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Zulfiqar U, Khokhar A, Maqsood MF, Shahbaz M, Naz N, Sara M, Maqsood S, Sahar S, Hussain S, Ahmad M. Genetic biofortification: advancing crop nutrition to tackle hidden hunger. Funct Integr Genomics 2024; 24:34. [PMID: 38365972 DOI: 10.1007/s10142-024-01308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Malnutrition, often termed "hidden hunger," represents a pervasive global issue carrying significant implications for health, development, and socioeconomic conditions. Addressing the challenge of inadequate essential nutrients, despite sufficient caloric intake, is crucial. Biofortification emerges as a promising solution by enhance the presence of vital nutrients like iron, zinc, iodine, and vitamin A in edible parts of different crop plants. Crop biofortification can be attained through either agronomic methods or genetic breeding techniques. Agronomic strategies for biofortification encompass the application of mineral fertilizers through foliar or soil methods, as well as leveraging microbe-mediated mechanisms to enhance nutrient uptake. On the other hand, genetic biofortification involves the strategic crossing of plants to achieve a desired combination of genes, promoting balanced nutrient uptake and bioavailability. Additionally, genetic biofortification encompasses innovative methods such as speed breeding, transgenic approaches, genome editing techniques, and integrated omics approaches. These diverse strategies collectively contribute to enhancing the nutritional profile of crops. This review highlights the above-said genetic biofortification strategies and it also covers the aspect of reduction in antinutritional components in food through genetic biofortification.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Amman Khokhar
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Maheen Sara
- Department of Nutritional Sciences, Government College Women University, Faisalabad, Pakistan
| | - Sana Maqsood
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sajila Sahar
- Department of Plant Breeding & Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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Avnee, Sood S, Chaudhary DR, Jhorar P, Rana RS. Biofortification: an approach to eradicate micronutrient deficiency. Front Nutr 2023; 10:1233070. [PMID: 37789898 PMCID: PMC10543656 DOI: 10.3389/fnut.2023.1233070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Micronutrient deficiency also known as "hidden hunger" refers to a condition that occurs when the body lacks essential vitamins and minerals that are required in small amounts for proper growth, development and overall health. These deficiencies are particularly common in developing countries, where a lack of access to a varied and nutritious diet makes it difficult for people to get the micronutrients they need. Micronutrient supplementation has been a topic of interest, especially during the Covid-19 pandemic, due to its potential role in supporting immune function and overall health. Iron (Fe), zinc (Zn), iodine (I), and selenium (Se) deficiency in humans are significant food-related issues worldwide. Biofortification is a sustainable strategy that has been developed to address micronutrient deficiencies by increasing the levels of essential vitamins and minerals in staple crops that are widely consumed by people in affected communities. There are a number of agricultural techniques for biofortification, including selective breeding of crops to have higher levels of specific nutrients, agronomic approach using fertilizers and other inputs to increase nutrient uptake by crops and transgenic approach. The agronomic approach offers a temporary but speedy solution while the genetic approach (breeding and transgenic) is the long-term solution but requires time to develop a nutrient-rich variety.
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Affiliation(s)
- Avnee
- Department of Agronomy, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Sonia Sood
- Department of Vegetable Science and Floriculture, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Desh Raj Chaudhary
- Department of Vegetable Science and Floriculture, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Pooja Jhorar
- Department of Agronomy, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Ranbir Singh Rana
- Department of Agronomy, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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Álvarez-Urdiola R, Matus JT, Riechmann JL. Multi-Omics Methods Applied to Flower Development. Methods Mol Biol 2023; 2686:495-508. [PMID: 37540374 DOI: 10.1007/978-1-0716-3299-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Developmental processes in multicellular organisms depend on the proficiency of cells to orchestrate different gene expression programs. Over the past years, several studies of reproductive organ development have considered genomic analyses of transcription factors and global gene expression changes, modeling complex gene regulatory networks. Nevertheless, the dynamic view of developmental processes requires, as well, the study of the proteome in its expression, complexity, and relationship with the transcriptome. In this chapter, we describe a dual extraction method-for protein and RNA-for the characterization of genome expression at proteome level and its correlation to transcript expression data. We also present a shotgun proteomic procedure (LC-MS/MS) followed by a pipeline for the imputation of missing values in mass spectrometry results.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Wan D, Wan Y, Zhang T, Wang R, Ding Y. Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis. FRONTIERS IN PLANT SCIENCE 2022; 13:995074. [PMID: 36407579 PMCID: PMC9673880 DOI: 10.3389/fpls.2022.995074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.
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Affiliation(s)
- Dongli Wan
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yongqing Wan
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Tongrui Zhang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ruigang Wang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong Ding
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
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Current Status and Potential of Biofortification to Enhance Crop Nutritional Quality: An Overview. SUSTAINABILITY 2022. [DOI: 10.3390/su14063301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Around 2 billion people are suffering from chronic malnutrition or “hidden hunger”, which is the result of many diseases and disorders, including cognitive degeneration, stunting growth, and mortality. Thus, biofortification of staple food crops enriched with micronutrients is a more sustainable option for providing nutritional supplements and managing malnutrition in a society. Since 2001, when the concept of biofortification came to light, different research activities have been carried out, like the development of target populations, breeding or genetic engineering, and the release of biofortified cultivars, in addition to conducting nutritional efficacy trials and delivery plan development. Although, being a cost-effective intervention, it still faces many challenges, like easy accessibility of biofortified cultivars, stakeholders’ acceptance, and the availability of biofortified germplasm in the public domain, which varies from region to region. Hence, this review is focused on the recent potential, efforts made to crop biofortification, impacts analysis on human health, cost-effectiveness, and future perspectives to further strengthen biofortification programs. Through regular interventions of sustainable techniques and methodologies, biofortification holds huge potential to solve the malnutrition problem through regular interventions of nutrient-enriched staple food options for billions of people globally.
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Pérez L, Alves R, Perez-Fons L, Albacete A, Farré G, Soto E, Vilaprinyó E, Martínez-Andújar C, Basallo O, Fraser PD, Medina V, Zhu C, Capell T, Christou P. Multilevel interactions between native and ectopic isoprenoid pathways affect global metabolism in rice. Transgenic Res 2022; 31:249-268. [PMID: 35201538 PMCID: PMC8993735 DOI: 10.1007/s11248-022-00299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/28/2022] [Indexed: 11/29/2022]
Abstract
Isoprenoids are natural products derived from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, these precursors are synthesized via the cytosolic mevalonate (MVA) and plastidial methylerythritol phosphate (MEP) pathways. The regulation of these pathways must therefore be understood in detail to develop effective strategies for isoprenoid metabolic engineering. We hypothesized that the strict regulation of the native MVA pathway could be circumvented by expressing an ectopic plastidial MVA pathway that increases the accumulation of IPP and DMAPP in plastids. We therefore introduced genes encoding the plastid-targeted enzymes HMGS, tHMGR, MK, PMK and MVD and the nuclear-targeted transcription factor WR1 into rice and evaluated the impact of their endosperm-specific expression on (1) endogenous metabolism at the transcriptomic and metabolomic levels, (2) the synthesis of phytohormones, carbohydrates and fatty acids, and (3) the macroscopic phenotype including seed morphology. We found that the ectopic plastidial MVA pathway enhanced the expression of endogenous cytosolic MVA pathway genes while suppressing the native plastidial MEP pathway, increasing the production of certain sterols and tocopherols. Plants carrying the ectopic MVA pathway only survived if WR1 was also expressed to replenish the plastid acetyl-CoA pool. The transgenic plants produced higher levels of fatty acids, abscisic acid, gibberellins and lutein, reflecting crosstalk between phytohormones and secondary metabolism.
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Affiliation(s)
- Lucía Pérez
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Rui Alves
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, UK
| | - Alfonso Albacete
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, 30100, Murcia, Espinardo, Spain
- Department of Plant Production and Agrotechnology, Institute for Agri-Food Research and Development of Murcia, Murcia, La Alberca, Spain
| | - Gemma Farré
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Erika Soto
- Department of Chemistry, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Ester Vilaprinyó
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
- IRBLleida, Lleida, Catalunya, Spain
| | - Cristina Martínez-Andújar
- Departament of Plant Nutrition, Center of Edaphology and Applied Biology of the Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, 30100, Murcia, Espinardo, Spain
| | - Oriol Basallo
- Departament de Cienciès Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham Hill, UK
| | - Vicente Medina
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Shahzad R, Jamil S, Ahmad S, Nisar A, Khan S, Amina Z, Kanwal S, Aslam HMU, Gill RA, Zhou W. Biofortification of Cereals and Pulses Using New Breeding Techniques: Current and Future Perspectives. Front Nutr 2021; 8:721728. [PMID: 34692743 PMCID: PMC8528959 DOI: 10.3389/fnut.2021.721728] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
Cereals and pulses are consumed as a staple food in low-income countries for the fulfillment of daily dietary requirements and as a source of micronutrients. However, they are failing to offer balanced nutrition due to deficiencies of some essential compounds, macronutrients, and micronutrients, i.e., cereals are deficient in iron, zinc, some essential amino acids, and quality proteins. Meanwhile, the pulses are rich in anti-nutrient compounds that restrict the bioavailability of micronutrients. As a result, the population is suffering from malnutrition and resultantly different diseases, i.e., anemia, beriberi, pellagra, night blindness, rickets, and scurvy are common in the society. These facts highlight the need for the biofortification of cereals and pulses for the provision of balanced diets to masses and reduction of malnutrition. Biofortification of crops may be achieved through conventional approaches or new breeding techniques (NBTs). Conventional approaches for biofortification cover mineral fertilization through foliar or soil application, microbe-mediated enhanced uptake of nutrients, and conventional crossing of plants to obtain the desired combination of genes for balanced nutrient uptake and bioavailability. Whereas, NBTs rely on gene silencing, gene editing, overexpression, and gene transfer from other species for the acquisition of balanced nutritional profiles in mutant plants. Thus, we have highlighted the significance of conventional and NBTs for the biofortification of cereals and pulses. Current and future perspectives and opportunities are also discussed. Further, the regulatory aspects of newly developed biofortified transgenic and/or non-transgenic crop varieties via NBTs are also presented.
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Affiliation(s)
- Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Amina Nisar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Sipper Khan
- Tropics and Subtropics Group, Institute of Agricultural Engineering, University of Hohenheim, Stuttgart, Germany
| | - Zarmaha Amina
- Tropics and Subtropics Group, Institute of Agricultural Engineering, University of Hohenheim, Stuttgart, Germany
| | - Shamsa Kanwal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | | | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weijun Zhou
- Key Laboratory of Spectroscopy Sensing, The Ministry of Agriculture and Rural Affairs, Institute of Crop Science, Zhejiang University, Hangzhou, China
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Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
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Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Girón-Calva PS, Pérez-Fons L, Sandmann G, Fraser PD, Christou P. Nitrogen inputs influence vegetative metabolism in maize engineered with a seed-specific carotenoid pathway. PLANT CELL REPORTS 2021; 40:899-911. [PMID: 33787959 DOI: 10.1007/s00299-021-02689-2] [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: 02/15/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Metabolomic profiling of a maize line engineered with an endosperm-specific carotenogenic pathway revealed unexpected metabolic readjustments of primary metabolism in leaves and roots. High-carotenoid (HC) maize was engineered to accumulate high levels of carotenoids in the endosperm. The metabolic interventions influenced the flux through non-target pathways in tissues that were not affected by the targeted intervention. HC maize at the vegetative stage also showed a reduced susceptibility to insect feeding. It is unknown, however, whether the metabolic history of the embryo has any impact on the metabolite composition in vegetative tissues. We, therefore, compared HC maize and its isogenic counterpart (M37W) to test the hypothesis that boosting the carotenoid content in the endosperm triggers compensatory effects in core metabolism in vegetative tissues. Specifically, we investigated whether the metabolite composition of leaves and roots at the V6 stage differs between HC and M37W, and whether N inputs further alter the core metabolism of HC compared to M37W. We found an increase in the abundance of organic acids from the tricarboxylic acid (TCA) cycle in HC even under restricted N conditions. In contrast, low levels of carotenoids and chlorophyll were measured regardless of N levels. Sugars were also significantly depleted in HC under low N. We propose a model explaining the observed genotype-dependent and input-dependent effects, in which organic acids derived from the TCA cycle accumulate during vegetative growth and contribute to the increased demand for pyruvate and/or acetyl-CoA in the endosperm and embryo. This response may in part reflect the transgenerational priming of vegetative tissues in the embryo induced by the increased demand for metabolic precursors during seed development in the previous generation.
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Affiliation(s)
- Patricia S Girón-Calva
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Laura Pérez-Fons
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK
| | - Gerhard Sandmann
- Institute of Molecular Bioscience, J. W. Goethe University, Frankfurt am Main, Germany
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway, University London, Egham, Surrey, UK.
| | - Paul Christou
- Department of Plant Production and Forestry Sciences, University of Lleida-Agrotecnio Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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12
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Engineered Maize Hybrids with Diverse Carotenoid Profiles and Potential Applications in Animal Feeding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33783733 DOI: 10.1007/978-981-15-7360-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Multi-gene transformation methods need to be able to introduce multiple transgenes into plants in order to reconstitute a transgenic locus where the introduced genes express in a coordinated manner and do not segregate in subsequent generations. This simultaneous multiple gene transfer enables the study and modulation of the entire metabolic pathways and the elucidation of complex genetic control circuits and regulatory hierarchies. We used combinatorial nuclear transformation to produce multiplex-transgenic maize plants. In proof of principle experiments, we co-expressed five carotenogenic genes in maize endosperm. The resulting combinatorial transgenic maize plant population, equivalent to a "mutant series," allowed us to identify and complement rate-limiting steps in the extended endosperm carotenoid pathway and to recover corn plants with extraordinary levels of β-carotene and other nutritionally important carotenoids. We then introgressed the induced (transgenic) carotenoid pathway in a transgenic line accumulating high levels of nutritionally important carotenoids into a wild-type yellow-endosperm variety with a high β:ε ratio. Novel hybrids accumulated zeaxanthin at unprecedented amounts. We introgressed the same pathway into a different yellow corn line with a low β:ε ratio. The resulting hybrids, in this case, had a very different carotenoid profile. The role of genetic background in determining carotenoid profiles in corn was elucidated, and further rate-limiting steps in the pathway were identified and resolved in hybrids. Astaxanthin accumulation was engineered by overexpression of a β-carotene ketolase in maize endosperm. In early experiments, limited astaxanthin accumulation in transgenic maize plants was attributed to a bottleneck in the conversion of adonixanthin (4-ketozeaxanthin) to astaxanthin. More recent experiments showed that a synthetic β-carotene ketolase with a superior β-carotene/zeaxanthin ketolase activity is critical for the high-yield production of astaxanthin in maize endosperm. Engineered lines were used in animal feeding experiments which demonstrated not only the safety of the engineered lines but also their efficacy in a range of different animal production applications.
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Baysal C, He W, Drapal M, Villorbina G, Medina V, Capell T, Khush GS, Zhu C, Fraser PD, Christou P. Inactivation of rice starch branching enzyme IIb triggers broad and unexpected changes in metabolism by transcriptional reprogramming. Proc Natl Acad Sci U S A 2020; 117:26503-26512. [PMID: 33020297 PMCID: PMC7584904 DOI: 10.1073/pnas.2014860117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Starch properties can be modified by mutating genes responsible for the synthesis of amylose and amylopectin in the endosperm. However, little is known about the effects of such targeted modifications on the overall starch biosynthesis pathway and broader metabolism. Here we investigated the effects of mutating the OsSBEIIb gene encoding starch branching enzyme IIb, which is required for amylopectin synthesis in the endosperm. As anticipated, homozygous mutant plants, in which OsSBEIIb was completely inactivated by abolishing the catalytic center and C-terminal regulatory domain, produced opaque seeds with depleted starch reserves. Amylose content in the mutant increased from 19.6 to 27.4% and resistant starch (RS) content increased from 0.2 to 17.2%. Many genes encoding isoforms of AGPase, soluble starch synthase, and other starch branching enzymes were up-regulated, either in their native tissues or in an ectopic manner, whereas genes encoding granule-bound starch synthase, debranching enzymes, pullulanase, and starch phosphorylases were largely down-regulated. There was a general increase in the accumulation of sugars, fatty acids, amino acids, and phytosterols in the mutant endosperm, suggesting that intermediates in the starch biosynthesis pathway increased flux through spillover pathways causing a profound impact on the accumulation of multiple primary and secondary metabolites. Our results provide insights into the broader implications of perturbing starch metabolism in rice endosperm and its impact on the whole plant, which will make it easier to predict the effect of metabolic engineering in cereals for nutritional improvement or the production of valuable metabolites.
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Affiliation(s)
- Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Margit Drapal
- Department of Biological Sciences, Royal Holloway University of London, TW20 0EX Egham, United Kingdom
| | - Gemma Villorbina
- Department of Chemistry, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA 95616;
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, TW20 0EX Egham, United Kingdom
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain;
- Catalan Institute for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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Durán-Soria S, Pott DM, Osorio S, Vallarino JG. Sugar Signaling During Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2020; 11:564917. [PMID: 32983216 PMCID: PMC7485278 DOI: 10.3389/fpls.2020.564917] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/13/2020] [Indexed: 05/14/2023]
Abstract
Sugars play a key role in fruit quality, as they directly influence taste, and thus consumer acceptance. Carbohydrates are the main resources needed by the plant for carbon and energy supply and have been suggested to be involved in all the important developmental processes, including embryogenesis, seed germination, stress responses, and vegetative and reproductive growth. Recently, considerable progresses have been made in understanding regulation of fruit ripening mechanisms, based on the role of ethylene, auxins, abscisic acid, gibberellins, or jasmonic acid, in both climacteric and non-climacteric fruits. However, the role of sugar and its associated molecular network with hormones in the control of fruit development and ripening is still poorly understood. In this review, we focus on sugar signaling mechanisms described up to date in fruits, describing their involvement in ripening-associated processes, such as pigments accumulation, and their association with hormone transduction pathways, as well as their role in stress-related responses.
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Affiliation(s)
| | | | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - José G. Vallarino
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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Chettry U, Chrungoo NK. A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains. Brief Funct Genomics 2020; 19:324-335. [PMID: 32240289 DOI: 10.1093/bfgp/elaa007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 11/12/2022] Open
Abstract
Carotenoids are mostly C40 terpenoids that participate in several important functions in plants including photosynthesis, responses to various forms of stress, signal transduction and photoprotection. While the antioxidant potential of carotenoids is of particular importance for human health, equally important is the role of β-carotene as the precursor for vitamin A in the human diet. Rice, which contributes upto 40% of dietary energy for mankind, contains very low level of β-carotene, thereby making it an important crop for enhancing β-carotene accumulation in its grains and consequently targeting vitamin A deficiency. Biosynthesis of carotenoids in the endosperm of white rice is blocked at the first enzymatic step wherein geranylgeranyl diphosphate is converted to phytoene by the action of phytoene synthase (PSY). Strategies aimed at enhancing β-carotene levels in the endosperm of white rice identified Narcissus pseudonarcissus (npPSY) and bacterial CRT1 as the regulators of the carotenoid biosynthetic pathway in rice. Besides transcriptional regulation of PSY, posttranscriptional regulation of PSY expression by OR gene, molecular synergism between ε-LCY and β-LCY and epigenetic control of CRITSO through SET DOMAIN containing protein appear to be the other regulatory nodes which regulate carotenoid biosynthesis and accumulation in rice grains. In this review, we elucidate a comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops that will enable us to identify an effective tool to alleviate carotenoid content in rice grains.
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Affiliation(s)
- Upasna Chettry
- Department of Botany, North-Eastern Hill University, Shillong 793022, India
| | - Nikhil K Chrungoo
- Department of Botany, North-Eastern Hill University, Shillong 793022, India
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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Zhou J, Lu M, Yu S, Liu Y, Yang J, Tan X. In-depth Understanding of Camellia oleifera Self-incompatibility by Comparative Transcriptome, Proteome and Metabolome. Int J Mol Sci 2020; 21:E1600. [PMID: 32111089 PMCID: PMC7084461 DOI: 10.3390/ijms21051600] [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: 12/19/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Oil-tea tree (Camellia oleifera) is the most important edible oil tree species in China with late-acting self-incompatibility (LSI) properties. The mechanism of LSI is uncertain, which seriously hinders the research on its genetic characteristics, construction of genetic map, selection of cross breeding parents and cultivar arrangement. To gain insights into the LSI mechanism, we performed cytological, transcriptomic, proteomic and metabolomic studies on self- and cross-pollinated pistils. The studies identified 166,591 transcripts, 6851 proteins and 6455 metabolites. Transcriptomic analysis revealed 1197 differentially expressed transcripts between self- and cross-pollinated pistils and 47 programmed cell death (PCD)-control transcripts. Trend analysis by Pearson correlation categorized nine trend graphs linked to 226 differentially expressed proteins and 38 differentially expressed metabolites. Functional enrichment analysis revealed that the LSI was closely associated with PCD-related genes, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, ATP-binding cassette (ABC) transporters and ubiquitin-mediated proteolysis. These particular trends in transcripts, proteins and metabolites suggested the involvement of PCD in LSI. The results provide a solid genetic foundation for elucidating the regulatory network of PCD-mediated self-incompatibility in C. oleifera.
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Affiliation(s)
| | | | | | | | | | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410001, China
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Jia Z, Zhao C, Wang M, Zhao X, Zhang W, Han T, Xia Q, Han Z, Lin R, Li X. Hepatotoxicity assessment of Rhizoma Paridis in adult zebrafish through proteomes and metabolome. Biomed Pharmacother 2020; 121:109558. [DOI: 10.1016/j.biopha.2019.109558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
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Chandra AK, Kumar A, Bharati A, Joshi R, Agrawal A, Kumar S. Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops. 3 Biotech 2020; 10:2. [PMID: 31824813 DOI: 10.1007/s13205-019-1994-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
Both human and animals, for their nutritional requirements, mainly rely on the plant-based foods, which provide a wide range of nutrients. Minerals, proteins, vitamins are among the nutrients which are essential and need to be available in adequate amount in edible portion of the staple crops. Increasing nutritional content in staple crops either through agronomic biofortification or through conventional plant-breeding strategies continue to be a huge task for scientists around the globe. Although some success has been achieved in recent past, in most cases, we have fallen short of expected targets. To maximize the nutrient uptake and partitioning to different economic part of plants, scientists have employed and tailored several biofortification strategies. But in present agricultural and environmental concerns, these approaches are not much effective. Henceforth, we are highlighting the recent developments and promising aspects of microbial-assisted and genomic-assisted breeding as candidate biofortification approach, that have contributed significantly in increasing nutritional content in grains of different crops. The methods used to date to accomplish nutrient enrichment with recently emerging strategies that we believe could be the most promising and holistic approach for future biofortification program. Results are encouraging, but for future perspective, the existing knowledge about the strategies needs to be confined. Concerted scientific investment are required to widen up these biofortification strategies, so that it could play an important role in ensuring nutritional security of ever-growing population in growing agricultural and environmental constraints.
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Integrated proteomic and metabolomic analysis suggests high rates of glycolysis are likely required to support high carotenoid accumulation in banana pulp. Food Chem 2019; 297:125016. [DOI: 10.1016/j.foodchem.2019.125016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022]
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21
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Ke Q, Kang L, Kim HS, Xie T, Liu C, Ji CY, Kim SH, Park WS, Ahn MJ, Wang S, Li H, Deng X, Kwak SS. Down-regulation of lycopene ε-cyclase expression in transgenic sweetpotato plants increases the carotenoid content and tolerance to abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:52-60. [PMID: 30824061 DOI: 10.1016/j.plantsci.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 05/13/2023]
Abstract
Carotenoids are required for many biological processes in plants and humans. Lycopene ε-cyclase (LCY-ε) catalyzes the conversion of lycopene into lutein via the α-branch carotenoid biosynthesis pathway. Down-regulation of IbLCY-ε by RNAi increases carotenoid accumulation and salt stress tolerance in transgenic sweetpotato calli. As the role of IbLCY-ε in carotenoid biosynthesis and environmental stress responses in whole plants is poorly understood, transgenic sweetpotato (RLE plants) with reduced expression of IbLCY-ε were developed. RLE plants contained higher levels of total carotenoid and β-carotene, due to an elevated β-carotene/lutein ratio rather than increased de novo biosynthesis. RLE plants showed high reactive oxygen species/radical-scavenging activity. They also exhibited an enhanced tolerance of both salt and drought stress, which was associated with lower membrane permeability and a higher photosynthetic rate, respectively. Elevated carotenoid accumulation in RLE plants mitigated the reductions in leaf photosystem II efficiency and chlorophyll induced by abiotic stress. Expression of the carotenoid cleavage genes 9-cis-epoxycarotenoid dioxygenase, carotenoid cleavage dioxygenase 1 (CCD1) and CCD4 was higher in RLE plants, as was abscisic acid accumulation. IbLCY-ε silencing thus offers an effective approach for developing sweetpotato plants with increased tolerance to abiotic stress that will grow on global marginal lands with no reduction in nutritional value.
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Affiliation(s)
- Qingbo Ke
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Le Kang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637002, China
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea
| | - Tian Xie
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Chunjuan Liu
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Chang Yoon Ji
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea
| | - Sun Ha Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea
| | - Woo Sung Park
- College of Pharmacy and Research Institute of Life Sciences, Gyeongsang National University, 501 Jinjudae-ro, Jinju 52828, Republic of Korea
| | - Mi-Jeong Ahn
- College of Pharmacy and Research Institute of Life Sciences, Gyeongsang National University, 501 Jinjudae-ro, Jinju 52828, Republic of Korea
| | - Shiwen Wang
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Hongbing Li
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Xiping Deng
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea.
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Wurtzel ET. Changing Form and Function through Carotenoids and Synthetic Biology. PLANT PHYSIOLOGY 2019; 179:830-843. [PMID: 30361256 PMCID: PMC6393808 DOI: 10.1104/pp.18.01122] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/06/2018] [Indexed: 05/06/2023]
Abstract
The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.
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Affiliation(s)
- Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York 10468
- The Graduate School and University Center-CUNY, New York, New York 10016-4309
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Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.). Sci Rep 2019; 9:1631. [PMID: 30733556 PMCID: PMC6367445 DOI: 10.1038/s41598-018-38233-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Estimation of phytoene, lycopene, β-carotene, lutein, and zeaxanthin in grains of white, brown and purple cultivars of rice revealed marked differences in the levels of these carotenoid intermediates amongst the cultivars. Grains of white rice did not show any significant accumulation of carotenoid intermediates at any stage of development. On the other hand, grains of the purple cultivar accumulated 49.16 ± 5 µg of β-carotene, 28.89 ± 3.2 µg of lutein and 34.65 ± 4.6 µg of zeaxanthin per gm of grain fresh weight. In addition to PSY1, higher expression of βLCY than εLCY appears to be an important factor in determining the flux of pathway towards synthesis of β-β branch carotenoids in purple rice. This cultivar showed a higher fold change in carotenoid precursors during transition from milky to doughing stages and an enhanced flux of lycopene towards β-carotene during grain maturation. Our results indicate that higher level of carotenoids in purple rice is a consequence of higher expression of genes involved in pyruvate metabolism as well as those involved in carotenoid biosynthesis such as PSY1, PDS and β-LCY. Co-expression networking revealed a strong positive relationship between the expression profiles of genes involved in carotenoid biosynthesis and genes coding for geranylgeranyl transferase type II, glutathione S-transferase, DnaJ and SET domain containing proteins as well as MADS26 and R2R3MYB family of transcription factors.
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Chen C, Zhang X, Zhang H, Ban Z, Li L, Dong C, Ji H, Xue W. Label-free quantitative proteomics to investigate the response of strawberry fruit after controlled ozone treatment. RSC Adv 2019; 9:676-689. [PMID: 35517630 PMCID: PMC9060875 DOI: 10.1039/c8ra08405j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/11/2018] [Indexed: 01/27/2023] Open
Abstract
To elucidate postharvest senescence in strawberry (Fragaria ananassa Duch. var. 'JingTaoXiang') fruit in response to ozone treatment at different concentrations (0, 2.144, 6.432, and 10.72 mg m-3), a label-free quantitative proteomic investigation was performed. Postharvest physiological quality traits including respiration rate, firmness, titratable acid, and anthocyanin content were characterized. The observed protein expression profile after storage was related to delayed senescence in strawberries. A total of 2413 proteins were identified in differentially treated strawberry fruits, and 382 proteins were differentially expressed between the four treatments on day 7 and the initial value (blank 0). Proteins related to carbohydrate and energy metabolism and anthocyanin biosynthesis, cell stress response, and fruit firmness were characterized and quantified. Ozone treatment at the concentration of 10.72 mg m-3 effectively delayed the senescence of the strawberry. The proteomic profiles were linked to physiological traits of strawberry fruit senescence to provide new insights into possible molecular mechanisms.
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Affiliation(s)
- Cunkun Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University Beijing China
- College of Food Science and Nutritional Engineering, China Agricultural University Beijing China
| | - Xiaojun Zhang
- National Engineering Technology Research Center for Preservation of Agricultural Products, Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Ministry of Agriculture of China, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products Tianjin China
| | - Huijie Zhang
- College of Food Engineering and Biotechnology, Tianjin University of Science and Technology Tianjin China
| | - Zhaojun Ban
- Zhejiang Provincial Key Laboratory of Chemical and Biological Processing Technology of Farm Products, Zhejiang University of Science and Technology Hangzhou China
| | - Li Li
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University Hangzhou China
| | - Chenghu Dong
- National Engineering Technology Research Center for Preservation of Agricultural Products, Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Ministry of Agriculture of China, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products Tianjin China
| | - Haipeng Ji
- National Engineering Technology Research Center for Preservation of Agricultural Products, Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Ministry of Agriculture of China, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products Tianjin China
| | - Wentong Xue
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University Beijing China
- College of Food Science and Nutritional Engineering, China Agricultural University Beijing China
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25
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Dussert S, Serret J, Bastos-Siqueira A, Morcillo F, Déchamp E, Rofidal V, Lashermes P, Etienne H, JOët T. Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1583-1597. [PMID: 29361125 PMCID: PMC5888931 DOI: 10.1093/jxb/erx492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 05/24/2023]
Abstract
The 'intermediate seed' category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage and has implications for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone contents, and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis, and respiration, and the up-regulation of genes coding for late-embryogenesis abundant (LEA) proteins, heat-shock proteins (HSPs), and antioxidant enzymes. Analysis of the heat-stable proteome in mature coffee seeds confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggested a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ, and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.
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Affiliation(s)
| | | | | | | | | | - Valérie Rofidal
- Biochimie et physiologie moléculaire des plantes, CNRS, INRA, Montpellier Supagro, Université Montpellier, France
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Garg M, Sharma N, Sharma S, Kapoor P, Kumar A, Chunduri V, Arora P. Biofortified Crops Generated by Breeding, Agronomy, and Transgenic Approaches Are Improving Lives of Millions of People around the World. Front Nutr 2018; 5:12. [PMID: 29492405 PMCID: PMC5817065 DOI: 10.3389/fnut.2018.00012] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022] Open
Abstract
Biofortification is an upcoming, promising, cost-effective, and sustainable technique of delivering micronutrients to a population that has limited access to diverse diets and other micronutrient interventions. Unfortunately, major food crops are poor sources of micronutrients required for normal human growth. The manuscript deals in all aspects of crop biofortification which includes-breeding, agronomy, and genetic modification. It tries to summarize all the biofortification research that has been conducted on different crops. Success stories of biofortification include lysine and tryptophan rich quality protein maize (World food prize 2000), Vitamin A rich orange sweet potato (World food prize 2016); generated by crop breeding, oleic acid, and stearidonic acid soybean enrichment; through genetic transformation and selenium, iodine, and zinc supplementation. The biofortified food crops, especially cereals, legumes, vegetables, and fruits, are providing sufficient levels of micronutrients to targeted populations. Although a greater emphasis is being laid on transgenic research, the success rate and acceptability of breeding is much higher. Besides the challenges biofortified crops hold a bright future to address the malnutrition challenge.
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Affiliation(s)
- Monika Garg
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Natasha Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Saloni Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Payal Kapoor
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Aman Kumar
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | | | - Priya Arora
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
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Pan L, Meng C, Wang J, Ma X, Fan X, Yang Z, Zhou M, Zhang X. Integrated omics data of two annual ryegrass (Lolium multiflorum L.) genotypes reveals core metabolic processes under drought stress. BMC PLANT BIOLOGY 2018; 18:26. [PMID: 29378511 PMCID: PMC5789592 DOI: 10.1186/s12870-018-1239-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Annual ryegrass (Lolium multiflorum L.) is a commercially important, widely distributed forage crop that is used in the production of hay and silage worldwide. Drought has been a severe environmental constraint in its production. Nevertheless, only a handful of studies have examined the impact of short-term drought stress on annual ryegrass. The aim of this study was to explore how stress-induced core metabolic processes enhance drought tolerance, or adaptation to drought, in annual ryegrass. RESULTS We profiled the transcriptomes, proteomes, and metabolomes of two annual ryegrass genotypes: the drought-resistant genotype "Abundant 10" and drought-susceptible genotype "Adrenalin 11." We identified differentially expressed metabolites and their corresponding proteins and transcripts that are involved in 23 core metabolic processes, in response to short-term drought stress. Protein-gene-metabolite correlation networks were built to reveal the relationships between the expression of transcripts, proteins, and metabolites in drought-resistant annual ryegrass. Furthermore, integrated metabolic pathways were used to observe changes in enzymes corresponding with levels of amino acids, lipids, carbohydrate conjugates, nucleosides, alkaloids and their derivatives, and pyridines and their derivatives. The resulting omics data underscored the significance of 23 core metabolic processes on the enhancement of drought tolerance or adaptation to drought in annual ryegrass. CONCLUSIONS The regulatory networks were inferred using MCoA and correlation analysis to reveal the relationships among the expression of transcripts, proteins, and metabolites that highlight the corresponding elements of these core metabolic pathways. Our results provide valuable insight into the molecular mechanisms of drought resistance, and represent a promising strategy toward the improvement of drought tolerance in annual ryegrass.
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Affiliation(s)
- Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, USA
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaomei Fan
- Vazyme Biotech Co., Ltd, Nanjing State Economy & Technology Development Zone, Red Maple Technology Industrial Park, Nanjing, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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29
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Obudulu O, Mähler N, Skotare T, Bygdell J, Abreu IN, Ahnlund M, Latha Gandla M, Petterle A, Moritz T, Hvidsten TR, Jönsson LJ, Wingsle G, Trygg J, Tuominen H. A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees. BMC Genomics 2018; 19:11. [PMID: 29298676 PMCID: PMC5753437 DOI: 10.1186/s12864-017-4411-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/21/2017] [Indexed: 01/03/2023] Open
Abstract
Background Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). Results The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis. Conclusions Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues. Electronic supplementary material The online version of this article (10.1186/s12864-017-4411-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ogonna Obudulu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden.,Present address: Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian, University of Life Sciences, 1432, Ås, Norway
| | - Tomas Skotare
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Ilka N Abreu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Maria Ahnlund
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | | | - Anna Petterle
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Torgeir R Hvidsten
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian, University of Life Sciences, 1432, Ås, Norway
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.
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Kang L, Ji CY, Kim SH, Ke Q, Park SC, Kim HS, Lee HU, Lee JS, Park WS, Ahn MJ, Lee HS, Deng X, Kwak SS. Suppression of the β-carotene hydroxylase gene increases β-carotene content and tolerance to abiotic stress in transgenic sweetpotato plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 117:24-33. [PMID: 28587990 DOI: 10.1016/j.plaphy.2017.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 05/13/2023]
Abstract
β-carotene, a carotenoid that plays a key photo-protective role in plants is converted into zeaxanthin by β-carotene hydroxylase (CHY-β). Previous work showed that down-regulation of IbCHY-β by RNA interference (RNAi) results in higher levels of β-carotene and total carotenoids, as well as salt stress tolerance, in cultured transgenic sweetpotato cells. In this study, we introduced the RNAi-IbCHY-β construct into a white-fleshed sweetpotato cultivar (cv. Yulmi) by Agrobacterium-mediated transformation. Among the 13 resultant transgenic sweetpotato plants (referred to as RC plants), three lines were selected for further characterization on the basis of IbCHY-β transcript levels. The RC plants had orange flesh, total carotenoid and β-carotene contents in storage roots were 2-fold and 16-fold higher, respectively, than those of non-transgenic (NT) plants. Unlike storage roots, total carotenoid and β-carotene levels in the leaves of RC plants were slightly increased compared to NT plants. The leaves of RC plants also exhibited tolerance to methyl viologen (MV)-mediated oxidative stress, which was associated with higher 2,2-diphenyl-1- picrylhydrazyl (DPPH) radical-scavenging activity. In addition, RC plants maintained higher levels of chlorophyll and higher photosystem II efficiency than NT plants after 250 mM NaCl stress. Yield of storage roots did not differ significantly between RC and NT plants. These observations suggest that RC plants might be useful as a nutritious and environmental stress-tolerant crop on marginal lands around the world.
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Affiliation(s)
- Le Kang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, South Korea
| | - Chang Yoon Ji
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, South Korea
| | - Sun Ha Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea
| | - Qingbo Ke
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea
| | - Sung-Chul Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, 199 Muan-ro, Muan-gun 58545, South Korea
| | - Joon Seol Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, 199 Muan-ro, Muan-gun 58545, South Korea
| | - Woo Sung Park
- College of Pharmacy and Research Institute of Life Sciences, Gyeongsang National University, 501 Jinjudae-ro, Jinju 52828, South Korea
| | - Mi-Jeong Ahn
- College of Pharmacy and Research Institute of Life Sciences, Gyeongsang National University, 501 Jinjudae-ro, Jinju 52828, South Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, South Korea
| | - Xiping Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Shaanxi, China
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, South Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, South Korea.
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Ge F, Hu H, Huang X, Zhang Y, Wang Y, Li Z, Zou C, Peng H, Li L, Gao S, Pan G, Shen Y. Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo. Sci Rep 2017; 7:1004. [PMID: 28432333 PMCID: PMC5430770 DOI: 10.1038/s41598-017-01280-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
The low ratio of embryonic callus (EC) induction has inhibited the rapid development of maize genetic engineering. Still, little is known to explain the genotype-dependence of EC induction. Here, we performed a large-scale, quantitative analysis of the maize EC metabolome and proteome at three typical induction stages in two inbred lines with a range of EC induction capabilities. Comparison of the metabolomes and proteomes suggests that the differential molecular responses begin at an early stage of development and continue throughout the process of EC formation. The two inbred lines show different responses under various conditions, such as metal ion binding, cell enlargement, stem cell formation, meristematic activity maintenance, somatic embryogenesis, cell wall synthesis, and hormone signal transduction. Furthermore, the differences in hormone (auxin, cytokinin, gibberellin, salicylic acid, jasmonic acid, brassinosteroid and ethylene) synthesis and transduction ability could partially explain the higher EC induction ratio in the inbred line 18-599R. During EC formation, repression of the "histone deacetylase 2 and ERF transcription factors" complex in 18-599R activated the expression of downstream genes, which further promoted EC induction. Together, our data provide new insights into the molecular regulatory mechanism responsible for efficient EC induction in maize.
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Affiliation(s)
- Fei Ge
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongmei Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xing Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanli Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanwei Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lujiang Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Provitamin A biofortification of crop plants: a gold rush with many miners. Curr Opin Biotechnol 2017; 44:169-180. [DOI: 10.1016/j.copbio.2017.02.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/11/2023]
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Zanga D, Capell T, Slafer GA, Christou P, Savin R. A carotenogenic mini-pathway introduced into white corn does not affect development or agronomic performance. Sci Rep 2016; 6:38288. [PMID: 27922071 PMCID: PMC5138849 DOI: 10.1038/srep38288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022] Open
Abstract
High-carotenoid corn (Carolight®) has been developed as a vehicle to deliver pro-vitamin A in the diet and thus address vitamin A deficiency in at-risk populations in developing countries. Like any other novel crop, the performance of Carolight® must be tested in different environments to ensure that optimal yields and productivity are maintained, particularly in this case to ensure that the engineered metabolic pathway does not attract a yield penalty. Here we compared the performance of Carolight® with its near isogenic white corn inbred parental line under greenhouse and field conditions, and monitored the stability of the introduced trait. We found that Carolight® was indistinguishable from its near isogenic line in terms of agronomic performance, particularly grain yield and its main components. We also established experimentally that the functionality of the introduced trait was indistinguishable when plants were grown in a controlled environment or in the field. Such thorough characterization under different agronomic conditions is rarely performed even for first-generation traits such as herbicide tolerance and pest resistance, and certainly not for complex second-generation traits such as the metabolic remodeling in the Carolight® variety. Our results therefore indicate that Carolight® can now be incorporated into breeding lines to generate hybrids with locally adapted varieties for further product development and assessment.
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Affiliation(s)
- Daniela Zanga
- Crop and Forestry Sciences, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Teresa Capell
- Crop and Forestry Sciences, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Gustavo A Slafer
- Crop and Forestry Sciences, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain.,ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Paul Christou
- Crop and Forestry Sciences, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain.,ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Roxana Savin
- Crop and Forestry Sciences, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Lleida, Spain
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Zhai S, Li G, Sun Y, Song J, Li J, Song G, Li Y, Ling H, He Z, Xia X. Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat. BMC PLANT BIOLOGY 2016; 16:228. [PMID: 27769185 PMCID: PMC5073469 DOI: 10.1186/s12870-016-0916-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/06/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches. RESULTS Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54-76 % and yellow pigment content (YPC) was reduced by 26-35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development. CONCLUSION The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products.
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Affiliation(s)
- Shengnan Zhai
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Youwei Sun
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Jihu Li
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Guoqi Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Yulian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
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35
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Engineered maize as a source of astaxanthin: processing and application as fish feed. Transgenic Res 2016; 25:785-793. [DOI: 10.1007/s11248-016-9971-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
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36
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Farré G, Perez-Fons L, Decourcelle M, Breitenbach J, Hem S, Zhu C, Capell T, Christou P, Fraser PD, Sandmann G. Metabolic engineering of astaxanthin biosynthesis in maize endosperm and characterization of a prototype high oil hybrid. Transgenic Res 2016; 25:477-89. [DOI: 10.1007/s11248-016-9943-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/19/2016] [Indexed: 11/29/2022]
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37
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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Gioria S, Lobo Vicente J, Barboro P, La Spina R, Tomasi G, Urbán P, Kinsner-Ovaskainen A, François R, Chassaigne H. A combined proteomics and metabolomics approach to assess the effects of gold nanoparticles in vitro. Nanotoxicology 2016; 10:736-48. [PMID: 26647645 PMCID: PMC4898143 DOI: 10.3109/17435390.2015.1121412] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Omics technologies, such as proteomics or metabolomics, have to date been applied in the field of nanomaterial safety assessment to a limited extent. To address this dearth, we developed an integrated approach combining the two techniques to study the effects of two sizes, 5 and 30 nm, of gold nanoparticles (AuNPs) in Caco-2 cells. We observed differences in cells exposed for 72 h to each size of AuNPs: 61 responsive (up/down-regulated) proteins were identified and 35 metabolites in the cell extract were tentatively annotated. Several altered biological pathways were highlighted by integrating the obtained multi-omics data with bioinformatic tools. This provided a unique set of molecular information on the effects of nanomaterials at cellular level. This information was supported by complementary data obtained by immunochemistry, microscopic analysis, and multiplexed assays. A part from increasing our knowledge on how the cellular processes and pathways are affected by nanomaterials (NMs), these findings could be used to identify specific biomarkers of toxicity or to support the safe-by-design concept in the development of new nanomedicines.
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Affiliation(s)
- Sabrina Gioria
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Joana Lobo Vicente
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Paola Barboro
- b IRCCS Azienda Ospedaliera Universitaria San Martino - IST Istituto Nazionale per la Ricerca sul Cancro , Genova , Italy
| | - Rita La Spina
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Giorgio Tomasi
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Patricia Urbán
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | | | - Rossi François
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
| | - Hubert Chassaigne
- a European Commission, Joint Research Centre, Institute for Health and Consumer Protection , Ispra , Italy and
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Gayen D, Ghosh S, Paul S, Sarkar SN, Datta SK, Datta K. Metabolic Regulation of Carotenoid-Enriched Golden Rice Line. FRONTIERS IN PLANT SCIENCE 2016; 7:1622. [PMID: 27840631 PMCID: PMC5083848 DOI: 10.3389/fpls.2016.01622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/13/2016] [Indexed: 05/21/2023]
Abstract
Vitamin A deficiency (VAD) is the leading cause of blindness among children and is associated with high risk of maternal mortality. In order to enhance the bioavailability of vitamin A, high carotenoid transgenic golden rice has been developed by manipulating enzymes, such as phytoene synthase (psy) and phytoene desaturase (crtI). In this study, proteome and metabolite analyses were carried out to comprehend metabolic regulation and adaptation of transgenic golden rice after the manipulation of endosperm specific carotenoid pathways. The main alteration was observed in carbohydrate metabolism pathways of the transgenic seeds. The 2D based proteomic studies demonstrated that carbohydrate metabolism-related enzymes, such as pullulanase, UDP-glucose pyrophosphorylase, and glucose-1-phosphate adenylyltransferase, were primarily up-regulated in transgenic rice seeds. In addition, the enzyme PPDK was also elevated in transgenic seeds thus enhancing pyruvate biosynthesis, which is the precursor in the carotenoids biosynthetic pathway. GC-MS based metabolite profiling demonstrated an increase in the levels of glyceric acid, fructo-furanose, and galactose, while decrease in galactonic acid and gentiobiose in the transgenic rice compared to WT. It is noteworthy to mention that the carotenoid content, especially β-carotene level in transgenic rice (4.3 μg/g) was significantly enhanced. The present study highlights the metabolic adaptation process of a transgenic golden rice line (homozygous T4 progeny of SKBR-244) after enhancing carotenoid biosynthesis. The presented information would be helpful in the development of crops enriched in carotenoids by expressing metabolic flux of pyruvate biosynthesis.
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Affiliation(s)
- Dipak Gayen
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Subhrajyoti Ghosh
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Soumitra Paul
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Sailendra N. Sarkar
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Swapan K. Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- Department of Crop Sciences, Institute of Agriculture, Visva Bharati UniversitySantiniketan, India
| | - Karabi Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- *Correspondence: Karabi Datta
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Chayut N, Yuan H, Ohali S, Meir A, Yeselson Y, Portnoy V, Zheng Y, Fei Z, Lewinsohn E, Katzir N, Schaffer AA, Gepstein S, Burger J, Li L, Tadmor Y. A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit. BMC PLANT BIOLOGY 2015; 15:274. [PMID: 26553015 PMCID: PMC4640158 DOI: 10.1186/s12870-015-0661-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/03/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Melon fruit flesh color is primarily controlled by the "golden" single nucleotide polymorhism of the "Orange" gene, CmOr, which dominantly triggers the accumulation of the pro-vitamin A molecule, β-carotene, in the fruit mesocarp. The mechanism by which CmOr operates is not fully understood. To identify cellular and metabolic processes associated with CmOr allelic variation, we compared the transcriptome of bulks of developing fruit of homozygous orange and green fruited F3 families derived from a cross between orange and green fruited parental lines. RESULTS Pooling together F3 families that share same fruit flesh color and thus the same CmOr allelic variation, normalized traits unrelated to CmOr allelic variation. RNA sequencing analysis of these bulks enabled the identification of differentially expressed genes. These genes were clustered into functional groups. The relatively enriched functional groups were those involved in photosynthesis, RNA and protein regulation, and response to stress. CONCLUSIONS The differentially expressed genes and the enriched processes identified here by bulk segregant RNA sequencing analysis are likely part of the regulatory network of CmOr. Our study demonstrates the resolution power of bulk segregant RNA sequencing in identifying genes related to commercially important traits and provides a useful tool for better understanding the mode of action of CmOr gene in the mediation of carotenoid accumulation.
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Affiliation(s)
- Noam Chayut
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel.
| | - Hui Yuan
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Shachar Ohali
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Ayala Meir
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Yelena Yeselson
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan, 50250, ISRAEL.
| | - Vitaly Portnoy
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
| | - Efraim Lewinsohn
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan, 50250, ISRAEL.
| | - Shimon Gepstein
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel.
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
- US Department of Agriculture-Agricultural Research Service, Robert W Holly Center for Agriculture and Health, Cornell University, Ithaca, NY, 14853, USA.
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.
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Breitkopf SB, Yuan M, Helenius KP, Lyssiotis CA, Asara JM. Triomics Analysis of Imatinib-Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis. Anal Chem 2015; 87:10995-1006. [PMID: 26434776 PMCID: PMC5585869 DOI: 10.1021/acs.analchem.5b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of metabolomics, lipidomics, and phosphoproteomics that incorporates triple stable isotope labeling by amino acids in cell culture (SILAC) protein labeling, as well as (13)C in vivo metabolite labeling, was demonstrated on BCR-ABL-positive H929 multiple myeloma cells. From 11 880 phosphorylation sites, we confirm that H929 cells are primarily signaling through the BCR-ABL-ERK pathway, and we show that imatinib treatment not only downregulates phosphosites in this pathway but also upregulates phosphosites on proteins involved in RNA expression. Metabolomics analyses reveal that BCR-ABL-ERK signaling in H929 cells drives the pentose phosphate pathway (PPP) and RNA biosynthesis, where pathway inhibition via imatinib results in marked PPP impairment and an accumulation of RNA nucleotides and negative regulation of mRNA. Lipidomics data also show an overall reduction in lipid biosynthesis and fatty acid incorporation with a significant decrease in lysophospholipids. RNA immunoprecipitation studies confirm that RNA degradation is inhibited with short imatinib treatment and transcription is inhibited upon long imatinib treatment, validating the triomics results. These data show the utility of combining mass spectrometry-based "-omics" technologies and reveals that kinase inhibitors may not only downregulate phosphorylation of their targets but also induce metabolic events via increased phosphorylation of other cellular components.
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Affiliation(s)
- Susanne B. Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
| | - Katja P. Helenius
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology and Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
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