1
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Ziaei N, Talebi M, Sayed Tabatabaei BE, Sabzalian MR, Soleimani M. Intra-canopy LED lighting outperformed top LED lighting in improving tomato yield and expression of the genes responsible for lycopene, phytoene and vitamin C synthesis. Sci Rep 2024; 14:19043. [PMID: 39152138 PMCID: PMC11329737 DOI: 10.1038/s41598-024-69210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 08/01/2024] [Indexed: 08/19/2024] Open
Abstract
Greenhouses located at high latitudes and in cloudy areas often experience a low quality and quantity of light, especially during autumn and winter. This low daily light integral (DLI) reduces production rate, quality, and nutritional value of many crops. This study was conducted on Sakhiya RZ F1 tomato plants to evaluate the impact of LED lights on the growth and nutritional value of tomatoes in a greenhouse with low daily light due to cloudy weather. The treatments included LED growth lights in three modes: top lighting, intra-canopy lighting, and combined top and intra-canopy lighting. The results showed that although the combined top and intra-canopy lighting reached the maximum increase in tomato yield, exposure to intra-canopy LED lighting alone outperformed in tomato fruit yield increase (28.46%) than exposure to top LED lighting alone (12.12%) when compared to no supplemental lighting during the entire production year. Intra-canopy exposure demonstrated the highest increase in tomato lycopene (31.3%), while top and intra-canopy lighting exhibited the highest increase in vitamin C content (123.4%) compared to the control. The LED light treatment also had a very positive effect on the expression of genes responsible for metabolic cycles, including Psy1, LCY-β, and VTC2 genes, which had collinearity with the increase in tomato fruit production.
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Affiliation(s)
- Negar Ziaei
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Majid Talebi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | | | - Mohammad R Sabzalian
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Masoud Soleimani
- Department of Bio-Light, Golnoor Scientific Corporation, Golnoor Sadra, Isfahan, 81636-54714, Iran
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2
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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3
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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.
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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.
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4
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Alseekh S, Fernie AR. Expanding our coverage: Strategies to detect a greater range of metabolites. CURRENT OPINION IN PLANT BIOLOGY 2023; 73:102335. [PMID: 36689903 DOI: 10.1016/j.pbi.2022.102335] [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: 10/18/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 06/10/2023]
Abstract
Whilst the study of metabolites can arguably be traced back several hundred years it began in earnest in the 20th century with studies based on single metabolites or simple metabolic pathways. The advent of metabolomics and in particular the adoption of high-resolution mass spectrometry now means we can faithfully annotate and quantify in excess of 1000 plant metabolites. Whilst this is an impressive leap it falls well short of the estimated number of metabolites in the plant kingdom. This, whilst considerable and important insights have been achieved using commonly utilized approaches, there is a need to improve the coverage of the metabolome. Here, we review three largely complementary strategies (i) methods based on using chemical libraries (ii) methods based on molecular networking and (iii) approaches that link metabolomics and genetic variance. It is our contention that using all three approaches in tandem represents the best approach to tackle this challenge.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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5
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Zhang F, Li X, Wu Q, Lu P, Kang Q, Zhao M, Wang A, Dong Q, Sun M, Yang Z, Gao Z. Selenium Application Enhances the Accumulation of Flavones and Anthocyanins in Bread Wheat ( Triticum aestivum L.) Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13431-13444. [PMID: 36198089 DOI: 10.1021/acs.jafc.2c04868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Selenium (Se) biofortification in wheat reduces the risk of Se deficiency in humans. Se biofortification increases the concentration of Se and anthocyanins in wheat grains. However, it is unknown whether Se biofortification can enhance flavonoids other than anthocyanins and the mechanism underlying flavonoid accumulation in wheat grains. Here, foliar application of selenite solution in wheat was conducted 10 days after flowering. Metabolite profiling and transcriptome sequencing were performed in Se-treated grains. A significant increase in the total contents of Se, anthocyanins, and flavonoids was observed in Se-treated mature grains. Twenty-seven significantly increased flavonoids were identified in Se-treated immature grains. The significant accumulation of flavones (tricin, tricin derivatives, and chrysoeriol derivatives) was detected, and six anthocyanins, dihydroquercetin (the precursor for anthocyanin biosynthesis) and catechins were also increased. Integrated analysis of metabolites and transcriptome revealed that Se application enhanced the biosynthesis of flavones, dihydroquercetin, anthocyanins, and catechins by increasing the expression levels of seven key structural genes in flavonoid biosynthesis (two TaF3Hs, two TaDFRs, one TaF3'5'H, one TaOMT, and one TaANR). Our findings shed new light on the molecular mechanism underlying the enhancement in flavonoid accumulation by Se supplementation and pave the way for further enhancing the nutritional value of wheat grains.
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Affiliation(s)
- Fengjie Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Xueyin Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Qiangqiang Wu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Ping Lu
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Qingfang Kang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Mengyao Zhao
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Aiping Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Qi Dong
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Min Sun
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhenping Yang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhiqiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
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6
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Wang S, Qiang Q, Xiang L, Fernie AR, Yang J. Targeted approaches to improve tomato fruit taste. HORTICULTURE RESEARCH 2022; 10:uhac229. [PMID: 36643745 PMCID: PMC9832879 DOI: 10.1093/hr/uhac229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.
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Affiliation(s)
- Shouchuang Wang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | | | - Lijun Xiang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Alisdair R Fernie
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | - Jun Yang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
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7
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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.
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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
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8
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Dzakovich MP, Francis DM, Cooperstone JL. Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red-fruited clade. THE PLANT GENOME 2022; 15:e20192. [PMID: 35184399 DOI: 10.1002/tpg2.20192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
The tomato (Solanum spp.) clade of Solanaceae features a unique assortment of cholesterol-derived steroidal alkaloids. However, little quantitative data exists reporting the profile and concentration of these alkaloids across diverse fruit germplasm. To address the lack of knowledge regarding the chemical diversity, concentration, and genetic architecture controlling tomato steroidal alkaloids, we quantitatively profiled and genotyped two tomato populations representing diversity in the red-fruited clade. We grew 107 genetically diverse fresh market, processing, landrace, and wild tomato in multiple environments. Nine steroidal alkaloid groups were quantified using ultra-high performance liquid chromatography tandem mass spectrometry. The diversity panel and a biparental population segregating for high alpha-tomatine were genotyped to identify and validate quantitative trait loci (QTL) associated with steroidal alkaloids. Landraces and wild material exhibited higher alkaloid concentrations and more chemical diversity. Average total content of steroidal alkaloids, often dominated by lycoperoside F/G/esculeoside A, ranged from 1.9 to 23.3 mg 100 g-1 fresh wt. across accessions. Landrace and wild cherry accessions distinctly clustered based on elevated concentrations of early or late-pathway steroidal alkaloids. Significant correlations were observed among alkaloids from the early and late parts of the biosynthetic pathway in a species-dependent manner. A QTL controlling multiple, early steroidal alkaloid pathway intermediates on chromosome 3 was identified by genome-wide association studies (GWAS) and validated in a backcross population. Overall, tomato steroidal alkaloids are diverse in the red-fruited clade and their biosynthesis is regulated in a coordinated manner.
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Affiliation(s)
- Michael P Dzakovich
- Dep. of Horticulture and Crop Science, The Ohio State Univ., 2001 Fyffe Court, Columbus, OH, 43210, USA
- USDA-ARS Children's Nutrition Research Center, Dep. of Pediatrics, Baylor College of Medicine, 1100 Bates Ave., Houston, TX, 77030, USA
| | - David M Francis
- Dep. of Horticulture and Crop Science, The Ohio State Univ./Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH, 44691, USA
| | - Jessica L Cooperstone
- Dep. of Horticulture and Crop Science, The Ohio State Univ., 2001 Fyffe Court, Columbus, OH, 43210, USA
- Dep. of Food Science and Technology, The Ohio State Univ., 2015 Fyffe Court., Columbus, OH, 43210, USA
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9
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Sonawane PD, Jozwiak A, Barbole R, Panda S, Abebie B, Kazachkova Y, Gharat SA, Ramot O, Unger T, Wizler G, Meir S, Rogachev I, Doron-Faigenboim A, Petreikov M, Schaffer A, Giri AP, Scherf T, Aharoni A. 2-oxoglutarate-dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum. THE NEW PHYTOLOGIST 2022; 234:1394-1410. [PMID: 35238413 DOI: 10.1111/nph.18064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Solanum steroidal glycoalkaloids (SGAs) are renowned defence metabolites exhibiting spectacular structural diversity. Genes and enzymes generating the SGA precursor pathway, SGA scaffold and glycosylated forms have been largely identified. Yet, the majority of downstream metabolic steps creating the vast repertoire of SGAs remain untapped. Here, we discovered that members of the 2-OXOGLUTARATE-DEPENDENT DIOXYGENASE (2-ODD) family play a prominent role in SGA metabolism, carrying out three distinct backbone-modifying oxidative steps in addition to the three formerly reported pathway reactions. The GLYCOALKALOID METABOLISM34 (GAME34) enzyme catalyses the conversion of core SGAs to habrochaitosides in wild tomato S. habrochaites. Cultivated tomato plants overexpressing GAME34 ectopically accumulate habrochaitosides. These habrochaitoside enriched plants extracts potently inhibit Puccinia spp. spore germination, a significant Solanaceae crops fungal pathogen. Another 2-ODD enzyme, GAME33, acts as a desaturase (via hydroxylation and E/F ring rearrangement) forming unique, yet unreported SGAs. Conversion of bitter α-tomatine to ripe fruit, nonbitter SGAs (e.g. esculeoside A) requires two hydroxylations; while the known GAME31 2-ODD enzyme catalyses hydroxytomatine formation, we find that GAME40 catalyses the penultimate step in the pathway and generates acetoxy-hydroxytomatine towards esculeosides accumulation. Our results highlight the significant contribution of 2-ODD enzymes to the remarkable structural diversity found in plant steroidal specialized metabolism.
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Affiliation(s)
- Prashant D Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Department of Natural Products, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - 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
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Gilat Research Center, Agricultural Research Organization (ARO), Rural delivery Negev, 85280, Israel
| | - Bekele Abebie
- Department of Plant Pathology and Weed Research, ARO-Volcani Center, Bet Dagan, 50250, Israel
| | - Yana Kazachkova
- 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
| | - Ofir Ramot
- Metabolic Insights Ltd, Ness Ziona, 7414001, Israel
| | - Tamar Unger
- Israel Structural Proteomics Centre, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Wizler
- 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
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Marina Petreikov
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Arthur Schaffer
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Ashok P Giri
- Department of Natural Products, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Tali Scherf
- NMR unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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10
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Ostreikova TO, Kalinkina OV, Bogomolov NG, Chernykh IV. Glycoalkaloids of Plants in the Family Solanaceae (Nightshade) as Potential Drugs. Pharm Chem J 2022; 56:948-957. [PMID: 36277854 PMCID: PMC9579588 DOI: 10.1007/s11094-022-02731-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/05/2022]
Abstract
Worldwide interest in medicinal plants and related drugs is growing because of the increased spectrum of new synthetic drugs. In this context, secondary plant metabolites are most significant. This review analyzes data on the structures and biosyntheses of metabolites such as glycoalkaloids; methods for their extraction from plants of the family Solanaceae, particularly potato S. tuberosum; their qualitative and quantitative analysis; biological activity; and toxicity. This information could be useful in the selection of methods for sample preparation and extraction of glycoalkaloids during the search for new plant sources with prospects of creating effective and safe pharmacological agents.
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Affiliation(s)
- T. O. Ostreikova
- grid.445664.10000 0004 0562 7304I. P. Pavlov Ryazan State Medical University, Ministry of Health of the Russian Federation, 8 Vysokovol’tnaya St, Ryazan, 390026 Russia
| | - O. V. Kalinkina
- grid.445664.10000 0004 0562 7304I. P. Pavlov Ryazan State Medical University, Ministry of Health of the Russian Federation, 8 Vysokovol’tnaya St, Ryazan, 390026 Russia
| | - N. G. Bogomolov
- grid.445664.10000 0004 0562 7304I. P. Pavlov Ryazan State Medical University, Ministry of Health of the Russian Federation, 8 Vysokovol’tnaya St, Ryazan, 390026 Russia
| | - I. V. Chernykh
- grid.445664.10000 0004 0562 7304I. P. Pavlov Ryazan State Medical University, Ministry of Health of the Russian Federation, 8 Vysokovol’tnaya St, Ryazan, 390026 Russia
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11
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Diversity: current and prospective secondary metabolites for nutrition and medicine. Curr Opin Biotechnol 2021; 74:164-170. [PMID: 34942505 DOI: 10.1016/j.copbio.2021.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/28/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022]
Abstract
Plants have been used as sources of food, feed and medicine for millennia. The ever-increasing population has, however, dramatically increased the burden on our arable land to meet nutritional demand. Concomitantly, and in part due to poor nutrition, we are faced with massive increases in chronic diseases, meaning the need for medicine has also increased. Here, we look back on research in these areas, surveying the polyphenols as a case study for health-conferring metabolites. We conclude that the tools that will allow us to breed more nutritious crops are all at hand. We stress that collaboration between plant and medical research needs to be intensified in order to improve our understanding of the bioactivities. In doing so, we attempt to draw a roadmap for the use of plants for mid-21st Century human health.
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12
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Akiyama R, Nakayasu M, Umemoto N, Kato J, Kobayashi M, Lee HJ, Sugimoto Y, Iijima Y, Saito K, Muranaka T, Mizutani M. Tomato E8 Encodes a C-27 Hydroxylase in Metabolic Detoxification of α-Tomatine during Fruit Ripening. PLANT & CELL PHYSIOLOGY 2021; 62:775-783. [PMID: 34100555 DOI: 10.1093/pcp/pcab080] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Tomato (Solanum lycopersicum) contains α-tomatine, a steroidal glycoalkaloid that contributes to the plant defense against pathogens and herbivores through its bitter taste and toxicity. It accumulates at high levels in all the plant tissues, especially in leaves and immature green fruits, whereas it decreases during fruit ripening through metabolic conversion to the nontoxic esculeoside A, which accumulates in the mature red fruit. This study aimed to identify the gene encoding a C-27 hydroxylase that is a key enzyme in the metabolic conversion of α-tomatine to esculeoside A. The E8 gene, encoding a 2-oxoglutalate-dependent dioxygenase, is well known as an inducible gene in response to ethylene during fruit ripening. The recombinant E8 was found to catalyze the C-27 hydroxylation of lycoperoside C to produce prosapogenin A and is designated as Sl27DOX. The ripe fruit of E8/Sl27DOX-silenced transgenic tomato plants accumulated lycoperoside C and exhibited decreased esculeoside A levels compared with the wild-type (WT) plants. Furthermore, E8/Sl27DOX deletion in tomato accessions resulted in higher lycoperoside C levels in ripe fruits than in WT plants. Thus, E8/Sl27DOX functions as a C-27 hydroxylase of lycoperoside C in the metabolic detoxification of α-tomatine during tomato fruit ripening, and the efficient detoxification by E8/27DOX may provide an advantage in the domestication of cultivated tomatoes.
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Affiliation(s)
- Ryota Akiyama
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Masaru Nakayasu
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Naoyuki Umemoto
- Department of Nutrition and Life Science, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa, 243-0292 Japan
| | - Junpei Kato
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Midori Kobayashi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Hyoung Jae Lee
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Yoko Iijima
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuki Saito
- Department of Nutrition and Life Science, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa, 243-0292 Japan
- Plant Molecular Science Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675 Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871 Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
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13
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Fernie AR, Alseekh S, Liu J, Yan J. Using precision phenotyping to inform de novo domestication. PLANT PHYSIOLOGY 2021; 186:1397-1411. [PMID: 33848336 PMCID: PMC8260140 DOI: 10.1093/plphys/kiab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
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14
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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.
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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.
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15
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Yadav A, Fennec A, Davidovich-Rikanati R, Meir S, Kochanek B, Lewinsohn E, Aharoni A, Alkan N, Friedman H. Phenylpropanoid Metabolism in Astringent and Nonastringent Persimmon ( Diospyros kaki) Cultivars Determines Sensitivity to Alternaria Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5628-5637. [PMID: 33983017 PMCID: PMC8278483 DOI: 10.1021/acs.jafc.1c01312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Fruits of nonastringent persimmon cultivars, as compared to astringent ones, were more resistant to Alternaria infection despite having lower polyphenol content. Metabolic analysis from the pulp of nonastringent "Shinshu", as compared to the astringent "Triumph", revealed a higher concentration of salicylic, coumaric, quinic, 5-o-feruloyl quinic, ferulic acids, β-glucogallin, gallocatechin, catechin, and procyanidins. Selected compounds like salicylic, ferulic, and ρ-coumaric acids inhibited in vitro Alternaria growth, and higher activity was demonstrated for methyl ferulic and methyl ρ-coumaric acids. These compounds also reduced in vivo Alternaria growth and the black spot disease in stored fruits. On the other hand, methyl gallic acid was a predominant compound in the "Triumph" pulp, as compared to the "Shinshu" pulp, and it augmented Alternaria growth in vitro and in vivo. Our results might explain the high sensitivity of the cultivar "Triumph" to Alternaria. It also emphasizes that specific phenolic compounds, and not the total phenol, affect susceptibility to fungal infection.
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Affiliation(s)
- Akhilesh Yadav
- Department
of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel
| | - Anton Fennec
- Department
of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel
| | | | - Sagit Meir
- Department
of Plant and Environmental Sciences, Weizmann
Institute, Rehovot 7610001, Israel
| | - Bettina Kochanek
- Department
of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel
| | - Efraim Lewinsohn
- Newe
Ya’ar Research Center, Agricultural
Research Organization (ARO), Ramat
Yishay 3009500, Israel
| | - Asaph Aharoni
- Department
of Plant and Environmental Sciences, Weizmann
Institute, Rehovot 7610001, Israel
| | - Noam Alkan
- Department
of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel
| | - Haya Friedman
- Department
of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel
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16
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Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
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Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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17
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Dong Y, Sonawane P, Cohen H, Polturak G, Feldberg L, Avivi SH, Rogachev I, Aharoni A. High mass resolution, spatial metabolite mapping enhances the current plant gene and pathway discovery toolbox. THE NEW PHYTOLOGIST 2020; 228:1986-2002. [PMID: 32654288 DOI: 10.1111/nph.16809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/06/2020] [Indexed: 05/21/2023]
Abstract
Understanding when and where metabolites accumulate provides important cues to the gene function. Mass spectrometry imaging (MSI) enables in situ temporal and spatial measurement of a large assortment of metabolites, providing mapping information regarding their cellular distribution. To describe the current state and technical advances using MSI in plant sciences, we employed MSI to demonstrate its significant contribution to the study of plant specialised metabolism. We show that coupling MSI with: (1) RNA interference (RNAi), (2) virus induced gene silencing (VIGS), (3) agroinfiltration or (4) samples derived from plant natural variation provides great opportunities to understand the accurate gene-metabolite relationship and discover novel gene-associated metabolites. This was exemplified in three plant species (i.e. tomato, tobacco and wheat) by mapping the distribution of metabolites possessing a range of polarities. In particular, we demonstrated that MSI is able to spatially map an entire metabolic pathway, including intermediates and final products, in the intricate biosynthetic route to tomato fruit steroidal glycoalkaloids. We therefore envisage MSI as a key component of the metabolome analysis arsenal employed in plant gene discovery strategies.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Prashant Sonawane
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Hagai Cohen
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Guy Polturak
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, 7410001, Israel
| | - Shelly Hen Avivi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
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18
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Vats S, Bansal R, Rana N, Kumawat S, Bhatt V, Jadhav P, Kale V, Sathe A, Sonah H, Jugdaohsingh R, Sharma TR, Deshmukh R. Unexplored nutritive potential of tomato to combat global malnutrition. Crit Rev Food Sci Nutr 2020; 62:1003-1034. [PMID: 33086895 DOI: 10.1080/10408398.2020.1832954] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tomato, a widely consumed vegetable crop, offers a real potential to combat human nutritional deficiencies. Tomatoes are rich in micronutrients and other bioactive compounds (including vitamins, carotenoids, and minerals) that are known to be essential or beneficial for human health. This review highlights the current state of the art in the molecular understanding of the nutritional aspects, conventional and molecular breeding efforts, and biofortification studies undertaken to improve the nutritional content and quality of tomato. Transcriptomics and metabolomics studies, which offer a deeper understanding of the molecular regulation of the tomato's nutrients, are discussed. The potential uses of the wastes from the tomato processing industry (i.e., the peels and seed extracts) that are particularly rich in oils and proteins are also discussed. Recent advancements with CRISPR/Cas mediated gene-editing technology provide enormous opportunities to enhance the nutritional content of agricultural produces, including tomatoes. In this regard, genome editing efforts with respect to biofortification in the tomato plant are also discussed. The recent technological advancements and knowledge gaps described herein aim to help explore the unexplored nutritional potential of the tomato.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vacha Bhatt
- Department of Botany, Savitribai Phule Pune University, Pune, MS, India
| | - Pravin Jadhav
- Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, MS, India
| | - Vijay Kale
- Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, MS, India
| | - Atul Sathe
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ravin Jugdaohsingh
- Biomineral Research Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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19
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Alseekh S, Ofner I, Liu Z, Osorio S, Vallarino J, Last RL, Zamir D, Tohge T, Fernie AR. Quantitative trait loci analysis of seed-specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2007-2024. [PMID: 32538521 DOI: 10.1111/tpj.14879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Given the potential health benefits (and adverse effects), of polyphenolic and steroidal glycoalkaloids in the diet there is a growing interest in fully elucidating the genetic control of their levels in foodstuffs. Here we carried out profiling of the specialized metabolites in the seeds of the Solanum pennellii introgression lines identifying 338 putative metabolite quantitative trait loci (mQTL) for flavonoids, steroidal glycoalkaloids and further specialized metabolites. Two putative mQTL for flavonols and one for steroidal glycoalkaloids were cross-validated by evaluation of the metabolite content of recombinants harboring smaller introgression in the corresponding QTL interval or by analysis of lines from an independently derived backcross inbred line population. The steroidal glycoalkaloid mQTL was localized to a chromosomal region spanning 14 genes, including a previously defined steroidal glycoalkaloid gene cluster. The flavonoid mQTL was further validated via the use of transient and stable overexpression of the Solyc12g098600 and Solyc12g096870 genes, which encode seed-specific uridine 5'-diphosphate-glycosyltransferases. The results are discussed in the context of our understanding of the accumulation of polyphenols and steroidal glycoalkaloids, and how this knowledge may be incorporated into breeding strategies aimed at improving nutritional aspects of plants as well as in fortifying them against abiotic stress.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Itai Ofner
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Zhongyuan Liu
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, 32611, USA
| | - Sonia Osorio
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruiticultura Subtropical y Mediterranea "La Major" - University of Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Campus de Teatinos, Malaga, 29071, Spain
| | - Jose Vallarino
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - 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
| | - Dani Zamir
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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20
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Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Hogstrand C, Hoogenboom L(R, Leblanc J, Nebbia CS, Nielsen E, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Brimer L, Cottrill B, Dusemund B, Mulder P, Vollmer G, Binaglia M, Ramos Bordajandi L, Riolo F, Roldán‐Torres R, Grasl‐Kraupp B. Risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products. EFSA J 2020; 18:e06222. [PMID: 32788943 PMCID: PMC7417869 DOI: 10.2903/j.efsa.2020.6222] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of glycoalkaloids (GAs) in feed and food. This risk assessment covers edible parts of potato plants and other food plants containing GAs, in particular, tomato and aubergine. In humans, acute toxic effects of potato GAs (α-solanine and α-chaconine) include gastrointestinal symptoms such as nausea, vomiting and diarrhoea. For these effects, the CONTAM Panel identified a lowest-observed-adverse-effect level of 1 mg total potato GAs/kg body weight (bw) per day as a reference point for the risk characterisation following acute exposure. In humans, no evidence of health problems associated with repeated or long-term intake of GAs via potatoes has been identified. No reference point for chronic exposure could be identified from the experimental animal studies. Occurrence data were available only for α-solanine and α-chaconine, mostly for potatoes. The acute dietary exposure to potato GAs was estimated using a probabilistic approach and applying processing factors for food. Due to the limited data available, a margin of exposure (MOE) approach was applied. The MOEs for the younger age groups indicate a health concern for the food consumption surveys with the highest mean exposure, as well as for the P95 exposure in all surveys. For adult age groups, the MOEs indicate a health concern only for the food consumption surveys with the highest P95 exposures. For tomato and aubergine GAs, the risk to human health could not be characterised due to the lack of occurrence data and the limited toxicity data. For horses, farm and companion animals, no risk characterisation for potato GAs could be performed due to insufficient data on occurrence in feed and on potential adverse effects of GAs in these species.
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21
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Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S, Jadhav SS, Delfin JC, Lohse M, Giavalisco P, Usadel B, Zhang Y, Luo J, Bouzayen M, Fernie AR. Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex. MOLECULAR PLANT 2020; 13:1027-1046. [PMID: 32305499 DOI: 10.1016/j.molp.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 02/01/2020] [Accepted: 04/11/2020] [Indexed: 05/10/2023]
Abstract
While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via Ardeatina 546 00178 Rome, Italy
| | - Regina Wendenburg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Pierre Frasse
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Ilse Balbo
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Sagar Sudam Jadhav
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jay C Delfin
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Marc Lohse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Bjoern Usadel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Mondher Bouzayen
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria.
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22
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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.
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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.
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23
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Yu G, Li C, Zhang L, Zhu G, Munir S, Shi C, Zhang H, Ai G, Gao S, Zhang Y, Yang C, Zhang J, Li H, Ye Z. An allelic variant of GAME9 determines its binding capacity with the GAME17 promoter in the regulation of steroidal glycoalkaloid biosynthesis in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2527-2536. [PMID: 31943062 PMCID: PMC7210767 DOI: 10.1093/jxb/eraa014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/13/2020] [Indexed: 05/19/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules found in the family Solanaceae. SGA content varies among different plant species and varieties. However, the genetic mechanisms regulating SGA content remain unclear. Here, we demonstrate that genetic variation in GLYCOALKALOID METABOLISM 9 (GAME9) is responsible for the variation in SGA content in tomato (Solanum lycopersicum). During a sequential analysis we found a 1 bp substitution in the AP2/ERF binding domain of GAME9. The 1 bp substitution in GAME9 was significantly associated with high SGA content and determined the binding capacity of GAME9 with the promoter of GAME17, a core SGA biosynthesis gene. The high-SGA GAME9 allele is mainly present in S. pimpinellifolium and S. lycopersicum var. cerasiforme populations and encodes a protein that can bind the GAME17 promoter. In contrast, the low-SGA GAME9 allele is mainly present in the big-fruited varieties of S. lycopersicum and encodes a protein that shows weak binding to the GAME17 promoter. Our findings provide new insight into the regulation of SGA biosynthesis and the factors that affect the accumulation of SGA in tomato.
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Affiliation(s)
- Gang Yu
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Lei Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guangtao Zhu
- The CAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Shoaib Munir
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Caixue Shi
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hongyan Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guo Ai
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shenghua Gao
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changxian Yang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Correspondence: , , or
| | - Hanxia Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Correspondence: , , or
| | - Zhibiao Ye
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Correspondence: , , or
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24
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Wen D, Liu Y, Yu Q. Metabolomic approach to measuring quality of chilled chicken meat during storage. Poult Sci 2020; 99:2543-2554. [PMID: 32359590 PMCID: PMC7597405 DOI: 10.1016/j.psj.2019.11.070] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 11/30/2022] Open
Abstract
The metabolites of stored, chilled chicken meat were analyzed using liquid chromatograph-mass spectrometry and metabolomics. The results showed significant differences in the metabolites of chicken meat stored at 4°C for 0 D and meat stored for longer periods of 2 D, 4 D, 6 D, and 10 D, when analyzed based on a variable of importance >2 and P < 0.05. These changed metabolites included amino acids, amines, nucleosides, nucleotides, carbohydrates, organic acids, and other substances. The data from this study provide a holistic understanding of food quality changes in chicken meat during deterioration in storage.
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Affiliation(s)
- Dongling Wen
- College of Food Science and Technology, Zhongkai University of Agriculture and Engineering, No. 501 Zhongkai Road, Haizhu District, Guangzhou, Guangdong Province, 510225, P.R. China
| | - Yue Liu
- College of Food Science and Technology, Zhongkai University of Agriculture and Engineering, No. 501 Zhongkai Road, Haizhu District, Guangzhou, Guangdong Province, 510225, P.R. China
| | - Qian Yu
- College of Food Science and Technology, Zhongkai University of Agriculture and Engineering, No. 501 Zhongkai Road, Haizhu District, Guangzhou, Guangdong Province, 510225, P.R. China.
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25
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Cortinovis G, Frascarelli G, Di Vittori V, Papa R. Current State and Perspectives in Population Genomics of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2020; 9:E330. [PMID: 32150958 PMCID: PMC7154925 DOI: 10.3390/plants9030330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
* Correspondence: r [...].
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Affiliation(s)
| | | | | | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.C.); (G.F.); (V.D.V.)
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26
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Price EJ, Drapal M, Perez‐Fons L, Amah D, Bhattacharjee R, Heider B, Rouard M, Swennen R, Becerra Lopez‐Lavalle LA, Fraser PD. Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1258-1268. [PMID: 31845400 PMCID: PMC7383867 DOI: 10.1111/tpj.14649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/09/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.
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Affiliation(s)
- Elliott J. Price
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
- Present address:
Masaryk UniversityBrno‐Bohunice625 00Czech Republic
| | - Margit Drapal
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Laura Perez‐Fons
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Delphine Amah
- International Institute of Tropical AgriculturePMB 5320IbadanNigeria
| | | | | | - Mathieu Rouard
- Bioversity InternationalParc Scientifique Agropolis II34397MontpellierFrance
| | - Rony Swennen
- Laboratory of Tropical Crop ImprovementDivision of Crop BiotechnicsKU LeuvenB‐3001LeuvenBelgium
- Bioversity InternationalWillem De Croylaan 42B‐3001LeuvenBelgium
- International Institute of Tropical Agriculture. C/0 The Nelson Mandela African Institution of Science and TechnologyP.O. Box 44ArushaTanzania
| | | | - Paul D. Fraser
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
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27
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Nakayasu M, Akiyama R, Kobayashi M, Lee HJ, Kawasaki T, Watanabe B, Urakawa S, Kato J, Sugimoto Y, Iijima Y, Saito K, Muranaka T, Umemoto N, Mizutani M. Identification of α-Tomatine 23-Hydroxylase Involved in the Detoxification of a Bitter Glycoalkaloid. PLANT & CELL PHYSIOLOGY 2020; 61:21-28. [PMID: 31816045 DOI: 10.1093/pcp/pcz224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/03/2019] [Indexed: 05/13/2023]
Abstract
Tomato plants (Solanum lycopersicum) contain steroidal glycoalkaloid α-tomatine, which functions as a chemical barrier to pathogens and predators. α-Tomatine accumulates in all tissues and at particularly high levels in leaves and immature green fruits. The compound is toxic and causes a bitter taste, but its presence decreases through metabolic conversion to nontoxic esculeoside A during fruit ripening. This study identifies the gene encoding a 23-hydroxylase of α-tomatine, which is a key to this process. Some 2-oxoglutarate-dependent dioxygenases were selected as candidates for the metabolic enzyme, and Solyc02g062460, designated Sl23DOX, was found to encode α-tomatine 23-hydroxylase. Biochemical analysis of the recombinant Sl23DOX protein demonstrated that it catalyzes the 23-hydroxylation of α-tomatine and the product spontaneously isomerizes to neorickiioside B, which is an intermediate in α-tomatine metabolism that appears during ripening. Leaves of transgenic tomato plants overexpressing Sl23DOX accumulated not only neorickiioside B but also another intermediate, lycoperoside C (23-O-acetylated neorickiioside B). Furthermore, the ripe fruits of Sl23DOX-silenced transgenic tomato plants contained lower levels of esculeoside A but substantially accumulated α-tomatine. Thus, Sl23DOX functions as α-tomatine 23-hydroxylase during the metabolic processing of toxic α-tomatine in tomato fruit ripening and is a key enzyme in the domestication of cultivated tomatoes.
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Affiliation(s)
- Masaru Nakayasu
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Ryota Akiyama
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Midori Kobayashi
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Hyoung Jae Lee
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Takashi Kawasaki
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Bunta Watanabe
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Shingo Urakawa
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Junpei Kato
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
| | - Yoko Iijima
- Department of Nutrition and Life Science, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa, 243-0292 Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675 Japan
- 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
| | - Naoyuki Umemoto
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkoudai 1-1, Nada-ku, Kobe, Hyogo, 657-8501 Japan
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28
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Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases. Nat Commun 2019; 10:5169. [PMID: 31727889 PMCID: PMC6856131 DOI: 10.1038/s41467-019-13211-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/06/2019] [Indexed: 11/09/2022] Open
Abstract
The genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic. Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.
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29
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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30
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Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR. Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1132-1153. [PMID: 30480348 PMCID: PMC6850281 DOI: 10.1111/tpj.14178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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Affiliation(s)
| | - Federico Scossa
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Consiglio per la ricerca in agricoltura e l′analisi dell′economia agrariaCREA‐OFAVia di Fioranello 5200134RomeItaly
| | - Sebastian Proost
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Takayuki Tohge
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, Nara630‐0192Japan
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
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Fang C, Luo J, Wang S. The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1028. [PMID: 31475024 PMCID: PMC6706459 DOI: 10.3389/fpls.2019.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 05/21/2023]
Abstract
The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Shouchuang Wang,
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Fang C, Fernie AR, Luo J. Exploring the Diversity of Plant Metabolism. TRENDS IN PLANT SCIENCE 2019; 24:83-98. [PMID: 30297176 DOI: 10.1016/j.tplants.2018.09.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
Plants produce a huge array of metabolites, far more than those produced by most other organisms. Unraveling this diversity and its underlying genetic variation has attracted increasing research attention. Post-genomic profiling platforms have enabled the marriage and mining of the enormous amount of phenotypic and genetic diversity. We review here achievements to date and challenges remaining that are associated with plant metabolic research using multi-omic strategies. We focus mainly on strategies adopted in investigating the diversity of plant metabolism and its underlying features. Recent advances in linking metabotypes with phenotypic and genotypic traits are also discussed. Taken together, we conclude that exploring the diversity of metabolism could provide new insights into plant evolution and domestication.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Zhu G, Wang S, Huang Z, Zhang S, Liao Q, Zhang C, Lin T, Qin M, Peng M, Yang C, Cao X, Han X, Wang X, van der Knaap E, Zhang Z, Cui X, Klee H, Fernie AR, Luo J, Huang S. Rewiring of the Fruit Metabolome in Tomato Breeding. Cell 2018; 172:249-261.e12. [PMID: 29328914 DOI: 10.1016/j.cell.2017.12.019] [Citation(s) in RCA: 470] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022]
Abstract
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.
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Affiliation(s)
- Guangtao Zhu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zejun Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinggang Liao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Chunzhi Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Tao Lin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Mao Qin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Han
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Xiaoxuan Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Harry Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL 32611, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, Hainan 572208, China.
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wang CC, Meng LH, Gao Y, Grierson D, Fu DQ. Manipulation of Light Signal Transduction Factors as a Means of Modifying Steroidal Glycoalkaloids Accumulation in Tomato Leaves. FRONTIERS IN PLANT SCIENCE 2018; 9:437. [PMID: 29706975 PMCID: PMC5906708 DOI: 10.3389/fpls.2018.00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/21/2018] [Indexed: 05/19/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are cholesterol-derived specialized metabolites produced by Solanaceous plant species. They contribute to pathogen defense but are considered as anti-nutritional compounds and toxic to humans. Although the genes involved in the SGA biosynthetic pathway have been successfully cloned and identified, transcription factors regulating this pathway are still poorly understood. We report that silencing tomato light signal transduction transcription factors ELONGATED HYPOCOTYL 5 (SlHY5) and PHYTOCHROME INTERACTING FACTOR3 (SlPIF3), by virus-induced gene silencing (VIGS), altered glycoalkaloids levels in tomato leaves compared to control plant. Electrophoretic mobility shift assay (EMSA) and Chromatin immunoprecipitation (ChIP) analysis confirmed that SlHY5 and SlPIF3 bind to the promoter of target genes of GLYCOALKALOID METABOLISM (GAME1, GAME4, GAME17), affecting the steady-state concentrations of transcripts coding for SGA pathway enzymes. The results indicate that light-signaling transcription factors HY5 and PIF3 regulate the abundance of SGAs by modulating the transcript levels of these GAME genes. This insight into the regulation of SGA biosynthesis can be used for manipulating the level of these metabolites in crops.
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Affiliation(s)
- Cui-cui Wang
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Lan-huan Meng
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Ying Gao
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Da-qi Fu
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- *Correspondence: Da-qi Fu
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Abstract
Recent technological developments and methodological advances of both liquid chromatography (LC) and mass spectrometry (MS) have allowed LC-MS-based plant metabolomics to become a common tool for investigating quantity, quality, and chemical diversity of plant metabolites. Targeted LC-MS metabolite analysis focuses on the detection and quantitation of the researcher's target metabolites. Whilst the word "target analysis" has been used for the analytical measurement to obtain the absolute concentrations evaluated by authentic and/or stable-isotope-labeled standards, over time the phrase came to be also used in a broad sense for the measurement of annotatable metabolites by structural information obtained from the combination of different strategies such as MS/MS analysis, reference extracts, mutant analysis and database search. Here, we describe a general protocol for targeted LC-MS metabolite profiling of plant secondary metabolites. Additionally, we introduce some examples of peak annotation using the combination approach.
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36
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The Importance of Experimental Design, Quality Assurance, and Control in Plant Metabolomics Experiments. Methods Mol Biol 2018; 1778:3-17. [PMID: 29761427 DOI: 10.1007/978-1-4939-7819-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The output of metabolomics relies to a great extent upon the methods and instrumentation to identify, quantify, and access spatial information on as many metabolites as possible. However, the most modern machines and sophisticated tools for data analysis cannot compensate for inappropriate harvesting and/or sample preparation procedures that modify metabolic composition and can lead to erroneous interpretation of results. In addition, plant metabolism has a remarkable degree of complexity, and the number of identified compounds easily surpasses the number of samples in metabolomics analyses, increasing false discovery risk. These aspects pose a large challenge when carrying out plant metabolomics experiments. In this chapter, we address the importance of a proper experimental design taking into consideration preventable complications and unavoidable factors to achieve success in metabolomics analysis. We also focus on quality control and standardized procedures during the metabolomics workflow.
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37
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Abstract
Plant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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38
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GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway. Nat Commun 2016; 7:10654. [PMID: 26876023 PMCID: PMC4756317 DOI: 10.1038/ncomms10654] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 01/07/2016] [Indexed: 12/31/2022] Open
Abstract
Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules produced by solanaceous species. They contribute to pathogen defence but are toxic to humans and considered as anti-nutritional compounds. Here we show that GLYCOALKALOID METABOLISM 9 (GAME9), an APETALA2/Ethylene Response Factor, related to regulators of alkaloid production in tobacco and Catharanthus roseus, controls SGA biosynthesis. GAME9 knockdown and overexpression in tomato and potato alters expression of SGAs and upstream mevalonate pathway genes including the cholesterol biosynthesis gene STEROL SIDE CHAIN REDUCTASE 2 (SSR2). Levels of SGAs, C24-alkylsterols and the upstream mevalonate and cholesterol pathways intermediates are modified in these plants. Δ(7)-STEROL-C5(6)-DESATURASE (C5-SD) in the hitherto unresolved cholesterol pathway is a direct target of GAME9. Transactivation and promoter-binding assays show that GAME9 exerts its activity either directly or cooperatively with the SlMYC2 transcription factor as in the case of the C5-SD gene promoter. Our findings provide insight into the regulation of SGA biosynthesis and means for manipulating these metabolites in crops.
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39
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Heiling S, Khanal S, Barsch A, Zurek G, Baldwin IT, Gaquerel E. Using the knowns to discover the unknowns: MS-based dereplication uncovers structural diversity in 17-hydroxygeranyllinalool diterpene glycoside production in the Solanaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:561-77. [PMID: 26749139 DOI: 10.1111/tpj.13119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 05/25/2023]
Abstract
Exploring the diversity of plant secondary metabolism requires efficient methods to obtain sufficient structural insights to discriminate previously known from unknown metabolites. De novo structure elucidation and confirmation of known metabolites (dereplication) remain a major bottleneck for mass spectrometry-based metabolomic workflows, and few systematic dereplication strategies have been developed for the analysis of entire compound classes across plant families, partly due to the complexity of plant metabolic profiles that complicates cross-species comparisons. 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) are abundant defensive secondary metabolites whose malonyl and glycosyl decorations are induced by jasmonate signaling in the ecological model plant Nicotiana attenuata. The multiple labile glycosidic bonds of HGL-DTGs result in extensive in-source fragmentation (IS-CID) during ionization. To reconstruct these IS-CID clusters from profiling data and identify precursor ions, we applied a deconvolution algorithm and created an MS/MS library from positive-ion spectra of purified HGL-DTGs. From this library, 251 non-redundant fragments were annotated, and a workflow to characterize leaf, flower and fruit extracts of 35 solanaceous species was established. These analyses predicted 105 novel HGL-DTGs that were restricted to Nicotiana, Capsicum and Lycium species. Interestingly, malonylation is a highly conserved step in HGL-DTG metabolism, but is differentially affected by jasmonate signaling among Nicotiana species. This MS-based workflow is readily applicable for cross-species re-identification/annotation of other compound classes with sufficient fragmentation knowledge, and therefore has the potential to support hypotheses regarding secondary metabolism diversification.
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Affiliation(s)
- Sven Heiling
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Santosh Khanal
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Aiko Barsch
- Bruker Daltonics, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Gabriela Zurek
- Bruker Daltonics, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Ian T Baldwin
- Molecular Ecology Department, Max Planck Institute for Chemical Ecology, Hans Knöll Straße 8, 07745, Jena, Germany
| | - Emmanuel Gaquerel
- Plant Defense Metabolism Research Group, Centre for Organismal Studies Heidelberg, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
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40
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Tohge T, Fernie AR. Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. PLANT & CELL PHYSIOLOGY 2015; 56:1681-96. [PMID: 26228272 DOI: 10.1093/pcp/pcv093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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42
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Tohge T, Zhang Y, Peterek S, Matros A, Rallapalli G, Tandrón YA, Butelli E, Kallam K, Hertkorn N, Mock HP, Martin C, Fernie AR. Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:686-704. [PMID: 26108615 DOI: 10.1111/tpj.12920] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 05/12/2023]
Abstract
Given the potential health benefits of polyphenolic compounds in the diet, there is a growing interest in the generation of food crops enriched with health-protective flavonoids. We undertook a series of metabolite analyses of tomatoes ectopically expressing the Delila and Rosea1 transcription factor genes from snapdragon (Antirrhinum majus), paying particular attention to changes in phenylpropanoids compared to controls. These analyses revealed multiple changes, including depletion of rutin and naringenin chalcone, and enhanced levels of anthocyanins and phenylacylated flavonol derivatives. We isolated and characterized the chemical structures of the two most abundant anthocyanins, which were shown by NMR spectroscopy to be delphinidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside and petunidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside. By performing RNA sequencing on both purple fruit and wild-type fruit, we obtained important information concerning the relative expression of both structural and transcription factor genes. Integrative analysis of the transcript and metabolite datasets provided compelling evidence of the nature of all anthocyanin biosynthetic genes, including those encoding species-specific anthocyanin decoration enzymes. One gene, SlFdAT1 (Solyc12g088170), predicted to encode a flavonoid-3-O-rutinoside-4'''-phenylacyltransferase, was characterized by assays of recombinant protein and over-expression assays in tobacco. The combined data are discussed in the context of both our current understanding of phenylpropanoid metabolism in Solanaceous species, and evolution of flavonoid decorating enzymes and their transcriptional networks in various plant species.
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Affiliation(s)
- Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Yang Zhang
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Silke Peterek
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Ghanasyam Rallapalli
- The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, UK NR4 7UH, UK
| | - Yudelsy A Tandrón
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Eugenio Butelli
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Kalyani Kallam
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Norbert Hertkorn
- German Research Center for Environment and Health, GmbH, Institute of Ecological Chemistry, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764, Neuherberg, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
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Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. THE PLANT CELL 2015; 27:485-512. [PMID: 25770107 PMCID: PMC4558650 DOI: 10.1105/tpc.114.132266] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Regina Wendenberg
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Federico Scossa
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy
| | - Nooshin Omranian
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sabrina Kleessen
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Tzili Pleban
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Bernd Mueller-Roeber
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Dani Zamir
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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Nakabayashi R, Tsugawa H, Kitajima M, Takayama H, Saito K. Boosting Sensitivity in Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Tandem Mass Spectrometry for Product Ion Analysis of Monoterpene Indole Alkaloids. FRONTIERS IN PLANT SCIENCE 2015; 6:1127. [PMID: 26734034 PMCID: PMC4681812 DOI: 10.3389/fpls.2015.01127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/27/2015] [Indexed: 05/05/2023]
Abstract
In metabolomics, the analysis of product ions in tandem mass spectrometry (MS/MS) is noteworthy to chemically assign structural information. However, the development of relevant analytical methods are less advanced. Here, we developed a method to boost sensitivity in liquid chromatography-Fourier transform ion cyclotron resonance-tandem mass spectrometry analysis (MS/MS boost analysis). To verify the MS/MS boost analysis, both quercetin and uniformly labeled (13)C quercetin were analyzed, revealing that the origin of the product ions is not the instrument, but the analyzed compounds resulting in sensitive product ions. Next, we applied this method to the analysis of monoterpene indole alkaloids (MIAs). The comparative analyses of MIAs having indole basic skeleton (ajmalicine, catharanthine, hirsuteine, and hirsutine) and oxindole skeleton (formosanine, isoformosanine, pteropodine, isopteropodine, rhynchophylline, isorhynchophylline, and mitraphylline) identified 86 and 73 common monoisotopic ions, respectively. The comparative analyses of the three pairs of stereoisomers showed more than 170 common monoisotopic ions in each pair. This method was also applied to the targeted analysis of MIAs in Catharanthus roseus and Uncaria rhynchophylla to profile indole and oxindole compounds using the product ions. This analysis is suitable for chemically assigning features of the metabolite groups, which contributes to targeted metabolome analysis.
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Affiliation(s)
- Ryo Nakabayashi
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Ryo Nakabayashi,
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Mariko Kitajima
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Hiromitsu Takayama
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
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Qi X, Zhang D. Plant metabolomics and metabolic biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:814-815. [PMID: 25088016 DOI: 10.1111/jipb.12247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Xiaoquan Qi
- Institute of Botany, the Chinese Academy of Sciences, Beijing, China
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