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Del Giúdice LZ, Falquetto-Gomes P, de Almeida Costa PM, Martins AO, Omena-Garcia RP, Araújo WL, Zsögön A, Picoli EADT, Nunes-Nesi A. Dynamic shifts in primary metabolism across fruit development stages in Capsicum chinense (cv. Habanero). JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154121. [PMID: 37924627 DOI: 10.1016/j.jplph.2023.154121] [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: 05/26/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023]
Abstract
The development of fleshy fruits involves changes in size and mass, followed by cell differentiation, which is associated with anatomical and histological changes. Parallel to these changes, metabolic alterations lead to the production of osmolytes and energy that modify cell turgor pressure, thereby promoting cell expansion and fruit growth. Detailed information is known about these processes in climacteric fruits (e.g. tomato); however, the regulation of metabolism and its association with anatomical changes in non-climacteric fruit development are poorly understood. In this study, we used detailed anatomical and histological analyses to define three developmental phases of chili pepper (Capsicum chinense cv. Habanero): cell division, cell expansion, and ripening. We showed that each was marked by distinct metabolic profiles, underpinning the switches in energy metabolism to support cellular processes. Interestingly, mitochondrial activity was high in the early stages of development and declined over time, with a modest increase in O2 consumption by pericarp tissues at the beginning of the ripening stage. This respiratory-like burst was associated with the degradation of starch and malate, which are the sources of energy and carbon required for other processes associated with fruit maturation.
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Affiliation(s)
- Luciana Zacour Del Giúdice
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Priscilla Falquetto-Gomes
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Auxiliadora O Martins
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Rebeca Patrícia Omena-Garcia
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Agustín Zsögön
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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2
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Bulut M, Wendenburg R, Bitocchi E, Bellucci E, Kroc M, Gioia T, Susek K, Papa R, Fernie AR, Alseekh S. A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1152-1171. [PMID: 37285370 DOI: 10.1111/tpj.16329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Legumes represent an important component of human and livestock diets; they are rich in macro- and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst several health-promoting and anti-nutritional properties have been associated with grain content, in-depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) and pearl lupin (Lupinus mutabilis), at the tissue level. We were able to detect and quantify over 3400 metabolites covering major nutritional and anti-nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics-assisted crop breeding and facilitate metabolite-based genome-wide association studies to dissect the genetic and biochemical bases of metabolism in legume species.
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Affiliation(s)
- Mustafa Bulut
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, 85100, Italy
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - 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
| | - 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
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3
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Lewis DC, van der Zwan T, Richards A, Little H, Coaker GL, Bostock RM. The Oomycete Microbe-Associated Molecular Pattern, Arachidonic Acid, and an Ascophyllum nodosum-Derived Plant Biostimulant Induce Defense Metabolome Remodeling in Tomato. PHYTOPATHOLOGY 2023; 113:1084-1092. [PMID: 36598344 PMCID: PMC10318118 DOI: 10.1094/phyto-10-22-0368-r] [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] [Indexed: 06/17/2023]
Abstract
Arachidonic acid (AA) is an oomycete-derived microbe-associated molecular pattern (MAMP) capable of eliciting robust defense responses and inducing resistance in plants. Similarly, Ascophylum nodosum extract (ANE) from the brown seaweed A. nodosum, a plant biostimulant that contains AA, can also prime plants for defense against pathogen challenges. A previous parallel study comparing the transcriptomes of AA- and ANE-root-treated tomatoes demonstrated significant overlap in transcriptional profiles, a shared induced resistance phenotype, and changes in the accumulation of various defense-related phytohormones. In this work, untargeted metabolomic analysis via liquid chromatography-mass spectrometry was conducted to investigate the local and systemic metabolome-wide remodeling events elicited by AA and ANE root treatment in tomatoes. Our study demonstrated AA and ANE's capacity to locally and systemically alter the metabolome of tomatoes with enrichment of chemical classes and accumulation of metabolites associated with defense-related secondary metabolism. AA- and ANE-root-treated plants showed enrichment of fatty acyl-glycosides and strong modulation of hydroxycinnamic acids and derivatives. Identification of specific metabolites whose accumulation was affected by AA and ANE treatment revealed shared metabolic changes related to ligno-suberin biosynthesis and the synthesis of phenolic compounds. This study highlights the extensive local and systemic metabolic changes in tomatoes induced by treatment with a fatty acid MAMP and a seaweed-derived plant biostimulant with implications for induced resistance and crop improvement.
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Affiliation(s)
- Domonique C. Lewis
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Timo van der Zwan
- Acadian Plant Health, Acadian Seaplants, Ltd., Dartmouth, Nova Scotia, Canada, B3B 1X8
| | - Andrew Richards
- Acadian Plant Health, Acadian Seaplants, Ltd., Dartmouth, Nova Scotia, Canada, B3B 1X8
| | - Holly Little
- Acadian Plant Health, Acadian Seaplants, Ltd., Dartmouth, Nova Scotia, Canada, B3B 1X8
| | - Gitta L. Coaker
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Richard M. Bostock
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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4
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Wang Y, Shi C, Ge P, Li F, Zhu L, Wang Y, Tao J, Zhang X, Dong H, Gai W, Wang F, Ye Z, Grierson D, Xu W, Zhang Y. A 21-bp InDel in the promoter of STP1 selected during tomato improvement accounts for soluble solid content in fruits. HORTICULTURE RESEARCH 2023; 10:uhad009. [PMID: 36960428 PMCID: PMC10028405 DOI: 10.1093/hr/uhad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement. Unfortunately, during selection for certain attributes, other valuable traits may be inadvertently discarded. One example is the decline in fruit soluble solids content (SSC) during tomato breeding. Several genetic loci for SSC have been identified, but few reports on the underlying mechanisms are available. In this study we performed a genome-wide association study (GWAS) for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus, STP1, encoding a sugar transporter protein. The causal variation of STP1, a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon, alters its expression. STP1 Insertion accessions with an 21-bp insertion have higher SSC than STP1 Deletion accessions with the 21-bp deletion. Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits. In vivo and in vitro assays demonstrated that ZAT10-LIKE, a zinc finger protein transcription factor (ZFP TF), can specifically bind to the promoter of STP1 Insertion to enhance STP1 expression, but not to the promoter of STP1 Deletion , leading to lower fruit SSC in modern tomatoes. Diversity analysis revealed that STP1 was selected during tomato improvement. Taking these results together, we identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich our understanding of tomato evolution and domestication, and provide a genetic basis for genome design for improving fruit taste.
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Affiliation(s)
- Ying Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingfei Ge
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangman Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihui Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaru Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinbao Tao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiqiang Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenxian Gai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Donald Grierson
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Wei Xu
- Corresponding authors. E-mail: ;
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5
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Zhang Y, Yun F, Man X, Huang D, Liao W. Effects of Hydrogen Sulfide on Sugar, Organic Acid, Carotenoid, and Polyphenol Level in Tomato Fruit. PLANTS (BASEL, SWITZERLAND) 2023; 12:719. [PMID: 36840068 PMCID: PMC9965552 DOI: 10.3390/plants12040719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen sulfide (H2S) is known to have a positive effect on the postharvest storage of vegetables and fruits, but limited results are available on its influence in fruit flavor quality. Here, we presented the effect of H2S on the flavor quality of tomato fruit during postharvest. H2S decreased the content of fructose, glucose, carotene and lycopene but increased that of soluble protein, organic acid, malic acid and citric acid. These differences were directly associated with the expression of their metabolism-related genes. Moreover, H2S treatment raised the contents of total phenolics, total flavonoids and most phenolic compounds, and up-regulated the expression level of their metabolism-related genes (PAL5, 4CL, CHS1, CHS2, F3H and FLS). However, the effects of the H2S scavenger hypotaurine on the above flavor quality parameters were opposite to that of H2S, thus confirming the role of H2S in tomato flavor quality. Thus, these results provide insight into the significant roles of H2S in tomato fruit quality regulation and implicate the potential application of H2S in reducing the flavor loss of tomato fruit during postharvest.
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6
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Application of Exogenous Melatonin Improves Tomato Fruit Quality by Promoting the Accumulation of Primary and Secondary Metabolites. Foods 2022; 11:foods11244097. [PMID: 36553839 PMCID: PMC9778358 DOI: 10.3390/foods11244097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Melatonin plays key roles in improving fruit quality and yield by regulating various aspects of plant growth. However, the effects of how melatonin regulates primary and secondary metabolites during fruit growth and development are poorly understood. In this study, the surfaces of tomato fruit were sprayed with different concentrations of melatonin (0, 50, and 100 µmol·L-1) on the 20th day after anthesis; we used high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS) to determine the changes in primary and secondary metabolite contents during fruit development and measured the activity of sucrose metabolizing enzymes during fruit development. Our results showed that 100 µmol·L-1 melatonin significantly promoted the accumulation of soluble sugar in tomato fruit by increasing the activities of sucrose synthase (SS), sucrose phosphate synthase (SPS), and acid convertase (AI). The application of 100 µmol·L-1 melatonin also increased the contents of ten amino acids in tomato fruit as well as decreased the contents of organic acids. In addition, 100 µmol·L-1 melatonin application also increased the accumulation of some secondary metabolites, such as six phenolic acids, three flavonoids, and volatile substances (including alcohols, aldehydes, and ketones). In conclusion, melatonin application improves the internal nutritional and flavor quality of tomato fruit by regulating the accumulation of primary and secondary metabolites during tomato fruit ripening. In the future, we need to further understand the molecular mechanism of melatonin in tomato fruit to lay a solid foundation for quality improvement breeding.
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7
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Perez BC, Bink MCAM, Svenson KL, Churchill GA, Calus MPL. Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence. G3 (BETHESDA, MD.) 2022; 12:jkac258. [PMID: 36161485 PMCID: PMC9635642 DOI: 10.1093/g3journal/jkac258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Recent developments allowed generating multiple high-quality 'omics' data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm. We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do that. While gradient boosting machine models captured more phenotypic variation, their predictive performance did not exceed the best linear unbiased prediction models for most traits. Models leveraging gene transcripts captured higher proportions of the phenotypic variance for almost all traits when these were measured closer to the moment of measuring gene transcripts in the liver. In most cases, the combination of layers was not able to outperform the best single-omics models to predict phenotypes. Using only gene transcripts, the gradient boosting machine model was able to outperform best linear unbiased prediction for most traits except body weight, but the same pattern was not observed when using both single nucleotide polymorphism genotypes and gene transcripts. Although the GTCBLUP model was not able to produce the most accurate phenotypic predictions, it showed the highest accuracies for breeding values for 9 out of 13 traits. We recommend using the GTBLUP model for prediction of phenotypes and using the GTCBLUP for prediction of breeding values.
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Affiliation(s)
- Bruno C Perez
- Hendrix Genetics B.V., Research and Technology Center (RTC), 5830 AC Boxmeer, The Netherlands
| | - Marco C A M Bink
- Hendrix Genetics B.V., Research and Technology Center (RTC), 5830 AC Boxmeer, The Netherlands
| | | | | | - Mario P L Calus
- Corresponding author: Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands.
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8
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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9
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Jammer A, Akhtar SS, Amby DB, Pandey C, Mekureyaw MF, Bak F, Roth PM, Roitsch T. Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5170-5198. [PMID: 35675172 DOI: 10.1093/jxb/erac215] [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] [Received: 11/22/2021] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.
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Affiliation(s)
- Alexandra Jammer
- Institute of Biology, University of Graz, NAWI Graz, Schubertstraße 51, 8010 Graz, Austria
| | - Saqib Saleem Akhtar
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Chandana Pandey
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Mengistu F Mekureyaw
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Sciences, Section of Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Peter M Roth
- Institute for Computational Medicine, University of Veterinary Medicine Vienna, Vienna, Austria
- International AI Future Lab, Technical University of Munich, Munich, Germany
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
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10
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Wang C, Li M, Duan X, Abu-Izneid T, Rauf A, Khan Z, Mitra S, Emran TB, Aljohani ASM, Alhumaydhi FA, Thiruvengadam M, Suleria HAR. Phytochemical and Nutritional Profiling of Tomatoes; Impact of Processing on Bioavailability - A Comprehensive Review. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2097692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Chuqi Wang
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Parkville, Victoria, Australia
| | - Minhao Li
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Parkville, Victoria, Australia
| | - Xinyu Duan
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Parkville, Victoria, Australia
| | - Tareq Abu-Izneid
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, Al Ain Campus, United Arab Emirates
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Zidan Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Abdullah S. M. Aljohani
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
- Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - Hafiz A. R. Suleria
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Parkville, Victoria, Australia
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11
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Chele KH, Steenkamp P, Piater LA, Dubery IA, Huyser J, Tugizimana F. A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions. Metabolites 2021; 11:metabo11120820. [PMID: 34940578 PMCID: PMC8709197 DOI: 10.3390/metabo11120820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/10/2021] [Accepted: 11/13/2021] [Indexed: 01/19/2023] Open
Abstract
The ongoing unpredictability of climate changes is exponentially exerting a negative impact on crop production, further aggravating detrimental abiotic stress effects. Several research studies have been focused on the genetic modification of crop plants to achieve more crop resilience against such stress factors; however, there has been a paradigm shift in modern agriculture focusing on more organic, eco-friendly and long-lasting systems to improve crop yield. As such, extensive research into the use of microbial and nonmicrobial biostimulants has been at the core of agricultural studies to improve crop growth and development, as well as to attain tolerance against several biotic and abiotic stresses. However, the molecular mechanisms underlying the biostimulant activity remain enigmatic. Thus, this study is a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics approach to unravel the hypothetical biochemical framework underlying effects of a nonmicrobial biostimulant (a silicon-based formulation) on tomato plants (Solanum lycopersium) under salinity stress conditions. This metabolomics study postulates that Si-based biostimulants could alleviate salinity stress in tomato plants through modulation of the primary metabolism involving changes in the tricarboxylic acid cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways including flavone and flavanol biosynthesis. Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively, explore, design, and fully implement Si-based formulations and strategies into agronomic practices for sustainable agriculture and food production.
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Affiliation(s)
- Kekeletso H. Chele
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
- Correspondence: ; Tel.: +27-011-559-7784
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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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A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis. Metabolites 2021; 11:metabo11050303. [PMID: 34064699 PMCID: PMC8151637 DOI: 10.3390/metabo11050303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 02/01/2023] Open
Abstract
Metabolomics plays an important role in various fields from health to agriculture. However, the comprehensive quantitative metabolomic analysis of plants and plant metabolites has not been widely performed. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based plant metabolomics offers the sensitivity and breadth of coverage for both phenotyping and disease diagnosis of plants. Here, we report a high-coverage and quantitative MS-based assay for plant metabolite analysis. The assay detects and quantifies 206 primary and secondary plant metabolites, including many key plant hormones. In total, it measures 28 amino acids and derivatives, 27 organic acids, 20 biogenic amines and derivatives, 40 acylcarnitines, 90 phospholipids and C-6 sugars. All the analysis methods in this assay are based on LC-MS/MS techniques using both positive and negative-mode multiple reaction monitoring (MRM). The recovery rates of spiked plant samples at three different concentration levels (low, medium and high) ranged from 80% to 120%, with satisfactory precision values of less than 20%. This targeted plant metabolomic assay has been successfully applied to the analysis of large numbers of pine and spruce needle samples, canola root samples, as well as cannabis samples. Moreover, the assay was specifically developed in a 96-well plate format, which enables automated, high-throughput sample analysis. This assay has already been used to analyze over 1500 crop plant samples in less than two months.
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14
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Ara T, Sakurai N, Takahashi S, Waki N, Suganuma H, Aizawa K, Matsumura Y, Kawada T, Shibata D. TOMATOMET: A metabolome database consists of 7118 accurate mass values detected in mature fruits of 25 tomato cultivars. PLANT DIRECT 2021; 5:e00318. [PMID: 33969254 PMCID: PMC8082711 DOI: 10.1002/pld3.318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/18/2021] [Accepted: 03/09/2021] [Indexed: 06/02/2023]
Abstract
The total number of low-molecular-weight compounds in the plant kingdom, most of which are secondary metabolites, is hypothesized to be over one million, although only a limited number of plant compounds have been characterized. Untargeted analysis, especially using mass spectrometry (MS), has been useful for understanding the plant metabolome; however, due to the limited availability of authentic compounds for MS-based identification, the identities of most of the ion peaks detected by MS remain unknown. Accurate mass values of peaks obtained by high accuracy mass measurement and, if available, MS/MS fragmentation patterns provide abundant annotation for each peak. Here, we carried out an untargeted analysis of compounds in the mature fruit of 25 tomato cultivars using liquid chromatography-Orbitrap MS for accurate mass measurement, followed by manual curation to construct the metabolome database TOMATOMET (http://metabolites.in/tomato-fruits/). The database contains 7,118 peaks with accurate mass values, in which 1,577 ion peaks are annotated as members of a chemical group. Remarkably, 71% of the mass values are not found in the accurate masses detected previously in Arabidopsis thaliana, Medicago truncatula or Jatropha curcas, indicating significant chemical diversity among plant species that remains to be solved. Interestingly, substantial chemical diversity exists also among tomato cultivars, indicating that chemical profiling from distinct cultivars contributes towards understanding the metabolome, even in a single organ of a species, and can prioritize some desirable metabolic targets for further applications such as breeding.
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Affiliation(s)
- Takeshi Ara
- Graduate School of AgricultureKyoto UniversityUjiJapan
| | - Nozomu Sakurai
- Kazusa DNA Research InstituteKisarazuJapan
- National Institute of GeneticsMishimaJapan
| | - Shingo Takahashi
- Graduate School of AgricultureKyoto UniversityUjiJapan
- KAGOME CO., LTD.NasushiobaraJapan
| | - Naoko Waki
- Graduate School of AgricultureKyoto UniversityUjiJapan
- KAGOME CO., LTD.NasushiobaraJapan
| | | | | | | | - Teruo Kawada
- Graduate School of AgricultureKyoto UniversityUjiJapan
| | - Daisuke Shibata
- Graduate School of AgricultureKyoto UniversityUjiJapan
- Kazusa DNA Research InstituteKisarazuJapan
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15
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Asakura H, Yamakawa T, Tamura T, Ueda R, Taira S, Saito Y, Abe K, Asakura T. Transcriptomic and Metabolomic Analyses Provide Insights into the Upregulation of Fatty Acid and Phospholipid Metabolism in Tomato Fruit under Drought Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2894-2905. [PMID: 33645220 DOI: 10.1021/acs.jafc.0c06168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transcriptome and metabolome analysis in tomato (Solanum lycopersicum) fruits cultivated under drought conditions showed that drought stress promoted fatty acid synthesis and increased the content of fatty acids in fruits. The accumulation of some phospholipids composed of palmitic acid and oleic acid also was significantly increased, especially in seeds. Moreover, inositol, which is a component of cell membranes and cell walls, was increased through the activity of the myoinositol monophosphatase 1-mediated pathway. In mature fruits, the levels of metabolic regulators such as β-alanine and 4-aminobutyric acid were elevated. These results showed that these compounds are drought-responsive and enhance drought tolerance and subsequently they could enhance the nutritional value and health benefits of tomato fruit.
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Affiliation(s)
- Hiroko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Yamakawa
- Department of Global Agricultural Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tomoko Tamura
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Reiko Ueda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shu Taira
- Faculty of Food and Agricultural Sciences, Cluster of Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan
| | - Yoshikazu Saito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Keiko Abe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Life Science & Environmental Research Center (LiSE), Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, Kanagawa 243-0435, Japan
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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16
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Composition and Antioxidant Activity, Supercritical Carbon Dioxide Extraction Extracts, and Residue after Extraction of Biologically Active Compounds from Freeze-Dried Tomato Matrix. Processes (Basel) 2021. [DOI: 10.3390/pr9030467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Supercritical carbon dioxide extraction (SCE-CO2) is an attractive, green technology that is used for the recovery of biologically active compounds from plant material. The antioxidant potential of lipophilic fractions (extract obtained with SCE-CO2) and hydrophilic fractions (extracts obtained from the residue after extraction) obtained from a matrix of freeze-dried tomatoes (cvs. “Admiro” F1, “Jurgiai”, “Vilina”, “Pirmutis”, and “Skariai”) was assessed via different antioxidant activity methods. The total amount of polyphenols, carotenoids, and carotenoid isomers before and after SCE-CO2 extraction was also determined. To investigate the effect of the SCE-CO2 extract on the viability of cancer cells, rat glioblastoma C6 cells were chosen. The SCE-CO2 yielded an average of 800 mg of lipophilic fraction per 100 g of freeze-dried tomatoes. The ABTS•+ scavenging activity of the extract was 251 ± 3.4 µmol TE/g. After SCE-CO2 extraction, the DPPH•-RSA of the freeze-dried tomato matrix was 7 to 12% higher. There was a strong positive correlation (R = 0.84) between the total polyphenolics content and the DPPH•-RSA of the tomato samples. The SCE-CO2 increased the radical scavenging activity of the extraction residue, indicating that a considerable fraction of the hydrophilic compounds with particular antioxidant capacity remain unextracted from the tomato matrix. Our results reveal the cytotoxic effect of lycopene extract rich in cis-isomers (62% cis-isomers of the total lycopene content) on rat glioblastoma C6 cells. The viability of the glioblastoma C6 cells significantly decreased (−42%) at a total lycopene concentration of 2.4 µM after 24 h of incubation.
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17
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Zheng S, Hao Y, Fan S, Cai J, Chen W, Li X, Zhu X. Metabolomic and Transcriptomic Profiling Provide Novel Insights into Fruit Ripening and Ripening Disorder Caused by 1-MCP Treatments in Papaya. Int J Mol Sci 2021; 22:ijms22020916. [PMID: 33477620 PMCID: PMC7831311 DOI: 10.3390/ijms22020916] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 01/10/2023] Open
Abstract
Treatment with 1-methylcyclopropylene (1-MCP) is an effective technique to preserve fruits, but inappropriate treatment with 1-MCP causes a ripening disorder (rubbery texture) in papaya fruit. In this study, a combined metabolomic and transcriptomic analysis was conducted to reveal the possible mechanism of the ripening disorder caused by unsuitable 1-MCP in papaya. A total of 203 differential accumulated metabolites (DAMs) were identified in the metabolome analysis. Only 24 DAMs were identified in the control (CK) vs. the 1-MCP 2 h group, and they were primarily flavonoids. Ninety and 89 DAMs were identified in the CK vs. 1-MCP 16 h and 1-MCP 2 h vs. 1-MCP 16 h groups, respectively, indicating that long-term 1-MCP treatment severely altered the metabolites during fruit ripening. 1-MCP 16 h treatment severely reduced the number of metabolites, which primarily consisted of flavonoids, lipids, phenolic acids, alkaloids, and organic acids. An integrated analysis of RNA-Seq and metabolomics showed that various energy metabolites for the tricarboxylic acid cycle were reduced by long-term treatment with 1-MCP, and the glycolic acid cycle was the most significantly affected, as well as the phenylpropane pathway. These results provide valuable information for fruit quality control and new insight into the ripening disorder caused by unsuitable treatment with 1-MCP in papaya.
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18
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Ali MY, Sina AAI, Khandker SS, Neesa L, Tanvir EM, Kabir A, Khalil MI, Gan SH. Nutritional Composition and Bioactive Compounds in Tomatoes and Their Impact on Human Health and Disease: A Review. Foods 2020; 10:E45. [PMID: 33375293 PMCID: PMC7823427 DOI: 10.3390/foods10010045] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Tomatoes are consumed worldwide as fresh vegetables because of their high contents of essential nutrients and antioxidant-rich phytochemicals. Tomatoes contain minerals, vitamins, proteins, essential amino acids (leucine, threonine, valine, histidine, lysine, arginine), monounsaturated fatty acids (linoleic and linolenic acids), carotenoids (lycopene and β-carotenoids) and phytosterols (β-sitosterol, campesterol and stigmasterol). Lycopene is the main dietary carotenoid in tomato and tomato-based food products and lycopene consumption by humans has been reported to protect against cancer, cardiovascular diseases, cognitive function and osteoporosis. Among the phenolic compounds present in tomato, quercetin, kaempferol, naringenin, caffeic acid and lutein are the most common. Many of these compounds have antioxidant activities and are effective in protecting the human body against various oxidative stress-related diseases. Dietary tomatoes increase the body's level of antioxidants, trapping reactive oxygen species and reducing oxidative damage to important biomolecules such as membrane lipids, enzymatic proteins and DNA, thereby ameliorating oxidative stress. We reviewed the nutritional and phytochemical compositions of tomatoes. In addition, the impacts of the constituents on human health, particularly in ameliorating some degenerative diseases, are also discussed.
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Affiliation(s)
- Md Yousuf Ali
- Laboratory of Preventive and Integrative Biomedicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (M.Y.A.); (S.S.K.); (A.K.)
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka 1344, Bangladesh
| | - Abu Ali Ibn Sina
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Shahad Saif Khandker
- Laboratory of Preventive and Integrative Biomedicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (M.Y.A.); (S.S.K.); (A.K.)
| | - Lutfun Neesa
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh;
| | - E. M. Tanvir
- Veterinary Drug Residue Analysis Division, Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Savar, Dhaka 1349, Bangladesh;
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Alamgir Kabir
- Laboratory of Preventive and Integrative Biomedicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (M.Y.A.); (S.S.K.); (A.K.)
| | - Md Ibrahim Khalil
- Laboratory of Preventive and Integrative Biomedicine, Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (M.Y.A.); (S.S.K.); (A.K.)
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka 1344, Bangladesh
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
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19
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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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20
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Roch L, Prigent S, Klose H, Cakpo CB, Beauvoit B, Deborde C, Fouillen L, van Delft P, Jacob D, Usadel B, Dai Z, Génard M, Vercambre G, Colombié S, Moing A, Gibon Y. Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5823-5836. [PMID: 32592486 PMCID: PMC7540837 DOI: 10.1093/jxb/eraa302] [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: 03/05/2020] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
Abstract
Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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Affiliation(s)
- Léa Roch
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Sylvain Prigent
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Holger Klose
- Institute for Biology, BioSC, RWTH Aachen University, Worringer Weg, Aachen, Germany
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Bertrand Beauvoit
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Catherine Deborde
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Laetitia Fouillen
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- UMR 5200, CNRS, Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Pierre van Delft
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- UMR 5200, CNRS, Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Daniel Jacob
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Björn Usadel
- Institute for Biology, BioSC, RWTH Aachen University, Worringer Weg, Aachen, Germany
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Zhanwu Dai
- UMR 1287 EGFV, INRAE, Univ. Bordeaux, Bordeaux Sci Agro, Villenave d’Ornon, France
| | | | | | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Annick Moing
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
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21
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Abreu AC, Fernández I. NMR Metabolomics Applied on the Discrimination of Variables Influencing Tomato ( Solanum lycopersicum). Molecules 2020; 25:E3738. [PMID: 32824282 PMCID: PMC7463728 DOI: 10.3390/molecules25163738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 02/07/2023] Open
Abstract
Tomato composition and nutritional value are attracting increasing attention and interest from both consumers and producers. The interest in enhancing fruits' quality with respect to beneficious nutrients and flavor/aroma components is based not only in their economic added value but also in their implications involving organoleptic and healthy properties and has generated considerable research interest among nutraceutical and horticultural industries. The present article reviews up to March 2020 some of the most relevant studies based on the application of NMR coupled to multivariate statistical analysis that have addressed the investigation on tomato (Solanum lycopersicum). Specifically, the NMR untargeted technique in the agri-food sector can generate comprehensive data on metabolic networks and is paving the way towards the understanding of variables affecting tomato crops and composition such as origin, variety, salt-water irrigation, cultivation techniques, stage of development, among many others. Such knowledge is helpful to improve fruit quality through cultural practices that divert the metabolism towards the desired pathways and, probably more importantly, drives further efforts towards the differentiation of those crops developed under controlled and desired agronomical conditions.
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Affiliation(s)
| | - Ignacio Fernández
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, 04120 Almería, Spain;
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22
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Bagley MC, Pace CL, Ekelöf M, Muddiman DC. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging analysis of endogenous metabolites in cherry tomatoes. Analyst 2020; 145:5516-5523. [PMID: 32602477 PMCID: PMC7423647 DOI: 10.1039/d0an00818d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the spatially resolved metabolic profiling of cherry tomatoes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI), a mass spectrometry imaging (MSI) technique that operates at ambient conditions and requires no sample derivatization. Tomatoes were flash frozen, cryosectioned and imaged with adequate spatial resolution to distinguish between the major tissue structures of a tomato including the skin, mesocarp, endocarp, locular tissue, septum, placenta, seed and seed coating. Metabolites were imaged from 100-1200 m/z, enabling significant coverage of a diverse array of metabolites including amino acids and lipids along with the major secondary metabolite classes: terpenes, phenolics, glycosides, and alkaloids. During the metabolic profiling, we found endogenous carotenoid hydrocarbons, namely lycopene or its structural isomer β-carotene, ionized as radical cations. To our knowledge, this is the first demonstration of ionizing hydrocarbons in the MSI field.
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Affiliation(s)
- M Caleb Bagley
- FTMS Laboratory for Human Health Research, Department of Chemistry, USA.
| | - Crystal L Pace
- FTMS Laboratory for Human Health Research, Department of Chemistry, USA.
| | - Måns Ekelöf
- FTMS Laboratory for Human Health Research, Department of Chemistry, USA.
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, USA. and Department of Plant and Microbial Biology, USA and Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA
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23
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24
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Mochida K, Nishii R, Hirayama T. Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. PLANT & CELL PHYSIOLOGY 2020; 61:1408-1418. [PMID: 32392328 PMCID: PMC7434589 DOI: 10.1093/pcp/pcaa064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/26/2020] [Indexed: 05/16/2023]
Abstract
To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants' later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant-environment interactions by elucidating plants' temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant-environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Corresponding author: E-mail, ; Fax, +81-45-503-9609
| | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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25
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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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26
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Fantini E, Facella P. Cryptochromes in the field: how blue light influences crop development. PHYSIOLOGIA PLANTARUM 2020; 169:336-346. [PMID: 32175597 DOI: 10.1111/ppl.13088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 05/02/2023]
Abstract
Light is a pivotal environmental element capable of influencing multiple physiological processes across the entire plant life cycle. Over the course of their evolution, plants have developed several families of photoreceptors such as phytochromes, phototropins, ultraviolet (UV) resistance locus 8 and cryptochromes (crys), in order to sense light stimuli and respond to their changes. Numerous genetic studies have demonstrated that functional alterations to these photoreceptors cause a change in important agronomical traits. In particular, crys, which absorb UVA/blue light, can influence seed germination, flowering induction, plant architecture, fruit metabolic content and resistance to biotic and abiotic stresses. In the years to come, the rising temperatures and alterations to precipitation patterns generated by climate change will present a dramatic challenge for our agricultural system, with its few varieties characterized by a narrow genetic pool derived from artificial selection. Here, we review the main roles of crys in determining important agronomic traits in crops, we discuss the opportunities of using these photoreceptors as genetic targets for tuning plant physiological responses to environmental change, and the molecular strategies used so far to manipulate this family of photoreceptors.
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Affiliation(s)
- Elio Fantini
- Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Trisaia Research Center, 75026, Rotondella (Matera), Italy
| | - Paolo Facella
- Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Trisaia Research Center, 75026, Rotondella (Matera), Italy
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27
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Bakir S, Capanoglu E, Hall RD, de Vos RCH. Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey. Food Chem 2020; 317:126406. [PMID: 32097823 DOI: 10.1016/j.foodchem.2020.126406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 01/28/2023]
Abstract
In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) of the relative abundance levels of >250 metabolites, it could be concluded that fruit size was the most influential to the biochemical composition, rather than the geographical origin of accessions. Results indicated substantial biodiversity in various metabolites generally regarded as key to fruit quality aspects, including sugars; phenolic compounds like phenylpropanoids and flavonoids; alkaloids and glycosides of flavour-related volatile compounds. The phytochemical data provides insight into which Turkish accessions might be most promising as starting materials for the tomato processing and breeding industries.
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Affiliation(s)
- Sena Bakir
- Istanbul Technical University, Faculty of Chemical and Metallurgical Engineering, Food Engineering Department, Maslak, Istanbul, Turkey; Recep Tayyip Erdogan University, Faculty of Engineering, Merkez, Rize, Turkey
| | - Esra Capanoglu
- Istanbul Technical University, Faculty of Chemical and Metallurgical Engineering, Food Engineering Department, Maslak, Istanbul, Turkey.
| | - Robert D Hall
- Bioscience, Wageningen University and Research Centre (Wageningen-UR), PO Box 16, 6700 AA Wageningen, The Netherlands; Laboratory of Plant Physiology, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Ric C H de Vos
- Bioscience, Wageningen University and Research Centre (Wageningen-UR), PO Box 16, 6700 AA Wageningen, The Netherlands.
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28
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Special Issue on "Fruit Metabolism and Metabolomics". Metabolites 2020; 10:metabo10060230. [PMID: 32503284 PMCID: PMC7344593 DOI: 10.3390/metabo10060230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.
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29
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Calumpang CLF, Saigo T, Watanabe M, Tohge T. Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops. Metabolites 2020; 10:E209. [PMID: 32438728 PMCID: PMC7281770 DOI: 10.3390/metabo10050209] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/03/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022] Open
Abstract
Many solanaceous crops are an important part of the human daily diet. Fruit polyphenolics are plant specialized metabolites that are recognized for their human health benefits and their defensive role against plant abiotic and biotic stressors. Flavonoids and chlorogenates are the major polyphenolic compounds found in solanaceous fruits that vary in quantity, physiological function, and structural diversity among and within plant species. Despite their biological significance, the elucidation of metabolic shifts of polyphenols during fruit ripening in different fruit tissues, has not yet been well-characterized in solanaceous crops, especially at a cross-species and cross-cultivar level. Here, we performed a cross-species comparison of fruit-metabolomics to elucidate the metabolic regulation of fruit polyphenolics from three representative crops of Solanaceae (tomato, eggplant, and pepper), and a cross-cultivar comparison among different pepper cultivars (Capsicum annuum cv.) using liquid chromatography-mass spectrometry (LC-MS). We observed a metabolic trade-off between hydroxycinnamates and flavonoids in pungent pepper and anthocyanin-type pepper cultivars and identified metabolic signatures of fruit polyphenolics in each species from each different tissue-type and fruit ripening stage. Our results provide additional information for metabolomics-assisted crop improvement of solanaceous fruits towards their improved nutritive properties and enhanced stress tolerance.
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Affiliation(s)
| | | | | | - Takayuki Tohge
- Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan; (C.L.F.C.); (T.S.); (M.W.)
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30
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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31
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Kuhalskaya A, Wijesingha Ahchige M, Perez de Souza L, Vallarino J, Brotman Y, Alseekh S. Network Analysis Provides Insight into Tomato Lipid Metabolism. Metabolites 2020; 10:metabo10040152. [PMID: 32295308 PMCID: PMC7240963 DOI: 10.3390/metabo10040152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.
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Affiliation(s)
- Anastasiya Kuhalskaya
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Micha Wijesingha Ahchige
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - José Vallarino
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +49-(0)331-567-8211
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32
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Zhang X, Tang H, Du H, Liu Z, Bao Z, Shi Q. Comparative N-glycoproteome analysis provides novel insights into the regulation mechanism in tomato (solanum lycopersicum L.) During fruit ripening process. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110413. [PMID: 32081262 DOI: 10.1016/j.plantsci.2020.110413] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/08/2020] [Accepted: 01/11/2020] [Indexed: 05/27/2023]
Abstract
Protein N-glycosylation plays key roles in protein folding, stability, solubility, biogenesis, and enzyme activity. Tomato (Solanum lycopersicum L.) is an important vegetable crop with abundant nutritional value, and the formation of tomato fruit qualities primarily occurs in the fruit ripening process. However, a large number of N-glycosylation-mediated mechanisms in regulating tomato fruit ripening have not been elucidated to date. In this study, western blot assays showed that the extents of mature N-glycoproteins were differentially expressed in mature green fruits (fruit start ripening) and ripe fruits (fruit stop ripening). Next, through performing a comparative N-glycoproteome analysis strategy, a total of 553 N-glycosites from 363 N-glycoproteins were identified in mature green fruits compared with ripe fruits. Among them, 252 N-glycosites from 191 N-glycoproteins were differentially expressed in mature green fruits compared with ripe fruits. The differentially expressed N-glycoproteins were mainly located in the chloroplast (30 %) and cytoplasm (16 %). Gene Ontology (GO) analysis showed that these N-glycoproteins were involved in various biological processes, cellular components and molecular functions. These N-glycoproteins participate in biological processes, such as metabolic processes, cellular processes and single-organism processes. These N-glycoproteins are also cellular components in biological process cells, membranes and organelles and have different molecular functions, such as catalytic activity and binding. Notably, these N-glycoproteins were enriched in starch and sucrose metabolism and galactose metabolism by KEGG pathway analysis. This community resource regarding N-glycoproteins is the first large-scale N-glycoproteome during plant fruit ripening. This study will contribute to understanding the function of N-glycosylation in regulating plant fruit ripening.
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Affiliation(s)
- Xu Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Huimeng Tang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Han Du
- College of food science and engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Zhen Liu
- Jingjie PTM Biolab Co. Ltd, Hangzhou 310018, PR China.
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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Quinet M, Angosto T, Yuste-Lisbona FJ, Blanchard-Gros R, Bigot S, Martinez JP, Lutts S. Tomato Fruit Development and Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:1554. [PMID: 31850035 PMCID: PMC6895250 DOI: 10.3389/fpls.2019.01554] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.
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Affiliation(s)
- Muriel Quinet
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Rémi Blanchard-Gros
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Servane Bigot
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Naves ER, de Ávila Silva L, Sulpice R, Araújo WL, Nunes-Nesi A, Peres LEP, Zsögön A. Capsaicinoids: Pungency beyond Capsicum. TRENDS IN PLANT SCIENCE 2019; 24:109-120. [PMID: 30630668 DOI: 10.1016/j.tplants.2018.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/22/2018] [Accepted: 11/09/2018] [Indexed: 05/08/2023]
Abstract
Capsaicinoids are metabolites responsible for the appealing pungency of Capsicum (chili pepper) species. The completion of the Capsicum annuum genome has sparked new interest into the development of biotechnological applications involving the manipulation of pungency levels. Pungent dishes are already part of the traditional cuisine in many countries, and numerous health benefits and industrial applications are associated to capsaicinoids. This raises the question of how to successfully produce more capsaicinoids, whose biosynthesis is strongly influenced by genotype-environment interactions in fruits of Capsicum. In this Opinion article we propose that activating the capsaicinoid biosynthetic pathway in a more amenable species such as tomato could be the next step in the fascinating story of pungent crops.
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Affiliation(s)
- Emmanuel Rezende Naves
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lucas de Ávila Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Ronan Sulpice
- Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre (PABC) and Ryan Institute, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lázaro E P Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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Cui L, Lu H, Lee YH. Challenges and emergent solutions for LC-MS/MS based untargeted metabolomics in diseases. MASS SPECTROMETRY REVIEWS 2018; 37:772-792. [PMID: 29486047 DOI: 10.1002/mas.21562] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023]
Abstract
In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks. Second, partial, incomplete metabolomes persist due to factors such as limitations in mass spectrometry data acquisition speeds, wide-range of metabolites concentrations, and cellular/tissue/temporal-specific expression changes that confound our understanding of metabolite perturbations. Third, to contextualize metabolites in pathways and biology is difficult because many metabolites partake in multiple pathways, have yet to be described species specificity, or possess unannotated or more-complex functions that are not easily characterized through metabolomics analyses. From a translational perspective, information related to novel metabolite biomarkers, metabolic pathways, and drug targets might be sparser than they should be. Thankfully, significant progress has been made and novel solutions are emerging, achieved through sustained academic and industrial community efforts in terms of hardware, computational, and experimental approaches. Given the rapidly growing utility of metabolomics, this review will offer new perspectives, increase awareness of the major challenges in LC-MS metabolomics that will significantly benefit the metabolomics community and also the broader the biomedical community metabolomics aspire to serve.
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Affiliation(s)
- Liang Cui
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- Infectious Diseases-Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Haitao Lu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yie Hou Lee
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- OBGYN-Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
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Genetic diversity of strawberry germplasm using metabolomic biomarkers. Sci Rep 2018; 8:14386. [PMID: 30258188 PMCID: PMC6158285 DOI: 10.1038/s41598-018-32212-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput metabolomics technologies can provide the quantification of metabolites levels across various biological processes in different tissues, organs and species, allowing the identification of genes underpinning these complex traits. Information about changes of metabolites during strawberry development and ripening processes is key to aiding the development of new approaches to improve fruit attributes. We used network-based methods and multivariate statistical approaches to characterize and investigate variation in the primary and secondary metabolism of seven domesticated and seven wild strawberry fruit accessions at three different fruit development and ripening stages. Our results demonstrated that Fragaria sub-species can be identified solely based on the gathered metabolic profiles. We also showed that domesticated accessions displayed highly similar metabolic changes due to shared domestication history. Differences between domesticated and wild accessions were detected at the level of metabolite associations which served to rank metabolites whose regulation was mostly altered in the process of domestication. The discovery of comprehensive metabolic variation among strawberry accessions offers opportunities to probe into the genetic basis of variation, providing insights into the pathways to relate metabolic variation with important traits.
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Paolo D, Bianchi G, Scalzo RL, Morelli CF, Rabuffetti M, Speranza G. The Chemistry behind Tomato Quality. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Tomato is one of the most widely consumed fresh vegetables in the industrialized world and an important source of healthy constituents of the human diet. Despite the unique flavor characteristics of tomatoes, which make them extremely valuable in cooking, and their recognized beneficial role in the diet, the quality of tomato was traditionally only considered in connection to external appearances. As it happened with other highly requested crops, breeding programs of tomato focused their efforts on developing new varieties with higher yields and stress resistance, with better uniformity in fruit size, brighter color and prolonged shelf life. The downside of these strategies was that organoleptic features and nutritional value were often neglected, with a detrimental effect on commercial tomatoes. Over the last years, there has been an increase in consumers’ demand for tasty and healthy products. This aspect, paired with novel and multidisciplinary approaches to tomato research, allowed both sensory and nutritional qualities to be reconsidered as valuable parameters in breeding. In this review we describe the main chemical constituents of tomato, focusing on the flavor compounds (both volatile and non-volatile compounds) and secondary metabolites. Particular attention is paid to their beneficial effects on human health and their relevance to the overall quality of tomato.
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Affiliation(s)
- Dario Paolo
- Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, CREA-IT, 20133 Milano, Italy
| | - Giulia Bianchi
- Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, CREA-IT, 20133 Milano, Italy
| | - Roberto Lo Scalzo
- Centro di Ricerca Ingegneria e Trasformazioni Agroalimentari, CREA-IT, 20133 Milano, Italy
| | - Carlo F. Morelli
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Marco Rabuffetti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, 20133 Milano, Italy
| | - Giovanna Speranza
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), CNR, 20133 Milano, Italy
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Chiu KH, Dong CD, Chen CF, Tsai ML, Ju YR, Chen TM, Chen CW. NMR-based metabolomics for the environmental assessment of Kaohsiung Harbor sediments exemplified by a marine amphipod (Hyalella azteca). MARINE POLLUTION BULLETIN 2017; 124:714-724. [PMID: 28267993 DOI: 10.1016/j.marpolbul.2017.02.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 02/21/2017] [Accepted: 02/24/2017] [Indexed: 05/08/2023]
Abstract
Inflow of wastewater from upstream causes a large flux of pollutants to enter Kaohsiung Harbor in Taiwan daily. To reveal the ecological risk posed by Kaohsiung Harbor sediments, an ecological metabolomic approach was employed to investigate environmental factors pertinent to the physiological regulation of the marine amphipod Hyalella azteca. The amphipods were exposed to sediments collected from different stream inlets of the Love River (LR), Canon River (CR), Jen-Gen River (JR), and Salt River (SR). Harbor entrance 1 (E1) was selected as a reference site. After 10-day exposure, metabolomic analysis of the Hyalella azteca revealed differences between two groups: {E1, LR, CR} and {JR, SR}. The metabolic pathways identified in the two groups of amphipods were significantly different. The results demonstrated that NMR-based metabolomics can be effectively used to characterize metabolic response related to sediment from polluted areas.
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Affiliation(s)
- K H Chiu
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - C D Dong
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan; Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - C F Chen
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - M L Tsai
- Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Y R Ju
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - T M Chen
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - C W Chen
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan.
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Marmiroli M, Mussi F, Imperiale D, Marmiroli N. Target proteins reprogrammed by As and As + Si treatments in Solanum lycopersicum L. fruit. BMC PLANT BIOLOGY 2017; 17:210. [PMID: 29157202 PMCID: PMC5696772 DOI: 10.1186/s12870-017-1168-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/10/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arsenic is an important contaminant of many arable soils worldwide, while silicon, one of the most abundant elements in the earth's crust, interacts with As in the context of plant metabolism. As toxicity results largely from its stimulation of reactive oxygen species, and it is believed that Si can mitigate this process through reduction of the level of oxidative stress. Experiments targeting the proteomic impact of exposure to As and Si have to date largely focused on analyses of root, shoot and seed of a range of mainly non-solanaceous species, thus it remains unclear whether oxidative stress is the most important manifestation of As toxicity in Solanum lycopersicum fruit which during ripening go through drastic physiological and molecular readjustments. The role of Si also needs to be re-evaluated. RESULTS A comparison was drawn between the proteomic responses to As and As + Si treatments of the fruit of two tomato cultivars (cvs. Aragon and Gladis) known to contrast for their ability to take up these elements and to translocate them into fruits. Treatments were applied at the beginning of the red ripening stage, and the fruit proteomes were captured after a 14 day period of exposure. For each cultivar, a set of differentially abundant fruit proteins (from non-treated and treated plants) were isolated by 2DGE and identified using mass spectrometry. In the fruit of cv. Aragon, the As treatment reprogrammed proteins largely involved in transcription regulation (growth- regulating factor 9-like), and cell structure (actin-51), while in the cv. Gladis, the majority of differentially expressed proteins were associated with protein ubiquitination and proteolysis (E3 ubiquitin protein, and hormones (1-aminocyclopropane 1-carboxylase). CONCLUSIONS The present experiments were intended to establish whether Si supplementation can be used to reverse the proteomic disturbance induced by the As treatment; this reprogram was only partial and more effective in the fruit of cv. Gladis than in that of cv. Aragon. Proteins responsible for the protection of the fruits' quality in the face of As-induced stress were identified. Moreover, supplementation with Si seemed to limit to a degree the accumulation of As in the tomato fruit of cv. Aragon.
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Affiliation(s)
- Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Francesca Mussi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Davide Imperiale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Sangireddy S, Okekeogbu I, Ye Z, Zhou S, Howe KJ, Fish T, Thannhauser TW. Effects of Al 3+ and La 3+ Trivalent Metal Ions on Tomato Fruit Proteomes. Proteomes 2017; 5:proteomes5010007. [PMID: 28248258 PMCID: PMC5372228 DOI: 10.3390/proteomes5010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/26/2017] [Accepted: 02/07/2017] [Indexed: 12/18/2022] Open
Abstract
The tomato (Solanum lycopersicum) ripening process from mature green (MG) to turning and then to red stages is accompanied by the occurrences of physiological and biochemical reactions, which ultimately result in the formation of the flavor, color and texture of ripe fruits. The two trivalent metal ions Al3+ and La3+ are known to induce different levels of phytotoxicity in suppressing root growth. This paper aims to understand the impacts of these two metal ions on tomato fruit proteomes. Tomato ‘Micro-Tom’ plants were grown in a hydroponic culture system supplemented with 50 μM aluminum sulfate (Al2 (SO4)3.18H2O) for Al3+ or La2(SO4)3 for La3+. Quantitative proteomics analysis, using isobaric tags for relative and absolute quantitation, were performed for fruits at MG, turning and red stages. Results show that in MG tomatoes, proteins involved in protein biosynthesis, photosynthesis and primary carbohydrate metabolisms were at a significantly lower level in Al-treated compared to La-treated plants. For the turning and red tomatoes, only a few proteins of significant differences between the two metal treatments were identified. Results from this study indicate that compared to La3+, Al3+ had a greater influence on the basic biological activities in green tomatoes, but such an impact became indistinguishable as tomatoes matured into the late ripening stages.
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Affiliation(s)
- Sasikiran Sangireddy
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Ikenna Okekeogbu
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Zhujia Ye
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Kevin J Howe
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
| | - Tara Fish
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
| | - Theodore W Thannhauser
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
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Rangel-Huerta OD, Gil A. Nutrimetabolomics: An Update on Analytical Approaches to Investigate the Role of Plant-Based Foods and Their Bioactive Compounds in Non-Communicable Chronic Diseases. Int J Mol Sci 2016; 17:ijms17122072. [PMID: 27941699 PMCID: PMC5187872 DOI: 10.3390/ijms17122072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/28/2016] [Accepted: 12/03/2016] [Indexed: 12/17/2022] Open
Abstract
Metabolomics is the study of low-weight molecules present in biological samples such as biofluids, tissue/cellular extracts, and culture media. Metabolomics research is increasing, and at the moment, it has several applications in the food science and nutrition fields. In the present review, we provide an update about the most frequently used methodologies and metabolomic platforms in these areas. Also, we discuss different metabolomic strategies regarding the discovery of new bioactive compounds (BACs) in plant-based foods. Furthermore, we review the existing literature related to the use of metabolomics to investigate the potential protective role of BACs in the prevention and treatment of non-communicable chronic diseases, namely cardiovascular disease, diabetes, and cancer.
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Affiliation(s)
- Oscar Daniel Rangel-Huerta
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology "José Mataix", Center for Biomedical Research, University of Granada, 18100 Granada, Spain.
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology "José Mataix", Center for Biomedical Research, University of Granada, 18100 Granada, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Ciberobn, 28029 Madrid, Spain.
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Ikeda H, Shibuya T, Imanishi S, Aso H, Nishiyama M, Kanayama Y. Dynamic Metabolic Regulation by a Chromosome Segment from a Wild Relative During Fruit Development in a Tomato Introgression Line, IL8-3. PLANT & CELL PHYSIOLOGY 2016; 57:1257-1270. [PMID: 27076398 DOI: 10.1093/pcp/pcw075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
We performed comparative metabolome and transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. Marked differences between M82 and IL8-3 were found not only in ripe fruits but also at 20 days after flowering (DAF) in the hierarchical clustering analysis of the metabolome, whereas patterns were similar between the two genotypes at 10 and 30 DAF. Our metabolome analysis conclusively showed that 20 DAF is an important stage of fruit metabolism and that the Solanum pennellii introgressed region in IL8-3 plays a key role in metabolic changes at this stage. Carbohydrate and amino acid metabolism were found to be promoted in IL8-3 at 20 DAF and the ripening stage, respectively, whereas transcriptome analysis showed no marked differences between the two genotypes, indicating that dynamic metabolic regulation at 20 DAF and the ripening stage was controlled by relatively few genes. The transcript levels of the cell wall invertase (LIN6) and sucrose synthase (TOMSSF) genes in starch and sucrose metabolic pathway and that of the glutamate synthase (SlGOGAT) gene in the amino acid metabolic pathway in IL8-3 fruit were higher than those in M82, and SlGOGAT expression was enhanced under high-sugar conditions. The results suggest that the promotion of carbohydrate metabolism by LIN6 and TOMSSF in IL8-3 fruit at 20 DAF affects SlGOGAT expression and amino acid accumulation via higher sugar concentration at the late stage of fruit development.
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Affiliation(s)
- Hiroki Ikeda
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan Present address: (H. Ikeda), NARO Tohoku Agricultural Research Center, Morioka 020-0198, Japan
| | - Tomoki Shibuya
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Shunsuke Imanishi
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, 514-2392 Japan
| | - Hisashi Aso
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Manabu Nishiyama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan
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Dai Z, Wu H, Baldazzi V, van Leeuwen C, Bertin N, Gautier H, Wu B, Duchêne E, Gomès E, Delrot S, Lescourret F, Génard M. Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits. FRONTIERS IN PLANT SCIENCE 2016; 7:649. [PMID: 27242850 PMCID: PMC4872523 DOI: 10.3389/fpls.2016.00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/28/2016] [Indexed: 05/03/2023]
Abstract
The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.
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Affiliation(s)
- Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | - Huan Wu
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | | | | | - Nadia Bertin
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
| | - Hélène Gautier
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
| | - Benhong Wu
- Institute of Botany – Chinese Academy of SciencesBeijing, China
| | | | - Eric Gomès
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | | | - Michel Génard
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
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46
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Dai Z, Wu H, Baldazzi V, van Leeuwen C, Bertin N, Gautier H, Wu B, Duchêne E, Gomès E, Delrot S, Lescourret F, Génard M. Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27242850 DOI: 10.3389/fcls.2016.00649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.
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Affiliation(s)
- Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | - Huan Wu
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | | | | | - Nadia Bertin
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
| | - Hélène Gautier
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
| | - Benhong Wu
- Institute of Botany - Chinese Academy of Sciences Beijing, China
| | | | - Eric Gomès
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | | | - Michel Génard
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
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