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Barboza Bispo R, Teixeira do Amaral A, Pinto VB, de Oliveira Santos T, Jário de Lima V, Rohem Simão B, Fischer A, Naldrett MJ, Alvarez S. Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn ( Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis. J Proteome Res 2024. [PMID: 38648199 DOI: 10.1021/acs.jproteome.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.
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Affiliation(s)
- Rosimeire Barboza Bispo
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Antônio Teixeira do Amaral
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biologia Celular e Tecidual (LBCT), UENF, Centro de Biociências e Biotecnologia (CBB), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Talles de Oliveira Santos
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Valter Jário de Lima
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Bruna Rohem Simão
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Anne Fischer
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
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Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [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: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
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Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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Huang Y, Wan X, Zhao Z, Liu H, Wen Y, Wu W, Ge X, Zhao C. Metabolomic analysis and pathway profiling of paramylon production in Euglena gracilis grown on different carbon sources. Int J Biol Macromol 2023; 246:125661. [PMID: 37399871 DOI: 10.1016/j.ijbiomac.2023.125661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/18/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Paramylon (β-1,3-glucan) produced by Euglena gracilis displays antioxidant, antitumor, and hypolipidaemic functions. The biological properties of paramylon production by E. gracilis can be understood by elucidating the metabolic changes within the algae. In this study, the carbon sources in AF-6 medium were replaced with glucose, sodium acetate, glycerol, or ethanol, and the paramylon yield was measured. Adding 0.1260 g/L glucose to the culture medium resulted in the highest paramylon yield of 70.48 %. The changes in metabolic pathways in E. gracilis grown on glucose were assessed via non-targeted metabolomics analysis using ultra-high-performance liquid chromatography coupled to high-resolution quadrupole-Orbitrap mass spectrometry. We found that glucose, as a carbon source, regulated some differentially expressed metabolites, including l-glutamic acid, γ-aminobutyric acid (GABA), and l-aspartic acid. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes further showed that glucose regulated the carbon and nitrogen balance through the GABA shunt, which enhanced photosynthesis, regulated the flux of carbon and nitrogen into the tricarboxylic acid cycle, promoted glucose uptake, and increased the accumulation of paramylon. This study provides new insights into E. gracilis metabolism during paramylon synthesis.
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Affiliation(s)
- Yajun Huang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuzhi Wan
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zexu Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanqi Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuxi Wen
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Sciences, 32004 Ourense, Spain
| | - Weihao Wu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaodong Ge
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Chao Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Han M, Xu X, Xiong Y, Wei H, Yao K, Huang T, Long Y, Su T. Genome-Wide Survey and Expression Analyses of Hexokinase Family in Poplar (Populus trichocarpa). PLANTS 2022; 11:plants11152025. [PMID: 35956502 PMCID: PMC9370503 DOI: 10.3390/plants11152025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022]
Abstract
Hexokinase (HXK) family proteins exert critical roles in catalyzing hexose phosphorylation, sugar sensing, and modulation of plant growth and stress adaptation. Nevertheless, a large amount remains unknown about the molecular profile of HXK enzymes in Populus trichocarpa, a woody model tree species. A genome-wide survey of HXK-encoding genes, including phylogenies, genomic structures, exon/intron organization, chromosomal distribution, and conserved features, was conducted, identifying six putative HXK isogenes (PtHXK1-6) in the Populus genome. The evolutionary tree demonstrated that 135 homologous HXKs between 17 plant species were categorized into four major subfamilies (type A, B, C, and D), clustering one plastidic (PtHXK3) and five mitochondrial PtHXKs grouped into type A and B, respectively. The in silico deduction prompted the presence of the conserved sugar-binding core (motif 4), phosphorylation sites (motif 2 and 3), and adenosine-binding domains (motif 7). The transcriptomic sequencing (RNA-seq) and the quantitative real-time PCR (qRT-PCR) assays revealed that three isogenes (PtHXK2, 3, and 6) were abundantly expressed in leaves, stems, and roots, while others appeared to be dominantly expressed in the reproductive tissues. Under the stress exposure, PtHXK2 and 6 displayed a significant induction upon the pathogenic fungi (Fusarium solani) infection and marked promotions by glucose feeding in roots. In contrast, the PtHXK3 and 6 are ABA-responsive genes, following a dose-dependent manner. The comprehensive analyses of the genomic patterns and expression profiling provide theoretical clues and lay a foundation for unraveling the physiological and signaling roles underlying the fine-tuned PtHXKs responding to diverse stressors.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Xianglei Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Yuan Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Haikun Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Kejun Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Tingting Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Yingle Long
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-1589-598-3381
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