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Xing J, Zhang J, Wang Y, Wei X, Yin Z, Zhang Y, Pu A, Dong Z, Long Y, Wan X. Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1148-1164. [PMID: 37967146 DOI: 10.1111/tpj.16550] [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: 08/18/2023] [Revised: 10/08/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
Nitrogen (N) is an essential factor for limiting crop yields, and cultivation of crops with low nitrogen-use efficiency (NUE) exhibits increasing environmental and ecological risks. Hence, it is crucial to mine valuable NUE improvement genes, which is very important to develop and breed new crop varieties with high NUE in sustainable agriculture system. Quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis are the most common methods for dissecting genetic variations underlying complex traits. In addition, with the advancement of biotechnology, multi-omics technologies can be used to accelerate the process of exploring genetic variations. In this study, we integrate the substantial data of QTLs, quantitative trait nucleotides (QTNs) from GWAS, and multi-omics data including transcriptome, proteome, and metabolome and further analyze their interactions to predict some NUE-related candidate genes. We also provide the genic resources for NUE improvement among maize, rice, wheat, and sorghum by homologous alignment and collinearity analysis. Furthermore, we propose to utilize the knowledge gained from classical cases to provide the frameworks for improving NUE and breeding N-efficient varieties through integrated genomics, systems biology, and modern breeding technologies.
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Affiliation(s)
- Jiapeng Xing
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Juan Zhang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Yanbo Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Zechao Yin
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yuqian Zhang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
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2
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Dong S, Tian Q, Hui M, Zhang S. Revealing the Antiperspirant Components of Floating Wheat and Their Mechanisms of Action through Metabolomics and Network Pharmacology. Molecules 2024; 29:553. [PMID: 38338298 PMCID: PMC10856516 DOI: 10.3390/molecules29030553] [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: 11/11/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Abstract
Floating wheat is a classical herbal with potential efficacy in the treatment of hyperhidrosis. Aiming at revealing the main components and potential mechanisms of floating wheat, a comprehensive and unique phytopharmacology profile study was carried out. First, common wheat was used as a control to look for chemical markers of floating wheat. In the screening analysis, a total of 180 shared compounds were characterized in common wheat and floating wheat, respectively. The results showed that floating wheat and common wheat contain similar types of compounds. In addition, in non-targeted metabolomic analysis, when taking the contents of the constituents into account, it was found that there indeed existed quite a difference between floating wheat and common wheat and 17 potential biomarkers for floating wheat. Meanwhile, a total of seven components targeted for hyperhidrosis were screened out based on network pharmacology. Seven key differential components were screened, among which kaempferol, asiatic acid, sclareol, enoxolone, and secoisolariciresinol had higher degree values than the others. The analysis of interacting genes revealed three key genes, namely, MAP2K1, ESR1, and ESR2. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that various signaling pathways were involved. Prolactin signaling, thyroid cancer, endocrine resistance, gonadotropin secretion, and estrogen signaling pathways were the main pathways of the intervention of floating wheat in excessive sweating, which was associated with the estrogenic response, hormone receptor binding, androgen metabolism, apoptosis, cancer, and many other biological processes. Molecular docking showed that the screened key components could form good bindings with the target proteins through intermolecular forces. This study reveals the active ingredients and potential molecular mechanism of floating wheat in the treatment of hyperhidrosis and provides a reference for subsequent basic research.
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Affiliation(s)
- Shengnan Dong
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China;
| | - Qing Tian
- Industrial Microorganism Preservation and Breeding Henan Engineering Laboratory, Zhengzhou 450001, China;
| | - Ming Hui
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China;
- Industrial Microorganism Preservation and Breeding Henan Engineering Laboratory, Zhengzhou 450001, China;
| | - Shouyu Zhang
- College of Smart Health, Henan Polytechnic, Zhengzhou 450046, China
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Tercé-Laforgue T, Lothier J, Limami AM, Rouster J, Lea PJ, Hirel B. The Key Role of Glutamate Dehydrogenase 2 (GDH2) in the Control of Kernel Production in Maize ( Zea mays L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2612. [PMID: 37514227 PMCID: PMC10385319 DOI: 10.3390/plants12142612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/02/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
The agronomic potential of glutamate dehydrogenase 2 (GDH2) in maize kernel production was investigated by examining the impact of a mutation on the corresponding gene. Mu-insertion homozygous and heterozygous mutant lines lacking GDH2 activity were isolated and characterized at the biochemical, physiological and agronomic levels. In comparison to the wild type and to the homozygous ghd2 mutants, the heterozygous gdh2 mutant plants were characterized by a decrease in the root amino acid content, whereas in the leaves an increase of a number of phenolic compounds was observed. On average, a 30 to 40% increase in kernel yield was obtained only in the heterozygous gdh2 mutant lines when plants were grown in the field over two years. The importance of GDH2 in the control of plant productivity is discussed in relation to the physiological impact of the mutation on amino acid content, with primary carbon metabolism mostly occurring in the roots and secondary metabolism occurring in the leaves.
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Affiliation(s)
- Thérèse Tercé-Laforgue
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique et de L'Environnement (INRAE), CEDEX, 78026 Versailles, France
| | - Jérémy Lothier
- Univ Angers, Institut National de Recherche Pour L'Agriculture et L'Environnement (INRAE), Institut de Recherche en Horticulture et Semence (IRHS), 49007 Angers, France
| | - Anis M Limami
- Univ Angers, Institut National de Recherche Pour L'Agriculture et L'Environnement (INRAE), Institut de Recherche en Horticulture et Semence (IRHS), 49007 Angers, France
| | - Jacques Rouster
- BIOGEMMA-LIMAGRAIN, Site de la Garenne, Route d'Ennezat, CS 90126, 63720 Chappes, France
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique et de L'Environnement (INRAE), CEDEX, 78026 Versailles, France
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Singh V, Gupta K, Singh S, Jain M, Garg R. Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1156606. [PMID: 37287713 PMCID: PMC10242046 DOI: 10.3389/fpls.2023.1156606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/18/2023] [Indexed: 06/09/2023]
Abstract
Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.
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Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Shubhangi Singh
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
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Tang J, Ma YC, Chen YL, Yang RQ, Liu HC, Wang X, Ni B, Zou CG, Zhang KQ. Vitellogenin accumulation leads to reproductive senescence by impairing lysosomal function. SCIENCE CHINA. LIFE SCIENCES 2023; 66:439-452. [PMID: 36680676 DOI: 10.1007/s11427-022-2242-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/19/2022] [Indexed: 01/22/2023]
Abstract
The maintenance of proteostasis is essential for cellular and organism healthspan. How proteostasis collapse influences reproductive span remains largely unclear. In Caenorhabditis elegans, excess accumulation of vitellogenins, the major components in yolk proteins, is crucial for the development of the embryo and occurs throughout the whole body during the aging process. Here, we show that vitellogenin accumulation leads to reproduction cessation. Excess vitellogenin is accumulated in the intestine and transported into the germline, impairing lysosomal activity in these tissues. The lysosomal function in the germline is required for reproductive span by maintaining oocyte quality. In contrast, autophagy and sperm depletion are not involved in vitellogenin accumulation-induced reproductive aging. Our findings provide insights into how proteome imbalance has an impact on reproductive aging and imply that improvement of lysosomal function is an effective approach for mid-life intervention for maintaining reproductive health in mammals.
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Affiliation(s)
- Jie Tang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), Kunming, 650118, China
| | - Yi-Cheng Ma
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yuan-Li Chen
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Faculty of Basic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Rui-Qiu Yang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Heng-Chen Liu
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Xin Wang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Baosen Ni
- Institute of Biology and Environmental Engineering, School of Chemistry, Biology & Environment, Yuxi Normal University, Yuxi, 653100, China
| | - Cheng-Gang Zou
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Ke-Qin Zhang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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Niu L, Liu L, Zhang J, Scali M, Wang W, Hu X, Wu X. Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production. Int J Mol Sci 2023; 24:ijms24043927. [PMID: 36835340 PMCID: PMC9967003 DOI: 10.3390/ijms24043927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/20/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Maize accumulates large amounts of starch in seeds which have been used as food for human and animals. Maize starch is an importantly industrial raw material for bioethanol production. One critical step in bioethanol production is degrading starch to oligosaccharides and glucose by α-amylase and glucoamylase. This step usually requires high temperature and additional equipment, leading to an increased production cost. Currently, there remains a lack of specially designed maize cultivars with optimized starch (amylose and amylopectin) compositions for bioethanol production. We discussed the features of starch granules suitable for efficient enzymatic digestion. Thus far, great advances have been made in molecular characterization of the key proteins involved in starch metabolism in maize seeds. The review explores how these proteins affect starch metabolism pathway, especially in controlling the composition, size and features of starch. We highlight the roles of key enzymes in controlling amylose/amylopectin ratio and granules architecture. Based on current technological process of bioethanol production using maize starch, we propose that several key enzymes can be modified in abundance or activities via genetic engineering to synthesize easily degraded starch granules in maize seeds. The review provides a clue for developing special maize cultivars as raw material in the bioethanol industry.
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Affiliation(s)
- Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Liangwei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Monica Scali
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence:
| | - Xiuli Hu
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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7
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Limami AM, Cukier C, Hirel B. 15N-labelling of Leaves Combined with GC-MS Analysis as a Tool for Monitoring the Dynamics of Nitrogen Incorporation into Amino Acids. Methods Mol Biol 2023; 2642:151-161. [PMID: 36944877 DOI: 10.1007/978-1-0716-3044-0_8] [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: 03/23/2023]
Abstract
Labeling plant material such as detached leaves with 15NH4+ is a very instrumental method for the characterization of metabolic pathways of mineral nitrogen assimilation and incorporation into amino acids. A procedure of labeling, followed by amino acid extraction, purification, and derivatization for gas chromatography coupled to mass spectrometry (GC/MS) analysis, is presented. The rationale of heavy isotope abundance calculations and amino acid quantification is detailed. This method is adaptable to various plant species and various kinds of investigations, such as elucidating physiological changes occurring as a result of gene mutations (overexpression or inhibition) in natural variants or genetically modified crops, or characterization of metabolic fluxes in genotypes exhibiting contrasted physiological or developmental adaptive responses to biotic and/or abiotic environmental stresses. Furthermore, the benefit of working on detached organs or pieces of organs is to investigate finely the metabolism of species that are not amenable to laboratory work, such as plants growing in natural environments or under agricultural conditions in the field.
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Affiliation(s)
- Anis M Limami
- Univ Angers, INRAE, IRHS, SFR QUASAV, Angers, France.
| | | | - Bertrand Hirel
- INRAE, Institut Jean-Pierre Bourgin, Agro-ParisTech, Université Paris-Saclay, Paris, France
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8
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Song G, Lu Y, Wang Y, Nie C, Xu M, Wang L, Bai Y. Analysis of metabolic differences in maize in different growth stages under nitrogen stress based on UPLC-QTOF-MS. FRONTIERS IN PLANT SCIENCE 2023; 14:1141232. [PMID: 37077647 PMCID: PMC10106645 DOI: 10.3389/fpls.2023.1141232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Introduction Maize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation. Methods In order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions. Results and discussion The results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.
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Grzybowski MW, Zwiener M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC. Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC PLANT BIOLOGY 2022; 22:433. [PMID: 36076172 PMCID: PMC9461132 DOI: 10.1186/s12870-022-03823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited. RESULTS Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions. CONCLUSION Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsw, Poland.
| | - Mackenzie Zwiener
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Nuwan K Wijewardane
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - Abbas Atefi
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, USA
- California Strawberry Commission, San Luis Obispo, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
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10
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Huang WT, Zheng ZC, Hua D, Chen XF, Zhang J, Chen HH, Ye X, Guo JX, Yang LT, Chen LS. Adaptive responses of carbon and nitrogen metabolisms to nitrogen-deficiency in Citrus sinensis seedlings. BMC PLANT BIOLOGY 2022; 22:370. [PMID: 35879653 PMCID: PMC9316421 DOI: 10.1186/s12870-022-03759-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In China, nitrogen (N)-deficiency often occurs in Citrus orchards, which is one of the main causes of yield loss and fruit quality decline. Little information is known about the adaptive responses of Citrus carbon (C) and N metabolisms to N-deficiency. Seedlings of 'Xuegan' (Citrus sinensis (L.) Osbeck) were supplied with nutrient solution at an N concentration of 0 (N-deficiency), 5, 10, 15 or 20 mM for 10 weeks. Thereafter, we examined the effects of N supply on the levels of C and N in roots, stems and leaves, and the levels of organic acids, nonstructural carbohydrates, NH4+-N, NO3--N, total soluble proteins, free amino acids (FAAs) and derivatives (FAADs), and the activities of key enzymes related to N assimilation and organic acid metabolism in roots and leaves. RESULTS N-deficiency elevated sucrose export from leaves to roots, C and N distributions in roots and C/N ratio in roots, stems and leaves, thus enhancing root dry weight/shoot dry weight ratio and N use efficiency. N-deficient leaves displayed decreased accumulation of starch and total nonstructural carbohydrates (TNC) and increased sucrose/starch ratio as well as a partitioning trend of assimilated C toward to sucrose, but N-deficient roots displayed elevated accumulation of starch and TNC and reduced sucrose/starch ratio as well as a partitioning trend of assimilated C toward to starch. N-deficiency reduced the concentrations of most FAADs and the ratios of total FAADs (TFAADs)/N in leaves and roots. N-deficiency reduced the demand for C skeleton precursors for amino acid biosynthesis, thus lowering TFAADs/C ratio in leaves and roots. N-deficiency increased (decreased) the relative amounts of C-rich (N-rich) FAADs, thus increasing the molar ratio of C/N in TFAADs in leaves and roots. CONCLUSIONS Our findings corroborated our hypothesis that C and N metabolisms displayed adaptive responses to N-deficiency in C. sinensis seedlings, and that some differences existed between roots and leaves in N-deficiency-induced alterations of and C and N metabolisms.
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Affiliation(s)
- Wei-Tao Huang
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Zhi-Chao Zheng
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Dan Hua
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Xu-Feng Chen
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Jiang Zhang
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Huan-Huan Chen
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Xin Ye
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Jiu-Xin Guo
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Lin-Tong Yang
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
| | - Li-Song Chen
- Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002 China
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11
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Chen D, Mubeen B, Hasnain A, Rizwan M, Adrees M, Naqvi SAH, Iqbal S, Kamran M, El-Sabrout AM, Elansary HO, Mahmoud EA, Alaklabi A, Sathish M, Din GMU. Role of Promising Secondary Metabolites to Confer Resistance Against Environmental Stresses in Crop Plants: Current Scenario and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:881032. [PMID: 35615133 PMCID: PMC9126561 DOI: 10.3389/fpls.2022.881032] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 05/22/2023]
Abstract
Plants often face incompatible growing environments like drought, salinity, cold, frost, and elevated temperatures that affect plant growth and development leading to low yield and, in worse circumstances, plant death. The arsenal of versatile compounds for plant consumption and structure is called metabolites, which allows them to develop strategies to stop enemies, fight pathogens, replace their competitors and go beyond environmental restraints. These elements are formed under particular abiotic stresses like flooding, heat, drought, cold, etc., and biotic stress such as a pathogenic attack, thus associated with survival strategy of plants. Stress responses of plants are vigorous and include multifaceted crosstalk between different levels of regulation, including regulation of metabolism and expression of genes for morphological and physiological adaptation. To date, many of these compounds and their biosynthetic pathways have been found in the plant kingdom. Metabolites like amino acids, phenolics, hormones, polyamines, compatible solutes, antioxidants, pathogen related proteins (PR proteins), etc. are crucial for growth, stress tolerance, and plant defense. This review focuses on promising metabolites involved in stress tolerance under severe conditions and events signaling the mediation of stress-induced metabolic changes are presented.
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Affiliation(s)
- Delai Chen
- College of Life Science and Technology, Longdong University, Qingyang, China
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang, China
| | - Bismillah Mubeen
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ammarah Hasnain
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Adrees
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Shehzad Iqbal
- Faculty of Agriculture Sciences, Universidad de Talca, Talca, Chile
| | - Muhammad Kamran
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Ahmed M. El-Sabrout
- Department of Applied Entomology and Zoology, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria, Egypt
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Abdullah Alaklabi
- Department of Biology, Faculty of Science, University of Bisha, Bisha, Saudi Arabia
| | - Manda Sathish
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | - Ghulam Muhae Ud Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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12
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Javed T, I I, Singhal RK, Shabbir R, Shah AN, Kumar P, Jinger D, Dharmappa PM, Shad MA, Saha D, Anuragi H, Adamski R, Siuta D. Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:877544. [PMID: 35574130 PMCID: PMC9106419 DOI: 10.3389/fpls.2022.877544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 05/05/2023]
Abstract
The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.
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Affiliation(s)
- Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Indu I
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rubab Shabbir
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Breeding and Genetics, Seed Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Pawan Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Arid Horticulture, Bikaner, India
| | - Dinesh Jinger
- Research Centre, Indian Council of Agricultural Research (ICAR)-Indian Institute of Soil and Water Conservation, Anand, India
| | - Prathibha M. Dharmappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Horticultural Research, Bengaluru, India
| | - Munsif Ali Shad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene, Hubei Hongshan Laboratory, Wuhan, China
| | - Debanjana Saha
- Centurion University of Technology and Management, Jatni, India
| | - Hirdayesh Anuragi
- Indian Council of Agricultural Research (ICAR)- Central Agroforestry Research Institute, Jhansi, India
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
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13
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Singh P, Kumar K, Jha AK, Yadava P, Pal M, Rakshit S, Singh I. Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.). Sci Rep 2022; 12:4211. [PMID: 35273237 PMCID: PMC8913646 DOI: 10.1038/s41598-022-07709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.
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Affiliation(s)
- Prabha Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Krishan Kumar
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Kumar Jha
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Madan Pal
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Ishwar Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
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14
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Mauceri A, Aci MM, Toppino L, Panda S, Meir S, Mercati F, Araniti F, Lupini A, Panuccio MR, Rotino GL, Aharoni A, Abenavoli MR, Sunseri F. Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant. PLANTS 2022; 11:plants11050700. [PMID: 35270170 PMCID: PMC8912549 DOI: 10.3390/plants11050700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 12/01/2022]
Abstract
Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30–40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant.
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Affiliation(s)
- Antonio Mauceri
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Correspondence: (A.M.); (M.R.A.)
| | - Meriem Miyassa Aci
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Laura Toppino
- CREA—Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (L.T.); (G.L.R.)
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Francesco Mercati
- Institute Bioscience and Bioresources—National Research Council CNR, 90129 Palermo, Italy;
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milano, 20133 Milan, Italy;
| | - Antonio Lupini
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Maria Rosaria Panuccio
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Giuseppe Leonardo Rotino
- CREA—Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (L.T.); (G.L.R.)
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Maria Rosa Abenavoli
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Correspondence: (A.M.); (M.R.A.)
| | - Francesco Sunseri
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Institute Bioscience and Bioresources—National Research Council CNR, 90129 Palermo, Italy;
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15
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Seaver SMD. Systems-level analysis of the plasticity of the maize metabolic network reveals novel hypotheses in the nitrogen-use efficiency of maize roots. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5-7. [PMID: 34986229 PMCID: PMC8730699 DOI: 10.1093/jxb/erab522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article comments on: Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. 2022. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions. Journal of Experimental Botany 73, 275–291.
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Affiliation(s)
- Samuel M D Seaver
- Argonne National Laboratory, Data Science and Learning Division, Argonne, IL, USA
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16
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Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:275-291. [PMID: 34554248 DOI: 10.1093/jxb/erab435] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N-) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes.
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Affiliation(s)
- Niaz Bahar Chowdhury
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wheaton L Schroeder
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Debolina Sarkar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Nardjis Amiour
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Isabelle Quilleré
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Bertrand Hirel
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
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17
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Wani SH, Vijayan R, Choudhary M, Kumar A, Zaid A, Singh V, Kumar P, Yasin JK. Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize ( Zea mays L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2875-2891. [PMID: 35035142 PMCID: PMC8720126 DOI: 10.1007/s12298-021-01113-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/22/2021] [Accepted: 12/07/2021] [Indexed: 05/22/2023]
Abstract
UNLABELLED Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C4 plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01113-z.
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Affiliation(s)
- Shabir H. Wani
- Genetics and Plant Breeding, Mountain Research Centre For Field Crops, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Anantnag, J&K 192101 India
| | - Roshni Vijayan
- Regional Agricultural Research Station-Central Zone, Kerala Agricultural University, MelePattambi, Palakkad, Kerala 679306 India
| | | | - Anuj Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002 India
| | - Vishal Singh
- Department of Plants, Soils and Climate, Utah State University, 4820 Old Main Hill, Logan, UT 84322 USA
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001 India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012 India
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18
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miRNAomic Approach to Plant Nitrogen Starvation. Int J Genomics 2021; 2021:8560323. [PMID: 34796230 PMCID: PMC8595019 DOI: 10.1155/2021/8560323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.
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19
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Liu J, Liu M, Fang H, Zhang Q, Ruan J. Accumulation of Amino Acids and Flavonoids in Young Tea Shoots Is Highly Correlated With Carbon and Nitrogen Metabolism in Roots and Mature Leaves. FRONTIERS IN PLANT SCIENCE 2021; 12:756433. [PMID: 34868150 PMCID: PMC8636729 DOI: 10.3389/fpls.2021.756433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The quality of tea product and the metabolism of quality-related compounds in young shoots are significantly affected by the nitrogen(N) supply. However, little is known of the metabolic changes that take place in tea roots and mature leaves under different supplies, which has a large effect on the accumulation of quality-related compounds in young shoots. In this study, young shoots, mature leaves, and roots under different N conditions were subjected to metabolite profiling using gas chromatography and ultraperformance liquid chromatography, coupled with quadrupole time-of-flight mass spectrometry. The contents of free amino acids (e.g., theanine and glutamate) involved in N metabolism were significantly greater under high N than under low N, while a high N supply reduced soluble sugars (e.g., glucose) in all three tissues. Organic acids (e.g., malate, fumarate, α-ketoglutatare, and succinate) involved in tricarboxylic acid cycle remarkably increased as the nitrogen supply increased, which confirms that carbon (C) allocation was restricted by increasing the nitrogen supply, especially in mature leaves. RT-PCR results indicated that gene expression related to nitrogen assimilation significantly increased in roots with increasing nitrogen supply, which had a significant positive relationship with the level of free amino acids in young shoots. In addition, the expression of most genes involved in flavonoid synthesis was significantly upregulated under conditions of low nitrogen supply relative to high nitrogen supply in young shoot and roots. These data suggest that enhanced assimilation of N in tea roots and the coordinated regulation of C (sugars, organic acids, and flavonoids) and N(amino acids) in mature leaves can lead to a high accumulation of amino acids in young shoots. Furthermore, as the N supply increased, more C was partitioned into compounds containing N in mature leaves and roots, resulting in a decrease in flavonoids in young shoots. In conclusion, the accumulation of amino acids and flavonoids in young tea shoots is highly correlated with carbon and nitrogen metabolism in roots and mature leaves.
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Affiliation(s)
- Jianwei Liu
- Key Laboratory for Plant Biology and Resource Application of Tea, The Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Technology Extension Center of Fuyang, Hangzhou, China
| | - Meiya Liu
- Key Laboratory for Plant Biology and Resource Application of Tea, The Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | | | - Qunfeng Zhang
- Key Laboratory for Plant Biology and Resource Application of Tea, The Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyun Ruan
- Key Laboratory for Plant Biology and Resource Application of Tea, The Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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20
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Farjad M, Clément G, Launay A, Jeridi R, Jolivet S, Citerne S, Rigault M, Soulie M, Dinant S, Fagard M. Plant nitrate supply regulates Erwinia amylovora virulence gene expression in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2021; 22:1332-1346. [PMID: 34382308 PMCID: PMC8518577 DOI: 10.1111/mpp.13114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/16/2021] [Accepted: 06/26/2021] [Indexed: 05/03/2023]
Abstract
We showed previously that nitrogen (N) limitation decreases Arabidopsis resistance to Erwinia amylovora (Ea). We show that decreased resistance to bacteria in low N is correlated with lower apoplastic reactive oxygen species (ROS) accumulation and lower jasmonic acid (JA) pathway expression. Consistently, pretreatment with methyl jasmonate (Me-JA) increased the resistance of plants grown under low N. In parallel, we show that in planta titres of a nonvirulent type III secretion system (T3SS)-deficient Ea mutant were lower than those of wildtype Ea in low N, as expected, but surprisingly not in high N. This lack of difference in high N was consistent with the low expression of the T3SS-encoding hrp virulence genes by wildtype Ea in plants grown in high N compared to plants grown in low N. This suggests that expressing its virulence factors in planta could be a major limiting factor for Ea in the nonhost Arabidopsis. To test this hypothesis, we preincubated Ea in an inducing medium that triggers expression of hrp genes in vitro, prior to inoculation. This preincubation strongly enhanced Ea titres in planta, independently of the plant N status, and was correlated to a significant repression of JA-dependent genes. Finally, we identify two clusters of metabolites associated with resistance or with susceptibility to Ea. Altogether, our data showed that high susceptibility of Arabidopsis to Ea, under low N or following preincubation in hrp-inducing medium, is correlated with high expression of the Ea hrp genes in planta and low expression of the JA signalling pathway, and is correlated with the accumulation of specific metabolites.
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Affiliation(s)
- Mahsa Farjad
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Gilles Clément
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Alban Launay
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Roua Jeridi
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
- Laboratoire des Risques Liés Aux Stress EnvironnementauxFaculté des Sciences de Bizerte, Université de CarthageBizerteTunisia
| | - Sylvie Jolivet
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Sylvie Citerne
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Martine Rigault
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Marie‐Christine Soulie
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
- Sorbonne UniversitéUPMC Université Paris 06ParisFrance
| | - Sylvie Dinant
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Mathilde Fagard
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
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21
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Guo J, Gu X, Lu W, Lu D. Multiomics analysis of kernel development in response to short-term heat stress at the grain formation stage in waxy maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6291-6304. [PMID: 34128533 DOI: 10.1093/jxb/erab286] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/11/2021] [Indexed: 06/12/2023]
Abstract
Understanding the adaptive changes in maize kernels under high-temperature stress during grain formation stage is critical for developing strategies to alleviate the negative effects on yield and quality. In this study, we subjected waxy maize (Zea mays L. sinensis Kulesh) to four different temperature regimes from 1-15 d after pollination (DAP), namely normal day/normal night (control), hot day/normal night, normal day/hot night, and hot day/hot night. Compared to the control, the three high-temperature treatments inhibited kernel development and starch deposition. To understand how the kernels responded to high-temperature stress, their transcriptomes, proteomes, and metabolomes were studied at 10 DAP and 25 DAP. This showed that genes and proteins related to kernel development and starch deposition were up- and down-regulated, respectively, at 10 DAP, but this pattern was reversed at 25 DAP. Metabolome profiling under high-temperature stress showed that the accumulation patterns of metabolites at 10 DAP and 25 DAP were inversely related. Our multiomics analyses indicated that the response to high-temperature stress of signaling pathways mediated by auxin, abscisic acid, and salicylic acid was more active at 10 DAP than at 25 DAP. These results confirmed that high-temperature stress during early kernel development has a carry-over effect on later development. Taken together, our multiomics profiles of developing kernels under high-temperature stress provide insights into the processes that underlie maize yield and quality under high-temperature conditions.
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Affiliation(s)
- Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, P.R. China
| | - Xiaotian Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, P.R. China
| | - Weiping Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, P.R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, P.R. China
| | - Dalei Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, P.R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, P.R. China
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22
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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23
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Impacts of environmental conditions, and allelic variation of cytosolic glutamine synthetase on maize hybrid kernel production. Commun Biol 2021; 4:1095. [PMID: 34535763 PMCID: PMC8448750 DOI: 10.1038/s42003-021-02598-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
Cytosolic glutamine synthetase (GS1) is the enzyme mainly responsible of ammonium assimilation and reassimilation in maize leaves. The agronomic potential of GS1 in maize kernel production was investigated by examining the impact of an overexpression of the enzyme in the leaf cells. Transgenic hybrids exhibiting a three-fold increase in leaf GS activity were produced and characterized using plants grown in the field. Several independent hybrids overexpressing Gln1-3, a gene encoding cytosolic (GS1), in the leaf and bundle sheath mesophyll cells were grown over five years in different locations. On average, a 3.8% increase in kernel yield was obtained in the transgenic hybrids compared to controls. However, we observed that such an increase was simultaneously dependent upon both the environmental conditions and the transgenic event for a given field trial. Although variable from one environment to another, significant associations were also found between two GS1 genes (Gln1-3 and Gln1-4) polymorphic regions and kernel yield in different locations. We propose that the GS1 enzyme is a potential lead for producing high yielding maize hybrids using either genetic engineering or marker-assisted selection. However, for these hybrids, yield increases will be largely dependent upon the environmental conditions used to grow the plants. Amiour et al. use a multi-year field trial evaluation and association mapping to determine if increased enzyme activity and native allelic variations at the GS1 loci in maize contribute to differences in grain yield. Overexpression of GS1 and polymorphisms in the corresponding loci were associated with kernel yield, indicating that GS1 expression can directly control kernel production and that GS1 has a potential lead in the production of high yielding maize hybrids depending on environmental conditions.
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24
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Metabolomics and Molecular Approaches Reveal Drought Stress Tolerance in Plants. Int J Mol Sci 2021; 22:ijms22179108. [PMID: 34502020 PMCID: PMC8431676 DOI: 10.3390/ijms22179108] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023] Open
Abstract
Metabolic regulation is the key mechanism implicated in plants maintaining cell osmotic potential under drought stress. Understanding drought stress tolerance in plants will have a significant impact on food security in the face of increasingly harsh climatic conditions. Plant primary and secondary metabolites and metabolic genes are key factors in drought tolerance through their involvement in diverse metabolic pathways. Physio-biochemical and molecular strategies involved in plant tolerance mechanisms could be exploited to increase plant survival under drought stress. This review summarizes the most updated findings on primary and secondary metabolites involved in drought stress. We also examine the application of useful metabolic genes and their molecular responses to drought tolerance in plants and discuss possible strategies to help plants to counteract unfavorable drought periods.
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25
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Sathasivam R, Yeo HJ, Park CH, Choi M, Kwon H, Sim JE, Park SU, Kim JK. Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L. PLANTS 2021; 10:plants10081753. [PMID: 34451798 PMCID: PMC8398043 DOI: 10.3390/plants10081753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022]
Abstract
Chelidonium majus L. is a perennial herbaceous plant that has various medicinal properties. However, the genomic information about its carotenoid biosynthesis pathway (CBP), xanthophyll biosynthesis pathway (XBP), and apocarotenoid biosynthesis pathway (ABP) genes were limited. Thus, the CBP, XBP, and ABP genes of C. majus were identified and analyzed. Among the 15 carotenoid pathway genes identified, 11 full and 4 partial open reading frames were determined. Phylogenetic analysis of these gene sequences showed higher similarity with higher plants. Through 3D structural analysis and multiple alignments, several distinct conserved motifs were identified, including dinucleotide binding motif, carotene binding motif, and aspartate or glutamate residues. Quantitative RT-PCR showed that CBP, XBP, and ABP genes were expressed in a tissue-specific manner; the highest expression levels were achieved in flowers, followed by those in leaves, roots, and stems. The HPLC analysis of the different organs showed the presence of eight different carotenoids. The highest total carotenoid content was found in leaves, followed by that in flowers, stems, and roots. This study provides information on the molecular mechanisms involved in CBP, XBP, and ABP genes, which might help optimize the carotenoid production in C. majus. The results could also be a basis of further studies on the molecular genetics and functional analysis of CBP, XBP, and ABP genes.
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Affiliation(s)
- Ramaraj Sathasivam
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Hyeon Ji Yeo
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Chang Ha Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Minsol Choi
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Haejin Kwon
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Ji Eun Sim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Korea;
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
- Department of Smart Agriculture Systems, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
- Correspondence: (S.U.P.); (J.K.K.); Tel.: +82-42-821-5730 (S.U.P.); +82-32-835-8241 (J.K.K.); Fax: +82-42-822-2631 (S.U.P.); +82-32-835-0763 (J.K.K.)
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Korea;
- Correspondence: (S.U.P.); (J.K.K.); Tel.: +82-42-821-5730 (S.U.P.); +82-32-835-8241 (J.K.K.); Fax: +82-42-822-2631 (S.U.P.); +82-32-835-0763 (J.K.K.)
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26
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He L, Teng L, Tang X, Long W, Wang Z, Wu Y, Liao L. Agro-morphological and metabolomics analysis of low nitrogen stress response in Axonopus compressus. AOB PLANTS 2021; 13:plab022. [PMID: 34234932 PMCID: PMC8256886 DOI: 10.1093/aobpla/plab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 05/14/2023]
Abstract
Axonopus compressus also known as carpet grass is a robust, stoloniferous grass that can grow in minimal fertilization and resists well to abiotic and biotic stresses including low nitrogen (LN) stress. This study aimed at characterizing the agro-morphological and metabolome responses to LN in carpet grass leaves. Under LN stress, carpet grass increased yellowness of leaves and root dry matter while reduced turf quality and shoot dry weight. The metabolome comparison between samples from optimum and LN conditions indicated 304 differentially accumulated metabolites (DAMs), which could be classified into 12 major and 31 subclasses. The results revealed that the leaf tissues accumulated more anthocyanins and other flavonoid metabolites under LN stress. Conversely, amino acids, nucleic acids and their derivatives were reduced in response to LN stress. The overall evaluation of individual metabolites and pathways, and previous studies on metabolomes indicated that carpet grass reduced its energy consumption in leaves and increased the level of organic acid metabolism and secondary metabolism in order to resist LN stress conditions.
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Affiliation(s)
- Li He
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Li Teng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Xiaomin Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Wanwan Long
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Yang Wu
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343009, China
| | - Li Liao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan 570228, 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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28
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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: 34] [Impact Index Per Article: 11.3] [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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Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
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30
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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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Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation. Int J Mol Sci 2021; 22:ijms22094790. [PMID: 33946478 PMCID: PMC8124848 DOI: 10.3390/ijms22094790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.
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Narvekar AS, Tharayil N. Nitrogen Fertilization Influences the Quantity, Composition, and Tissue Association of Foliar Phenolics in Strawberries. FRONTIERS IN PLANT SCIENCE 2021; 12:613839. [PMID: 33959135 PMCID: PMC8093403 DOI: 10.3389/fpls.2021.613839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Unlike quantitative changes, the compositional changes of plant phenolics and changes in their tissue association as influenced by the nutrient supply are less well understood. We evaluated the quantity, composition, and tissue association of phenolics in leaves of two Fragaria ananassa cultivars in response to different levels of nitrogen (N) fertilization using global metabolomic approaches. Influence of N supply on phenolic content in both cultivars was similar, but the magnitude of this response was compound specific. Ellagitannins, the most abundant class of phenolic oligomers, were less responsive to the applied N treatments, whereas proanthocyanidins, the less abundant class of phenolic oligomers, exhibited higher fold change. Within mono-phenolics, the hydroxycinnamates were more abundant but showed lower fold change than the hydroxybenzoates. Among flavonoids, the hydroxylated flavonols showed higher abundances than the flavones, with a preferential accumulation of dihydroxylated flavonol at lower N levels. Furthermore, glycosylated flavonols were higher than the acylated forms. The extractable fraction of phenolics was more influenced by the N treatment than the fiber-bound fraction. The extensive compositional modification of phenolics and a greater response of non-bound fractions in response to N rates highlight the potential to use precise management of N supply as an effective strategy to enhance the bioactive compounds in crops.
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Transcriptome Analysis for Fraxinus mandshurica Rupr. Seedlings from Different Carbon Sequestration Provenances in Response to Nitrogen Deficiency. FORESTS 2021. [DOI: 10.3390/f12020257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To explore the molecular regulatory mechanism of high-carbon (C) sequestration Fraxinus mandshurica Rupr. (F. mandshurica) provenance and the expression profile of F. mandshurica during nitrogen (N) starvation, the foliage and roots of the annual Wuchang (WC) seedlings with greater C amount and Hailin (HL) seedlings with smaller C amount, which were grown in N-deficient nutrition and complete N, were used for RNA-seq and physiological determination, respectively. One thousand and fifty-seven differentially expressed genes (DEGs) between WC and HL and 8173 DEGs related to N deficiency were identified, respectively. The root of F. mandshurica responded to N deficiency more strongly than foliar. The target genes that responded to N deficiency in roots were mainly regulatory genes (transcription factors, hormones and protein kinases), and their response patterns were upregulated. The growth and N concentration in both WC and HL were reduced by the N deficiency, which might result from the decrease of the leaf Nitrate reductase (NR) and glutamine synthetase (GS) enzyme activity and ABA content, although the root-to-shoot ratio; lateral root number; lignin content; endogenous hormones content (GA, IAA and ZR); root GS and glutamate synthetase activity and transcriptional level of most of the regulatory genes were increased. The C sequestration capacity in WC was greater than that in HL, which related to the higher GS enzymes activity and transcriptional levels of regulatory genes and metabolic genes (terpenes, carbohydrates, and lipid energy). However, the C sequestration advantage of WC was significantly reduced by the N deficiency, which was due to the smaller response to N deficiency compared to HL.
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Sun X, Guo Z, Jiang Y, Qin L, Shi Z, Dong L, Xiong L, Yuan R, Deng W, Wu H, Liu Q, Xie F, Chen Y. Differential Metabolomic Responses of Kentucky Bluegrass Cultivars to Low Nitrogen Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:808772. [PMID: 35154204 PMCID: PMC8831703 DOI: 10.3389/fpls.2021.808772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 05/12/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) is a cool-season turfgrass species that responds strongly to nitrogen (N), but the metabolomic responses of this grass species to N supply is unknown. The N-tolerant cultivar Bluemoon and N-sensitive cultivar Balin were exposed to normal N (15 mM) and low N (0.5 mM) for 21 days for identification of differentially expressed metabolites (DEMs) between normal N and low N treatments. Balin had more reductions of chlorophyll and total soluble protein concentrations and a higher accumulation of superoxide radicals under low N stress. A total of 99 known DEMs were identified in either cultivar or both including 22 amino acids and derivatives, 16 carbohydrates, 29 organic acids, and 32 other metabolites. In Bluemoon, β-alanine metabolism was most enriched, followed by alanine, aspartate, and glutamate metabolism, biosynthesis of valine, leucine, and isoleucine biosynthesis, and glycine, serine, and threonine metabolism. In Balin, alanine, aspartate, and glutamate metabolism were most enriched, followed by the tricarboxylic acid (TCA), glyoxylate and decarbohydrate metabolism, and carbon fixation. Bluemoon generally maintained higher TCA cycle capacity and had more downregulated amino acids, while changes in more organic acids occurred in Balin under low N stress. Some metabolite changes by low-N stress were cultivar-specific. The results suggested that regulation of metabolites related to energy production or energy saving could contribute to low N tolerance in Kentucky bluegrass.
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Affiliation(s)
- Xiaoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhixin Guo
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Ligang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhenjie Shi
- College of Horticulture, Northeast Agricultural University, Harbin, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lili Dong
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Liangbing Xiong
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Runli Yuan
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Wenjing Deng
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Hanfu Wu
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Qingqing Liu
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Fuchun Xie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Fuchun Xie,
| | - Yajun Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- College of Horticulture, Northeast Agricultural University, Harbin, China
- *Correspondence: Yajun Chen,
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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Chang W, Zhao H, Yu S, Yu J, Cai K, Sun W, Liu X, Li X, Yu M, Ali S, Zhang K, Qu C, Lei B, Lu K. Comparative transcriptome and metabolomic profiling reveal the complex mechanisms underlying the developmental dynamics of tobacco leaves. Genomics 2020; 112:4009-4022. [PMID: 32650092 DOI: 10.1016/j.ygeno.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/31/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022]
Abstract
Although the leaf is the most important photosynthetic organ in most plants, many of the molecular mechanisms underlying leaf developmental dynamics remain to be explored. To better understand the transcriptional regulatory mechanisms involved in leaf development, we conducted comparative transcriptomic and metabolomic analysis of leaves from seven positions on tobacco (Nicotiana tabacum) plants. A total of 35,622 unique differentially expressed genes and 79 metabolites were identified. A time-series expression analysis detected two interesting transcriptional profiles, one comprising 10,197 genes that displayed continual up-regulation during leaf development and another comprising 4696 genes that displayed continual down-regulation. Combining these data with co-expression network results identified four important regulatory networks involved in photorespiration and the tricarboxylic acid cycle; these networks may regulate carbon/nitrogen balance during leaf development. We also found that the transcription factor NtGATA5 acts as a hub associated with C and N metabolism and chloroplast development during leaf development through regulation of phytohormones. Furthermore, we investigated the transcriptional dynamics of genes involved in the auxin, cytokinin, and jasmonic acid biosynthesis and signaling pathways during tobacco leaf development. Overall, our study greatly expands the understanding of the regulatory network controlling developmental dynamics in plant leaves.
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Affiliation(s)
- Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Huina Zhao
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Jing Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Kai Cai
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xumei Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Shahzad Ali
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Bo Lei
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China.
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Ganie AH, Pandey R, Kumar MN, Chinnusamy V, Iqbal M, Ahmad A. Metabolite Profiling and Network Analysis Reveal Coordinated Changes in Low-N Tolerant and Low-N Sensitive Maize Genotypes under Nitrogen Deficiency and Restoration Conditions. PLANTS 2020; 9:plants9111459. [PMID: 33137957 PMCID: PMC7716227 DOI: 10.3390/plants9111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 11/16/2022]
Abstract
Nitrogen (N), applied in the form of a nitrogenous fertilizer, is one of the main inputs for agricultural production. Food production is closely associated with the application of N. However, the application of nitrogenous fertilizers to agricultural fields is associated with heavy production of nitrous oxide because agricultural crops can only utilize 30-40% of applied N, leaving behind unused 60-70% N in the environment. The global warming effect of this greenhouse gas is approximately 300 times more than of carbon dioxide. Under the present scenario of climate change, it is critical to maintain the natural balance between food production and environmental sustainability by targeting traits responsible for improving nitrogen-use-efficiency (NUE). Understanding of the molecular mechanisms behind the metabolic alterations due to nitrogen status needs to be addressed. Additionally, mineral nutrient deficiencies and their associated metabolic networks have not yet been studied well. Given this, the alterations in core metabolic pathways of low-N tolerant (LNT) and low-N sensitive (LNS) genotypes of maize under N-deficiency and their efficiency of recovering the changes upon resupplying N were investigated by us, using the GC-MS and LC-MS based metabolomic approach. Significant genotype-specific changes were noted in response to low-N. The N limitation affected the whole plant metabolism, most significantly the precursors of primary metabolic pathways. These precursors may act as important targets for improving the NUE. Limited availability of N reduced the levels of N-containing metabolites, organic acids and amino acids, but soluble sugars increased. Major variations were encountered in LNS, as compared to LNT. This study has revealed potential metabolic targets in response to the N status, which are indeed the prospective targets for crop improvement.
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Affiliation(s)
| | - Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - M. Nagaraj Kumar
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Muhammad Iqbal
- Department of Botany, Jamia Hamdard, New Delhi 110062, India; (A.H.G.); (M.I.)
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
- Correspondence: ; Tel.: +00-91-9999886334
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Gong X, Liu X, Pan Q, Mi G, Chen F, Yuan L. Combined physiological, transcriptome, and genetic analysis reveals a molecular network of nitrogen remobilization in maize. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5061-5073. [PMID: 32392584 DOI: 10.1093/jxb/eraa229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/06/2020] [Indexed: 05/28/2023]
Abstract
In plants, nitrogen remobilization from source to sink organs is an important process regulated by complex transcriptional regulatory networks. However, the relationship between nitrogen remobilization and leaf senescence and the molecular regulatory network that controls them are unknown in maize. Here, using 15N labeling and a transcriptome approach, a dynamic analysis of the nitrogen remobilization process was conducted in two elite maize inbred lines (PH4CV and PH6WC) with contrasting leaf senescence. PH4CV showed higher nitrogen remobilization efficiency (NRE) than PH6WC, mainly in the middle and lower leaves from 15 d to 35 d after silking. The co-expression network analysis revealed that ethylene and cytokinin metabolism-related genes triggered the onset of nitrogen remobilization, while abscisic acid and jasmonic acid biosynthesis-related genes controlled the progression of nitrogen remobilization. By integrating genetic analysis, functional annotation, and gene expression, two candidate genes underlying a major quantitative trait locus of NRE were identified, namely an early senescence acting gene (ZmASR6) and an ATP-dependent Clp protease gene (GRMZM2G172230). Hormone-coupled transcription factors and downstream target genes reveal a gene regulatory network for the nitrogen remobilization process after silking in maize. These results uncovered a sophisticated regulatory mechanism for nitrogen remobilization, and further provided characterization of valuable genes for genetic improvement of nitrogen use efficiency in maize.
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Affiliation(s)
- Xiaoping Gong
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Xiaoyang Liu
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Qingchun Pan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Guohua Mi
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Fanjun Chen
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Lixing Yuan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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39
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Dellagi A, Quillere I, Hirel B. Beneficial soil-borne bacteria and fungi: a promising way to improve plant nitrogen acquisition. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4469-4479. [PMID: 32157312 PMCID: PMC7475097 DOI: 10.1093/jxb/eraa112] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/09/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative impacts on the environment. Exploiting the potential of beneficial microbes and identifying crop genotypes that can capitalize on symbiotic associations may be possible ways to significantly reduce the use of N fertilizers. The best-known example of symbiotic association that can reduce the use of N fertilizers is the N2-fixing rhizobial bacteria and legumes. Bacterial taxa other than rhizobial species can develop associative symbiotic interactions with plants and also fix N. These include bacteria of the genera Azospirillum, Azotobacter, and Bacillus, some of which are commercialized as bio-inoculants. Arbuscular mycorrhizal fungi are other microorganisms that can develop symbiotic associations with most terrestrial plants, favoring access to nutrients in a larger soil volume through their extraradical mycelium. Using combinations of different beneficial microbial species is a promising strategy to boost plant N acquisition and foster a synergistic beneficial effect between symbiotic microorganisms. Complex biological mechanisms including molecular, metabolic, and physiological processes dictate the establishment and efficiency of such multipartite symbiotic associations. In this review, we present an overview of the current knowledge and future prospects regarding plant N nutrition improvement through the use of beneficial bacteria and fungi associated with plants, individually or in combination.
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Affiliation(s)
- Alia Dellagi
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Quillere
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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Kareya MS, Mariam I, Shaikh KM, Nesamma AA, Jutur PP. Photosynthetic Carbon Partitioning and Metabolic Regulation in Response to Very-Low and High CO 2 in Microchloropsis gaditana NIES 2587. FRONTIERS IN PLANT SCIENCE 2020; 11:981. [PMID: 32719702 PMCID: PMC7348049 DOI: 10.3389/fpls.2020.00981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/16/2020] [Indexed: 05/06/2023]
Abstract
Photosynthetic organisms fix inorganic carbon through carbon capture machinery (CCM) that regulates the assimilation and accumulation of carbon around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, few constraints that govern the central carbon metabolism are regulated by the carbon capture and partitioning machinery. In order to divert the cellular metabolism toward lipids and/or biorenewables it is important to investigate and understand the molecular mechanisms of the CO2-driven carbon partitioning. In this context, strategies for enhancement of CO2 fixation which will increase the overall biomass and lipid yields, can provide clues on understanding the carbon assimilation pathway, and may lead to new targets for genetic engineering in microalgae. In the present study, we have focused on the physiological and metabolomic response occurring within marine oleaginous microalgae Microchloropsis gaditana NIES 2587, under the influence of very-low CO2 (VLC; 300 ppm, or 0.03%) and high CO2 (HC; 30,000 ppm, or 3% v/v). Our results demonstrate that HC supplementation in M. gaditana channelizes the carbon flux toward the production of long chain polyunsaturated fatty acids (LC-PUFAs) and also increases the overall biomass productivities (up to 2.0 fold). Also, the qualitative metabolomics has identified nearly 31 essential metabolites, among which there is a significant fold change observed in accumulation of sugars and alcohols such as galactose and phytol in VLC as compared to HC. In conclusion, our focus is to understand the entire carbon partitioning and metabolic regulation within these photosynthetic cell factories, which will be further evaluated through multiomics approach for enhanced productivities of biomass, biofuels, and bioproducts (B3).
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Affiliation(s)
| | | | | | | | - Pannaga Pavan Jutur
- Omics of Algae Group, Industrial Biotechnology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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41
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Zhang JY, Cun Z, Chen JW. Photosynthetic performance and photosynthesis-related gene expression coordinated in a shade-tolerant species Panax notoginseng under nitrogen regimes. BMC PLANT BIOLOGY 2020; 20:273. [PMID: 32593292 PMCID: PMC7321538 DOI: 10.1186/s12870-020-02434-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Nitrogen (N) is an essential component of photosynthetic apparatus. However, the mechanism that photosynthetic capacity is suppressed by N is not completely understood. Photosynthetic capacity and photosynthesis-related genes were comparatively analyzed in a shade-tolerant species Panax notoginseng grown under the levels of low N (LN), moderate N (MN) and high N (HN). RESULTS Photosynthetic assimilation was significantly suppressed in the LN- and HN-grown plants. Compared with the MN-grown plants, the HN-grown plants showed thicker anatomic structure and larger chloroplast accompanied with decreased ratio of mesophyll conductance (gm) to Rubisco content (gm/Rubisco) and lower Rubisco activity. Meanwhile, LN-grown plants displayed smaller chloroplast and accordingly lower internal conductance (gi). LN- and HN-grown individuals allocated less N to light-harvesting system (NL) and carboxylation system (NC), respectively. N surplus negatively affected the expression of genes in Car biosynthesis (GGPS, DXR, PSY, IPI and DXS). The LN individuals outperformed others with respect to non-photochemical quenching. The expression of genes (FBA, PGK, RAF2, GAPC, CAB, PsbA and PsbH) encoding enzymes of Calvin cycle and structural protein of light reaction were obviously repressed in the LN individuals, accompanying with a reduction in Rubisco content and activity. Correspondingly, the expression of genes encoding RAF2, RPI4, CAB and PetE were repressed in the HN-grown plants. CONCLUSIONS LN-induced depression of photosynthetic capacity might be caused by the deceleration on Calvin cycle and light reaction of photosynthesis, and HN-induced depression of ones might derive from an increase in the form of inactivated Rubisco.
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Affiliation(s)
- Jin-Yan Zhang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medical Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhu Cun
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Medical Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Wen Chen
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
- Key Laboratory of Medical Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China.
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Wang Y, Xu J, Ge M, Ning L, Hu M, Zhao H. High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize. BMC Genomics 2020; 21:353. [PMID: 32393171 PMCID: PMC7216474 DOI: 10.1186/s12864-020-6769-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Background The fluctuation of nitrogen (N) contents profoundly affects the root growth and architecture in maize by altering the expression of thousands of genes. The differentially expressed genes (DEGs) in response to N have been extensively reported. However, information about the effects of N variation on the alternative splicing in genes is limited. Results To reveal the effects of N on the transcriptome comprehensively, we studied the N-starved roots of B73 in response to nitrate treatment, using a combination of short-read sequencing (RNA-seq) and long-read sequencing (PacBio-sequencing) techniques. Samples were collected before and 30 min after nitrate supply. RNA-seq analysis revealed that the DEGs in response to N treatment were mainly associated with N metabolism and signal transduction. In addition, we developed a workflow that utilizes the RNA-seq data to improve the quality of long reads, increasing the number of high-quality long reads to about 2.5 times. Using this workflow, we identified thousands of novel isoforms; most of them encoded the known functional domains and were supported by the RNA-seq data. Moreover, we found more than 1000 genes that experienced AS events specifically in the N-treated samples, most of them were not differentially expressed after nitrate supply-these genes mainly related to immunity, molecular modification, and transportation. Notably, we found a transcription factor ZmNLP6, a homolog of AtNLP7-a well-known regulator for N-response and root growth-generates several isoforms varied in capacities of activating downstream targets specifically after nitrate supply. We found that one of its isoforms has an increased ability to activate downstream genes. Overlaying DEGs and DAP-seq results revealed that many putative targets of ZmNLP6 are involved in regulating N metabolism, suggesting the involvement of ZmNLP6 in the N-response. Conclusions Our study shows that many genes, including the transcription factor ZmNLP6, are involved in modulating early N-responses in maize through the mechanism of AS rather than altering the transcriptional abundance. Thus, AS plays an important role in maize to adapt N fluctuation.
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Affiliation(s)
- Yuancong Wang
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jinyan Xu
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Min Ge
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lihua Ning
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Mengmei Hu
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Han Zhao
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Tucker SL, Dohleman FG, Grapov D, Flagel L, Yang S, Wegener KM, Kosola K, Swarup S, Rapp RA, Bedair M, Halls SC, Glenn KC, Hall MA, Allen E, Rice EA. Evaluating maize phenotypic variance, heritability, and yield relationships at multiple biological scales across agronomically relevant environments. PLANT, CELL & ENVIRONMENT 2020; 43:880-902. [PMID: 31733168 DOI: 10.1111/pce.13681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 05/22/2023]
Abstract
A challenge to improve an integrative phenotype, like yield, is the interaction between the broad range of possible molecular and physiological traits that contribute to yield and the multitude of potential environmental conditions in which they are expressed. This study collected data on 31 phenotypic traits, 83 annotated metabolites, and nearly 22,000 transcripts from a set of 57 diverse, commercially relevant maize hybrids across three years in central U.S. Corn Belt environments. Although variability in characteristics created a complex picture of how traits interact produce yield, phenotypic traits and gene expression were more consistent across environments, while metabolite levels showed low repeatability. Phenology traits, such as green leaf number and grain moisture and whole plant nitrogen content showed the most consistent correlation with yield. A machine learning predictive analysis of phenotypic traits revealed that ear traits, phenology, and root traits were most important to predicting yield. Analysis suggested little correlation between biomass traits and yield, suggesting there is more of a sink limitation to yield under the conditions studied here. This work suggests that continued improvement of maize yields requires a strong understanding of baseline variation of plant characteristics across commercially-relevant germplasm to drive strategies for consistently improving yield.
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Affiliation(s)
| | | | | | - Lex Flagel
- Bayer Crop Science, Chesterfield, Missouri
| | - Sean Yang
- Bayer Crop Science, Chesterfield, Missouri
| | | | | | | | - Ryan A Rapp
- Pairwise, Research Triangle Park, North Carolina
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Chin EL, Ramsey JS, Mishchuk DO, Saha S, Foster E, Chavez JD, Howe K, Zhong X, Polek M, Godfrey KE, Mueller LA, Bruce JE, Heck M, Slupsky CM. Longitudinal Transcriptomic, Proteomic, and Metabolomic Analyses of Citrus sinensis (L.) Osbeck Graft-Inoculated with " Candidatus Liberibacter asiaticus". J Proteome Res 2020; 19:719-732. [PMID: 31885275 DOI: 10.1021/acs.jproteome.9b00616] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
"Candidatus Liberibacter asiaticus" (CLas) is the bacterium associated with the citrus disease Huanglongbing (HLB). Current CLas detection methods are unreliable during presymptomatic infection, and understanding CLas pathogenicity to help develop new detection techniques is challenging because CLas has yet to be isolated in pure culture. To understand how CLas affects citrus metabolism and whether infected plants produce systemic signals that can be used to develop improved detection techniques, leaves from Washington Navel orange (Citrus sinensis (L.) Osbeck) plants were graft-inoculated with CLas and longitudinally studied using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry), and metabolomics (proton nuclear magnetic resonance). Photosynthesis gene expression and protein levels were lower in infected plants compared to controls during late infection, and lower levels of photosynthesis proteins were identified as early as 8 weeks post-grafting. These changes coordinated with higher sugar concentrations, which have been shown to accumulate during HLB. Cell wall modification and degradation gene expression and proteins were higher in infected plants during late infection. Changes in gene expression and proteins related to plant defense were observed in infected plants as early as 8 weeks post-grafting. These results reveal coordinated changes in greenhouse navel leaves during CLas infection at the transcript, protein, and metabolite levels, which can inform of biomarkers of early infection.
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Affiliation(s)
- Elizabeth L Chin
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
| | - John S Ramsey
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Darya O Mishchuk
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
| | - Surya Saha
- Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Elizabeth Foster
- Contained Research Facility , University of California, Davis , Davis , California 95616 , United States
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Kevin Howe
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - Xuefei Zhong
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - MaryLou Polek
- National Clonal Germplasm Repository for Citrus & Dates , Riverside , California 92507 , United States
| | - Kris E Godfrey
- Contained Research Facility , University of California, Davis , Davis , California 95616 , United States
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health , USDA Agricultural Research Service , Ithaca , New York 14853 , United States.,Boyce Thompson Institute for Plant Research , Ithaca , New York 14853 , United States.,Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science , Cornell University , Ithaca , New York 14853 , United States
| | - Carolyn M Slupsky
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
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Sun CX, Hao L, Wang D, Li C, Zhang C, Chen X, Fu J, Zhang YL. Nitrogen utilisation and metabolism in maize (Zea mays L.) plants under different rates of biochar addition and nitrogen input conditions. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:882-890. [PMID: 31002433 DOI: 10.1111/plb.12997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/11/2019] [Indexed: 05/26/2023]
Abstract
Biochar (BC) application could improve plant nitrogen (N) utilisation and potentially reduce N fertiliser requirements. However, the fate of N in crop-soil systems and the metabolic responses of crops under conditions of BC co-applied with reduced N are not well understood. The urea-15 N isotope and pot experiments with three BC rates (0%, 5% and 15%; w/w) combined with three N fertiliser levels (100% N, 85% N and 55% N) were conducted for maize. The metabolome, 15 N abundance and gene expression in plants were analysed using nuclear magnetic resonance, gas isotope mass spectrometry and quantitative real-time reverse transcription PCR, respectively. The results showed that recovery of N by maize ranged from 27.4% to 23.6% and decreased as the N application rate decreased (from 100% to 55%) without BC addition, but ranged from 24.6% to 29.4% when BC was added at a rate of 5% and increased as the N application rate decreased. BC addition had major effects on global metabolic profiles and metabolic networks at the metabolomics level as well as on the expression of related genes (zmGS1and zmAS1) and the content of mineral N (NO3 - , NO2 - and NH4 + ) in maize seedlings; moreover, the interaction effects of the BC application rates and N fertiliser levels were evident (P ≤ 0.001). BC addition induced a decrease in the flux toward sugar hydrolysis and maintained homeostasis in the amino acid pool, which was perturbed by reduced N levels; after which the maize plants adapted to the reduced N condition, and the N recovery efficiency ultimately improved with reduced N loss.
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Affiliation(s)
- C X Sun
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - L Hao
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - D Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - C Li
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - C Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - X Chen
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - J Fu
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - Y L Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning Province, China
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46
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Stanley L, Yuan YW. Transcriptional Regulation of Carotenoid Biosynthesis in Plants: So Many Regulators, So Little Consensus. FRONTIERS IN PLANT SCIENCE 2019; 10:1017. [PMID: 31447877 PMCID: PMC6695471 DOI: 10.3389/fpls.2019.01017] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/22/2019] [Indexed: 05/19/2023]
Abstract
In plants, the carotenoid biosynthesis pathway (CBP) is essential for the production of photosynthetic and protective pigments, plant hormones, and visual/olfactory attractants for animal pollinators and seed dispersers. The regulation of carotenoid biosynthesis at the transcriptional level is vitally important for all of these functions and has been the subject of intensive research. Many putative transcriptional regulators, both direct and indirect, have been identified through conventional mutant analysis, transcriptome profiling, yeast one-hybrid screening, and candidate gene approaches. Despite this progress, our understanding of the transcriptional regulation of carotenoid biosynthesis remains fragmented and incomplete. Frequently, a stimulus or regulator is known, but the mechanism by which it affects transcription has not been elucidated. In other cases, mechanisms have been proposed (such as direct binding of a CBP gene promoter by a transcription factor), but function was tested only in vitro or in heterologous systems, making it unclear whether these proteins actually play a role in carotenoid regulation in their endogenous environments. Even in cases where the mechanism is relatively well understood, regulators are often studied in isolation, either in a single plant species or outside the context of other known regulators. This presents a conundrum: why so many candidate regulators but so little consensus? Here we summarize current knowledge on transcriptional regulation of the CBP, lay out the challenges contributing to this conundrum, identify remaining knowledge gaps, and suggest future research directions to address these challenges and knowledge gaps.
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Affiliation(s)
- Lauren Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
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Qu C, Zuo Z, Cao L, Huang J, Sun X, Zhang P, Yang C, Li L, Xu Z, Liu G. Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar. BMC PLANT BIOLOGY 2019; 19:279. [PMID: 31242858 PMCID: PMC6595626 DOI: 10.1186/s12870-019-1862-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant. RESULTS In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites. CONCLUSIONS Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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Casartelli A, Melino VJ, Baumann U, Riboni M, Suchecki R, Jayasinghe NS, Mendis H, Watanabe M, Erban A, Zuther E, Hoefgen R, Roessner U, Okamoto M, Heuer S. Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. PLANT MOLECULAR BIOLOGY 2019; 99:477-497. [PMID: 30721380 DOI: 10.1007/s11103-019-00831-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/24/2019] [Indexed: 05/06/2023]
Abstract
Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH4+) thereby preventing N losses. On the other hand, under N deficiency, increasing the NH4+ liberated via allantoin catabolism contributes towards the maintenance of N homeostasis.
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Affiliation(s)
- Alberto Casartelli
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Strube Research GmbH & Co. KG, 38387, Söllingen, Germany
| | - Vanessa J Melino
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- School of Agriculture and Food, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Nirupama S Jayasinghe
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Himasha Mendis
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mutsumi Watanabe
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alexander Erban
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ellen Zuther
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Rainer Hoefgen
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ute Roessner
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mamoru Okamoto
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
- Rothamsted Research, Plant Science Department, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Kaur H, Peel A, Acosta K, Gebril S, Ortega JL, Sengupta‐Gopalan C. Comparison of alfalfa plants overexpressing glutamine synthetase with those overexpressing sucrose phosphate synthase demonstrates a signaling mechanism integrating carbon and nitrogen metabolism between the leaves and nodules. PLANT DIRECT 2019; 3:e00115. [PMID: 31245757 PMCID: PMC6508842 DOI: 10.1002/pld3.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 05/29/2023]
Abstract
Alfalfa, like other legumes, establishes a symbiotic relationship with the soil bacteria, Sinorhizobium meliloti, which results in the formation of the root nodules. Nodules contain the bacteria enclosed in a membrane-bound vesicle, the symbiosome where it fixes atmospheric N2 and converts it into ammonia using the bacterial enzyme, nitrogenase. The ammonia released into the cytoplasm from the symbiosome is assimilated into glutamine (Gln) using carbon skeletons produced by the metabolism of sucrose (Suc), which is imported into the nodules from the leaves. The key enzyme involved in the synthesis of Suc in the leaves is sucrose phosphate synthase (SPS) and glutamine synthetase (GS) is the enzyme with a role in ammonia assimilation in the root nodules. Alfalfa plants, overexpressing SPS or GS, or both showed increased growth and an increase in nodule function. The endogenous genes for the key enzymes in C/N metabolism showed increased expression in the nodules of both sets of transformants. Furthermore, the endogenous SPS and GS genes were also induced in the leaves and nodules of the transformants, irrespective of the transgene, suggesting that the two classes of plants share a common signaling pathway regulating C/N metabolism in the nodules. This study reaffirms the utility of the nodulated legume plant to study C/N interaction and the cross talk between the source and sink for C and N.
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Affiliation(s)
- Harmanpreet Kaur
- Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesNew Mexico
| | - Amanda Peel
- Department of Learning, Teaching and CurriculumUniversity of MissouriColumbiaMissouri
| | - Karen Acosta
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Sayed Gebril
- Department of HorticultureSohag UniversitySohagEgypt
| | - Jose Luis Ortega
- Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesNew Mexico
| | - Champa Sengupta‐Gopalan
- Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesNew Mexico
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50
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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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