localization directly influence chemical phenotypes. We review a variety of mechanisms that modulate substrate availability for promiscuous plant enzymes. We focus on examples where evolution led to modification of the 'cellular context' through changes in cell-type expression, subcellular relocalization, pathway sequestration, and cellular mixing via tissue damage. These varied mechanisms contributed to the emergence of structurally diverse plant specialized metabolites and inform future metabolic engineering approaches.
Collapse
Affiliation(s)
- Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
49
|
Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
Collapse
Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
50
|
Ainsworth EA, Carmo-Silva E. Editorial overview: Harnessing genetic variation in metabolic traits to understand trait evolution and improve the sustainability of crop production. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:A1-A3. [PMID: 31395142 DOI: 10.1016/j.pbi.2019.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, 1201 W. Gregory Drive, Urbana, IL 61801, USA.
| | | |
Collapse
|