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Chen L, Kuai P, Lu J, Li L, Lou Y. A Cytosolic Phosphoglucose Isomerase, OsPGI1c, Enhances Plant Growth and Herbivore Resistance in Rice. Int J Mol Sci 2024; 26:169. [PMID: 39796027 PMCID: PMC11720589 DOI: 10.3390/ijms26010169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 12/19/2024] [Accepted: 12/26/2024] [Indexed: 01/13/2025] Open
Abstract
Glucose-6-phosphate isomerase (PGI), a key enzyme that catalyzes the reversible conversion of glucose-6-phosphate and fructose-6-phosphate, plays an important role in plant growth, development, and responses to abiotic stresses and pathogen infections. However, whether and how PGI modulates herbivore-induced plant defenses remain largely unknown. The Brown planthopper (BPH, Nilaparvata lugens) is a devastating insect pest of rice, causing significant damage to rice plants through feeding, oviposition, and disease transmission, resulting in great yield losses. Here, we isolated a rice cytosolic PGI gene, OsPGI1c, which is ubiquitously expressed in rice plants; the highest transcript levels are found in leaves, outer leaf sheaths, and seeds. The expression of OsPGI1c was induced by infestation by gravid females of the BPH, mechanical wounding, and treatment with jasmonic acid (JA). Overexpressing OsPGI1c in rice (oePGI) enhanced both the masses of plant shoots and roots and basal levels of trehalose; however, when infested by gravid BPH females for 2 days, trehalose levels were significantly lower in oePGI plants than in wild-type (WT) plants. Additionally, the overexpression of OsPGI1c increased the BPH-induced levels of JA, jasmonoyl-L-isoleucine, and abscisic acid, but decreased the levels of ethylene and H2O2. Bioassays revealed that gravid BPH females preferred WT plants over oePGI plants for laying eggs; moreover, BPH eggs exhibited lower hatching rates and required longer developmental durations on oePGI plants than WT plants. These results indicate that OsPGI1c positively modulates both rice growth and BPH resistance.
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Affiliation(s)
- Lin Chen
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China;
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (P.K.); (J.L.); (L.L.)
| | - Peng Kuai
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (P.K.); (J.L.); (L.L.)
| | - Jing Lu
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (P.K.); (J.L.); (L.L.)
| | - Leilei Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (P.K.); (J.L.); (L.L.)
| | - Yonggen Lou
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (P.K.); (J.L.); (L.L.)
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Chen L, Wang P, Tan L, Li H, Wang D. Genetic Transformation of Torenia fournieri L. with the Bacillus thuringiensis Cry1Ab Gene Confers Resistance to Mythimna separata (Walker). PLANTS (BASEL, SWITZERLAND) 2024; 13:3568. [PMID: 39771266 PMCID: PMC11678925 DOI: 10.3390/plants13243568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/16/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]
Abstract
Torenia fournieri L. is a popular ornamental plant in the genus Torenia, widely used in commercial landscaping, especially during the summer. Additionally, Torenia has served as a model ornamental plant in many studies exploring ornamental characteristics and pest control through genetic engineering. To date, no research has been reported on developing insect-resistant Torenia expressing genes from Bacillus thuringiensis (Bt). In this study, a recombinant vector carrying the Cry1Ab gene from Bt, pBI121-Cry1Ab, was constructed and transferred into T. fournieri via Agrobacterium tumefaciens-mediated transformation. A total of 13 shoots survived on the kanamycin selection medium, among which four putative transgenic lines, designated L1, L2, L7, and L11, were molecularly confirmed by PCR and Southern blot analysis, indicating successful integration of the Cry1Ab gene into the genomes of these lines. Quantitative real-time PCR and ELISA results further verified the successful expression of the Cry1Ab gene in the leaves of all four transgenic lines. Insect bioassay results demonstrated that all four transgenic lines showed strong resistance to the insect pest, Mythimna separata, with mortality rates ranging from 59.9% to 100.0%, in contrast to a larval mortality rate of 16.2% in the wild-type Torenia. Additionally, these transgenic lines significantly decreased in larval survival rates compared to those fed on wild-type plants. Furthermore, these transgenic lines activated superoxide dismutase (SOD) activity at 12 and 24 h, and catalase (CAT) activity at 72 h, while suppressing SOD activity at 72 h, and peroxidase (POD) activity over time. Our findings indicate that these transgenic lines exhibit high resistance to the insect pest and provide new insights into controlling insect pests in ornamental plants through genetic approaches.
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Affiliation(s)
- Lin Chen
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China; (P.W.); (L.T.)
| | - Pei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China; (P.W.); (L.T.)
- Qingdao Smart Village Development Service Center, Qingdao 266000, China
| | - Lixia Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China; (P.W.); (L.T.)
| | - Houhua Li
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China; (P.W.); (L.T.)
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Ye Y, Xiong S, Guan X, Tang T, Zhu Z, Zhu X, Hu J, Wu J, Zhang S. Insight into Rice Resistance to the Brown Planthopper: Gene Cloning, Functional Analysis, and Breeding Applications. Int J Mol Sci 2024; 25:13397. [PMID: 39769161 PMCID: PMC11678690 DOI: 10.3390/ijms252413397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
This review provides a comprehensive overview of the current understanding of rice resistance to the brown planthopper (BPH), a major pest that poses significant threats to rice production through direct feeding damage and by transmitting viruses such as Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). We highlight the emergence of various BPH biotypes that have overcome specific resistance genes in rice. Advances in genetic mapping and cloning have identified 17 BPH resistance genes, classified into typical R genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins and atypical R genes such as lectin receptor kinases and proteins affecting cell wall composition. The molecular mechanisms of these genes involve the activation of plant defense pathways mediated by phytohormones like jasmonic acid (JA), salicylic acid (SA), and ethylene, as well as the production of defensive metabolites. We also examine the complex interactions between BPH salivary proteins and rice defense responses, noting how salivary effectors can both suppress and trigger plant immunity. The development and improvement of BPH-resistant rice varieties through conventional breeding and molecular marker-assisted selection are discussed, including strategies like gene pyramiding to enhance resistance durability. Finally, we outline the challenges and future directions in breeding for durable BPH resistance, emphasizing the need for continued research on resistance mechanisms and the development of rice varieties with broad-spectrum and long-lasting resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Y.); (S.X.); (X.G.); (T.T.); (Z.Z.); (X.Z.); (J.H.)
| | - Shuai Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Y.); (S.X.); (X.G.); (T.T.); (Z.Z.); (X.Z.); (J.H.)
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Varandas R, Barroso C, Conceição IL, Egas C. Molecular insights into Solanum sisymbriifolium's resistance against Globodera pallida via RNA-seq. BMC PLANT BIOLOGY 2024; 24:1005. [PMID: 39455908 PMCID: PMC11515252 DOI: 10.1186/s12870-024-05694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024]
Abstract
BACKGROUND The presence of potato cyst nematodes (PCN) causes a significant risk to potato crops globally, leading to reduced yields and economic losses. While the plant Solanum sisymbriifolium is known for its resistance to PCN and can be used as a trap crop, the molecular mechanisms behind this resistance remain poorly understood. In this study, genes differentially expressed were identified in control and infected plants during the early stages of the S. sisymbriifolium - G. pallida interaction. RESULTS Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. Gene ontology (GO) enrichment analysis provided insights into the response of the plant to nematode infection, indicating an activation of the plant metabolism, oxidative stress leading to defence mechanism activation, and modification of the plant cell wall. Genes associated with the jasmonic and salicylic acid pathways were also found to be differentially expressed, suggesting their involvement in the plant's defence response. In addition, the analysis of NBS-LRR domain-containing transcripts that play an important role in hypersensitive response and programmed cell death led to the identification of ten transcripts that had no annotations from the databases, with emphasis on TRINITY_DN52667_C1_G1, found to be upregulated in both cultivars. CONCLUSIONS These findings represent an important step towards understanding the molecular basis underlying plant resistance to nematodes and facilitating the development of more effective control strategies against PCN.
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Affiliation(s)
- Raquel Varandas
- Centre for Functional Ecology-Science for People & the Planet (CFE), Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, 3000-456, Portugal.
| | - Cristina Barroso
- Next Generation Sequencing Unit, Biocant Park, Núcleo 04, Lote 8, Cantanhede, 3060-197, Portugal
- Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, Pólo I, Coimbra, 3004-504, Portugal
| | - Isabel Luci Conceição
- Centre for Functional Ecology-Science for People & the Planet (CFE), Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, 3000-456, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant Park, Núcleo 04, Lote 8, Cantanhede, 3060-197, Portugal
- Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, Pólo I, Coimbra, 3004-504, Portugal
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Peng B, Liu Y, Qiu J, Peng J, Sun X, Tian X, Zhang Z, Huang Y, Pang R, Zhou W, Zhao J, Sun Y, Wang Q. OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1436998. [PMID: 39049859 PMCID: PMC11267625 DOI: 10.3389/fpls.2024.1436998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.
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Affiliation(s)
- Bo Peng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yan Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jing Qiu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jing Peng
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Xiaoyu Sun
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xiayu Tian
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Zhiguo Zhang
- Henan Lingrui Pharmaceutical Company Limited, Xinyang, China
| | - Yaqin Huang
- School of Pharmacy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Ruihua Pang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yanfang Sun
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Quanxiu Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Uribe-López B, Barraza A, Cabrera-Ponce JL. Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions. Genes (Basel) 2023; 14:1463. [PMID: 37510367 PMCID: PMC10379993 DOI: 10.3390/genes14071463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Braulio Uribe-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC., Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz CP 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
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Vuong UT, Iswanto ABB, Nguyen Q, Kang H, Lee J, Moon J, Kim SH. Engineering plant immune circuit: walking to the bright future with a novel toolbox. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:17-45. [PMID: 36036862 PMCID: PMC9829404 DOI: 10.1111/pbi.13916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.
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Affiliation(s)
- Uyen Thi Vuong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Quang‐Minh Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Hobin Kang
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jihyun Lee
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jiyun Moon
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
- Division of Life ScienceGyeongsang National UniversityJinjuRepublic of Korea
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Fatty acyl-CoA reductase influences wax biosynthesis in the cotton mealybug, Phenacoccus solenopsis Tinsley. Commun Biol 2022; 5:1108. [PMID: 36261606 PMCID: PMC9582030 DOI: 10.1038/s42003-022-03956-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Mealybugs are highly aggressive to a diversity of plants. The waxy layer covering the outermost part of the integument is an important protective defense of these pests. However, the molecular mechanisms underlying wax biosynthesis in mealybugs remain largely unknown. Here, we analyzed multi-omics data on wax biosynthesis by the cotton mealybug, Phenacoccus solenopsis Tinsley, and found that a fatty acyl-CoA reductase (PsFAR) gene, which was highly expressed in the fat bodies of female mealybugs, contributed to wax biosynthesis by regulating the production of the dominant chemical components of wax, cuticular hydrocarbons (CHCs). RNA interference (RNAi) against PsFAR by dsRNA microinjection and allowing mealybugs to feed on transgenic tobacco expressing target dsRNA resulted in a reduction of CHC contents in the waxy layer, and an increase in mealybug mortality under desiccation and deltamethrin treatments. In conclusion, PsFAR plays crucial roles in the wax biosynthesis of mealybugs, thereby contributing to their adaptation to water loss and insecticide stress. The role of a fatty acyl-CoA reductase (PsFAR) in wax biosynthesis of cotton mealybug is investigated, RNAi against PsFAR resulted in insects with lower generation of waxy filaments and higher mortality under desiccation and deltamethrin treatments.
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Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava. Sci Rep 2021; 11:8758. [PMID: 33888810 PMCID: PMC8062692 DOI: 10.1038/s41598-021-88129-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 02/02/2023] Open
Abstract
The existing genome-scale metabolic model of carbon metabolism in cassava storage roots, rMeCBM, has proven particularly resourceful in exploring the metabolic basis for the phenotypic differences between high and low-yield cassava cultivars. However, experimental validation of predicted metabolic fluxes by carbon labeling is quite challenging. Here, we incorporated gene expression data of developing storage roots into the basic flux-balance model to minimize infeasible metabolic fluxes, denoted as rMeCBMx, thereby improving the plausibility of the simulation and predictive power. Three different conceptual algorithms, GIMME, E-Flux, and HPCOF were evaluated. The rMeCBMx-HPCOF model outperformed others in predicting carbon fluxes in the metabolism of storage roots and, in particular, was highly consistent with transcriptome of high-yield cultivars. The flux prediction was improved through the oxidative pentose phosphate pathway in cytosol, as has been reported in various studies on root metabolism, but hardly captured by simple FBA models. Moreover, the presence of fluxes through cytosolic glycolysis and alanine biosynthesis pathways were predicted with high consistency with gene expression levels. This study sheds light on the importance of prediction power in the modeling of complex plant metabolism. Integration of multi-omics data would further help mitigate the ill-posed problem of constraint-based modeling, allowing more realistic simulation.
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