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Yuan T, Zhu C, Li G, Liu Y, Yang K, Li Z, Song X, Gao Z. An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo. Front Genet 2022; 13:854346. [PMID: 35651936 PMCID: PMC9149284 DOI: 10.3389/fgene.2022.854346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.
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Affiliation(s)
- Tingting Yuan
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Guangzhu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Yan Liu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Zhen Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Hangzhou, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
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Singh P, Kumar K, Jha AK, Yadava P, Pal M, Rakshit S, Singh I. Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.). Sci Rep 2022; 12:4211. [PMID: 35273237 PMCID: PMC8913646 DOI: 10.1038/s41598-022-07709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.
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Affiliation(s)
- Prabha Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Krishan Kumar
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Kumar Jha
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Madan Pal
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Ishwar Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
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Buet A, Luquet M, Santa-María GE, Galatro A. Can NO Signaling and Its Metabolism Be Used to Improve Nutrient Use Efficiency? Toward a Research Agenda. FRONTIERS IN PLANT SCIENCE 2022; 13:787594. [PMID: 35242150 PMCID: PMC8885532 DOI: 10.3389/fpls.2022.787594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Agustina Buet
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue (CITAAC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, subsede Instituto de Biotecnología Agropecuaria del Comahue (IBAC), Cinco Saltos, Argentina
- Facultad de Ciencias Agrarias y Forestales (FCAyF), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Melisa Luquet
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata (UNLP)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
| | - Guillermo E. Santa-María
- Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús, Argentina
| | - Andrea Galatro
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata (UNLP)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
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Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms. Int J Mol Sci 2021; 22:ijms22179527. [PMID: 34502437 PMCID: PMC8431222 DOI: 10.3390/ijms22179527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
Maize root responds to nitrate by modulating its development through the coordinated action of many interacting players. Nitric oxide is produced in primary root early after the nitrate provision, thus inducing root elongation. In this study, RNA sequencing was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency on, or independency of, nitric oxide, thus discriminating the signaling pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to gain further information and the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led us to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, shared and specific features for the six clusters were identified, allowing us to determine the overall root response to nitrate according to its dependency on nitric oxide.
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Molecular mechanisms of mesocotyl elongation induced by brassinosteroid in maize under deep-seeding stress by RNA-sequencing, microstructure observation, and physiological metabolism. Genomics 2021; 113:3565-3581. [PMID: 34455034 DOI: 10.1016/j.ygeno.2021.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/25/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022]
Abstract
Deep-seeding is an important way to improve maize drought resistance, mesocotyl elongation can significantly enhance its seedling germination. To improve our understanding of transcription-mediated maize mesocotyl elongation under deep-seeding stress. RNA-sequencing was used to identify differentially expressed genes (DEGs) in both deep-seeding tolerant W64A and intolerant K12 mesocotyls following culture for 10 days after 2.0 mg·L-1 24-epibrassinolide (EBR) induced stress at the depths of 3 and 20 cm. Phenotypically, the mesocotyl length of both maize significantly increased under 20 cm stress and in the presence of EBR. Microstructure observations revealed that the mesocotyls underwent programmed cell death under deep-seeding stress, which was alleviated by EBR. This was found to be regulated by multiple DEGs encoding cysteine protease/senescence-specific cysteine protease, aspartic protease family protein, phospholipase D, etc. and transcription factors (TFs; MYB, NAC). Additionally, some DEGs associated with cell wall components, i.e., cellulose synthase/cellulose synthase like protein (CESA/CSL), fasciclin-like arabinogalactan (APG), leucine-rich repeat protein (LRR) and lignin biosynthesis enzymes including phenylalanine ammonia-lyase, S-adenosyl-L-methionine-dependent methyltransferases, 4-coumarate-CoA ligase, cinnamoyl CoA reductase, cinnamyl alcohol dehydrogenase, catalase, peroxiredoxin/peroxidase were found to control cell wall sclerosis. Moreover, in auxin, ethylene, brassinosteriod, cytokinin, zeatin, abscisic acid, gibberellin, jasmonic acid, and salicylic acid signaling transduction pathways, the corresponding DEGs were activated/inhibited by TFs (ARF, BZR1/2, B-ARR, A-ARR, MYC2, ABF, TGA) and synthesis of phytohormones-related metabolites. These findings provide information on the molecular mechanisms controlling maize deep-seeding tolerance and will aid in the breeding of deep-seeding maize varieties.
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6
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Torres-Rodríguez JV, Salazar-Vidal MN, Chávez Montes RA, Massange-Sánchez JA, Gillmor CS, Sawers RJH. Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.). BMC PLANT BIOLOGY 2021; 21:259. [PMID: 34090337 PMCID: PMC8178920 DOI: 10.1186/s12870-021-02997-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized. RESULTS We characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation. CONCLUSIONS Transcriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.
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Affiliation(s)
- J Vladimir Torres-Rodríguez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
| | - M Nancy Salazar-Vidal
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Ricardo A Chávez Montes
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Julio A Massange-Sánchez
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ) Subsede Zapopan, Guadalajara, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico
| | - Ruairidh J H Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, C.P, 36824, Guanajuato, Mexico.
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA.
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Huang J, Zhu C, Hussain S, Huang J, Liang Q, Zhu L, Cao X, Kong Y, Li Y, Wang L, Li J, Zhang J. Effects of nitric oxide on nitrogen metabolism and the salt resistance of rice (Oryza sativa L.) seedlings with different salt tolerances. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:374-383. [PMID: 32805614 DOI: 10.1016/j.plaphy.2020.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/27/2020] [Accepted: 06/08/2020] [Indexed: 05/04/2023]
Abstract
Salt stress inhibits rice productivity seriously. Nitric oxide (NO) is an endogenous signaling molecule in plants that can improve the resistance of rice to abiotic stresses. Previous studies also showed that nitrogen metabolism is essential for rice stress-tolerance. However, the physiological and molecular mechanisms by how NO affects the nitrogen metabolisms of rice seedlings remain unclear. A hydroponic experiment with two rice varieties, Jinyuan85 (salt tolerant) and Liaojing763 (salt sensitive), was carried out to explore whether NO could alleviate the negative effects of salt stress on nitrogen metabolism and increase salt resistance of rice seedlings. The results showed that (1) the application of NO alleviated the inhibitory effects of salt stress on plant height and biomass accumulation, and increased the nitrogen content of rice leaf. (2) the accumulation of the sucrose and proline was markedly increased in salt stress after application of NO, and peroxidase activities was increased by 107% and 67.7% for Jinyuan85 and Liaojing763, respectively. (3) NO significantly increased the activities of glutamate dehydrogenase, sucrose synthase and sucrose phosphate synthase in both rice varieties under salt stress. (4) Additionally, NO regulated the expression levels of AMT, NIA and SUT genes, but these regulation effects are different with rice varieties and treatments. The results suggested that NO mainly increased the glutamate dehydrogenase and peroxidase activities and sucrose accumulation to enhance the nitrogen metabolism and antioxidative capacity, and alleviated the negative effects of salt stress on rice performance.
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Affiliation(s)
- Jie Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Chunquan Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Sajid Hussain
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jing Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qingduo Liang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lianfeng Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaochuang Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yali Kong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yefeng Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Liping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jianwu Li
- College of Environmental and Resource Science, Zhejiang Agricultural and Forestry University, Hangzhou, 311300, China.
| | - Junhua Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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8
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Shao CH, Qiu CF, Qian YF, Liu GR. Nitrate deficiency decreased photosynthesis and oxidation-reduction processes, but increased cellular transport, lignin biosynthesis and flavonoid metabolism revealed by RNA-Seq in Oryza sativa leaves. PLoS One 2020; 15:e0235975. [PMID: 32649704 PMCID: PMC7351185 DOI: 10.1371/journal.pone.0235975] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Rice cultivar "Weiyou916" (Oryza sativa L. ssp. Indica) were cultured with control (10 mM NO3-) and nitrate deficient solution (0 mM NO3-) for four weeks. Nitrogen (N) deficiency significantly decreased the content of N and P, dry weight (DW) of the shoots and roots, but increased the ratio of root to shoot in O. sativa. N deficiency decreased the photosynthesis rate and the maximum quantum yield of primary photochemistry (Fv/Fm), however, increased the intercellular CO2 concentration and primary fluorescence (Fo). N deficiency significantly increased the production of H2O2 and membrane lipid peroxidation revealed as increased MDA content in O. sativa leaves. N deficiency significantly increased the contents of starch, sucrose, fructose, and malate, but did not change that of glucose and total soluble protein in O. sativa leaves. The accumulated carbohydrates and H2O2 might further accelerate biosynthesis of lignin in O. sativa leaves under N limitation. A total of 1635 genes showed differential expression in response to N deficiency revealed by Illumina sequencing. Gene Ontology (GO) analysis showed that 195 DEGs were found to highly enrich in nine GO terms. Most of DEGs involved in photosynthesis, biosynthesis of ethylene and gibberellins were downregulated, whereas most of DEGs involved in cellular transport, lignin biosynthesis and flavonoid metabolism were upregulated by N deficiency in O. sativa leaves. Results of real-time quantitative PCR (RT-qPCR) further verified the RNA-Seq data. For the first time, DEGs involved oxygen-evolving complex, phosphorus response and lignin biosynthesis were identified in rice leaves. Our RNA-Seq data provided a global view of transcriptomic profile of principal processes implicated in the adaptation of N deficiency in O. sativa and shed light on the candidate direction in rice breeding for green and sustainable agriculture.
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Affiliation(s)
- Cai-Hong Shao
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Cai-Fei Qiu
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yin-Fei Qian
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Guang-Rong Liu
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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9
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Shang H, Xu H, Jin L, Wang C, Chen C, Song T, Du Y. 3D ZnIn2S4 nanosheets decorated ZnCdS dodecahedral cages as multifunctional signal amplification matrix combined with electroactive/photoactive materials for dual mode electrochemical – photoelectrochemical detection of bovine hemoglobin. Biosens Bioelectron 2020; 159:112202. [DOI: 10.1016/j.bios.2020.112202] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022]
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10
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Ge M, Wang Y, Liu Y, Jiang L, He B, Ning L, Du H, Lv Y, Zhou L, Lin F, Zhang T, Liang S, Lu H, Zhao H. The NIN-like protein 5 (ZmNLP5) transcription factor is involved in modulating the nitrogen response in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:353-368. [PMID: 31793100 PMCID: PMC7217196 DOI: 10.1111/tpj.14628] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 05/12/2023]
Abstract
Maize exhibits marked growth and yield response to supplemental nitrogen (N). Here, we report the functional characterization of a maize NIN-like protein ZmNLP5 as a central hub in a molecular network associated with N metabolism. Predominantly expressed and accumulated in roots and vascular tissues, ZmNLP5 was shown to rapidly respond to nitrate treatment. Under limited N supply, compared with that of wild-type (WT) seedlings, the zmnlp5 mutant seedlings accumulated less nitrate and nitrite in the root tissues and ammonium in the shoot tissues. The zmnlp5 mutant plants accumulated less nitrogen than the WT plants in the ear leaves and seed kernels. Furthermore, the mutants carrying the transgenic ZmNLP5 cDNA fragment significantly increased the nitrate content in the root tissues compared with that of the zmnlp5 mutants. In the zmnlp5 mutant plants, loss of the ZmNLP5 function led to changes in expression for a significant number of genes involved in N signalling and metabolism. We further show that ZmNLP5 directly regulates the expression of nitrite reductase 1.1 (ZmNIR1.1) by binding to the nitrate-responsive cis-element at the 5' UTR of the gene. Interestingly, a natural loss-of-function allele of ZmNLP5 in Mo17 conferred less N accumulation in the ear leaves and seed kernels resembling that of the zmnlp5 mutant plants. Our findings show that ZmNLP5 is involved in mediating the plant response to N in maize.
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Affiliation(s)
- Min Ge
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Yuancong Wang
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Yuhe Liu
- Department of Crop SciencesUniversity of IllinoisUrbana‐ChampaignILUSA
| | - Lu Jiang
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Bing He
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Lihua Ning
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Hongyang Du
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Yuanda Lv
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Ling Zhou
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Feng Lin
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Tifu Zhang
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Shuaiqiang Liang
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Haiyan Lu
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
| | - Han Zhao
- Institute of Crop Germplasm and BiotechnologyProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing210014China
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11
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Ravazzolo L, Trevisan S, Forestan C, Varotto S, Sut S, Dall’Acqua S, Malagoli M, Quaggiotti S. Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots. Int J Mol Sci 2020; 21:ijms21020686. [PMID: 31968691 PMCID: PMC7013554 DOI: 10.3390/ijms21020686] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.
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Affiliation(s)
- Laura Ravazzolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Sara Trevisan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Cristian Forestan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Stefania Sut
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Stefano Dall’Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova—Via Marzolo 5, 35121 Padova, Italy;
| | - Mario Malagoli
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
- Correspondence: ; Tel.: +39-049-8272913
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12
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León J, Costa-Broseta Á. Present knowledge and controversies, deficiencies, and misconceptions on nitric oxide synthesis, sensing, and signaling in plants. PLANT, CELL & ENVIRONMENT 2020; 43. [PMID: 31323702 DOI: 10.1111/pce.13617] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/15/2019] [Indexed: 05/17/2023]
Abstract
After 30 years of intensive work, nitric oxide (NO) has just started to be characterized as a relevant regulatory molecule on plant development and responses to stress. Its reactivity as a free radical determines its mode of action as an inducer of posttranslational modifications of key target proteins through cysteine S-nitrosylation and tyrosine nitration. Many of the NO-triggered regulatory actions are exerted in tight coordination with phytohormone signaling. This review not only summarizes and updates the information accumulated on how NO is synthesized, sensed, and transduced in plants but also makes emphasis on controversies, deficiencies, and misconceptions that are hampering our present knowledge on the biology of NO in plants. The development of noninvasive accurate tools for the endogenous NO quantitation as well as the implementation of genetic approaches that overcome misleading pharmacological experiments will be critical for getting significant advances in better knowledge of NO homeostasis and regulatory actions in plants.
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Affiliation(s)
- José León
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Álvaro Costa-Broseta
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022, Valencia, Spain
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13
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Jindo K, Olivares FL, Malcher DJDP, Sánchez-Monedero MA, Kempenaar C, Canellas LP. From Lab to Field: Role of Humic Substances Under Open-Field and Greenhouse Conditions as Biostimulant and Biocontrol Agent. FRONTIERS IN PLANT SCIENCE 2020; 11:426. [PMID: 32528482 PMCID: PMC7247854 DOI: 10.3389/fpls.2020.00426] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 05/21/2023]
Abstract
The demand for biostimulants has been growing at an annual rate of 10 and 12.4% in Europe and Northern America, respectively. The beneficial effects of humic substances (HS) as biostimulants of plant growth have been well-known since the 1980s, and they can be supportive to a circular economy if they are extracted from different renewable resources of organic matter including harvest residues, wastewater, sewage sludge, and manure. This paper presents an overview of the scientific outputs on application methods of HS in different conditions. Firstly, the functionality of HS in the primary and secondary metabolism under stressed and non-stressed cropping conditions is discussed along with crop protection against pathogens. Secondly, the advantages and limitations of five different types of HS application under open-fields and greenhouse conditions are described. Key factors, such as the chemical structure of HS, application method, optimal rate, and field circumstances, play a crucial role in enhancing plant growth by HS treatment as a biostimulant. If we can get a better grip on these factors, HS has the potential to become a part of circular agriculture.
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Affiliation(s)
- Keiji Jindo
- Agrosystems Research, Wageningen University and Research, Wageningen, Netherlands
| | - Fábio Lopes Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro, UENF, Rio de Janeiro, Brazil
| | - Deyse Jacqueline da Paixão Malcher
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro, UENF, Rio de Janeiro, Brazil
| | - Miguel Angel Sánchez-Monedero
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafolog a y Biología Aplicada del Segura (CEBAS)-Consejo Superior de Investigaciones Cient ficas (CSIC), Campus Universitario de Espinardo, Murcia, Spain
- *Correspondence: Miguel Angel Sánchez-Monedero,
| | - Corné Kempenaar
- Agrosystems Research, Wageningen University and Research, Wageningen, Netherlands
| | - Luciano Pasqualoto Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro, UENF, Rio de Janeiro, Brazil
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14
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Ravazzolo L, Trevisan S, Manoli A, Boutet-Mercey SP, Perreau FO, Quaggiotti S. The Control of Zealactone Biosynthesis and Exudation is Involved in the Response to Nitrogen in Maize Root. PLANT & CELL PHYSIOLOGY 2019; 60:2100-2112. [PMID: 31147714 DOI: 10.1093/pcp/pcz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Nitrate acts as a signal in regulating plant development in response to environment. In particular nitric oxide, auxin and strigolactones (SLs) were supposed to cooperate to regulate the maize root response to this anion. In this study, a combined approach based on liquid chromatography-quadrupole/time-of-flight tandem mass spectrometry and on physiological and molecular analyses was adopted to specify the involvement of SLs in the maize response to N. Our results showed that N deficiency strongly induces SL exudation, likely through stimulating their biosynthesis. Nitrate provision early counteracts and also ammonium lowers SL exudation, but less markedly. Exudates obtained from N-starved and ammonium-provided seedlings stimulated Phelipanche germination, whereas when seeds were treated with exudates harvested from nitrate-provided plants no germination was observed. Furthermore, our findings support the idea that the inhibition of SL production observed in response to nitrate and ammonium would contribute to the regulation of lateral root development. Moreover, the transcriptional regulation of a gene encoding a putative maize WBC transporter, in response to various nitrogen supplies, together with its mRNA tissue localization, supported its role in SL allocation. Our results highlight the dual role of SLs as molecules able to signal outwards a nutritional need and as endogenous regulators of root architecture adjustments to N, thus synchronizing plant growth with nitrogen acquisition.
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Affiliation(s)
- Laura Ravazzolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Sara Trevisan
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Alessandro Manoli
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Stï Phanie Boutet-Mercey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Franï Ois Perreau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
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15
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Buet A, Galatro A, Ramos-Artuso F, Simontacchi M. Nitric oxide and plant mineral nutrition: current knowledge. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4461-4476. [PMID: 30903155 DOI: 10.1093/jxb/erz129] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/14/2019] [Indexed: 05/20/2023]
Abstract
Plants under conditions of essential mineral deficiency trigger signaling mechanisms that involve common components. Among these components, nitric oxide (NO) has been identified as a key participant in responses to changes in nutrient availability. Usually, nutrient imbalances affect the levels of NO in specific plant tissues, via modification of its rate of synthesis or degradation. Changes in the level of NO affect plant morphology and/or trigger responses associated with nutrient homeostasis, mediated by its interaction with reactive oxygen species, phytohormones, and through post-translational modification of proteins. NO-related events constitute an exciting field of research to understand how plants adapt and respond to conditions of nutrient shortage. This review summarizes the current knowledge on NO as a component of the multiple processes related to plant performance under conditions of deficiency in mineral nutrients, focusing on macronutrients such as nitrogen, phosphate, potassium, and magnesium, as well as micronutrients such as iron and zinc.
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Affiliation(s)
- Agustina Buet
- Instituto de Fisiología Vegetal, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrea Galatro
- Instituto de Fisiología Vegetal, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
| | - Facundo Ramos-Artuso
- Instituto de Fisiología Vegetal, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Marcela Simontacchi
- Instituto de Fisiología Vegetal, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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16
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Trevisan S, Trentin AR, Ghisi R, Masi A, Quaggiotti S. Nitrate affects transcriptional regulation of UPBEAT1 and ROS localisation in roots of Zea mays L. PHYSIOLOGIA PLANTARUM 2019; 166:794-811. [PMID: 30238472 DOI: 10.1111/ppl.12839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/23/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Nitrogen (N) is an indispensable nutrient for crops but its availability in agricultural soils is subject to considerable fluctuation. Plants have developed plastic responses to external N fluctuations in order to optimise their development. The coordinated action of nitric oxide and auxin seems to allow the cells of the root apex transition zone (TZ) of N-deprived maize to rapidly sense nitrate (NO3 - ). Preliminary results support the hypothesis that reactive oxygen species (ROS) signalling might also have a role in this pathway, probably through a putative maize orthologue of UPBEAT1 (UPB1). To expand on this hypothesis and better understand the different roles played by different root portions, we investigated the dynamics of ROS production, and the molecular and biochemical regulation of the main components of ROS production and scavenging in tissues of the meristem, transition zone, elongation zone and maturation zone of maize roots. The results suggest that the inverse regulation of ZmUPB1 and ZmPRX112 transcription observed in cells of the TZ in response to nitrogen depletion or NO3 - supply affects the balance between superoxide (O2 •- ) and hydrogen peroxide (H2 O2 ) in the root apex and consequently triggers differential root growth. This explanation is supported by additional results on the overall metabolic and transcriptional regulation of ROS homeostasis.
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Affiliation(s)
- Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy
| | - Anna R Trentin
- Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy
| | - Rossella Ghisi
- Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy
| | - Antonio Masi
- Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy
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17
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Tejada-Jimenez M, Llamas A, Galván A, Fernández E. Role of Nitrate Reductase in NO Production in Photosynthetic Eukaryotes. PLANTS 2019; 8:plants8030056. [PMID: 30845759 PMCID: PMC6473468 DOI: 10.3390/plants8030056] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
Nitric oxide is a gaseous secondary messenger that is critical for proper cell signaling and plant survival when exposed to stress. Nitric oxide (NO) synthesis in plants, under standard phototrophic oxygenic conditions, has long been a very controversial issue. A few algal strains contain NO synthase (NOS), which appears to be absent in all other algae and land plants. The experimental data have led to the hypothesis that molybdoenzyme nitrate reductase (NR) is the main enzyme responsible for NO production in most plants. Recently, NR was found to be a necessary partner in a dual system that also includes another molybdoenzyme, which was renamed NO-forming nitrite reductase (NOFNiR). This enzyme produces NO independently of the molybdenum center of NR and depends on the NR electron transport chain from NAD(P)H to heme. Under the circumstances in which NR is not present or active, the existence of another NO-forming system that is similar to the NOS system would account for NO production and NO effects. PII protein, which senses and integrates the signals of the C–N balance in the cell, likely has an important role in organizing cell responses. Here, we critically analyze these topics.
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Affiliation(s)
- Manuel Tejada-Jimenez
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain.
| | - Angel Llamas
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain.
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain.
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales y Campus Internacional de Excelencia Agroalimentario (CeiA3), Edif. Severo Ochoa, Universidad de Córdoba, 14071 Córdoba, Spain.
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18
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Uchida N, Torii KU. Stem cells within the shoot apical meristem: identity, arrangement and communication. Cell Mol Life Sci 2019; 76:1067-1080. [PMID: 30523363 PMCID: PMC11105333 DOI: 10.1007/s00018-018-2980-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
Stem cells are specific cells that renew themselves and also provide daughter cells for organ formation. In plants, primary stem cell populations are nurtured within shoot and root apical meristems (SAM and RAM) for the production of aerial and underground parts, respectively. This review article summarizes recent progress on control of stem cells in the SAM from studies of the model plant Arabidopsis thaliana. To that end, a brief overview of the RAM is provided first to emphasize similarities and differences between the two apical meristems, which would help in better understanding of stem cells in the SAM. Subsequently, we will discuss in depth how stem cells are arranged in an organized manner in the SAM, how dynamically the stem cell identity is regulated, what factors participate in stem cell control, and how intercellular communication by mobile signals modulates stem cell behaviors within the SAM. Remaining questions and perspectives are also presented for future studies.
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Affiliation(s)
- Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Keiko U Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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19
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Sun H, Feng F, Liu J, Zhao Q. Nitric Oxide Affects Rice Root Growth by Regulating Auxin Transport Under Nitrate Supply. FRONTIERS IN PLANT SCIENCE 2018; 9:659. [PMID: 29875779 PMCID: PMC5974057 DOI: 10.3389/fpls.2018.00659] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/30/2018] [Indexed: 05/08/2023]
Abstract
Nitrogen (N) is a major essential nutrient for plant growth, and rice is an important food crop globally. Although ammonium (NH4+) is the main N source for rice, nitrate (NO3-) is also absorbed and utilized. Rice responds to NO3- supply by changing root morphology. However, the mechanisms of rice root growth and formation under NO3- supply are unclear. Nitric oxide (NO) and auxin are important regulators of root growth and development under NO3- supply. How the interactions between NO and auxin in regulating root growth in response to NO3- are unknown. In this study, the levels of indole-3-acetic acid (IAA) and NO in roots, and the responses of lateral roots (LRs) and seminal roots (SRs) to NH4+ and NO3-, were investigated using wild-type (WT) rice, as well as osnia2 and ospin1b mutants. NO3- supply promoted LR formation and SR elongation. The effects of NO donor and NO inhibitor/scavenger supply on NO levels and the root morphology of WT and nia2 mutants under NH4+ or NO3- suggest that NO3--induced NO is generated by the nitrate reductase (NR) pathway rather than the NO synthase (NOS)-like pathway. IAA levels, [3H] IAA transport, and PIN gene expression in roots were enhanced under NO3- relative to NH4+ supply. These results suggest that NO3- regulates auxin transport in roots. Application of SNP under NH4+ supply, or of cPTIO under NO3- supply, resulted in auxin levels in roots similar to those under NO3- and NH4+ supply, respectively. Compared to WT, the roots of the ospin1b mutant had lower auxin levels, fewer LRs, and shorter SRs. Thus, NO affects root growth by regulating auxin transport in response to NO3-. Overall, our findings suggest that NO3- influences LR formation and SR elongation by regulating auxin transport via a mechanism involving NO.
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Affiliation(s)
- Huwei Sun
- *Correspondence: Huwei Sun, Quanzhi Zhao,
| | | | | | - Quanzhi Zhao
- Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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20
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Singh BN, Dwivedi P, Sarma BK, Singh GS, Singh HB. Trichoderma asperellum T42 Reprograms Tobacco for Enhanced Nitrogen Utilization Efficiency and Plant Growth When Fed with N Nutrients. FRONTIERS IN PLANT SCIENCE 2018; 9:163. [PMID: 29527216 PMCID: PMC5829606 DOI: 10.3389/fpls.2018.00163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/29/2018] [Indexed: 05/29/2023]
Abstract
Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca2+ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO3- and NH4+ nutrients to tobacco at 40 and 70 days, particularly in NO3- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO3- nutrient confirming NO generation was dependent on NR pathway. NO3- dependent NO production contributed to increase in lateral root initiation, Ca2+ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO3- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO3-/NH4+ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO3-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil.
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Affiliation(s)
- Bansh N. Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal S. Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
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21
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Chamizo-Ampudia A, Sanz-Luque E, Llamas A, Galvan A, Fernandez E. Nitrate Reductase Regulates Plant Nitric Oxide Homeostasis. TRENDS IN PLANT SCIENCE 2017; 22:163-174. [PMID: 28065651 DOI: 10.1016/j.tplants.2016.12.001] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/16/2016] [Accepted: 12/04/2016] [Indexed: 05/18/2023]
Abstract
Nitrate reductase (NR) is a key enzyme for nitrogen acquisition by plants, algae, yeasts, and fungi. Nitrate, its main substrate, is required for signaling and is widely distributed in diverse tissues in plants. In addition, NR has been proposed as an important enzymatic source of nitric oxide (NO). Recently, NR has been shown to play a role in NO homeostasis by supplying electrons from NAD(P)H through its diaphorase/dehydrogenase domain both to a truncated hemoglobin THB1, which scavenges NO by its dioxygenase activity, and to the molybdoenzyme NO-forming nitrite reductase (NOFNiR) that is responsible for NO synthesis from nitrite. We review how NR may play a central role in plant biology by controlling the amounts of NO, a key signaling molecule in plant cells.
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Affiliation(s)
- Alejandro Chamizo-Ampudia
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, School of Sciences, Campus de Excelencia Internacional (CeiA3), Edifico Severo Ochoa, Cordoba, Spain
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, School of Sciences, Campus de Excelencia Internacional (CeiA3), Edifico Severo Ochoa, Cordoba, Spain; Present address: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, School of Sciences, Campus de Excelencia Internacional (CeiA3), Edifico Severo Ochoa, Cordoba, Spain
| | - Aurora Galvan
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, School of Sciences, Campus de Excelencia Internacional (CeiA3), Edifico Severo Ochoa, Cordoba, Spain
| | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, School of Sciences, Campus de Excelencia Internacional (CeiA3), Edifico Severo Ochoa, Cordoba, Spain.
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Overexpression of spinach non-symbiotic hemoglobin in Arabidopsis resulted in decreased NO content and lowered nitrate and other abiotic stresses tolerance. Sci Rep 2016; 6:26400. [PMID: 27211528 PMCID: PMC4876387 DOI: 10.1038/srep26400] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 05/03/2016] [Indexed: 11/29/2022] Open
Abstract
A class 1 non-symbiotic hemoglobin family gene, SoHb, was isolated from spinach. qRT-PCR showed that SoHb was induced by excess nitrate, polyethylene glycol, NaCl, H2O2, and salicylic acid. Besides, SoHb was strongly induced by application of nitric oxide (NO) donor, while was suppressed by NO scavenger, nitrate reductase inhibitor, and nitric oxide synthase inhibitor. Overexpression of SoHb in Arabidopsis resulted in decreased NO level and sensitivity to nitrate stress, as shown by reduced root length, fresh weight, the maximum photosystem II quantum ratio of variable to maximum fluorescence (Fv/Fm), and higher malondialdehyde contents. The activities and gene transcription of superoxide dioxidase, and catalase decreased under nitrate stress. Expression levels of RD22, RD29A, DREB2A, and P5CS1 decreased after nitrate treatment in SoHb-overexpressing plants, while increased in the WT plants. Moreover, SoHb-overexpressing plants showed decreased tolerance to NaCl and osmotic stress. In addition, the SoHb-overexpression lines showed earlier flower by regulating the expression of SOC, GI and FLC genes. Our results indicated that the decreasing NO content in Arabidopsis by overexpressing SoHb might be responsible for lowered tolerance to nitrate and other abiotic stresses.
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Zhu Y, Liao W, Wang M, Niu L, Xu Q, Jin X. Nitric oxide is required for hydrogen gas-induced adventitious root formation in cucumber. JOURNAL OF PLANT PHYSIOLOGY 2016; 195:50-8. [PMID: 27010347 DOI: 10.1016/j.jplph.2016.02.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 05/24/2023]
Abstract
Hydrogen gas (H2) is involved in plant development and stress responses. Cucumber explants were used to study whether nitric oxide (NO) is involved in H2-induced adventitious root development. The results revealed that 50% and 100% hydrogen-rich water (HRW) apparently promoted the development of adventitious root in cucumber. While, the responses of HRW-induced adventitious rooting were blocked by a specific NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt (cPTIO), NO synthase (NOS) enzyme inhibitor N(G)-nitro-l-arginine methylester hydrochloride (l-NAME) and nitrate reductase (NR) inhibitor NaN3. HRW also increased NO content and NOS and NR activity both in a dose- and time-dependent fashion. Moreover, molecular evidence showed that HRW up-regulated NR genes expression in explants. The results indicate the importance of NOS and NR enzymes, which might be responsible for NO production in explants during H2-induced root organogenesis. Additionally, peroxidase (POD) and indoleacetic acid oxidase (IAAO) activity was significantly decreased in the explants treated with HRW, while HRW treatment significantly increased polyphenol oxidase (PPO) activity. In addition, cPTIO, l-NAME and NaN3 inhibited the actions of HRW on the activity of these enzymes. Together, NO may be involved in H2-induced adventitious rooting, and NO may be acting downstream in plant H2 signaling cascade.
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Affiliation(s)
- Yongchao Zhu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Meng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Lijuan Niu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Qingqing Xu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xin Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
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Manoli A, Trevisan S, Voigt B, Yokawa K, Baluška F, Quaggiotti S. Nitric Oxide-Mediated Maize Root Apex Responses to Nitrate are Regulated by Auxin and Strigolactones. FRONTIERS IN PLANT SCIENCE 2016; 6:1269. [PMID: 26834770 PMCID: PMC4722128 DOI: 10.3389/fpls.2015.01269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/28/2015] [Indexed: 05/20/2023]
Abstract
Nitrate (NO3 (-)) is a key element for crop production but its levels in agricultural soils are limited. Plants have developed mechanisms to cope with these NO3 (-) fluctuations based on sensing nitrate at the root apex. Particularly, the transition zone (TZ) of root apex has been suggested as a signaling-response zone. This study dissects cellular and molecular mechanisms underlying NO3 (-) resupply effects on primary root (PR) growth in maize, confirming nitric oxide (NO) as a putative modulator. Nitrate restoration induced PR elongation within the first 2 h, corresponding to a stimulation of cell elongation at the basal border of the TZ. Xyloglucans (XGs) immunolocalization together with Brefeldin A applications demonstrated that nitrate resupply induces XG accumulation. This effect was blocked by cPTIO (NO scavenger). Transcriptional analysis of ZmXET1 confirmed the stimulatory effect of nitrate on XGs accumulation in cells of the TZ. Immunolocalization analyses revealed a positive effect of nitrate resupply on auxin and PIN1 accumulation, but a transcriptional regulation of auxin biosynthesis/transport/signaling genes was excluded. Short-term nitrate treatment repressed the transcription of genes involved in strigolactones (SLs) biosynthesis and transport, mainly in the TZ. Enhancement of carotenoid cleavage dioxygenases (CCDs) transcription in presence of cPTIO indicated endogenous NO as a negative modulator of CCDs activity. Finally, treatment with the SLs-biosynthesis inhibitor (TIS108) restored the root growth in the nitrate-starved seedlings. Present report suggests that the NO-mediated root apex responses to nitrate are accomplished in cells of the TZ via integrative actions of auxin, NO and SLs.
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Affiliation(s)
- Alessandro Manoli
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
| | - Sara Trevisan
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
| | - Boris Voigt
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
| | - Ken Yokawa
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
- Department of Biological Sciences, Tokyo Metropolitan UniversityTokyo, Japan
| | - František Baluška
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
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Trevisan S, Manoli A, Ravazzolo L, Botton A, Pivato M, Masi A, Quaggiotti S. Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3699-715. [PMID: 25911739 PMCID: PMC4473975 DOI: 10.1093/jxb/erv165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nitrate is an essential nutrient for plants, and crops depend on its availability for growth and development, but its presence in agricultural soils is far from stable. In order to overcome nitrate fluctuations in soil, plants have developed adaptive mechanisms allowing them to grow despite changes in external nitrate availability. Nitrate can act as both nutrient and signal, regulating global gene expression in plants, and the root tip has been proposed as the sensory organ. A set of genome-wide studies has demonstrated several nitrate-regulated genes in the roots of many plants, although only a few studies have been carried out on distinct root zones. To unravel new details of the transcriptomic and proteomic responses to nitrate availability in a major food crop, a double untargeted approach was conducted on a transition zone-enriched root portion of maize seedlings subjected to differing nitrate supplies. The results highlighted a complex transcriptomic and proteomic reprogramming that occurs in response to nitrate, emphasizing the role of this root zone in sensing and transducing nitrate signal. Our findings indicated a relationship of nitrate with biosynthesis and signalling of several phytohormones, such as auxin, strigolactones, and brassinosteroids. Moreover, the already hypothesized involvement of nitric oxide in the early response to nitrate was confirmed with the use of nitric oxide inhibitors. Our results also suggested that cytoskeleton activation and cell wall modification occurred in response to nitrate provision in the transition zone.
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Affiliation(s)
- Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Alessandro Manoli
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Laura Ravazzolo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Alessandro Botton
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Micaela Pivato
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy Proteomics Centre of Padova University, VIMM and Padova University Hospital, Via Giuseppe Orus, 2, 35129 Padova, Italy
| | - Antonio Masi
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
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26
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Sun H, Li J, Song W, Tao J, Huang S, Chen S, Hou M, Xu G, Zhang Y. Nitric oxide generated by nitrate reductase increases nitrogen uptake capacity by inducing lateral root formation and inorganic nitrogen uptake under partial nitrate nutrition in rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2449-59. [PMID: 25784715 PMCID: PMC4986861 DOI: 10.1093/jxb/erv030] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Increasing evidence shows that partial nitrate nutrition (PNN) can be attributed to improved plant growth and nitrogen-use efficiency (NUE) in rice. Nitric oxide (NO) is a signalling molecule involved in many physiological processes during plant development and nitrogen (N) assimilation. It remains unclear whether molecular NO improves NUE through PNN. Two rice cultivars (cvs Nanguang and Elio), with high and low NUE, respectively, were used in the analysis of NO production, nitrate reductase (NR) activity, lateral root (LR) density, and (15)N uptake under PNN, with or without NO production donor and inhibitors. PNN increased NO accumulation in cv. Nanguang possibly through the NIA2-dependent NR pathway. PNN-mediated NO increases contributed to LR initiation, (15)NH₄(+)/(15)NO₃(-) influx into the root, and levels of ammonium and nitrate transporters in cv. Nanguang but not cv. Elio. Further results revealed marked and specific induction of LR initiation and (15)NH₄(+)/(15)NO₃(-) influx into the roots of plants supplied with NH₄(+)+sodium nitroprusside (SNP) relative to those supplied with NH₄(+) alone, and considerable inhibition upon the application of cPTIO or tungstate (NR inhibitor) in addition to PNN, which is in agreement with the change in NO fluorescence in the two rice cultivars. The findings suggest that NO generated by the NR pathway plays a pivotal role in improving the N acquisition capacity by increasing LR initiation and the inorganic N uptake rate, which may represent a strategy for rice plants to adapt to a fluctuating nitrate supply and increase NUE.
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Affiliation(s)
- Huwei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Song
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Jinyuan Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuangjie Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Si Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengmeng Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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27
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Sanz-Luque E, Ocaña-Calahorro F, de Montaigu A, Chamizo-Ampudia A, Llamas Á, Galván A, Fernández E. THB1, a truncated hemoglobin, modulates nitric oxide levels and nitrate reductase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:467-79. [PMID: 25494936 DOI: 10.1111/tpj.12744] [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: 06/18/2014] [Revised: 11/21/2014] [Accepted: 12/02/2014] [Indexed: 05/18/2023]
Abstract
Hemoglobins are ubiquitous proteins that sense, store and transport oxygen, but the physiological processes in which they are implicated is currently expanding. Recent examples of previously unknown hemoglobin functions, which include scavenging of the signaling molecule nitric oxide (NO), illustrate how the implication of hemoglobins in different cell signaling processes is only starting to be unraveled. The extent and diversity of the hemoglobin protein family suggest that hemoglobins have diverged and have potentially evolved specialized functions in certain organisms. A unique model organism to study this functional diversity at the cellular level is the green alga Chlamydomonas reinhardtii because, among other reasons, it contains an unusually high number of a particular type of hemoglobins known as truncated hemoglobins (THB1-THB12). Here, we reveal a cell signaling function for a truncated hemoglobin of Chlamydomonas that affects the nitrogen assimilation pathway by simultaneously modulating NO levels and nitrate reductase (NR) activity. First, we found that THB1 and THB2 expression is modulated by the nitrogen source and depends on NIT2, a transcription factor required for nitrate assimilation genes expression. Furthermore, THB1 is highly expressed in the presence of NO and is able to convert NO into nitrate in vitro. Finally, THB1 is maintained on its active and reduced form by NR, and in vivo lower expression of THB1 results in increased NR activity. Thus, THB1 plays a dual role in NO detoxification and in the modulation of NR activity. This mechanism can partly explain how NO inhibits NR post-translationally.
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Affiliation(s)
- Emanuel Sanz-Luque
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Campus de excelencia internacional (CeiA3), Edif. Severo Ochoa, 14071, Córdoba, Spain
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28
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Abstract
To quantitate the gene expression, real-time RT-PCR or quantitative PCR (qPCR) is one of the most sensitive, reliable, and commonly used methods in molecular biology. The reliability and success of a real-time PCR assay depend on the optimal experiment design. Primers are the most important constituents of real-time PCR experiments such as in SYBR Green-based detection assays. Designing of an appropriate and specific primer pair is extremely crucial for correct estimation of transcript abundance of any gene in a given sample. Here, we are presenting a quick, easy, and reliable method for designing target-specific primers using Primer Express(®) software for real-time PCR (qPCR) experiments.
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29
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Sanz-Luque E, Ocaña-Calahorro F, Galván A, Fernández E. THB1 regulates nitrate reductase activity and THB1 and THB2 transcription differentially respond to NO and the nitrate/ammonium balance in Chlamydomonas. PLANT SIGNALING & BEHAVIOR 2015; 10:e1042638. [PMID: 26252500 PMCID: PMC4622704 DOI: 10.1080/15592324.2015.1042638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nitric oxide (NO) has emerged as an important regulator of the nitrogen assimilation pathway in plants. Nevertheless, this free radical is a double-edged sword for cells due to its high reactivity and toxicity. Hemoglobins, which belong to a vast and ancestral family of proteins present in all kingdoms of life, have arisen as important NO scavengers, through their NO dioxygenase (NOD) activity. The green alga Chlamydomonas reinhardtii has 12 hemoglobins (THB1-12) belonging to the truncated hemoglobins family. THB1 and THB2 are regulated by the nitrogen source and respond differentially to NO and the nitrate/ammonium balance. THB1 expression is upregulated by NO in contrast to THB2, which is downregulated. THB1 has NOD activity and thus a role in nitrate assimilation. In fact, THB1 is upregulated by nitrate and is under the control of NIT2, the major transcription factor in nitrate assimilation. In Chlamydomonas, it has been reported that nitrate reductase (NR) has a redox regulation and is inhibited by NO through an unknown mechanism. Now, a model in which THB1 interacts with NR is proposed for its regulation. THB1 takes electrons from NR redirecting them to NO dioxygenation. Thus, when cells are assimilating nitrate and NO appears (i.e. as a consequence of nitrite accumulation), THB1 has a double role: 1) to scavenge NO avoiding its toxic effects and 2) to control the nitrate reduction activity.
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Affiliation(s)
- Emanuel Sanz-Luque
- Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad de Córdoba; Campus de Rabanales; Campus de excelencia internacional (CeiA3); Córdoba, Spain
| | - Francisco Ocaña-Calahorro
- Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad de Córdoba; Campus de Rabanales; Campus de excelencia internacional (CeiA3); Córdoba, Spain
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad de Córdoba; Campus de Rabanales; Campus de excelencia internacional (CeiA3); Córdoba, Spain
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad de Córdoba; Campus de Rabanales; Campus de excelencia internacional (CeiA3); Córdoba, Spain
- Correspondence to: Emilio Fernández;
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30
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Zanin L, Zamboni A, Monte R, Tomasi N, Varanini Z, Cesco S, Pinton R. Transcriptomic Analysis Highlights Reciprocal Interactions of Urea and Nitrate for Nitrogen Acquisition by Maize Roots. ACTA ACUST UNITED AC 2014; 56:532-48. [DOI: 10.1093/pcp/pcu202] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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31
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Feng H, Sun Y, Zhi Y, Wei X, Luo Y, Mao L, Zhou P. Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD-1. Microb Cell Fact 2014; 13:174. [PMID: 25492123 PMCID: PMC4272520 DOI: 10.1186/s12934-014-0174-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/24/2014] [Indexed: 11/19/2022] Open
Abstract
Background Streptomyces griseorubens JSD-1 is a novel actinomycete isolated from soil that can utilize nitrate as its sole nitrogen source for growth and these nitrate assimilation genes active in this biotransformation are expected to be crucial. However, little is known about its genomic or genetic background related to nitrogen metabolism in this isolate. Thus, this study concentrates on identification and characterization of genes involved in nitrate assimilation. Results To investigate the molecular mechanism of nitrate metabolism, genome sequencing was performed by Illumina Miseq platform. Then the draft genome of a single linear chromosome with 8,463,223 bp and an average G+C content of 72.42% was obtained, which has been deposited at GenBank under the accession number JJMG00000000. Sequences of nitrate assimilation proteins such as nitrate reductase (EC 1.7.99.4), nitrite reductase (EC 1.7.1.4), glutamine synthetase (EC 6.3.1.2), glutamate synthase (EC 1.4.1.13) and glutamate dehydrogenase (EC 1.4.1.2) were acquired. All proteins were predicted to be intracellular enzymes and their sequences were highly identical to those from their similar species owing to the conservative character. Putative 3D structures of these proteins were also modeled based on the templates with the most identities in the PDB database. Through KEGG annotated map, these proteins proved to be located on the key positions of nitrogen metabolic signaling pathway. Finally, quantitative RT-PCR indicated that expression responses of all genes were up-regulated generally and significantly when stimulated with nitrate. Conclusion In this manuscript, we describe the genome features of an isolate of S. griseorubens JSD-1 following with identification and characterization of these nitrate assimilation proteins such as nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase and glutamate dehydrogenase accounts for the ability to utilize nitrate as its sole nitrogen source for growth through cellular localization, multiple sequence alignment, putative 3D modeling and quantitative RT-PCR. In summary, our findings provide the genomic and genetic background of utilizing nitrate of this strain. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0174-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiwei Feng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yujing Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yuee Zhi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xing Wei
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yanqing Luo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Liang Mao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Pei Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
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32
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Yu P, White PJ, Hochholdinger F, Li C. Phenotypic plasticity of the maize root system in response to heterogeneous nitrogen availability. PLANTA 2014; 240:667-78. [PMID: 25143250 DOI: 10.1007/s00425-014-2150-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 08/08/2014] [Indexed: 05/03/2023]
Abstract
Mineral nutrients are distributed in a non-uniform manner in the soil. Plasticity in root responses to the availability of mineral nutrients is believed to be important for optimizing nutrient acquisition. The response of root architecture to heterogeneous nutrient availability has been documented in various plant species, and the molecular mechanisms coordinating these responses have been investigated particularly in Arabidopsis, a model dicotyledonous plant. Recently, progress has been made in describing the phenotypic plasticity of root architecture in maize, a monocotyledonous crop. This article reviews aspects of phenotypic plasticity of maize root system architecture, with special emphasis on describing (1) the development of its complex root system; (2) phenotypic responses in root system architecture to heterogeneous N availability; (3) the importance of phenotypic plasticity for N acquisition; (4) different regulation of root growth and nutrients uptake by shoot; and (5) root traits in maize breeding. This knowledge will inform breeding strategies for root traits enabling more efficient acquisition of soil resources and synchronizing crop growth demand, root resource acquisition and fertilizer application during crop growing season, thereby maximizing crop yields and nutrient-use efficiency and minimizing environmental pollution.
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Affiliation(s)
- Peng Yu
- Department of Plant Nutrition, China Agricultural University, Yuanmingyuan West Road 2, Beijing, 100193, People's Republic of China
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33
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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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Camargo ELO, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJPL, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GAG. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. BMC PLANT BIOLOGY 2014; 14:256. [PMID: 25260963 PMCID: PMC4189757 DOI: 10.1186/s12870-014-0256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/20/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns. RESULTS Histological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants. CONCLUSIONS This work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.
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Affiliation(s)
- Eduardo Leal Oliveira Camargo
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Leandro Costa Nascimento
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Marçal Soler
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Marcela Mendes Salazar
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Jorge Lepikson-Neto
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Wesley Leoricy Marques
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Ana Alves
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Paulo José Pereira Lima Teixeira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | | | - Marcelo Falsarella Carazzolle
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Yves Martinez
- />Fédération de Recherche “Agrobiosciences, Interactions et Biodiversité”, 24 Chemin de borde rouge, BP 42617, 31326 Castanet-Tolosan, France
| | - Ana Carolina Deckmann
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - José Carlos Rodrigues
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Jacqueline Grima-Pettenati
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Gonçalo Amarante Guimarães Pereira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
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Hebelstrup KH, Shah JK, Simpson C, Schjoerring JK, Mandon J, Cristescu SM, Harren FJM, Christiansen MW, Mur LAJ, Igamberdiev AU. An assessment of the biotechnological use of hemoglobin modulation in cereals. PHYSIOLOGIA PLANTARUM 2014; 150:593-603. [PMID: 24118006 DOI: 10.1111/ppl.12115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 05/11/2023]
Abstract
Non-symbiotic hemoglobin (nsHb) genes are ubiquitous in plants, but their biological functions have mostly been studied in model plant species rather than in crops. nsHb influences cell signaling and metabolism by modulating the levels of nitric oxide (NO). Class 1 nsHb is upregulated under hypoxia and is involved in various biotic and abiotic stress responses. Ectopic overexpression of nsHb in Arabidopsis thaliana accelerates development, whilst targeted overexpression in seeds can increase seed yield. Such observations suggest that manipulating nsHb could be a valid biotechnological target. We studied the effects of overexpression of class 1 nsHb in the monocotyledonous crop plant barley (Hordeum vulgare cv. Golden Promise). nsHb was shown to be involved in NO metabolism in barley, as ectopic overexpression reduced the amount of NO released during hypoxia. Further, as in Arabidopsis, nsHb overexpression compromised basal resistance toward pathogens in barley. However, unlike Arabidopsis, nsHb ectopic overexpression delayed growth and development in barley, and seed specific overexpression reduced seed yield. Thus, nsHb overexpression in barley does not seem to be an efficient strategy for increasing yield in cereal crops. These findings highlight the necessity for using actual crop plants rather than laboratory model plants when assessing the effects of biotechnological approaches to crop improvement.
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Affiliation(s)
- Kim H Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, Denmark
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Trevisan S, Manoli A, Quaggiotti S. NO signaling is a key component of the root growth response to nitrate in Zea mays L. PLANT SIGNALING & BEHAVIOR 2014; 9:e28290. [PMID: 24613869 PMCID: PMC4091522 DOI: 10.4161/psb.28290] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 02/19/2014] [Indexed: 05/18/2023]
Abstract
Roots are considered to be a vital organ system of plants due to their involvement in water and nutrient uptake, anchorage, propagation, storage functions, secondary metabolite (including hormones) biosynthesis, and accumulation. Crops are strongly dependent on the availability of nitrogen in soil and on the efficiency of nitrogen utilization for biomass production and yield. However, knowledge about molecular responses to nitrogen fluctuations mainly derives from the study of model species. Nitric oxide (NO) has been proposed to be implicated in plant adaptation to environment, but its exact role in the response of plants to nutritional stress is still under evaluation. Recently a novel role for NO production and scavenging, thanks to the coordinate spatio-temporal expression of nitrate reductase and non-symbiotic hemoglobins, in the maize root response to nitrate has been postulated. This control of NO homeostasis is preferentially accomplished by the cells of the root transition zone (TZ) which seem to represent the most nitrate responsive portion of maize root. The TZ is already known to function as a sensory center able to gather information from the external environment and to re-elaborate them in an adequate response. These results indicate that it could play a central role also for nitrate sensing by roots. A lot of work is still needed to identify and characterize other upstream and downstream signals involved in the "nitrate-NO" pathway, leading to root architecture adjustments and finally to stress adaptation.
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Affiliation(s)
- Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals, and Environment (DAFNAE); University of Padua; Agripolis, Legnaro (PD), Italy
| | - Alessandro Manoli
- Department of Agriculture, Food, Natural Resources, Animals, and Environment (DAFNAE); University of Padua; Agripolis, Legnaro (PD), Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals, and Environment (DAFNAE); University of Padua; Agripolis, Legnaro (PD), Italy
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Manoli A, Begheldo M, Genre A, Lanfranco L, Trevisan S, Quaggiotti S. NO homeostasis is a key regulator of early nitrate perception and root elongation in maize. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:185-200. [PMID: 24220653 PMCID: PMC3883287 DOI: 10.1093/jxb/ert358] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Crop plant development is strongly dependent on nitrogen availability in the soil and on the efficiency of its recruitment by roots. For this reason, the understanding of the molecular events underlying root adaptation to nitrogen fluctuations is a primary goal to develop biotechnological tools for sustainable agriculture. However, knowledge about molecular responses to nitrogen availability is derived mainly from the study of model species. Nitric oxide (NO) has been recently proposed to be implicated in plant responses to environmental stresses, but its exact role in the response of plants to nutritional stress is still under evaluation. In this work, the role of NO production by maize roots after nitrate perception was investigated by focusing on the regulation of transcription of genes involved in NO homeostasis and by measuring NO production in roots. Moreover, its involvement in the root growth response to nitrate was also investigated. The results provide evidence that NO is produced by nitrate reductase as an early response to nitrate supply and that the coordinated induction of non-symbiotic haemoglobins (nsHbs) could finely regulate the NO steady state. This mechanism seems to be implicated on the modulation of the root elongation in response to nitrate perception. Moreover, an improved agar-plate system for growing maize seedlings was developed. This system, which allows localized treatments to be performed on specific root portions, gave the opportunity to discern between localized and systemic effects of nitrate supply to roots.
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Affiliation(s)
- Alessandro Manoli
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Maura Begheldo
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
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38
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Pinosa F, Begheldo M, Pasternak T, Zermiani M, Paponov IA, Dovzhenko A, Barcaccia G, Ruperti B, Palme K. The Arabidopsis thaliana Mob1A gene is required for organ growth and correct tissue patterning of the root tip. ANNALS OF BOTANY 2013; 112:1803-14. [PMID: 24201137 PMCID: PMC3838559 DOI: 10.1093/aob/mct235] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/22/2013] [Accepted: 08/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS The Mob1 family includes a group of kinase regulators conserved throughout eukaryotes. In multicellular organisms, Mob1 is involved in cell proliferation and apoptosis, thus controlling appropriate cell number and organ size. These functions are also of great importance for plants, which employ co-ordinated growth processes to explore the surrounding environment and respond to changing external conditions. Therefore, this study set out to investigate the role of two Arabidopsis thaliana Mob1-like genes, namely Mob1A and Mob1B, in plant development. METHODS A detailed spatio-temporal analysis of Mob1A and Mob1B gene expression was performed by means of bioinformatic tools, the generation of expression reporter lines and in situ hybridization of gene-specific probes. To explore the function of the two genes in plant development, knock-out and knock-down mutants were isolated and their phenotype quantitatively characterized. KEY RESULTS Transcripts of the two genes were detected in specific sets of cells in all plant organs. Mob1A was upregulated by several stress conditions as well as by abscisic acid and salicylic acid. A knock-out mutation in Mob1B did not cause any visible defect in plant development, whereas suppression of Mob1A expression affected organ growth and reproduction. In the primary root, reduced levels of Mob1A expression brought about severe defects in tissue patterning of the stem cell niche and columella and led to a decrease in meristem size. Moreover, loss of Mob1A function resulted in a higher sensitivity of root growth to abscisic acid. CONCLUSIONS Taken together, the results indicate that arabidopsis Mob1A is involved in the co-ordination of tissue patterning and organ growth, similarly to its orthologues in other multicellular eukaryotes. In addition, Mob1A serves a plant-specific function by contributing to growth adjustments in response to stress conditions.
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Affiliation(s)
- Francesco Pinosa
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Maura Begheldo
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Monica Zermiani
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Ivan A. Paponov
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Alexander Dovzhenko
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Gianni Barcaccia
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Benedetto Ruperti
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
- Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, Habsburgerstrasse 49, D-79104 Freiburg, Germany
- Freiburg Institute for Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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39
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Mur LAJ, Mandon J, Persijn S, Cristescu SM, Moshkov IE, Novikova GV, Hall MA, Harren FJM, Hebelstrup KH, Gupta KJ. Nitric oxide in plants: an assessment of the current state of knowledge. AOB PLANTS 2013; 5:pls052. [PMID: 23372921 PMCID: PMC3560241 DOI: 10.1093/aobpla/pls052] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/12/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS After a series of seminal works during the last decade of the 20th century, nitric oxide (NO) is now firmly placed in the pantheon of plant signals. Nitric oxide acts in plant-microbe interactions, responses to abiotic stress, stomatal regulation and a range of developmental processes. By considering the recent advances in plant NO biology, this review will highlight certain key aspects that require further attention. SCOPE AND CONCLUSIONS The following questions will be considered. While cytosolic nitrate reductase is an important source of NO, the contributions of other mechanisms, including a poorly defined arginine oxidizing activity, need to be characterized at the molecular level. Other oxidative pathways utilizing polyamine and hydroxylamine also need further attention. Nitric oxide action is dependent on its concentration and spatial generation patterns. However, no single technology currently available is able to provide accurate in planta measurements of spatio-temporal patterns of NO production. It is also the case that pharmaceutical NO donors are used in studies, sometimes with little consideration of the kinetics of NO production. We here include in planta assessments of NO production from diethylamine nitric oxide, S-nitrosoglutathione and sodium nitroprusside following infiltration of tobacco leaves, which could aid workers in their experiments. Further, based on current data it is difficult to define a bespoke plant NO signalling pathway, but rather NO appears to act as a modifier of other signalling pathways. Thus, early reports that NO signalling involves cGMP-as in animal systems-require revisiting. Finally, as plants are exposed to NO from a number of external sources, investigations into the control of NO scavenging by such as non-symbiotic haemoglobins and other sinks for NO should feature more highly. By crystallizing these questions the authors encourage their resolution through the concerted efforts of the plant NO community.
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Affiliation(s)
- Luis A. J. Mur
- Institute of Environmental and Rural Science, Aberystwyth University, Edward Llwyd Building, Aberystwyth SY23 3DA, UK
- Corresponding author's e-mail address:
| | - Julien Mandon
- Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, Radboud University, PO Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Stefan Persijn
- Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, Radboud University, PO Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Simona M. Cristescu
- Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, Radboud University, PO Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Igor E. Moshkov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow 127276, Russia
| | - Galina V. Novikova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow 127276, Russia
| | - Michael A. Hall
- Institute of Environmental and Rural Science, Aberystwyth University, Edward Llwyd Building, Aberystwyth SY23 3DA, UK
| | - Frans J. M. Harren
- Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, Radboud University, PO Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Kapuganti J. Gupta
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Begheldo M, Ditengou FA, Cimoli G, Trevisan S, Quaggiotti S, Nonis A, Palme K, Ruperti B. Whole-mount in situ detection of microRNAs on Arabidopsis tissues using Zip Nucleic Acid probes. Anal Biochem 2012; 434:60-6. [PMID: 23149232 DOI: 10.1016/j.ab.2012.10.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/26/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) affect fundamental processes of development. In plants miRNAs regulate organ development, transition to flowering, and responses to abiotic/biotic stresses. To understand the biological role of miRNAs, in addition to identifying their targeted transcripts, it is necessary to characterize the spatiotemporal regulation of their expression. Many methods have been used to define the set of organ-specific miRNAs by tissue dissection and miRNA profiling but none of them can describe their tissue and cellular distribution at the high resolution provided by in situ hybridization (ISH). This article describes the setup and optimization of a whole-mount ISH protocol to target endogenous miRNAs on intact Arabidopsis seedlings using DIG-labeled Zip Nucleic Acid (ZNA) oligonucleotide probes. Automation of the main steps of the procedure by robotized liquid handling has also been implemented in the protocol for best reproducibility of results, enabling running of ISH experiments at high throughput.
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Affiliation(s)
- M Begheldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro (Padova), Italy.
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Trevisan S, Nonis A, Begheldo M, Manoli A, Palme K, Caporale G, Ruperti B, Quaggiotti S. Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings. PLANT, CELL & ENVIRONMENT 2012; 35:1137-55. [PMID: 22211437 DOI: 10.1111/j.1365-3040.2011.02478.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nitrogen availability seriously affects crop productivity and environment. The knowledge of post-transcriptional regulation of plant response to nutrients is important to improve nitrogen use efficiency of crop. This research was aimed at understanding the role of miRNAs in the molecular control of plant response to nitrate. The expression profiles of six mature miRNAs were deeply studied by quantitative real time polymerase chain reaction and in situ hybridization (ISH). To this aim, a novel optimized protocol was set up for the use of digoxygenin-labelled Zip Nucleic Acid-modified oligonucleotides as probes for ISH. Significant differences in miRNAs' transcripts accumulation were evidenced between nitrate-supplied and nitrate-depleted roots. Real-time PCR analyses and in situ detection of miRNA confirmed the array data and allowed us to evidence distinct miRNAs spatio-temporal expression patterns in maize roots. Our results suggest that a prolonged nitrate depletion may induce post-transcriptionally the expression of target genes by repressing the transcription of specific miRNAs. In particular, the repression of the transcription of miR528a/b, miR528a*/b*, miR169i/j/k, miR169i*/j*/k*, miR166j/k/n and miR408/b upon nitrate shortage could represent a crucial step integrating nitrate signals into developmental changes in maize roots.
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Affiliation(s)
- Sara Trevisan
- Agricultural Biotechnology Department, University of Padua, 35020 Legnaro (PD), Italy
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Manoli A, Sturaro A, Trevisan S, Quaggiotti S, Nonis A. Evaluation of candidate reference genes for qPCR in maize. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:807-15. [PMID: 22459324 DOI: 10.1016/j.jplph.2012.01.019] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 05/18/2023]
Abstract
Quantitative real-time PCR (qPCR) is a powerful tool to measure gene expression levels. Accurate and reproducible results are dependent on the correct choice of the reference genes for data normalization. To date, screenings evaluating candidate reference gene stability for expression studies in maize have not been reported. In the present work, we analyzed the expression patterns of 12 genes in a set of 20 maize samples, obtained from different tissues of plants grown at various experimental conditions. Using genorm(PLUS), NormFinder and BestKeeper algorithms, the expression stability of three "classical" reference genes, such as ACT, TUB and 18S rRNA, and the newly identified candidates, was assessed. With respect to the algorithms, our results showed similar performance among genorm(PLUS), NormFinder and BestKeeper in evaluating the suitability of reference genes. Our data therefore showed that the currently and widely used reference genes for data normalization in maize were not the most stable expressed transcripts. Five of the new putative reference genes (CUL, FPGS, LUG, MEP and UBCP) exhibited the highest expression stability according to all algorithms. In conclusion, with this study, we provide a list of validated reference genes and their relative primer sequences to conduct reliable qPCR experiments in maize.
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Affiliation(s)
- Alessandro Manoli
- Department of Agricultural Biotechnologies, University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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Gupta KJ, Hebelstrup KH, Mur LAJ, Igamberdiev AU. Plant hemoglobins: important players at the crossroads between oxygen and nitric oxide. FEBS Lett 2011; 585:3843-9. [PMID: 22036787 DOI: 10.1016/j.febslet.2011.10.036] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 11/16/2022]
Abstract
Plant hemoglobins constitute a diverse group of hemeproteins and evolutionarily belong to three different classes. Class 1 hemoglobins possess an extremely high affinity to oxygen and their main function consists in scavenging of nitric oxide (NO) at very low oxygen levels. Class 2 hemoglobins have a lower oxygen affinity and they facilitate oxygen supply to developing tissues. Symbiotic hemoglobins in nodules have mostly evolved from class 2 hemoglobins. Class 3 hemoglobins are truncated and represent a clade with a very low similarity to class 1 and 2 hemoglobins. They may regulate oxygen delivery at high O(2) concentrations. Depending on their physical properties, hemoglobins belong either to hexacoordinate non-symbiotic or pentacoordinate symbiotic groups. Plant hemoglobins are plausible targets for improving resistance to multiple stresses.
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Affiliation(s)
- Kapuganti J Gupta
- Department of Plant Physiology, University of Rostock, Rostock, Germany
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