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Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions. Int J Mol Sci 2023; 24:ijms24065290. [PMID: 36982364 PMCID: PMC10048922 DOI: 10.3390/ijms24065290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.
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Nazir F, Mahajan M, Khatoon S, Albaqami M, Ashfaque F, Chhillar H, Chopra P, Khan MIR. Sustaining nitrogen dynamics: A critical aspect for improving salt tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1087946. [PMID: 36909406 PMCID: PMC9996754 DOI: 10.3389/fpls.2023.1087946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
In the current changing environment, salt stress has become a major concern for plant growth and food production worldwide. Understanding the mechanisms of how plants function in saline environments is critical for initiating efforts to mitigate the detrimental effects of salt stress. Agricultural productivity is linked to nutrient availability, and it is expected that the judicious metabolism of mineral nutrients has a positive impact on alleviating salt-induced losses in crop plants. Nitrogen (N) is a macronutrient that contributes significantly to sustainable agriculture by maintaining productivity and plant growth in both optimal and stressful environments. Significant progress has been made in comprehending the fundamental physiological and molecular mechanisms associated with N-mediated plant responses to salt stress. This review provided an (a) overview of N-sensing, transportation, and assimilation in plants; (b) assess the salt stress-mediated regulation of N dynamics and nitrogen use- efficiency; (c) critically appraise the role of N in plants exposed to salt stress. Furthermore, the existing but less explored crosstalk between N and phytohormones has been discussed that may be utilized to gain a better understanding of plant adaptive responses to salt stress. In addition, the shade of a small beam of light on the manipulation of N dynamics through genetic engineering with an aim of developing salt-tolerant plants is also highlighted.
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Affiliation(s)
- Faroza Nazir
- Department of Botany, Jamia Hamdard, New Delhi, India
| | - Moksh Mahajan
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Mohammed Albaqami
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Farha Ashfaque
- Department of Botany, Aligarh Muslim University, Aligarh, India
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Aluko OO, Kant S, Adedire OM, Li C, Yuan G, Liu H, Wang Q. Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1074839. [PMID: 36895876 PMCID: PMC9989036 DOI: 10.3389/fpls.2023.1074839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.
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Affiliation(s)
- Oluwaseun Olayemi Aluko
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Chuanzong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haobao Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Hamdan MF, Mohd Noor SN, Abd-Aziz N, Pua TL, Tan BC. Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World. PLANTS (BASEL, SWITZERLAND) 2022; 11:1297. [PMID: 35631721 PMCID: PMC9146367 DOI: 10.3390/plants11101297] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022]
Abstract
Technological applications in agriculture have evolved substantially to increase crop yields and quality to meet global food demand. Conventional techniques, such as seed saving, selective breeding, and mutation breeding (variation breeding), have dramatically increased crop production, especially during the 'Green Revolution' in the 1990s. However, newer issues, such as limited arable lands, climate change, and ever-increasing food demand, pose challenges to agricultural production and threaten food security. In the following 'Gene Revolution' era, rapid innovations in the biotechnology field provide alternative strategies to further improve crop yield, quality, and resilience towards biotic and abiotic stresses. These innovations include the introduction of DNA recombinant technology and applications of genome editing techniques, such as transcription activator-like effector (TALEN), zinc-finger nucleases (ZFN), and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas) systems. However, the acceptance and future of these modern tools rely on the regulatory frameworks governing their development and production in various countries. Herein, we examine the evolution of technological applications in agriculture, focusing on the motivations for their introduction, technical challenges, possible benefits and concerns, and regulatory frameworks governing genetically engineered product development and production.
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Affiliation(s)
- Mohd Fadhli Hamdan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Siti Nurfadhlina Mohd Noor
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nazrin Abd-Aziz
- Innovation Centre in Agritechnology for Advanced Bioprocessing (ICA), Universiti Teknologi Malaysia, Pagoh 84600, Malaysia;
| | - Teen-Lee Pua
- Topplant Laboratories Sdn. Bhd., Jalan Ulu Beranang, Negeri Sembilan 71750, Malaysia;
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
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Wang L, Gao J, Wang C, Xu Y, Li X, Yang J, Chen K, Kang Y, Wang Y, Cao P, Xie X. Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:809435. [PMID: 35237286 PMCID: PMC8884251 DOI: 10.3389/fpls.2022.809435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression and are crucial for plant growth and development. However, the mechanisms underlying the effects of activated lncRNAs on axillary bud development remain largely unknown. By lncRNA transcriptomes of axillary buds in topped and untopped tobacco plants, we identified a total of 13,694 lncRNAs. LncRNA analysis indicated that the promoted growth of axillary bud by topping might be partially ascribed to the genes related to hormone signal transduction and glycometabolism, trans-regulated by differentially expressed lncRNAs, such as MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1. Metabolite profiling indicated that auxin, abscisic acid and gibberellin were decreased in axillary buds of topped tobacco lines, while cytokinin was increased, consistent with the expression levels of related lncRNAs. MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1 were shown to be influenced by hormones and sucrose treatments, and were associated with changes of axillary bud growth in the overexpression of NtCCD8 plants (with reduced axillary buds) and RNA interference of NtTB1 plants (with increased axillary buds). Moreover, MSTRG.28151.1 was identified as the antisense lncRNA of NtTB1. Silencing of MSTRG.28151.1 in tobacco significantly attenuated the expression of NtTB1 and resulted in larger axillary buds, suggesting the vital function of MSTRG.28151.1 axillary bud developmen by NtTB1. Our findings shed light on lncRNA-mRNA interactions and their functional roles in axillary bud growth, which would improve our understanding of lncRNAs as important regulators of axillary bud development and plant architecture.
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Affiliation(s)
- Lin Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Chen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Kai Chen
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yile Kang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yaofu Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
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Khan S, Pinto VB, do Amaral Júnior AT, Gonçalves GMB, Corrêa CCG, Ferreira FRA, de Souza GAR, Campostrini E, Freitas MSM, Vieira ME, de Oliveira Santos T, de Lima VJ, Kamphorst SH, do Amaral JFT, Mora-Poblete F, de Souza Filho GA, Silveira V. Revealing the differential protein profiles behind the nitrogen use efficiency in popcorn (Zea mays var. everta). Sci Rep 2022; 12:1521. [PMID: 35087128 PMCID: PMC8795358 DOI: 10.1038/s41598-022-05545-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
We investigated the proteomic profiles of two popcorn inbred lines, P2 (N-efficient and N-responsive) and L80 (N-inefficient and nonresponsive to N), under low (10% of N supply) and high (100% of N supply) nitrogen environments, associated with agronomic- and physiological-related traits to NUE. The comparative proteomic analysis allowed the identification of 79 differentially accumulated proteins (DAPs) in the comparison of high/low N for P2 and 96 DAPs in the comparison of high/low N for L80. The NUE and N uptake efficiency (NUpE) presented high means in P2 in comparison to L80 at both N levels, but the NUE, NUpE, and N utilization efficiency (NUtE) rates decreased in P2 under a high N supply. DAPs involved in energy and carbohydrate metabolism suggested that N regulates enzymes of alternative pathways to adapt to energy shortages and that fructose-bisphosphate aldolase may act as one of the key primary nitrate responsive proteins in P2. Proteins related to ascorbate biosynthesis and nitrogen metabolism increased their regulation in P2, and the interaction of L-ascorbate peroxidase and Fd-NiR may play an important role in the NUE trait. Taken together, our results provide new insights into the proteomic changes taking place in contrasting inbred lines, providing useful information on the genetic improvement of NUE in popcorn.
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Affiliation(s)
- Shahid Khan
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica. Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.
| | - Antônio Teixeira do Amaral Júnior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.
| | - Gabriel Moreno Bernardo Gonçalves
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Caio Cézar Guedes Corrêa
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Fernando Rafael Alves Ferreira
- Laboratório de Fitotecnia-Setor de Nutrição Mineral de Plantas, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Guilherme Augusto Rodrigues de Souza
- Laboratório de Melhoramento Genético Vegetal-Setor de Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Eliemar Campostrini
- Laboratório de Melhoramento Genético Vegetal-Setor de Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Marta Simone Mendonça Freitas
- Laboratório de Fitotecnia-Setor de Nutrição Mineral de Plantas, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Marlene Evangelista Vieira
- Laboratório de Fitotecnia-Setor de Nutrição Mineral de Plantas, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Talles de Oliveira Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Valter Jário de Lima
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Samuel Henrique Kamphorst
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - José Francisco Teixeira do Amaral
- Departamento de Engenharia Rural, Centro de Ciências Agrárias, Universidade Federal do Espírito Santo (UFES), Alto Universitário, s/nº, Alegre, Espírito Santo, 29500-000, Brazil
| | - Freddy Mora-Poblete
- Instituto de Ciencias Biológicas, Universidad de Talca, 1 Poniente 1141, 3460000, Talca, Chile
| | - Gonçalo Apolinário de Souza Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica. Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica. Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
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Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021; 10:cells10020346. [PMID: 33562333 PMCID: PMC7915772 DOI: 10.3390/cells10020346] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
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Ji PT, Li XL, Peng YJ, Zhang YC, Tao PJ. Effect of polyaspartic acid and different dosages of controlled-release fertilizers on nitrogen uptake, utilization, and yield of maize cultivars. Bioengineered 2021; 12:527-539. [PMID: 33535880 PMCID: PMC8806278 DOI: 10.1080/21655979.2020.1865608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effects of polyaspartic acid and different controlled-release fertilizers with urea on dry matter accumulation and distribution, nitrogen absorption and accumulation, and the activities of enzymes involved nitrogen metabolism and yield of corn were studied by using xianyu (XY688), a maize nitrogen efficient cultivar, and Jifeng NO.2 (JF2), a maize nitrogen-inefficient cultivar, as experimental materials and through random blocks experimental design in 2019. For XY688, polyaspartic acid chelated nitrogen fertilizer (PASPN) had the highest yield, which was 21.34% higher than N0 treatment. For JF2, it also had the highest yield under PASPN combined urea treatment, which was 23.44% higher than N0 (no nitrogen fertilizer), and JF2 had a 9.7% lower yield under XY688 treatment. For XY688, PASPN treatment had the largest nitrogen uptake in grain, up to 3.14 kg/hm2, and PASPN treatment increased 17.4% compared with N0. For JF2, grain nitrogen uptake was also the highest under PASPN treatment, which was significantly different from other treatments. Nitrogen uptake was 3.16 kg/hm2, which increased 37.4% compared with N0. Compared with JF2, XY688 showed higher nitrogen uptake efficiency, nitrogen utilization efficiency, and partial nitrogen productivity. For XY688, the highest nitrogen absorption efficiency was SU3 (slow-release urea and ordinary urea) treatment (0.36 kg/kg). The partial nitrogen productivity and harvest index of PASPN treatment were the highest and significantly different from other treatments. The partial nitrogen productivity of PASPN treatment was 57.02 kg/kg. These results can provide help for the further researches of the rational utilization and absorption of nitrogen fertilizer.
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Affiliation(s)
- Peng-Tao Ji
- College of Agronomy, Hebei Agricultural University , Baoding, Hebei, China
| | - Xiang-Ling Li
- Hebei Normal University of Science & Technology , Changli, P.R. China
| | - Yu-Juan Peng
- College of Agronomy, Hebei Agricultural University , Baoding, Hebei, China
| | - Yue-Chen Zhang
- College of Agronomy, Hebei Agricultural University , Baoding, Hebei, China
| | - Pei-Jun Tao
- College of Agronomy, Hebei Agricultural University , Baoding, Hebei, China
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Neeraja CN, Barbadikar KM, Krishnakanth T, Bej S, Rao IS, Srikanth B, Rao DS, Subrahmanyam D, Rao PR, Voleti SR. Down regulation of transcripts involved in selective metabolic pathways as an acclimation strategy in nitrogen use efficient genotypes of rice under low nitrogen. 3 Biotech 2021; 11:80. [PMID: 33505835 DOI: 10.1007/s13205-020-02631-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022] Open
Abstract
To understand the molecular mechanism of nitrogen use efficiency (NUE) in rice, two nitrogen (N) use efficient genotypes and two non-efficient genotypes were characterized using transcriptome analyses. The four genotypes were evaluated for 3 years under low and recommended N field conditions for 12 traits/parameters of yield, straw, nitrogen content along with NUE indices and 2 promising donors for rice NUE were identified. Using the transcriptome data generated from GS FLX 454 Roche and Illumina HiSeq 2000 of two efficient and two non-efficient genotypes grown under field conditions of low N and recommended N and their de novo assembly, differentially expressed transcripts and pathways during the panicle development were identified. Down regulation was observed in 30% of metabolic pathways in efficient genotypes and is being proposed as an acclimation strategy to low N. Ten sub metabolic pathways significantly enriched with additional transcripts either in the direction of the common expression or contra-regulated to the common expression were found to be critical for NUE in rice. Among the up-regulated transcripts in efficient genotypes, a hypothetical protein OsI_17904 with 2 alternative forms suggested the role of alternative splicing in NUE of rice and a potassium channel SKOR transcript (LOC_Os06g14030) has shown a positive correlation (0.62) with single plant yield under low N in a set of 16 rice genotypes. From the present study, we propose that the efficient genotypes appear to down regulate several not so critical metabolic pathways and divert the thus conserved energy to produce seed/yield under long-term N starvation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02631-5.
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Affiliation(s)
- C N Neeraja
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - Kalyani M Barbadikar
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - T Krishnakanth
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - Sonali Bej
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - I Subhakara Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - B Srikanth
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - D Sanjeeva Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - D Subrahmanyam
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - P Raghuveer Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - S R Voleti
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
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Kumari S, Sharma N, Raghuram N. Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:627955. [PMID: 34168661 PMCID: PMC8217879 DOI: 10.3389/fpls.2021.627955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/04/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein-protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.
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11
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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: 44] [Impact Index Per Article: 11.0] [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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Li M, Xu J, Gao Z, Tian H, Gao Y, Kariman K. Genetically modified crops are superior in their nitrogen use efficiency-A meta-analysis of three major cereals. Sci Rep 2020; 10:8568. [PMID: 32444783 PMCID: PMC7244766 DOI: 10.1038/s41598-020-65684-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 05/08/2020] [Indexed: 11/30/2022] Open
Abstract
It is currently uncertain to what extent genetic transformations of strategic crops (targeting diverse traits) have improved their N use efficiency (NUE), and what the key factors affecting their NUE are. Based on data collected from 130 publications, the effect sizes of genetic transformations and the key factors influencing NUE for three major cereal crops (rice, maize, and wheat), were investigated using a meta-analysis approach. Genetic transformations increased yield, shoot biomass, N uptake efficiency (NUpE), and partial factor productivity of N (PFPN) in the crops, but decreased shoot NUE (SNUE) and grain NUE (GNUE). Transporter genes improved yield and NUE parameters more efficiently, than did the other gene types. The effect sizes for some NUE parameters varied according to crop species and experimental conditions but did not differ between the overexpression and ectopic expression methods. Most effect sizes did not correlate with gene overexpression levels. These results indicate a promising potential of genetic transformations approaches for improving certain NUE parameters.
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Affiliation(s)
- Mengjiao Li
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Jili Xu
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiyuan Gao
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Tian
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yajun Gao
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Khalil Kariman
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
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Schaarschmidt S, Lawas LMF, Glaubitz U, Li X, Erban A, Kopka J, Jagadish SVK, Hincha DK, Zuther E. Season Affects Yield and Metabolic Profiles of Rice ( Oryza sativa) under High Night Temperature Stress in the Field. Int J Mol Sci 2020; 21:E3187. [PMID: 32366031 PMCID: PMC7247591 DOI: 10.3390/ijms21093187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- International Rice Research Institute, Metro Manila 1301, Philippines;
| | - Ulrike Glaubitz
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Xia Li
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Dirk K. Hincha
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
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Abstract
Nitrogen (N) is a macro-nutrient that is essential for growth development and resistance against biotic and abiotic stresses of plants. Nitrogen is a constituent of amino acids, proteins, nucleic acids, chlorophyll, and various primary and secondary metabolites. The atmosphere contains huge amounts of nitrogen but it cannot be taken up directly by plants. Plants can take up nitrogen in the form of nitrate, ammonium, urea, nitrite, or a combination of all these forms. In addition, in various leguminous rhizobia, bacteria can convert atmospheric nitrogen to ammonia and supply it to the plants. The form of nitrogen nutrition is also important in plant growth and resistance against pathogens. Nitrogen content has an important function in crop yield. Nitrogen deficiency can cause reduced root growth, change in root architecture, reduced plant biomass, and reduced photosynthesis. Hence, understanding the function and regulation of N metabolism is important. Several enzymes and intermediates are involved in nitrogen assimilation. Here we provide an overview of the important enzymes such as nitrate reductase, nitrite reductase, glutamine synthase, GOGAT, glutamate dehydrogenase, and alanine aminotransferase that are involved in nitrogen metabolism.
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Sisharmini A, Apriana A, Khumaida N, Trijatmiko KR, Purwoko BS. Expression of a cucumber alanine aminotransferase2 gene improves nitrogen use efficiency in transgenic rice. J Genet Eng Biotechnol 2019; 17:9. [PMID: 31712914 PMCID: PMC6848643 DOI: 10.1186/s43141-019-0010-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
Abstract
Background Rice can absorb less than 40% of applied nitrogen fertilizer, whereas the unabsorbed nitrogen fertilizer may cause environmental problems, such as algal blooms in freshwater and increased production of nitrous oxide, a greenhouse gas which is 300 times more potent than carbon dioxide. Development of nitrogen use efficient (NUE) rice is essential for more environmentally friendly rice production. Recently, NUE rice has been developed by root-specific expression of alanine aminotransferase (AlaAT) gene from barley, a monocot plant. Therefore, we tested the efficacy of AlaAT gene from cucumber in transgenic rice, aiming to provide evidence for the conservation of AlaAT gene function in monocot and dicot. Results AlaAT gene from cucumber (CsAlaAT2) has been successfully cloned and constructed on pCAMBIA1300 plant expression vectors under the control of tissue-specific promoter OsAnt1. Agrobacterium tumefaciens-mediated transformation of Indonesian rice cv. Fatmawati using this construct produced 14 transgenic events. Pre-screening of T1 seedlings grown in the agar medium containing low nitrogen concentration identified selected events that were superior in the root dry weight. Southern hybridization confirmed the integration of T-DNA in the selected event genomes, each of them carried 1, 2, or 3 T-DNA insertions. Efficacy assay of three lead events in the greenhouse showed that in general transgenic events had increased biomass, tiller number, nitrogen content, and grain yield compared to WT. One event, i.e., FAM13, showed an increase in yield as much as 27.9% and higher plant biomass as much as 27.4% compared to WT under the low nitrogen condition. The lead events also showed higher absorption NUE, agronomical NUE, and grain NUE as compared to WT under the low nitrogen condition. Conclusions The results of this study showed that root-specific expression of cucumber alanine aminotransferase2 gene improved nitrogen use efficiency in transgenic rice, which indicate the conservation of function of this gene in monocot and dicot.
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Affiliation(s)
- Atmitri Sisharmini
- Plant Breeding and Biotechnology Study Program, Departement of Agronomy and Horticulture, IPB University (Bogor Agricultural University), Jl. Meranti, Kampus IPB Darmaga, Bogor, 16680, Indonesia.,Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar 3A, Bogor, 16111, Indonesia
| | - Aniversari Apriana
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar 3A, Bogor, 16111, Indonesia
| | - Nurul Khumaida
- Plant Breeding and Biotechnology Study Program, Departement of Agronomy and Horticulture, IPB University (Bogor Agricultural University), Jl. Meranti, Kampus IPB Darmaga, Bogor, 16680, Indonesia
| | - Kurniawan Rudi Trijatmiko
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar 3A, Bogor, 16111, Indonesia
| | - Bambang Sapta Purwoko
- Plant Breeding and Biotechnology Study Program, Departement of Agronomy and Horticulture, IPB University (Bogor Agricultural University), Jl. Meranti, Kampus IPB Darmaga, Bogor, 16680, Indonesia.
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16
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Boschiero BN, Mariano E, Azevedo RA, Ocheuze Trivelin PC. Influence of nitrate - ammonium ratio on the growth, nutrition, and metabolism of sugarcane. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:246-255. [PMID: 30921736 DOI: 10.1016/j.plaphy.2019.03.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 05/13/2023]
Abstract
Although ammonium (NH4+) has been claimed as the preferential N source for sugarcane (Saccharum spp.), the intense uptake of this mineral form by plants can impair metabolic processes and crop yield. We aimed to assess the growth, nutrition, and metabolic responses of sugarcane grown under different amounts of nitrate (NO3-) and NH4+. Sugarcane setts were grown in nutrient solution at a total concentration of 15 mM N using different NO3-/NH4+ ratios (100/0, 75/25, 50/50, 25/75, and 0/100, respectively) for 163 d under controlled conditions. The pH of the medium was daily adjusted to 5.8 ± 0.1, with replacement of the hydroponic solution every 10 d. NH4+-only fed plants showed lower dry biomass yield, nutrient content, leaf surface area, and leaf gas exchange than those under sole NO3- supply, in addition to favoring the development of brown rust (Puccinia melanocephala). However, there was no indication that NH4+ is directly related to oxidative stress in sugarcane. On the other hand, the highest N utilization efficiency was obtained with NO3--only fed plants, which also resulted in the highest biomass yield, leaf surface area, nutrient content, leaf gas exchange, and root growth. Since NO3- was not stored in plant tissues, we therefore suggested that most of this N form is assimilated following its uptake. Despite the well-known preference of the crop for NH4+, the optimal growth response of sugarcane plants to NO3-/NH4+ ratios was observed under NO3- supply.
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Affiliation(s)
- Beatriz Nastaro Boschiero
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil; Laboratory of Stable Isotopes, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
| | - Eduardo Mariano
- Laboratory of Stable Isotopes, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Ricardo Antunes Azevedo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Paulo Cesar Ocheuze Trivelin
- Laboratory of Stable Isotopes, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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17
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2D-DIGE comparative proteomic analysis of developing wheat grains under high-nitrogen fertilization revealed key differentially accumulated proteins that promote storage protein and starch biosyntheses. Anal Bioanal Chem 2018; 410:6219-6235. [PMID: 30058028 DOI: 10.1007/s00216-018-1230-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022]
Abstract
Nitrogen (N) serves as a macronutrient that is essential to plant growth and development, and significantly influences storage protein and starch biosyntheses and, ultimately, grain yield and quality. In this study, we performed the first comparative proteomic analysis of developing wheat grains under high-N conditions using 2D-DIGE and tandem mass spectrometry. High-N fertilizer application caused significant increases in ear number, ear grain number, and grain yield. 2D-DIGE identified 142 differentially accumulated proteins (DAPs) during grain development in the elite Chinese bread wheat cultivar Zhongmai 175, of which 132 (93%) were identified by MALDI-TOF/TOF-MS, representing 92 unique proteins. These proteins are involved mainly in energy, N and protein metabolism, carbon metabolism, and starch biosynthesis. Subcellular localization prediction and fluorescence confocal microscopic analysis showed that the DAPs identified were localized mainly in the cytosol and chloroplast. Principal component analysis (PCA) revealed a greater proteomic difference among grain developmental periods than between the high-N and control groups. Protein-protein interaction analysis highlighted a complex network centered around enzymes involved in energy, N and protein metabolism, and starch biosynthesis. Six key DAP genes showed expression patterns consistent with their protein accumulation trends during grain development. A putative metabolic pathway was proposed, with synergistic regulatory networks of grain storage protein and starch biosyntheses in response to high-N application.
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18
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Ali J, Jewel ZA, Mahender A, Anandan A, Hernandez J, Li Z. Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice. Int J Mol Sci 2018; 19:E1762. [PMID: 29899204 PMCID: PMC6032200 DOI: 10.3390/ijms19061762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022] Open
Abstract
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.
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Affiliation(s)
- Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Zilhas Ahmed Jewel
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jose Hernandez
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
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Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
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20
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Peña PA, Quach T, Sato S, Ge Z, Nersesian N, Dweikat IM, Soundararajan M, Clemente T. Molecular and phenotypic characterization of transgenic wheat and sorghum events expressing the barley alanine aminotransferase. PLANTA 2017; 246:1097-1107. [PMID: 28801748 DOI: 10.1007/s00425-017-2753-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 05/03/2023]
Abstract
The expression of a barley alanine aminotransferase gene impacts agronomic outcomes in a C3 crop, wheat. The use of nitrogen-based fertilizers has become one of the major agronomic inputs in crop production systems. Strategies to enhance nitrogen assimilation and flux in planta are being pursued through the introduction of novel genetic alleles. Here an Agrobacterium-mediated approach was employed to introduce the alanine aminotransferase from barley (Hordeum vulgare), HvAlaAT, into wheat (Triticum aestivum) and sorghum (Sorghum bicolor), regulated by either constitutive or root preferred promoter elements. Plants harboring the transgenic HvAlaAT alleles displayed increased alanine aminotransferase (alt) activity. The enhanced alt activity impacted height, tillering and significantly boosted vegetative biomass relative to controls in wheat evaluated under hydroponic conditions, where the phenotypic outcome across these parameters varied relative to time of year study was conducted. Constitutive expression of HvAlaAT translated to elevation in wheat grain yield under field conditions. In sorghum, expression of HvAlaAT enhanced enzymatic activity, but no changes in phenotypic outcomes were observed. Taken together these results suggest that positive agronomic outcomes can be achieved through enhanced alt activity in a C3 crop, wheat. However, the variability observed across experiments under greenhouse conditions implies the phenotypic outcomes imparted by the HvAlaAT allele in wheat may be impacted by environment.
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Affiliation(s)
- Pamela A Peña
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Truyen Quach
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Natalya Nersesian
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | | | - Tom Clemente
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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21
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Li H, Hu B, Chu C. Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2477-2488. [PMID: 28419301 DOI: 10.1093/jxb/erx101] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Xu Z, Ma J, Qu C, Hu Y, Hao B, Sun Y, Liu Z, Yang H, Yang C, Wang H, Li Y, Liu G. Identification and expression analyses of the alanine aminotransferase (AlaAT) gene family in poplar seedlings. Sci Rep 2017; 7:45933. [PMID: 28378825 PMCID: PMC5380993 DOI: 10.1038/srep45933] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
Alanine aminotransferase (AlaAT, E.C.2.6.1.2) catalyzes the reversible conversion of pyruvate and glutamate to alanine and α-oxoglutarate. The AlaAT gene family has been well studied in some herbaceous plants, but has not been well characterized in woody plants. In this study, we identified four alanine aminotransferase homologues in Populus trichocarpa, which could be classified into two subgroups, A and B. AlaAT3 and AlaAT4 in subgroup A encode AlaAT, while AlaAT1 and AlaAT2 in subgroup B encode glutamate:glyoxylate aminotransferase (GGAT), which catalyzes the reaction of glutamate and glyoxylate to α-oxoglutarate and glycine. Four AlaAT genes were cloned from P. simonii × P. nigra. PnAlaAT1 and PnAlaAT2 were expressed predominantly in leaves and induced by exogenous nitrogen and exhibited a diurnal fluctuation in leaves, but was inhibited in roots. PnAlaAT3 and PnAlaAT4 were mainly expressed in roots, stems and leaves, and was induced by exogenous nitrogen. The expression of PnAlaAT3 gene could be regulated by glutamine or its related metabolites in roots. Our results suggest that PnAlaAT3 gene may play an important role in nitrogen metabolism and is regulated by glutamine or its related metabolites in the roots of P. simonii × P. nigra.
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Affiliation(s)
- Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.,College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jing Ma
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.,School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yanbo Hu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Bingqing Hao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yan Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhongye Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Han Yang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Hongwei Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China.,School of Forestry, Northeast Forestry University, Harbin 150040, China
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23
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Plett D, Holtham L, Baumann U, Kalashyan E, Francis K, Enju A, Toubia J, Roessner U, Bacic A, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN. Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms. PLANT MOLECULAR BIOLOGY 2016; 92:293-312. [PMID: 27511191 DOI: 10.1007/s11103-016-0512-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/10/2016] [Indexed: 05/21/2023]
Abstract
We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been hampered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 (-) throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or individual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants.
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Affiliation(s)
- Darren Plett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Luke Holtham
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Elena Kalashyan
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Karen Francis
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Akiko Enju
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - John Toubia
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- ACRF South Australian Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, 5000, Australia
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Ute Roessner
- Australian Centre for Plant Functional Genomics, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Antony Bacic
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Kanwarpal S Dhugga
- DuPont Pioneer, Johnston, IA, 50131, USA
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México Veracruz, Km. 45, El Batán, Texcoco, Estado De México, 56237, USA
| | - Mark Tester
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Trevor Garnett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia.
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia.
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, PMB 1, Glen Osmond, 5064, Australia.
| | - Brent N Kaiser
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- Centre For Carbon Water and Food, The Faculty of Agriculture and Environment, The University of Sydney, Camden, NSW, 2570, Australia
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24
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Ghaffari MR, Shahinnia F, Usadel B, Junker B, Schreiber F, Sreenivasulu N, Hajirezaei MR. The Metabolic Signature of Biomass Formation in Barley. PLANT & CELL PHYSIOLOGY 2016; 57:1943-60. [PMID: 27388338 DOI: 10.1093/pcp/pcw117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
The network analysis of genome-wide transcriptome responses, metabolic signatures and enzymes' relationship to biomass formation has been studied in a diverse panel of 12 barley accessions during vegetative and reproductive stages. The primary metabolites and enzymes involved in central metabolism that determine the accumulation of shoot biomass at the vegetative stage of barley development are primarily being linked to sucrose accumulation and sucrose synthase activity. Interestingly, the metabolic and enzyme links which are strongly associated with biomass accumulation during reproductive stages are related to starch accumulation and tricarboxylic acid (TCA) cycle intermediates citrate, malate, trans-aconitate and isocitrate. Additional significant associations were also found for UDP glucose, ATP and the amino acids isoleucine, valine, glutamate and histidine during the reproductive stage. A network analysis resulted in a combined identification of metabolite and enzyme signatures indicative for grain weight accumulation that was correlated with the activity of ADP-glucose pyrophosphorylase (AGPase), a rate-limiting enzyme involved in starch biosynthesis, and with that of alanine amino transferase involved in the synthesis of storage proteins. We propose that the mechanism related to vegetative and reproductive biomass formation vs. seed biomass formation is being linked to distinct fluxes regulating sucrose, starch, sugars and amino acids as central resources. These distinct biomarkers can be used to engineer biomass production and grain weight in barley.
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Affiliation(s)
- Mohammad R Ghaffari
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREO), Tehran, Iran Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466 Gatersleben, Germany
| | - Fahimeh Shahinnia
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466 Gatersleben, Germany
| | - Björn Usadel
- Institute of Botany, RWTH Aachen University, BioSC Germany and IBG-2 Plant Sciences, Forschungszentrum Jülich, D-52428 Jülich, Germany
| | - Björn Junker
- Institute of Pharmacy/Biosynthesis of Active Substances, Hoher Weg 8, Halle (Saale), Germany
| | - Falk Schreiber
- Monash University, Clayton Campus, Wellington Road, Clayton, VIC 3800, Australia
| | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Mohammad R Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466 Gatersleben, Germany
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25
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Qu CP, Xu ZR, Hu YB, Lu Y, Yang CJ, Sun GY, Liu GJ. RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments. FRONTIERS IN PLANT SCIENCE 2016; 7:51. [PMID: 26870068 PMCID: PMC4735414 DOI: 10.3389/fpls.2016.00051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/13/2016] [Indexed: 05/07/2023]
Abstract
Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.
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Affiliation(s)
- Chun-Pu Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Zhi-Ru Xu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yan-Bo Hu
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yao Lu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Cheng-Jun Yang
- School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Guang-Yu Sun
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Guan-Jun Liu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- *Correspondence: Guan-Jun Liu
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26
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McAllister CH, Good AG. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana. PLoS One 2015; 10:e0121830. [PMID: 25830496 PMCID: PMC4382294 DOI: 10.1371/journal.pone.0121830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/04/2015] [Indexed: 01/08/2023] Open
Abstract
Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.
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Affiliation(s)
- Chandra H. McAllister
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- * E-mail:
| | - Allen G. Good
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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27
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Yang W, Yoon J, Choi H, Fan Y, Chen R, An G. Transcriptome analysis of nitrogen-starvation-responsive genes in rice. BMC PLANT BIOLOGY 2015; 15:31. [PMID: 25644226 PMCID: PMC4333837 DOI: 10.1186/s12870-015-0425-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 01/15/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. RESULTS We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-change ≥ 2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down). Among the 36 deficiency-induced genes first identified via RNA-Seq analyses, 34 were subsequently confirmed by qRT-PCR. Our RNA-Seq data identified 8,509 multi-exonic genes with 19,628 alternative splicing events. However, we saw no significant difference in alternative splicing between N-sufficient and -deficient conditions. We found 2,986 novel transcripts, of which 192 were regulated under the N-deficiency. CONCLUSION We identified 1,650 genes that were differentially expressed after 12 h of N-starvation. Responses by those genes to a limited supply of N were confirmed by RT-PCR and GUS assays. Our results provide valuable information about N-starvation-responsive genes and will be useful when investigating the signal transduction pathway of N-utilization.
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Affiliation(s)
- Wenzhu Yang
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jinmi Yoon
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
| | - Heebak Choi
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
| | - Yunliu Fan
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rumei Chen
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
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28
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Tian H, Fu J, Drijber RA, Gao Y. Expression patterns of five genes involved in nitrogen metabolism in two winter wheat (Triticum aestivum L.) genotypes with high and low nitrogen utilization efficiencies. J Cereal Sci 2015. [DOI: 10.1016/j.jcs.2014.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Coneva V, Simopoulos C, Casaretto JA, El-Kereamy A, Guevara DR, Cohn J, Zhu T, Guo L, Alexander DC, Bi YM, McNicholas PD, Rothstein SJ. Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics 2014; 15:1056. [PMID: 25471115 PMCID: PMC4301927 DOI: 10.1186/1471-2164-15-1056] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions. RESULTS A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation. CONCLUSIONS The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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30
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Simons M, Saha R, Guillard L, Clément G, Armengaud P, Cañas R, Maranas CD, Lea PJ, Hirel B. Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5657-71. [PMID: 24863438 DOI: 10.1093/jxb/eru227] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this review, we will present the latest developments in systems biology with particular emphasis on improving nitrogen-use efficiency (NUE) in crops such as maize and demonstrating the application of metabolic models. The review highlights the importance of improving NUE in crops and provides an overview of the transcriptome, proteome, and metabolome datasets available, focusing on a comprehensive understanding of nitrogen regulation. 'Omics' data are hard to interpret in the absence of metabolic flux information within genome-scale models. These models, when integrated with 'omics' data, can serve as a basis for generating predictions that focus and guide further experimental studies. By simulating different nitrogen (N) conditions at a pseudo-steady state, the reactions affecting NUE and additional gene regulations can be determined. Such models thus provide a framework for improving our understanding of the metabolic processes underlying the more efficient use of N-based fertilizers.
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Affiliation(s)
- Margaret Simons
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rajib Saha
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lenaïg Guillard
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Gilles Clément
- Plateau Technique Spécifique de Chimie du Végétal, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Route de St Cyr, F-78026 Versailles Cedex, France
| | - Patrick Armengaud
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Rafael Cañas
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Bertrand Hirel
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
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31
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Valdés A, Simó C, Ibáñez C, García-Cañas V. Foodomics strategies for the analysis of transgenic foods. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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McAllister CH, Facette M, Holt A, Good AG. Analysis of the enzymatic properties of a broad family of alanine aminotransferases. PLoS One 2013; 8:e55032. [PMID: 23408955 PMCID: PMC3567105 DOI: 10.1371/journal.pone.0055032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/17/2012] [Indexed: 01/04/2023] Open
Abstract
Alanine aminotransferase (AlaAT) has been studied in a variety of organisms due to the involvement of this enzyme in mammalian processes such as non-alcoholic hepatocellular damage, and in plant processes such as C4 photosynthesis, post-hypoxic stress response and nitrogen use efficiency. To date, very few studies have made direct comparisons of AlaAT enzymes and fewer still have made direct comparisons of this enzyme across a broad spectrum of organisms. In this study we present a direct kinetic comparison of glutamate:pyruvate aminotransferase (GPAT) activity for seven AlaATs and two glutamate:glyoxylate aminotransferases (GGAT), measuring the KM values for the enzymes analyzed. We also demonstrate that recombinant expression of AlaAT enzymes in Eschericia coli results in differences in bacterial growth inhibition, supporting previous reports of AlaAT possessing bactericidal properties, attributed to lipopolysaccharide endotoxin recognition and binding. A probable lipopolysaccharide binding region within the AlaAT enzymes, homologous to a region of a lipopolysaccharide binding protein (LBP) in humans, was also identified in this study. The AlaAT enzyme differences identified here indicate that AlaAT homologues have differentiated significantly and the roles these homologues play in vivo may also have diverged significantly. Specifically, the differing kinetics of AlaAT enzymes and how this may alter the nitrogen use efficiency in plants is discussed.
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Hakeem KR, Chandna R, Ahmad A, Qureshi MI, Iqbal M. Proteomic analysis for low and high nitrogen-responsive proteins in the leaves of rice genotypes grown at three nitrogen levels. Appl Biochem Biotechnol 2012; 168:834-50. [PMID: 22903322 DOI: 10.1007/s12010-012-9823-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
Abstract
Nitrogen (N) is an essential nutrient for plants. Increase in crop production is associated with increase in N fertilizers. Excessive use of N fertilizers and the low nitrogen utilization efficiency by crop plants is a major cause for environmental damage. Therefore, to reduce the N-fertilizer pollution, there is an urgent need to improve nitrogen use efficiency. Identification and/or development of genotypes which can grow and yield well at low nitrogen levels may provide a solution. Understanding the molecular mechanism of differential nitrogen use efficiency of the genotypes may provide some clues. Keeping the above facts in mind, in this study we have identified the high N-responsive and low N-responsive contrasting rice genotypes, out of 20 genotypes that were grown at low (1 mM), moderate (10 mM), and high (25 mM) levels of N (KNO(3)). Proteome analysis of leaves revealed that the proteins involved in the energy production/regulation and metabolism in plant leaf tissues are differentially expressed under N treatments. Moreover, some disease-resistant and stress-induced proteins were found to be overexpressed at high levels of N. The present study could be useful in identifying proteins responding to different levels of nitrogen fertilization, which may open new avenues for a better understanding of N use efficiency, and for developing new strategies to enhance N efficiency in cereal crops.
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Affiliation(s)
- Khalid Rehman Hakeem
- Department of Botany, Molecular Ecology Laboratory, Faculty of Science, Hamdard University, New Delhi 110062, India.
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Møller ALB, Pedas P, Andersen B, Svensson B, Schjoerring JK, Finnie C. Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium. PLANT, CELL & ENVIRONMENT 2011; 34:2024-37. [PMID: 21736591 DOI: 10.1111/j.1365-3040.2011.02396.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Cereals are major crops worldwide, and improvement of their nitrogen use efficiency is a crucial challenge. In this study proteins responding to N supply in barley roots and shoots were analysed using a proteomics approach, to provide insight into mechanisms of N uptake and assimilation. Control plants grown hydroponically for 33 d with 5 mm nitrate, plants grown under N deficiency (0.5 mm nitrate, 33 d) or short-term N starvation (28 d with 5 mm nitrate followed by 5 d with no N source) were compared. N deficiency caused changes in C and N metabolism and ascorbate-glutathione cycle enzymes in shoots and roots. N starvation altered proteins of amino acid metabolism in roots. Both treatments caused proteome changes in roots that could affect growth. Shoots of plants grown with ammonium as N source (28 d with 5 mm nitrate followed by 5 d with 5 mm ammonium) showed responses similar to N deficient shoots, characterized by turnover of ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and increases in proteins of the chloroplastic transcription and translation machinery. Identified proteins in 67 and 49 varying spots in roots and shoots respectively, corresponded to 62 functions and over 80 gene products, considerably advancing knowledge of N responses in barley.
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Affiliation(s)
- Anders L B Møller
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Building 224, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
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Yang XS, Wu J, Ziegler TE, Yang X, Zayed A, Rajani M, Zhou D, Basra AS, Schachtman DP, Peng M, Armstrong CL, Caldo RA, Morrell JA, Lacy M, Staub JM. Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize. PLANT PHYSIOLOGY 2011; 157:1841-52. [PMID: 21980173 PMCID: PMC3327211 DOI: 10.1104/pp.111.187898] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the last several decades, increased agricultural production has been driven by improved agronomic practices and a dramatic increase in the use of nitrogen-containing fertilizers to maximize the yield potential of crops. To reduce input costs and to minimize the potential environmental impacts of nitrogen fertilizer that has been used to optimize yield, an increased understanding of the molecular responses to nitrogen under field conditions is critical for our ability to further improve agricultural sustainability. Using maize (Zea mays) as a model, we have characterized the transcriptional response of plants grown under limiting and sufficient nitrogen conditions and during the recovery of nitrogen-starved plants. We show that a large percentage (approximately 7%) of the maize transcriptome is nitrogen responsive, similar to previous observations in other plant species. Furthermore, we have used statistical approaches to identify a small set of genes whose expression profiles can quantitatively assess the response of plants to varying nitrogen conditions. Using a composite gene expression scoring system, this single set of biomarker genes can accurately assess nitrogen responses independently of genotype, developmental stage, tissue type, or environment, including in plants grown under controlled environments or in the field. Importantly, the biomarker composite expression response is much more rapid and quantitative than phenotypic observations. Consequently, we have successfully used these biomarkers to monitor nitrogen status in real-time assays of field-grown maize plants under typical production conditions. Our results suggest that biomarkers have the potential to be used as agronomic tools to monitor and optimize nitrogen fertilizer usage to help achieve maximal crop yields.
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Tcherkez G, Mahé A, Boex-Fontvieille E, Gout E, Guérard F, Bligny R. Experimental evidence of phosphoenolpyruvate resynthesis from pyruvate in illuminated leaves. PLANT PHYSIOLOGY 2011; 157:86-95. [PMID: 21730197 PMCID: PMC3165900 DOI: 10.1104/pp.111.180711] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 06/30/2011] [Indexed: 05/18/2023]
Abstract
Day respiration is the cornerstone of nitrogen assimilation since it provides carbon skeletons to primary metabolism for glutamate (Glu) and glutamine synthesis. However, recent studies have suggested that the tricarboxylic acid pathway is rate limiting and mitochondrial pyruvate dehydrogenation is partly inhibited in the light. Pyruvate may serve as a carbon source for amino acid (e.g. alanine) or fatty acid synthesis, but pyruvate metabolism is not well documented, and neither is the possible resynthesis of phosphoenolpyruvate (PEP). Here, we examined the capacity of pyruvate to convert back to PEP using (13)C and (2)H labeling in illuminated cocklebur (Xanthium strumarium) leaves. We show that the intramolecular labeling pattern in Glu, 2-oxoglutarate, and malate after (13)C-3-pyruvate feeding was consistent with (13)C redistribution from PEP via the PEP-carboxylase reaction. Furthermore, the deuterium loss in Glu after (2)H(3)-(13)C-3-pyruvate feeding suggests that conversion to PEP and back to pyruvate washed out (2)H atoms to the solvent. Our results demonstrate that in cocklebur leaves, PEP resynthesis occurred as a flux from pyruvate, approximately 0.5‰ of the net CO(2) assimilation rate. This is likely to involve pyruvate inorganic phosphate dikinase and the fundamental importance of this flux for PEP and inorganic phosphate homeostasis is discussed.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8618, France.
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Rolletschek H, Melkus G, Grafahrend-Belau E, Fuchs J, Heinzel N, Schreiber F, Jakob PM, Borisjuk L. Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. THE PLANT CELL 2011; 23:3041-54. [PMID: 21856793 PMCID: PMC3180809 DOI: 10.1105/tpc.111.087015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The starchy endosperm of cereals is a priori taken as a metabolically uniform tissue. By applying a noninvasive assay based on (13)C/(1)H-magnetic resonance imaging (MRI) to barley (Hordeum vulgare) grains, we uncovered metabolic compartmentation in the endosperm. (13)C-Suc feeding during grain filling showed that the primary site of Ala synthesis was the central region of the endosperm, the part of the caryopsis experiencing the highest level of hypoxia. Region-specific metabolism in the endosperm was characterized by flux balance analysis (FBA) and metabolite profiling. FBA predicts that in the central region of the endosperm, the tricarboxylic acid cycle shifts to a noncyclic mode, accompanied by elevated glycolytic flux and the accumulation of Ala. The metabolic compartmentation within the endosperm is advantageous for the grain's carbon and energy economy, with a prominent role being played by Ala aminotransferase. An investigation of caryopses with a genetically perturbed tissue pattern demonstrated that Ala accumulation is a consequence of oxygen status, rather than being either tissue specific or dependent on the supply of Suc. Hence the (13)C-Ala gradient can be used as an in vivo marker for hypoxia. The combination of MRI and metabolic modeling offers opportunities for the noninvasive analysis of metabolic compartmentation in plants.
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Affiliation(s)
- Hardy Rolletschek
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
| | - Gerd Melkus
- University of California–San Francisco, Radiology and Biomedical Imaging, San Francisco, California 94107
| | - Eva Grafahrend-Belau
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
| | - Johannes Fuchs
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
- University of Würzburg, Institute of Experimental Physics 5, 97074 Wuerzburg, Germany
| | - Nicolas Heinzel
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
| | - Falk Schreiber
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
| | - Peter M. Jakob
- University of Würzburg, Institute of Experimental Physics 5, 97074 Wuerzburg, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, 06466 Gatersleben, Germany
- Address correspondence to
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Ricroch AE, Bergé JB, Kuntz M. Evaluation of genetically engineered crops using transcriptomic, proteomic, and metabolomic profiling techniques. PLANT PHYSIOLOGY 2011; 155:1752-61. [PMID: 21350035 PMCID: PMC3091128 DOI: 10.1104/pp.111.173609] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 02/17/2011] [Indexed: 05/18/2023]
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Rocha M, Sodek L, Licausi F, Hameed MW, Dornelas MC, van Dongen JT. Analysis of alanine aminotransferase in various organs of soybean (Glycine max) and in dependence of different nitrogen fertilisers during hypoxic stress. Amino Acids 2010; 39:1043-53. [PMID: 20414691 PMCID: PMC2945468 DOI: 10.1007/s00726-010-0596-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 04/08/2010] [Indexed: 11/28/2022]
Abstract
Alanine aminotransferase (AlaAT) catalyses the reversible conversion of pyruvate and glutamate into alanine and oxoglutarate. In soybean, two subclasses were identified, each represented by two highly similar members. To investigate the role of AlaAT during hypoxic stress in soybean, changes in transcript level of both subclasses were analysed together with the enzyme activity and alanine content of the tissue. Moreover, the dependency of AlaAT activity and gene expression was investigated in relation to the source of nitrogen supplied to the plants. Using semi-quantitative PCR, GmAlaAT genes were determined to be highest expressed in roots and nodules. Under normal growth conditions, enzyme activity of AlaAT was detected in all organs tested, with lowest activity in the roots. Upon waterlogging-induced hypoxia, AlaAT activity increased strongly. Concomitantly, alanine accumulated. During re-oxygenation, AlaAT activity remained high, but the transcript level and the alanine content decreased. Our results show a role for AlaAT in the catabolism of alanine during the initial period of re-oxygenation following hypoxia. GmAlaAT also responded to nitrogen availability in the solution during waterlogging. Ammonium as nitrogen source induced both gene expression and enzyme activity of AlaAT more than when nitrate was supplied in the nutrient solution. The work presented here indicates that AlaAT might not only be important during hypoxia, but also during the recovery phase after waterlogging, when oxygen is available to the tissue again.
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Affiliation(s)
- Marcio Rocha
- Energy Metabolism Research Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departamento de Fisiologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, C.P. 6109, Campinas, SP 13083-970 Brazil
| | - Ladaslav Sodek
- Departamento de Fisiologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, C.P. 6109, Campinas, SP 13083-970 Brazil
| | - Francesco Licausi
- Energy Metabolism Research Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Plant Lab, Scuola Superiore Sant’Anna, Piazza Martiri della Liberta 33, 56127 Pisa, Italy
| | - Muhammad Waqar Hameed
- Energy Metabolism Research Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Marcelo Carnier Dornelas
- Departamento de Fisiologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, C.P. 6109, Campinas, SP 13083-970 Brazil
| | - Joost T. van Dongen
- Energy Metabolism Research Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Beatty PH, Anbessa Y, Juskiw P, Carroll RT, Wang J, Good AG. Nitrogen use efficiencies of spring barley grown under varying nitrogen conditions in the field and growth chamber. ANNALS OF BOTANY 2010; 105:1171-82. [PMID: 20308048 PMCID: PMC2887063 DOI: 10.1093/aob/mcq025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/11/2009] [Accepted: 12/14/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Nitrogen-use efficiency (NUE) of cereals needs to be improved by nitrogen (N) management, traditional plant breeding methods and/or biotechnology, while maintaining or, optimally, increasing crop yields. The aims of this study were to compare spring-barley genotypes grown on different nitrogen levels in field and growth-chamber conditions to determine the effects on N uptake (NUpE) and N utilization efficiency (NUtE) and ultimately, NUE. METHODS Morphological characteristics, seed yield and metabolite levels of 12 spring barley (Hordeum vulgare) genotypes were compared when grown at high and low nitrogen levels in field conditions during the 2007 and 2008 Canadian growing seasons, and in potted and hydroponic growth-chamber conditions. Genotypic NUpE, NUtE and NUE were calculated and compared between field and growth-chamber environments. KEY RESULTS Growth chamber and field tests generally showed consistent NUE characteristics. In the field, Vivar, Excel and Ponoka, showed high NUE phenotypes across years and N levels. Vivar also had high NUE in growth-chamber trials, showing NUE across complex to simplistic growth environments. With the high NUE genotypes grown at low N in the field, NUtE predominates over NUpE. N metabolism-associated amino acid levels were different between roots (elevated glutamine) and shoots (elevated glutamate and alanine) of hydroponically grown genotypes. In field trials, metabolite levels were different between Kasota grown at high N (elevated glutamine) and Kasota at low N plus Vivar at either N condition. CONCLUSIONS Determining which trait(s) or gene(s) to target to improve barley NUE is important and can be facilitated using simplified growth approaches to help determine the NUE phenotype of various genotypes. The genotypes studied showed similar growth and NUE characteristics across field and growth-chamber tests demonstrating that simplified, low-variable growth environments can help pinpoint genetic targets for improving spring barley NUE.
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Affiliation(s)
- Perrin H Beatty
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9, Canada.
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Castillejo MA, Kirchev HK, Jorrín JV. Differences in the triticale (X Triticosecale Wittmack) flag leaf 2-DE protein profile between varieties and nitrogen fertilization levels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:5698-707. [PMID: 20334342 DOI: 10.1021/jf100215t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nitrogen nutrition is one of the major factors limiting the growth and production of crop plants. Limited information on proteome changes occurring in response to nitrogen amount have been available up to now. We used 2-DE to investigate proteome differences between two triticale varieties and the changes caused by nitrogen nutrition deficit in the flag leaf tissue. Some physiological features, such as the number of tillers per plant, SPAD index, dry weight, and protein content were measured previous to the proteomic analysis. Statistical analysis identified 29 differential protein spots in the selected pairwise comparisons of experimental conditions and correlated with the expression cluster revealed by the principal component analysis. The 29 protein spots were subjected to matrix-assisted laser desorption ionization time of flight (MALDI-TOF) to deduce their possible functions. Many of these changes referred to enzymes involved in photosynthesis, metabolic pathways implicated in the balance of the energy, and redox status of the cell. This work provides a first characterization of the proteome changes that occur in response to nitrogen deficit in flag leaves of triticale plants.
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