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de Souza LP, Borghi M, Fernie A. Plant Single-Cell Metabolomics-Challenges and Perspectives. Int J Mol Sci 2020; 21:E8987. [PMID: 33256100 PMCID: PMC7730874 DOI: 10.3390/ijms21238987] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.
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Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| | - Monica Borghi
- Department of Biology, Utah State University, 1435 Old Main Hill, Logan, UT 84322, USA;
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
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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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53
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Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response. Nat Genet 2020; 52:1111-1121. [PMID: 32989321 DOI: 10.1038/s41588-020-0690-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.
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Li Y, Chen Y, Zhou L, You S, Deng H, Chen Y, Alseekh S, Yuan Y, Fu R, Zhang Z, Su D, Fernie AR, Bouzayen M, Ma T, Liu M, Zhang Y. MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle. MOLECULAR PLANT 2020; 13:1203-1218. [PMID: 32561360 DOI: 10.1016/j.molp.2020.06.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/07/2020] [Accepted: 06/10/2020] [Indexed: 05/21/2023]
Abstract
Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants.
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Affiliation(s)
- Yan Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Yang Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Lu Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Shengjie You
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Heng Deng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Ya Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Plant Biotechnology, 4000 Plovdiv, Bulgaria
| | - Yong Yuan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Zixin Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Dan Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Plant Biotechnology, 4000 Plovdiv, Bulgaria
| | - Mondher Bouzayen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China; GBF, University of Toulouse, INRA, Castanet-Tolosan, France
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China.
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China.
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