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Zuluaga DL, Blanco E, Mangini G, Sonnante G, Curci PL. A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation. PLANTS (BASEL, SWITZERLAND) 2023; 12:1267. [PMID: 36986956 PMCID: PMC10056183 DOI: 10.3390/plants12061267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 06/19/2023]
Abstract
Durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) is an allotetraploid cereal crop of worldwide importance, given its use for making pasta, couscous, and bulgur. Under climate change scenarios, abiotic (e.g., high and low temperatures, salinity, drought) and biotic (mainly exemplified by fungal pathogens) stresses represent a significant limit for durum cultivation because they can severely affect yield and grain quality. The advent of next-generation sequencing technologies has brought a huge development in transcriptomic resources with many relevant datasets now available for durum wheat, at various anatomical levels, also focusing on phenological phases and environmental conditions. In this review, we cover all the transcriptomic resources generated on durum wheat to date and focus on the corresponding scientific insights gained into abiotic and biotic stress responses. We describe relevant databases, tools and approaches, including connections with other "omics" that could assist data integration for candidate gene discovery for bio-agronomical traits. The biological knowledge summarized here will ultimately help in accelerating durum wheat breeding.
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Lyu J, Jin N, Meng X, Jin L, Wang S, Xiao X, Liu Z, Tang Z, Yu J. Exogenous silicon alleviates the adverse effects of cinnamic acid-induced autotoxicity stress on cucumber seedling growth. FRONTIERS IN PLANT SCIENCE 2022; 13:968514. [PMID: 36035700 PMCID: PMC9399776 DOI: 10.3389/fpls.2022.968514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Autotoxicity is a key factor that leads to obstacles in continuous cropping systems. Although Si is known to improve plant resistance to biotic and abiotic stresses, little is known about its role in regulating leaf water status, mineral nutrients, nitrogen metabolism, and root morphology of cucumber under autotoxicity stress. Here, we used cucumber seeds (Cucumis sativus L. cv. "Xinchun No. 4") to evaluate how exogenous Si (1 mmol L-1) affected the leaf water status, mineral nutrient uptake, N metabolism-related enzyme activities, root morphology, and shoot growth of cucumber seedlings under 0.8 mmol L-1 CA-induced autotoxicity stress. We found that CA-induced autotoxicity significantly reduced the relative water content and water potential of leaves and increase their cell sap concentration. CA-induced stress also inhibited the absorption of major (N, P, K, Ca, Mg) and trace elements (Fe, Mn, Zn). However, exogenous Si significantly improved the leaf water status (relative water content and water potential) of cucumber leaves under CA-induced stress. Exogenous Si also promoted the absorption of mineral elements by seedlings under CA-induced stress and alleviated the CA-induced inhibition of N metabolism-related enzyme activities (including nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase, glutamate dehydrogenase). Moreover, exogenous Si improved N uptake and utilization, promoted root morphogenesis, and increased the growth indexes of cucumber seedlings under CA-induced stress. Our findings have far-reaching implications for overcoming the obstacles to continuous cropping in cucumber cultivation.
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Affiliation(s)
- Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Xin Meng
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Li Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Shuya Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Xuemei Xiao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zeci Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhongqi Tang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou, China
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Yan S, Yu B, Ming F, Liang Y, Zhong Y, Wang Z, Zhang X, Li X, Qiu Z, Cao B. CsIVP Modulates Low Nitrogen and High-Temperature Resistance in Cucumber. PLANT & CELL PHYSIOLOGY 2022; 63:605-617. [PMID: 35137209 DOI: 10.1093/pcp/pcac020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Crop plants experience various abiotic stresses that reduce yield and quality. Although several adaptative physiological and defense responses to single stress have been identified, the behavior and mechanisms of plant response to multiple stresses remain underexamined. Herein, we determined that the leaf and vascular changes in Cucumis sativus Irregular Vasculature Patterning (CsIVP)-RNAi cucumber plants can enhance resistance to nitrogen deficiency and high-temperature stress. CsIVP negatively regulated high nitrate affinity transporters (NRT2.1, NRT2.5) and reallocation transporters (NRT1.7, NRT1.9, NRT1.12) under low nitrogen stress. Furthermore, CsIVP-RNAi plants have high survival rate with low heat injury level under high-temperature condition. Several key high-temperature regulators, including Hsfs, Hsps, DREB2C, MBF1b and WRKY33 have significant expression in CsIVP-RNAi plants. CsIVP negatively mediated high-temperature responses by physically interacting with CsDREB2C. Altogether, these results indicated that CsIVP integrates innate programming of plant development, nutrient transport and high-temperature resistance, providing a potentially valuable target for breeding nutrient-efficient and heat-resistant crops.
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Affiliation(s)
- Shuangshuang Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bingwei Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Fangyan Ming
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yonggui Liang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yanting Zhong
- Department of Plant Nutrition, The Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China
| | - Zhongyi Wang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaolan Zhang
- State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuexian Li
- Department of Plant Nutrition, The Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China
| | - Zhengkun Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Gülüt KY. Nitrogen and boron nutrition in grafted watermelon I: Impact on pomological attributes, yield and fruit quality. PLoS One 2021; 16:e0252396. [PMID: 34048470 PMCID: PMC8162669 DOI: 10.1371/journal.pone.0252396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/14/2021] [Indexed: 11/18/2022] Open
Abstract
Watermelon is extensively consumed fruit across the globe. However, limited is known about interactive effect of nitrogen (N) and boron (B) nutrition on pomological, yield and fruit quality attributes of grafted watermelon. This two-year study tested the influence of different N and B doses on pomological, yield and fruit quality attributes of grafted watermelon under field conditions in Çukurova plains of Turkey. Four different N (0, 90, 180 and 270 kg ha-1) and two B doses (0 and 2 kg ha-1 B) were tested. The individual and interactive effects of N and B significantly altered pomological, yield and fruit quality attributes during both years. Overall, application of 270 kg ha-1 N and 2 kg ha-1 B improved yield, pomological and fruit quality attributes during both years. The highest values for yield, main stem length, stem diameter, fruit weight, fruit width, number nodes and branches per stem were recorded for 270 kg ha-1 N during both years. However, rind thickness was not altered by N application. Similarly, the highest values for quality attributes such as sucrose, glucose, fructose, citric acid, tartaric acid and ascorbic acid were noted for 270 kg ha-1 N during both years. Interestingly, no N application and 90 kg ha-1 N recorded the highest values of maleic acid during both years. The highest values of rind thickness, fruit length, fruit width and fruit weight were noted for 2 kg ha-1 B during both years, while B application had no effect on main stem length, main stem diameter, number of nodes and number of branches. Regarding N by B interactions, 180 and 270 kg ha-1 N with both B doses observed the highest values for yield, pomological and quality attributes during each year. These results indicate that N has significant contribution towards yield, pomological attributes and fruit quality of grafted watermelon. Therefore, N should be applied at the rate of 270 kg ha-1 for better yield, pomological attributes and fruit quality. Nonetheless, where necessary grafted watermelon should be fertilized with 2 kg ha-1 B for better fruit quality and pomological attributes.
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Affiliation(s)
- Kemal Yalçın Gülüt
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Çukurova University, Adana, Turkey
- * E-mail:
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5
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Gülüt KY, Duymuş E, Solmaz İ, Torun AA. Nitrogen and boron nutrition in grafted watermelon II: Impact on nutrient accumulation in fruit rind and flesh. PLoS One 2021; 16:e0252437. [PMID: 34043729 PMCID: PMC8158982 DOI: 10.1371/journal.pone.0252437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/14/2021] [Indexed: 11/18/2022] Open
Abstract
Turkey ranks second in watermelon (Citrullus lunatus L.) production globally and the highest production is witnessed for Çukurova plains the country. Although watermelon is extensively cultivated in the Çukurova region, studies on optimum nitrogen (N) and boron (B) doses for watermelon cultivation are quite limited. This study, evaluated the impact of increasing N (0, 90, 180 and 270 kg ha-1) and B (0 and 2 kg ha-1 B) doses on nutrient uptake in rind (exocarp) and flesh (endocarp) of watermelon fruit. Grafted watermelon variety ‘Starburst’, widely cultivated in the region was used as experimental material. The concentrations of different macro and micronutrients were analyzed from fruit rind and flesh. Individual and interactive effect of N and B doses significantly altered macro and micronutrients’ uptake in rind and flesh. Higher amounts of macro and micronutrients were accumulated in rind than flesh. Nutrients’ uptake was increased with increasing N doses, whereas B had limited impact. The accumulated nutrients were within the safe limits for human consumption. The N concentrations of rind and flesh increased with increasing N dose. Similarly, B concentration in rind and flesh and N concentration in rind significantly increased, while N concentration in flesh decreased with B application. It was concluded that 270 kg ha-1 N and 2 kg ha-1 B are optimum for better nutrient uptake in watermelon fruit. Thus, these doses must be used for watermelon cultivation in Çukurova plains of the country.
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Affiliation(s)
- Kemal Yalçın Gülüt
- Faculty of Agriculture, Department of Soil Science and Plant Nutrition, Çukurova University, Adana, Turkey
- * E-mail:
| | - Ebru Duymuş
- Faculty of Agriculture, Department of Soil Science and Plant Nutrition, Çukurova University, Adana, Turkey
| | - İlknur Solmaz
- Faculty of Agriculture, Department of Horticulture, Çukurova University, Adana, Turkey
| | - Ayfer Alkan Torun
- Faculty of Agriculture, Department of Soil Science and Plant Nutrition, Çukurova University, Adana, Turkey
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Prinsi B, Muratore C, Espen L. Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040792. [PMID: 33920578 PMCID: PMC8073184 DOI: 10.3390/plants10040792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
In agricultural soils, nitrate (NO3-) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO3- acquisition is strictly dependent on rootstock. To improve the knowledge about N nutrition in grapevine, this study analyzed biochemical and proteomic changes induced by, NO3- availability, in a hydroponic system, in the roots of M4, a recently selected grapevine rootstock. The evaluation of biochemical parameters, such as NO3-, sugar and amino acid contents in roots, and the abundance of nitrate reductase, allowed us to define the time course of the metabolic adaptations to NO3- supply. On the basis of these results, the proteomic analysis was conducted by comparing the root profiles in N-starved plants and after 30 h of NO3- resupply. The analysis quantified 461 proteins, 26% of which differed in abundance between conditions. Overall, this approach highlighted, together with an increased N assimilatory metabolism, a concomitant rise in the oxidative pentose phosphate pathway and glycolysis, needed to fulfill the redox power and carbon skeleton demands, respectively. Moreover, a wide modulation of protein and amino acid metabolisms and changes of proteins involved in root development were observed. Finally, some results open new questions about the importance of redox-related post-translational modifications and of NO3- availability in modulating the dialog between root and rhizosphere.
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Affiliation(s)
| | | | - Luca Espen
- Correspondence: ; Tel.: +39-02-503-16610
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Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective. PLANTS 2021; 10:plants10040681. [PMID: 33916130 PMCID: PMC8066207 DOI: 10.3390/plants10040681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022]
Abstract
Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H+-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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Ganie AH, Pandey R, Kumar MN, Chinnusamy V, Iqbal M, Ahmad A. Metabolite Profiling and Network Analysis Reveal Coordinated Changes in Low-N Tolerant and Low-N Sensitive Maize Genotypes under Nitrogen Deficiency and Restoration Conditions. PLANTS 2020; 9:plants9111459. [PMID: 33137957 PMCID: PMC7716227 DOI: 10.3390/plants9111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 11/16/2022]
Abstract
Nitrogen (N), applied in the form of a nitrogenous fertilizer, is one of the main inputs for agricultural production. Food production is closely associated with the application of N. However, the application of nitrogenous fertilizers to agricultural fields is associated with heavy production of nitrous oxide because agricultural crops can only utilize 30-40% of applied N, leaving behind unused 60-70% N in the environment. The global warming effect of this greenhouse gas is approximately 300 times more than of carbon dioxide. Under the present scenario of climate change, it is critical to maintain the natural balance between food production and environmental sustainability by targeting traits responsible for improving nitrogen-use-efficiency (NUE). Understanding of the molecular mechanisms behind the metabolic alterations due to nitrogen status needs to be addressed. Additionally, mineral nutrient deficiencies and their associated metabolic networks have not yet been studied well. Given this, the alterations in core metabolic pathways of low-N tolerant (LNT) and low-N sensitive (LNS) genotypes of maize under N-deficiency and their efficiency of recovering the changes upon resupplying N were investigated by us, using the GC-MS and LC-MS based metabolomic approach. Significant genotype-specific changes were noted in response to low-N. The N limitation affected the whole plant metabolism, most significantly the precursors of primary metabolic pathways. These precursors may act as important targets for improving the NUE. Limited availability of N reduced the levels of N-containing metabolites, organic acids and amino acids, but soluble sugars increased. Major variations were encountered in LNS, as compared to LNT. This study has revealed potential metabolic targets in response to the N status, which are indeed the prospective targets for crop improvement.
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Affiliation(s)
| | - Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - M. Nagaraj Kumar
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Muhammad Iqbal
- Department of Botany, Jamia Hamdard, New Delhi 110062, India; (A.H.G.); (M.I.)
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
- Correspondence: ; Tel.: +00-91-9999886334
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Prinsi B, Failla O, Scienza A, Espen L. Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress. Int J Mol Sci 2020; 21:ijms21031076. [PMID: 32041176 PMCID: PMC7037071 DOI: 10.3390/ijms21031076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022] Open
Abstract
Salinity represents a very limiting factor that affects the fertility of agricultural soils. Although grapevine is moderately susceptible to salinity, both natural causes and agricultural practices could worsen the impact of this abiotic stress. A promising possibility to reduce this problem in vineyards is the use of appropriate graft combinations. The responses of grapevine rootstocks to this abiotic stress at the root level still remain poorly investigated. In order to obtain further information on the multifaceted responses induced by salt stress at the biochemical level, in the present work we analyzed the changes that occurred under control and salt conditions in the root proteomes of two grapevine rootstock genotypes, M4 and 101.14. Moreover, we compared the results considering that M4 and 101.14 were previously described to have lower and higher susceptibility to salt stress, respectively. This study highlighted the greater capability of M4 to maintain and adapt energy metabolism (i.e., synthesis of ATP and NAD(P)H) and to sustain the activation of salt-protective mechanisms (i.e., Na sequestration into the vacuole and synthesis of osmoprotectant compounds). Comparitively, in 101.14 the energy metabolism was deeply affected and there was an evident induction of the enzymatic antioxidant system that occurred, pointing to a metabolic scenario typical of a suffering tissue. Overall, this study describes for the first time in grapevine roots some of the more crucial events that characterize positive (M4) or negative (101.14) responses evoked by salt stress conditions.
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Affiliation(s)
| | | | | | - Luca Espen
- Correspondence: ; Tel.: +39-02-503-16610
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11
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Evaluation of the effects of humic acids on maize root architecture by label-free proteomics analysis. Sci Rep 2019; 9:12019. [PMID: 31427667 PMCID: PMC6700139 DOI: 10.1038/s41598-019-48509-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 08/07/2019] [Indexed: 01/07/2023] Open
Abstract
Humic substances have been widely used as plant growth promoters to improve the yield of agricultural crops. However, the mechanisms underlying this effect remain unclear. Root soluble protein profiles in plants 11 days after planting and cultivated with and without humic acids (HA, 50 mg CL-1), were analyzed using the label-free quantitative proteomic approach. Cultivation of maize with HA resulted in higher fresh weight of roots than in untreated plants (control). Plants treated with HA showed increased number, diameter and length of roots. In the proteomics analysis, differences were detected in the following categories: energy metabolism, cytoskeleton, cellular transport, conformation and degradation of proteins, and DNA replication. Thirty-four proteins were significantly more abundant in the seedlings treated with HA, whereas only nine proteins were abundant in the control. The effects on root architecture, such as the induction of lateral roots and biomass increase were accompanied by changes in the energy metabolism-associated proteins. The results show that the main effect of HA is protective, mainly associated with increased expression of the 2-cys peroxidase, putative VHS/GAT, and glutathione proteins. Indeed, these proteins had the highest fold-difference. Overall, these results improve our understanding of the molecular mechanisms of HA-promoted plant growth.
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12
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Nunes RO, Domiciano GA, Alves WS, Melo ACA, Nogueira FCS, Canellas LP, Olivares FL, Zingali RB, Soares MR. Evaluation of the effects of humic acids on maize root architecture by label-free proteomics analysis. Sci Rep 2019. [PMID: 31427667 DOI: 10.1038/s41598-019-48509-48502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Humic substances have been widely used as plant growth promoters to improve the yield of agricultural crops. However, the mechanisms underlying this effect remain unclear. Root soluble protein profiles in plants 11 days after planting and cultivated with and without humic acids (HA, 50 mg CL-1), were analyzed using the label-free quantitative proteomic approach. Cultivation of maize with HA resulted in higher fresh weight of roots than in untreated plants (control). Plants treated with HA showed increased number, diameter and length of roots. In the proteomics analysis, differences were detected in the following categories: energy metabolism, cytoskeleton, cellular transport, conformation and degradation of proteins, and DNA replication. Thirty-four proteins were significantly more abundant in the seedlings treated with HA, whereas only nine proteins were abundant in the control. The effects on root architecture, such as the induction of lateral roots and biomass increase were accompanied by changes in the energy metabolism-associated proteins. The results show that the main effect of HA is protective, mainly associated with increased expression of the 2-cys peroxidase, putative VHS/GAT, and glutathione proteins. Indeed, these proteins had the highest fold-difference. Overall, these results improve our understanding of the molecular mechanisms of HA-promoted plant growth.
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Affiliation(s)
- Rosane Oliveira Nunes
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giselli Abrahão Domiciano
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilber Sousa Alves
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Claudia Amaral Melo
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio Cesar Sousa Nogueira
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciano Pasqualoto Canellas
- Biological Inputs to Agriculture Development Center, State University of Northern of Rio de Janeiro, UENF, Rio de Janeiro, Brazil
| | - Fábio Lopes Olivares
- Biological Inputs to Agriculture Development Center, State University of Northern of Rio de Janeiro, UENF, Rio de Janeiro, Brazil
| | - Russolina Benedeta Zingali
- Medical Biochemistry Institute Leopoldo De Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia Regina Soares
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Vita F, Giuntoli B, Arena S, Quaranta F, Bertolini E, Lucarotti V, Guglielminetti L, Alessio M, Scaloni A, Alpi A. Effects of different nitrogen fertilizers on two wheat cultivars: An integrated approach. PLANT DIRECT 2018; 2:e00089. [PMID: 31245689 PMCID: PMC6508776 DOI: 10.1002/pld3.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/06/2018] [Accepted: 10/01/2018] [Indexed: 06/09/2023]
Abstract
Investigation of cultivated plant physiology grown under low energy input plays an important role to indicate their fitness to the new environmental conditions. The durum-wheat cultivars Creso and Dylan were tested to evaluate the growth, production, and proteomic and transcriptomic profiles of the crop under different synthetic and organic nitrogen fertilization regimes. In this work, a two-dimensional gel electrophoresis (2-DE) approach combined with liquid chromatography-mass spectrometry (LC-MS) was used to investigate the protein changes induced by the use of different nitrogen sources (hydrolysate of proteins 1 and 2, rhizovit, synthesis, leather) on wheat plants. Proteomic studies were integrated with qPCR analysis of genes related to glutamine synthetase/glutamine-2-oxoglutarate aminotransferase (GS-GOGAT) and tricarboxylic acid (TCA) metabolic pathways because most relevant for nitrogen-dependent plants growth. The proteomic analysis lead to the isolation of 23 spots that were able to distinguish the analyzed samples. These spots yielded the identification of 60 proteins involved in photosynthesis, glycolysis, and nitrogen metabolism. As an example, the quinone oxidoreductase-like protein and probable glutathione S-transferase GSTU proteins were identified in two spots that represents the most statistically significant ones in Dylan samples. Transcript analysis indicated that related genes exhibited different expression trends; the heat map also revealed the different behaviors of the hydrolysates of the proteins 1 and 2 nitrogen sources. The effects of nitrogenous fertilizers at the proteomic and agronomic levels revealed that plants fertilized with synthesis or rhizovit gave the best results concerning yield, whereas rhizovit and protein hydrolysates were most effective for proteins content in the grain (% of dry weight). Therefore, all parameters measured in this study indicated that different kinds of nitrogen fertilization used have a relevant impact on plant growth and production.
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Affiliation(s)
- Federico Vita
- LINV-Department of Plant Soil and Environmental Science University of Florence Florence Italy
- A.R.E.A. Foundation Pisa Italy
| | - Beatrice Giuntoli
- Biology Department University of Pisa Pisa Italy
- Institute of Life Sciences Scuola Superiore Sant'Anna Pisa Italy
| | - Simona Arena
- Proteomics and Mass Spectrometry Laboratory I.S.P.A.A.M. National Research Council Napoli Italy
| | - Fabrizio Quaranta
- Council for Agricultural Research and Agricultural Economics Analysis Unità di ricerca per la valorizzazione qualitativa dei cereali (CREA-QCE) Rome Italy
| | - Edoardo Bertolini
- Institute of Life Sciences Scuola Superiore Sant'Anna Pisa Italy
- Present address: Donald Danforth Plant Science Center Saint Louis Missouri
| | - Valentina Lucarotti
- Department of Agriculture, Food and Environment (DiSAAA) University of Pisa Pisa Italy
| | | | - Massimo Alessio
- Proteome Biochemistry Unit IRCCS-San Raffaele Scientific Institute Milan Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory I.S.P.A.A.M. National Research Council Napoli Italy
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Waqas M, Feng S, Amjad H, Letuma P, Zhan W, Li Z, Fang C, Arafat Y, Khan MU, Tayyab M, Lin W. Protein Phosphatase ( PP2C9) Induces Protein Expression Differentially to Mediate Nitrogen Utilization Efficiency in Rice under Nitrogen-Deficient Condition. Int J Mol Sci 2018; 19:E2827. [PMID: 30235789 PMCID: PMC6163212 DOI: 10.3390/ijms19092827] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 02/05/2023] Open
Abstract
Nitrogen (N) is an essential element usually limiting in plant growth and a basic factor for increasing the input cost in agriculture. To ensure the food security and environmental sustainability it is urgently required to manage the N fertilizer. The identification or development of genotypes with high nitrogen utilization efficiency (NUE) which can grow efficiently and sustain yield in low N conditions is a possible solution. In this study, two isogenic rice genotypes i.e., wild-type rice kitaake and its transgenic line PP2C9TL overexpressed protein phosphatase gene (PP2C9) were used for comparative proteomics analysis at control and low level of N to identify specific proteins and encoding genes related to high NUE. 2D gel electrophoresis was used to perform the differential proteome analysis. In the leaf proteome, 30 protein spots were differentially expressed between the two isogenic lines under low N level which were involved in the process of energy, photosynthesis, N metabolism, signaling, and defense mechanisms. In addition, we have found that protein phosphatase enhances nitrate reductase activation by downregulation of SnRK1 and 14-3-3 proteins. Furthermore, we showed that PP2C9TL exhibits higher NUE than WT due to higher activity of nitrate reductase. This study provides new insights on the rice proteome which would be useful in the development of new strategies to increase NUE in cereal crops.
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Affiliation(s)
- Muhammad Waqas
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shizhong Feng
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Hira Amjad
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Puleng Letuma
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Wenshan Zhan
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Zhong Li
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Changxun Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Yasir Arafat
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Muhammad Umar Khan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Muhammad Tayyab
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenxiong Lin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
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15
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Prinsi B, Espen L. Time-Course of Metabolic and Proteomic Responses to Different Nitrate/Ammonium Availabilities in Roots and Leaves of Maize. Int J Mol Sci 2018; 19:ijms19082202. [PMID: 30060519 PMCID: PMC6121299 DOI: 10.3390/ijms19082202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/16/2022] Open
Abstract
The availability of nitrate and ammonium significantly affects plant growth. Co-provision of both nutrients is generally the best nutritional condition, due to metabolic interactions not yet fully elucidated. In this study, maize grown in hydroponics was exposed to different nitrogen (N) availabilities, consisting of nitrate, ammonium and co-provision. Roots and leaves were analyzed after 6, 30, and 54 h by biochemical evaluations and proteomics. The ammonium-fed plants showed the lowest biomass accumulation and the lowest ratio of inorganic to organic N content, suggesting a metabolic need to assimilate ammonium that was not evident in plants grown in co-provision. The N sources differently affected the root proteome, inducing changes in abundance of proteins involved in N and carbon (C) metabolisms, cell water homeostasis, and cell wall metabolism. Notable among these changes was that some root enzymes, such as asparagine synthetase, phosphoenolpyruvate (PEP) carboxylase, and formate dehydrogenase showed a relevant upsurge only under the sole ammonium nutrition. However, the leaf proteome appeared mainly influenced by total N availability, showing changes in the abundance of several proteins involved in photosynthesis and in energy metabolism. Overall, the study provides novel information about the biochemical determinants involved in plant adaptation to different N mineral forms.
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Affiliation(s)
- Bhakti Prinsi
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Luca Espen
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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16
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Jozefowicz AM, Hartmann A, Matros A, Schum A, Mock HP. Nitrogen Deficiency Induced Alterations in the Root Proteome of a Pair of Potato (Solanum tuberosum L.) Varieties Contrasting for their Response to Low N. Proteomics 2018; 17. [PMID: 29087609 DOI: 10.1002/pmic.201700231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/13/2017] [Indexed: 12/20/2022]
Abstract
Improving crop nitrogen use efficiency is important both from the economic and the environmental viewpoint. Here, the aim is to highlight differences between the proteomic response of the roots of two potato cultivars contrasting in their response to nitrogen (N) deficiency, in an effort to understand which proteins and metabolic pathways contribute to the tolerance of N deprivation. The two cultivars ''Topas'' (tolerant) and ''Lambada'' (sensitive) are grown under both an N sufficient and an N deficient regime, using an in vitro-based cultivation system. Responsive proteins are identified and quantified using label-free quantitative shotgun proteomics. The contrasting cultivars differed with respect to components of the glutamine synthetase/glutamine oxoglutarate aminotransferase pathway, tricarboxylic acid cycle, the glycolysis/gluconeogenesis pathway as well as protein and amino acid synthesis machinery. Additional differences are associated with protein catabolism and defense mechanisms.
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Affiliation(s)
- Anna Maria Jozefowicz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Annegret Schum
- Julius Kühn-Institut (JKI) Bundesforschungsinstitut für Kulturpflanzen, Sanitz, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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17
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Prinsi B, Negri AS, Failla O, Scienza A, Espen L. Root proteomic and metabolic analyses reveal specific responses to drought stress in differently tolerant grapevine rootstocks. BMC PLANT BIOLOGY 2018; 18:126. [PMID: 29925320 PMCID: PMC6011575 DOI: 10.1186/s12870-018-1343-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/06/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Roots play a central role in plant response to water stress (WS). They are involved in its perception and signalling to the leaf as well as in allowing the plant to adapt to maintaining an adequate water balance. Only a few studies have investigated the molecular/biochemical responses to WS in roots of perennial plants, such as grapevine. This study compares two grapevine rootstock genotypes (i.e. 101.14 and M4) with different tolerance to WS, evaluating the responses at proteomic and metabolite levels. RESULTS WS induced changes in the abundance of several proteins in both genotypes (17 and 22% of the detected proteins in 101.14 and M4, respectively). The proteomic analysis revealed changes in many metabolic pathways that fitted well with the metabolite data. M4 showed metabolic responses which were potentially able to counteract the WS effects, such as the drop in cell turgor, increased oxidative stress and loss of cell structure integrity/functionality. However, in 101.14 it was evident that the roots were suffering more severely from these effects. We found that many proteins classified as active in energy metabolism, hormone metabolism, protein, secondary metabolism and stress functional classes showed particular differences between the two rootstocks. CONCLUSION The proteomic/metabolite comparative analysis carried out provides new information on the possible biochemical and molecular strategies adopted by grapevine roots to counteract WS. Although further work is needed to define in detail the role(s) of the proteins and metabolites that characterize WS response, this study, involving the M4 rootstock genotype, highlights that osmotic responses, modulations of C metabolism, mitochondrial functionality and some specific responses to stress occurring in the roots play a primary role in Vitis spp. tolerance to this type of abiotic stress.
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Affiliation(s)
- Bhakti Prinsi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Via Celoria, 2, 20133 Milano, Italy
| | - Alfredo Simone Negri
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Via Celoria, 2, 20133 Milano, Italy
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Via Celoria, 2, 20133 Milano, Italy
| | - Attilio Scienza
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Via Celoria, 2, 20133 Milano, Italy
| | - Luca Espen
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Via Celoria, 2, 20133 Milano, Italy
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18
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Nawaz MA, Chen C, Shireen F, Zheng Z, Sohail H, Afzal M, Ali MA, Bie Z, Huang Y. Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen. BMC Genomics 2018; 19:456. [PMID: 29898660 PMCID: PMC6001020 DOI: 10.1186/s12864-018-4856-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/06/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days. RESULTS Dry weight and photosynthetic assimilation at low N (0.2 mM) was reduced by 29 and 74% compared with high N (9 mM). The photochemical activity (Fv/Fm) was also reduced from 0.78 at high N to 0.71 at low N. The N concentration in the leaf, stem, and root of watermelon under low N conditions was reduced by 68, 104, and 108%, respectively compared with 9 mM N treatment after 14 days of N treatment. In the leaf tissues of watermelon grown under low N conditions, 9598 genes were differentially expressed, out of which 4533 genes (47.22%) were up-regulated whereas, 5065 genes (52.78%) were down-regulated compared with high N. Similarly in the root tissues, 3956 genes were differentially expressed, out of which 1605 genes were up-regulated (40.57%) and 2351 genes were down-regulated (59.43%), compared with high N. Our results suggest that leaf tissues are more sensitive to N deficiency compared with root tissues. The gene ontology (GO) analysis showed that the availability of N significantly affected 19 biological processes, 8 cell component metabolic pathways, and 3 molecular functions in the leaves; and 13 biological processes, 12 molecular functions, and 5 cell component metabolic pathways in the roots of watermelon. The low affinity nitrate transporters, high affinity nitrate transporters, ammonium transporters, genes related with nitrogen assimilation, and chlorophyll and photosynthesis were expressed differentially in response to low N. Three nitrate transporters (Cla010066, Cla009721, Cla012765) substantially responded to low nitrate supply in the root and leaf tissues. Additionally, a large number of transcription factors (1365) were involved in adaptation to low N availability. The major transcription factor families identified in this study includes MYB, AP2-EREBP, bHLH, C2H2 and NAC. CONCLUSION Candidate genes identified in this study for nitrate uptake and transport can be targeted and utilized for further studies in watermelon breeding and improvement programs to improve N uptake and utilization efficiency.
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Affiliation(s)
- Muhammad Azher Nawaz
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- University College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Chen Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Fareeha Shireen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhuhua Zheng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hamza Sohail
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Muhammad Afzal
- University College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, and Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zhilong Bie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yuan Huang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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19
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Meise P, Jozefowicz AM, Uptmoor R, Mock HP, Ordon F, Schum A. Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro. J Proteomics 2017; 166:68-82. [PMID: 28733104 DOI: 10.1016/j.jprot.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/10/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
Abstract
Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific. SIGNIFICANCE Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars.
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Affiliation(s)
- Philipp Meise
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany
| | - Anna Maria Jozefowicz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Physiology and Cell Biology, Applied Biochemistry, OT Gatersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Ralf Uptmoor
- University of Rostock, Faculty of Agricultural and Environmental Science, Justus-von-Liebig-Weg 6, 18055 Rostock, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Physiology and Cell Biology, Applied Biochemistry, OT Gatersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Frank Ordon
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany
| | - Annegret Schum
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany.
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20
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Nazaralian S, Majd A, Irian S, Najafi F, Ghahremaninejad F, Landberg T, Greger M. Comparison of silicon nanoparticles and silicate treatments in fenugreek. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 115:25-33. [PMID: 28300729 DOI: 10.1016/j.plaphy.2017.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 05/03/2023]
Abstract
Silicon (Si) fertilization improves crop cultivation and is commonly added in the form of soluble silicates. However, most natural plant-available Si originates from plant formed amorphous SiO2 particles, phytoliths, similar to SiO2-nanoparticles (SiNP). In this work we, therefore, compared the effect by sodium silicate and that of SiNP on Si accumulation, activity of antioxidative stress enzymes catalase, peroxidase, superoxide dismutase, lignification of xylem cell walls and activity of phenylalanine ammonia-lyase (PAL) as well as expression of genes for the putative silicon transporter (PST), defensive (Tfgd 1) and phosphoenolpyruvate carboxykinase (PEPCK) and protein in fenugreek (Trigonella foenum-graecum L.) grown in hydroponics. The results showed that Si was taken up from both silicate and SiNP treatments and increasing sodium silicate addition increased the translocation of Si to the shoot, while this was not shown with increasing SiNP addition. The silicon transporter PST was upregulated at a greater level when sodium silicate was added compared with SiNP addition. There were no differences in effects between sodium silicate and SiNP treatments on the other parameters measured. Both treatments increased the uptake and accumulation of Si, xylem cell wall lignification, cell wall thickness, PAL activity and protein concentration in seedlings, while there was no effect on antioxidative enzyme activity. Tfgd 1 expression was strongly downregulated in leaves at Si addition. The similarity in effects by silicate and SiNP would be due to that SiNP releases silicate, which may be taken up, shown by a decrease in SiNP particle size with time in the medium.
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Affiliation(s)
- Sanam Nazaralian
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, 15719-14911, Tehran, Iran.
| | - Ahmad Majd
- Department of Biology, Faculty of Science, North Tehran Branch of Islamic Azad University, 16679-34783, Tehran, Iran
| | - Saeed Irian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, 15719-14911, Tehran, Iran
| | - Farzaneh Najafi
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, 15719-14911, Tehran, Iran
| | - Farrokh Ghahremaninejad
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, 15719-14911, Tehran, Iran
| | - Tommy Landberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Maria Greger
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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21
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Transcriptomic response of durum wheat to nitrogen starvation. Sci Rep 2017; 7:1176. [PMID: 28446759 PMCID: PMC5430780 DOI: 10.1038/s41598-017-01377-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/27/2017] [Indexed: 11/29/2022] Open
Abstract
Nitrogen (N) is a key macronutrient representing a limiting factor for plant growth and development and affects productivity in wheat. In this study, durum wheat response to N chronic starvation during grain filling was investigated through a transcriptomic approach in roots, leaves/stems, flag leaf and spikes of cv. Svevo. Nitrogen stress negatively influenced plant height, tillering, flag leaf area, spike and seed traits, and total N content. RNA-seq data revealed 4,626 differentially expressed genes (DEGs). Most transcriptomic changes were observed in roots, with 3,270 DEGs, while 963 were found in leaves/stems, 470 in flag leaf, and 355 in spike tissues. A total of 799 gene ontology (GO) terms were identified, 180 and 619 among the upregulated and downregulated genes, respectively. Among the most addressed GO categories, N compound metabolism, carbon metabolism, and photosynthesis were mostly represented. Interesting DEGs, such as N transporters, genes involved in N assimilation, along with transcription factors, protein kinases and other genes related to stress were highlighted. These results provide valuable information about the transcriptomic response to chronic N stress in durum wheat, which could be useful for future improvement of N use efficiency.
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Lin ZH, Zhong QS, Chen CS, Ruan QC, Chen ZH, You XM. Carbon dioxide assimilation and photosynthetic electron transport of tea leaves under nitrogen deficiency. BOTANICAL STUDIES 2016; 57:37. [PMID: 28597447 PMCID: PMC5432892 DOI: 10.1186/s40529-016-0152-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/05/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Tea plant is famed in humid and sub-humid of tropical regions, sub-tropical regions, and is a leaf-harvested crop. Nitrogen is the most important nutrient for increasing quality of tea leaves. Therefore, large amounts of nitrogen fertilizer are increasingly applied by tea farmers. Appropriate application of nitrogen fertilizer aroused people's concern. This research of physiological response to N deficiency stress will be helpful for appropriate application of nitrogen fertilizer for tea farmers and elucidate a mechanistic basis for the reductions in carbon dioxide (CO2) assimilation. RESULTS To elucidate a mechanistic basis for the reductions in carbon dioxide (CO2) assimilation under nitrogen (N) deficiency tea leaves, changes in chlorophyll (Chl), carbohydrates, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and chlorophyll fluorescence transient were examined together with six N treatment (0, 50, 100, 300, 1200 or 6000 μM N). Root, stem and leaves dry weight (DW) increased as N supply increased from 0 to 300 μM, then remained unchanged. The reductions in CO2 assimilation of N-deficient leaves paralleled with high intercellular CO2 concentration. Rubisco activity, protein and Chl content increased linearly or curvilinearly over the range of leaf N content examined except unchanged as leaf N from 2.15 to 2.79 g m-2. Chlorophyll fluorescence transient from N-deficient leaves displayed a depression at the P-step, accompanied by a new step at about 150 μs (L-step). Fv/Fm, REo/ETo, ETo/ABS, Sm, ETo/CSo, PIabs, PItot, abs, were decreased in N-deficient leaves but increased DIo/CSo, DIo/RC and DIo/ABS. Regressive analysis showed that CO2 assimilation decreased linearly or curvilinearly with decreasing initial rubisco, PIabs and Leaf Chl, respectively. Therefore, we concluded the decreased photosynthetic electron transport capacity, leaf chl content and initial rubisco activity are probably the main factors contributing to decreased CO2 assimilation under N deficiency. CONCLUSIONS The decreased photosynthetic electron transport capacity, leaf Chl content and initial rubisco activity are probably the main factors contributing to decreased CO2 assimilation under N deficiency.
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Affiliation(s)
- Zheng-he Lin
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
| | - Qiu-sheng Zhong
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
| | - Chang-song Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
| | - Qi-chun Ruan
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
| | - Zhi-hui Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
| | - Xiao-mei You
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuan, 355000 China
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Wei S, Wang X, Shi D, Li Y, Zhang J, Liu P, Zhao B, Dong S. The mechanisms of low nitrogen induced weakened photosynthesis in summer maize (Zea mays L.) under field conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:118-128. [PMID: 27101123 DOI: 10.1016/j.plaphy.2016.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 05/21/2023]
Abstract
Soil nitrogen (N) shortage is a problem which affects many developing nations. Crops grown with low soil N levels show a marked decrease in the rate of photosynthesis and this deficiency reduces crop yield significantly. Therefore, developing a better understanding of the mechanisms by which low N levels cause decreased photosynthesis is crucial for maize agriculture. To better understand this process, we assessed the responses of photosynthesis traits and enzymatic activities in the summer maize cultivar Denghai 618 under field conditions with and without the use of N fertilisers. We measured photosynthesis parameters, and compared proteome compositions to identify the mechanisms of physiological and biochemical adaptations to N deficiency in maize. We observed that parameters that indicated the rate of photosynthesis decreased significantly under N deficiency, and this response was associated with leaf senescence. Moreover, we identified 37 proteins involved in leaf photosynthesis, and found that N deficiency significantly affected light-dependent and light-independent reactions in maize leaf photosynthesis. Although further analysis is required to fully elucidate the roles of these proteins in the response to N deficiency, our study identified candidate proteins which may be involved in the regulatory mechanisms involved in reduced photosynthesis under low N conditions in maize.
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Affiliation(s)
- Shanshan Wei
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Xiangyu Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Deyang Shi
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Yanhong Li
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Peng Liu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Bin Zhao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China
| | - Shuting Dong
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an 271018, Shandong Province, PR China.
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Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:581-601. [PMID: 26484978 DOI: 10.1089/omi.2015.0106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes.
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Affiliation(s)
| | - Rajesh Kumar Pathak
- 2 Department of Biotechnology, G. B. Pant Engineering College , Pauri Garhwal-246194, Uttarakhand, India
| | - Sanjay Mohan Gupta
- 3 Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research , DRDO, Haldwani, Uttarakhand, India
| | - Vikram Singh Gaur
- 4 College of Agriculture , Waraseoni, Balaghat, Madhya Pradesh, India
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Naidoo RK, Rafudeen MS, Coyne VE. Investigation of the Gracilaria gracilis (Gracilariales, Rhodophyta) proteome response to nitrogen limitation. JOURNAL OF PHYCOLOGY 2016; 52:369-383. [PMID: 27273530 DOI: 10.1111/jpy.12400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/02/2016] [Indexed: 06/06/2023]
Abstract
Inorganic nitrogen has been identified as the major growth-limiting nutritional factor affecting Gracilaria gracilis populations in South Africa. Although the physiological mechanisms implemented by G. gracilis for adaption to low nitrogen environments have been investigated, little is known about the molecular mechanisms of these adaptions. This study provides the first investigation of G. gracilis proteome changes in response to nitrogen limitation and subsequent recovery. A differential proteomics approach employing two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry was used to investigate G. gracilis proteome changes in response to nitrogen limitation and recovery. The putative identity of 22 proteins that changed significantly (P < 0.05) in abundance in response to nitrogen limitation and recovery was determined. The identified proteins function in a range of biological processes including glycolysis, photosynthesis, ATP synthesis, galactose metabolism, protein-refolding and biosynthesis, nitrogen metabolism and cytoskeleton remodeling. The identity of fructose 1,6 biphosphate (FBP) aldolase was confirmed by western blot analysis and the decreased abundance of FBP aldolase observed with two-dimensional gel electrophoresis was validated by enzyme assays and western blots. The identification of key proteins and pathways involved in the G. gracilis nitrogen stress response provide a better understanding of G. gracilis proteome responses to varying degrees of nitrogen limitation and is the first step in the identification of biomarkers for monitoring the nitrogen status of cultivated G. gracilis populations.
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Affiliation(s)
- Rene K Naidoo
- Molecular and Cell Biology Department, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Muhammad S Rafudeen
- Molecular and Cell Biology Department, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Vernon E Coyne
- Molecular and Cell Biology Department, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
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Sun C, Li Y, Zhao W, Song X, Lu M, Li X, Li X, Liu R, Yan L, Zhang X. Integration of Hormonal and Nutritional Cues Orchestrates Progressive Corolla Opening. PLANT PHYSIOLOGY 2016; 171:1209-29. [PMID: 27208289 PMCID: PMC4902604 DOI: 10.1104/pp.16.00209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/24/2016] [Indexed: 05/19/2023]
Abstract
Flower opening is essential for pollination and thus successful sexual reproduction; however, the underlying mechanisms of its timing control remain largely elusive. We identify a unique cucumber (Cucumis sativus) line '6457' that produces normal ovaries when nutrients are under-supplied, and super ovaries (87%) with delayed corolla opening when nutrients are oversupplied. Corolla opening in both normal and super ovaries is divided into four distinct phases, namely the green bud, green-yellow bud, yellow bud, and flowering stages, along with progressive color transition, cytological tuning, and differential expression of 14,282 genes. In the super ovary, cell division and cell expansion persisted for a significantly longer period of time; the expressions of genes related to photosynthesis, protein degradation, and signaling kinases were dramatically up-regulated, whereas the activities of most transcription factors and stress-related genes were significantly down-regulated; concentrations of cytokinins (CKs) and gibberellins were higher in accordance with reduced cytokinin conjugation and degradation and increased expression of gibberellin biosynthesis genes. Exogenous CK application was sufficient for the genesis of super ovaries, suggesting a decisive role of CKs in controlling the timing of corolla opening. Furthermore, 194 out of 11,127 differentially expressed genes identified in pairwise comparisons, including critical developmental, signaling, and cytological regulators, contained all three types of cis-elements for CK, nitrate, and phosphorus responses in their promoter regions, indicating that the integration of hormone modulation and nutritional regulation orchestrated the precise control of corolla opening in cucumber. Our findings provide a valuable framework for dissecting the regulatory pathways for flower opening in plants.
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Affiliation(s)
- Chengzhen Sun
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Yanqiang Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Wensheng Zhao
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaofei Song
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Man Lu
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaoli Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xuexian Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Renyi Liu
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Liying Yan
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaolan Zhang
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
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Prinsi B, Negri AS, Espen L, Piagnani MC. Proteomic Comparison of Fruit Ripening between 'Hedelfinger' Sweet Cherry (Prunus avium L.) and Its Somaclonal Variant 'HS'. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4171-81. [PMID: 27144542 DOI: 10.1021/acs.jafc.6b01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The somaclonal variant HS, from sweet cherry (Prunus avium L.) 'Hedelfinger' (H), was previously selected for reduced tree vegetative vigor and lesser canopy density. In this work, we compared H and HS fruits at early unripe (green) and full ripe (dark red) stages by biochemical and proteomic approaches. The main biochemical parameters showed that fruit quality was not affected by somaclonal variation. The proteomic analysis identified 39 proteins differentially accumulated between H and HS fruits at the two ripening stages, embracing enzymes involved in several pathways, such as carbon metabolism, cell wall modification, stress response, and secondary metabolism. The evaluation of fruit phenolic composition by mass spectrometry showed that HS sweet cherries have higher levels of procyanidin, flavonol, and anthocyanin compounds. This work provides the first proteomic characterization of fruit ripening in sweet cherry, revealing new positive traits of the HS somaclonal variant.
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Affiliation(s)
- Bhakti Prinsi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), Università degli Studi di Milano , Via Celoria 2, 20133 Milano, Italy
| | - Alfredo S Negri
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), Università degli Studi di Milano , Via Celoria 2, 20133 Milano, Italy
| | - Luca Espen
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), Università degli Studi di Milano , Via Celoria 2, 20133 Milano, Italy
| | - M Claudia Piagnani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), Università degli Studi di Milano , Via Celoria 2, 20133 Milano, Italy
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Nazir M, Pandey R, Siddiqi TO, Ibrahim MM, Qureshi MI, Abraham G, Vengavasi K, Ahmad A. Nitrogen-Deficiency Stress Induces Protein Expression Differentially in Low-N Tolerant and Low-N Sensitive Maize Genotypes. FRONTIERS IN PLANT SCIENCE 2016; 7:298. [PMID: 27047497 PMCID: PMC4800187 DOI: 10.3389/fpls.2016.00298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/25/2016] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is essential for proper plant growth and its application has proven to be critical for agricultural produce. However, for unavoidable economic and environmental problems associated with excessive use of N-fertilizers, it is an urgent demand to manage application of fertilizers. Improving the N-use efficiency (NUE) of crop plants to sustain productivity even at low N levels is the possible solution. In the present investigation, contrasting low-N sensitive (HM-4) and low-N tolerant (PEHM-2) genotypes were identified and used for comparative proteome-profiling of leaves under optimum and low N as well as restoration of low N on 3rd (NR3) and 5th (NR5) days after re-supplying N. The analysis of differential expression pattern of proteins was performed by 2-D gel electrophoresis. Significant variations in the expression of proteins were observed under low N, which were genotype specific. In the leaf proteome, 25 spots were influenced by N treatment and four spots were different between the two genotypes. Most of the proteins that were differentially accumulated in response to N level and were involved in photosynthesis and metabolism, affirming the relationship between N and carbon metabolism. In addition to this, greater intensity of some defense proteins in the low N tolerant genotype was found that may have a possible role in imparting it tolerance under N starvation conditions. The new insights generated on maize proteome in response to N-starvation and restoration would be useful toward improvement of NUE in maize.
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Affiliation(s)
- Muslima Nazir
- Department of Botany, Faculty of Science, Jamia HamdardNew Delhi, India
| | - Renu Pandey
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Tariq O. Siddiqi
- Department of Botany, Faculty of Science, Jamia HamdardNew Delhi, India
| | - Mohamed M. Ibrahim
- Department of Botany and Microbiology, Science College, King Saud UniversityRiyadh, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Alexandria UniversityAlexandria, Egypt
| | - Mohammad I. Qureshi
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia IslamiaNew Delhi, India
| | - Gerard Abraham
- Centre for Conservation and Utilization of Blue Green Algae, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Krishnapriya Vengavasi
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim UniversityAligarh, India
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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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Prinsi B, Negri AS, Quattrocchio FM, Koes RE, Espen L. Proteomics of red and white corolla limbs in petunia reveals a novel function of the anthocyanin regulator ANTHOCYANIN1 in determining flower longevity. J Proteomics 2016; 131:38-47. [DOI: 10.1016/j.jprot.2015.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/23/2015] [Accepted: 10/08/2015] [Indexed: 01/11/2023]
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Gong F, Yang L, Tai F, Hu X, Wang W. "Omics" of maize stress response for sustainable food production: opportunities and challenges. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:714-32. [PMID: 25401749 DOI: 10.1089/omi.2014.0125] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.
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Affiliation(s)
- Fangping Gong
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Science, Henan Agricultural University , Zhengzhou, China
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Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y. MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice. PLoS One 2015; 10:e0135196. [PMID: 26258667 PMCID: PMC4530940 DOI: 10.1371/journal.pone.0135196] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/19/2015] [Indexed: 12/30/2022] Open
Abstract
MADS-box transcription factors are vital regulators participating in plant growth and development process and the functions of most of them are still unknown. ANR1 was reported to play a key role in controlling lateral root development through nitrate signal in Arabidopsis. OsMADS25 is one of five ANR1-like genes in Oryza Sativa and belongs to the ANR1 clade. Here we have investigated the role of OsMADS25 in the plant’s responses to external nitrate in Oryza Sativa. Our results showed that OsMADS25 protein was found in the nucleus as well as in the cytoplasm. Over-expression of OsMADS25 significantly promoted lateral and primary root growth as well as shoot growth in a nitrate-dependent manner in Arabidopsis. OsMADS25 overexpression in transgenic rice resulted in significantly increased primary root length, lateral root number, lateral root length and shoot fresh weight in the presence of nitrate. Down-regulation of OsMADS25 in transgenic rice exhibited significantly reduced shoot and root growth in the presence of nitrate. Furthermore, over-expression of OsMADS25 in transgenic rice promoted nitrate accumulation and significantly increased the expressions of nitrate transporter genes at high rates of nitrate supply while down-regulation of OsMADS25 produced the opposite effect. Taken together, our findings suggest that OsMADS25 is a positive regulator control lateral and primary root development in rice.
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Affiliation(s)
- Chunyan Yu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yihua Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Aidong Zhang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sha Su
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - An Yan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Linli Huang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Ali
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Brian G. Forde
- Centre for Sustainable Agriculture, Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail:
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Nie L, Feng J, Fan P, Chen X, Guo J, Lv S, Bao H, Jia W, Tai F, Jiang P, Wang J, Li Y. Comparative proteomics of root plasma membrane proteins reveals the involvement of calcium signalling in NaCl-facilitated nitrate uptake in Salicornia europaea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4497-510. [PMID: 25956883 PMCID: PMC4507759 DOI: 10.1093/jxb/erv216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Improving crop nitrogen (N) use efficiency under salinity is essential for the development of sustainable agriculture in marginal lands. Salicornia europaea is a succulent euhalophyte that can survive under high salinity and N-deficient habitat conditions, implying that a special N assimilation mechanism may exist in this plant. In this study, phenotypic and physiological changes of S. europaea were investigated under different nitrate and NaCl levels. The results showed that NaCl had a synergetic effect with nitrate on the growth of S. europaea. In addition, the shoot nitrate concentration and nitrate uptake rate of S. europaea were increased by NaCl treatment under both low N and high N conditions, suggesting that nitrate uptake in S. europaea was NaCl facilitated. Comparative proteomic analysis of root plasma membrane (PM) proteins revealed 81 proteins, whose abundance changed significantly in response to NaCl and nitrate. These proteins are involved in metabolism, cell signalling, transport, protein folding, membrane trafficking, and cell structure. Among them, eight proteins were calcium signalling components, and the accumulation of seven of the above-mentioned proteins was significantly elevated by NaCl treatment. Furthermore, cytosolic Ca(2+) concentration ([Ca(2+)]cyt) was significantly elevated in S. europaea under NaCl treatment. The application of the Ca(2+) channel blocker LaCl3 not only caused a decrease in nitrate uptake rate, but also attenuated the promoting effects of NaCl on nitrate uptake rates. Based on these results, a possible regulatory network of NaCl-facilitated nitrate uptake in S. europaea focusing on the involvement of Ca(2+) signalling was proposed.
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Affiliation(s)
- Lingling Nie
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Pengxiang Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - Xianyang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Hexigeduleng Bao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China Shanghai Center for Plant Stress Biology (PSC), Chinese Academy of Sciences, No. 3888 Chenhua Road, Songjiang District, Shanghai 201602, PR China
| | - Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
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Microscopic and proteomic analysis of Zea mays roots (P30F53 variety) inoculated with Azospirillum brasilense strain FP2. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s12892-014-0061-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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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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Rogato A, Amato A, Iudicone D, Chiurazzi M, Ferrante MI, d'Alcalà MR. The diatom molecular toolkit to handle nitrogen uptake. Mar Genomics 2015; 24 Pt 1:95-108. [PMID: 26055207 DOI: 10.1016/j.margen.2015.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/26/2015] [Accepted: 05/26/2015] [Indexed: 11/16/2022]
Abstract
Nutrient concentrations in the oceans display significant temporal and spatial variability, which strongly affects growth, distribution and survival of phytoplankton. Nitrogen (N) in particular is often considered a limiting resource for prominent marine microalgae, such as diatoms. Diatoms possess a suite of N-related transporters and enzymes and utilize a variety of inorganic (e.g., nitrate, NO3(-); ammonium, NH4(+)) and organic (e.g., urea; amino acids) N sources for growth. However, the molecular mechanisms allowing diatoms to cope efficiently with N oscillations by controlling uptake capacities and signaling pathways involved in the perception of external and internal clues remain largely unknown. Data reported in the literature suggest that the regulation and the characteristic of the genes, and their products, involved in N metabolism are often diatom-specific, which correlates with the peculiar physiology of these organisms for what N utilization concerns. Our study reveals that diatoms host a larger suite of N transporters than one would expected for a unicellular organism, which may warrant flexible responses to variable conditions, possibly also correlated to the phases of life cycle of the cells. All this makes N transporters a crucial key to reveal the balance between proximate and ultimate factors in diatom life.
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Affiliation(s)
- Alessandra Rogato
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy.
| | - Alberto Amato
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy.
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
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Liu H, Sultan MARF, Liu XL, Zhang J, Yu F, Zhao HX. Physiological and comparative proteomic analysis reveals different drought responses in roots and leaves of drought-tolerant wild wheat (Triticum boeoticum). PLoS One 2015; 10:e0121852. [PMID: 25859656 PMCID: PMC4393031 DOI: 10.1371/journal.pone.0121852] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum), physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control), 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA) level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs) (corresponding to 87 and 80 unique proteins, respectively) in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism was down-regulated in the roots, but enhanced in the leaves. These results will contribute to the existing knowledge on the complexity of root and leaf protein changes that occur in response to drought, and also provide a framework for further functional studies on the identified proteins.
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Affiliation(s)
- Hui Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | | | - Xiang li Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hui xian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
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Prinsi B, Espen L. Mineral nitrogen sources differently affect root glutamine synthetase isoforms and amino acid balance among organs in maize. BMC PLANT BIOLOGY 2015; 15:96. [PMID: 25886826 PMCID: PMC4393875 DOI: 10.1186/s12870-015-0482-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/24/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Glutamine synthetase (GS) catalyzes the first step of nitrogen assimilation in plant cell. The main GS are classified as cytosolic GS1 and plastidial GS2, of which the functionality is variable according to the nitrogen sources, organs and developmental stages. In maize (Zea mays L.) one gene for GS2 and five genes for GS1 subunits are known, but their roles in root metabolism are not yet well defined. In this work, proteomic and biochemical approaches have been used to study root GS enzymes and nitrogen assimilation in maize plants re-supplied with nitrate, ammonium or both. RESULTS The plant metabolic status highlighted the relevance of root system in maize nitrogen assimilation during both nitrate and ammonium nutrition. The analysis of root proteomes allowed a study to be made of the accumulation and phosphorylation of six GS proteins. Three forms of GS2 were identified, among which only the phosphorylated one showed an accumulation trend consistent with plastidial GS activity. Nitrogen availabilities enabled increments in root total GS synthetase activity, associated with different GS1 isoforms according to the nitrogen sources. Nitrate nutrition induced the specific accumulation of GS1-5 while ammonium led to up-accumulation of both GS1-1 and GS1-5, highlighting co-participation. Moreover, the changes in thermal sensitivity of root GS transferase activity suggested differential rearrangements of the native enzyme. The amino acid accumulation and composition in roots, xylem sap and leaves deeply changed in response to mineral sources. Glutamine showed the prevalent changes in all nitrogen nutritions. Besides, the ammonium nutrition was associated with an accumulation of asparagine and reducing sugars and a drop in glutamic acid level, significantly alleviated by the co-provision with nitrate. CONCLUSION This work provides new information about the multifaceted regulation of the GS enzyme in maize roots, indicating the involvement of specific isoenzymes/isoforms, post-translational events and biochemical factors. For the first time, the proteomic approach allowed to discriminate the individual contribution of the GS1 isoforms, highlighting the participation of GS1-5 in nitrate metabolism. Moreover, the results give new insights about the influence of amino acid metabolism in plant C/N balance.
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Affiliation(s)
- Bhakti Prinsi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DISAA), Università degli Studi di Milano, Via Celoria, 2, 20133, Milano, Italy.
| | - Luca Espen
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DISAA), Università degli Studi di Milano, Via Celoria, 2, 20133, Milano, Italy.
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Wei S, Wang X, Zhang J, Liu P, Zhao B, Li G, Dong S. The role of nitrogen in leaf senescence of summer maize and analysis of underlying mechanisms using comparative proteomics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:72-81. [PMID: 25711815 DOI: 10.1016/j.plantsci.2015.01.002] [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] [Received: 10/12/2014] [Revised: 12/29/2014] [Accepted: 01/03/2015] [Indexed: 05/24/2023]
Abstract
Leaf senescence is associated with fundamental changes on the level of the proteome and it can be modulated by nitrogen. To determine the precise regulatory mechanisms underlying these effects, we conducted a comparative proteomics study using 2-dimensional gel electrophoresis and MALDI-TOF/TOF MS. Based on our study of the maize leaf proteome, leaf senescence induces complex responses including the degradation of 32 senescence-associated proteins that are involved in many biological processes, especially energy, metabolism and cell rescue, defense and virulence pathways. Although similar conclusions have been highlighted in other crops, this study filled the knowledge gap in maize leaf senescence. Moreover, we discovered, for the first time, 29 "nitrogen-regulated senescence proteins" had significant (P≤0.05) interaction term for nitrogen×stage. Although further study of nitrogen-related senescence proteins, such as 30S ribosomal protein, will be required to fully elucidate their complex functions, the surprising results in our study provide a new vision to research the relationship between nitrogen and senescence.
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Affiliation(s)
- Shanshan Wei
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Xiangyu Wang
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Jiwang Zhang
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Peng Liu
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Bin Zhao
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Geng Li
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China
| | - Shuting Dong
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai-an, Shandong 271018, PR China.
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Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wüthrich S, Blösch R, Rindisbacher A, Rafudeen S, Tadele Z. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]. FRONTIERS IN PLANT SCIENCE 2015; 6:177. [PMID: 25859251 PMCID: PMC4374454 DOI: 10.3389/fpls.2015.00177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/05/2015] [Indexed: 05/26/2023]
Abstract
Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.
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Affiliation(s)
- Kebebew Assefa
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Gina Cannarozzi
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Dejene Girma
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
- National Agricultural Biotechnology Laboratory, Holetta Agricultural Research Center, Ethiopian Institute of Agricultural ResearchHoletta, Ethiopia
| | - Rizqah Kamies
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Solomon Chanyalew
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Sonia Plaza-Wüthrich
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Regula Blösch
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Abiel Rindisbacher
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Suhail Rafudeen
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Zerihun Tadele
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
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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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Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Quilleré I, Tercé-Laforgue T, Dargel-Graffin C, Hirel B. An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase. BMC Genomics 2014; 15:1005. [PMID: 25410248 PMCID: PMC4247748 DOI: 10.1186/1471-2164-15-1005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022] Open
Abstract
Background To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. Results The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the “omics” considered at the vegetative stage of plant development, or during the grain filling period. Conclusions This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three “omics” procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1005) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique 3559, RD10, F-78026 Versailles, Cedex, France.
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Zamboni A, Astolfi S, Zuchi S, Pii Y, Guardini K, Tononi P, Varanini Z. Nitrate induction triggers different transcriptional changes in a high and a low nitrogen use efficiency maize inbred line. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:1080-94. [PMID: 24805158 DOI: 10.1111/jipb.12214] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/05/2014] [Indexed: 05/07/2023]
Abstract
In higher plants, NO3(-) can induce its own uptake and the magnitude of this induction is positively related to the external anion concentration. This phenomenon has been characterized in both herbaceous and woody plants. Here, different adaptation strategies of roots from two maize (Zea mays L., ZmAGOs) inbred lines differing in nitrogen use efficiency (NUE) and exhibiting different timing of induction were discussed by investigating NO3(-) -induced changes in their transcriptome. Lo5 line (high NUE) showing the maximum rate of NO3(-) uptake 4 h after the provision of 200 μmol/L NO3(-) treatment modulated a higher number of transcripts relative to T250 (low NUE) that peaked after 12 h. The two inbred lines share only 368 transcripts that are modulated by the treatment with NO3(-) and behaved differently when transcripts involved in anion uptake and assimilation were analyzed. T250 line responded to the NO3(-) induction modulating this group of genes as reported for several plant species. On the contrary, the Lo5 line did not exhibit during the induction changes in this set of genes. Obtained data suggest the importance of exploring the physiological and molecular variations among different maize genotypes in response to environmental clues like NO3(-) provision, in order to understand mechanisms underlying NUE.
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Affiliation(s)
- Anita Zamboni
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
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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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Expressed Proteins of Herbaspirillum seropedicae in Maize (DKB240) Roots-Bacteria Interaction Revealed Using Proteomics. Appl Biochem Biotechnol 2014; 174:2267-77. [DOI: 10.1007/s12010-014-1197-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/22/2014] [Indexed: 12/22/2022]
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Deng G, Liu LJ, Zhong XY, Lao CY, Wang HY, Wang B, Zhu C, Shah F, Peng DX. Comparative proteome analysis of the response of ramie under N, P and K deficiency. PLANTA 2014; 239:1175-86. [PMID: 24573224 DOI: 10.1007/s00425-014-2040-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/03/2014] [Indexed: 05/08/2023]
Abstract
Ramie is an important natural fiber. There has been little research on the molecular mechanisms of ramie related to the absorption, utilization and metabolism of nitrogen (N), phosphorus (P) and potassium (K). One approach to reveal the mechanisms of N, P and K (NPK) utilization and metabolism in ramie is comparative proteome analysis. The differentially expressed proteins in the leaves of ramie were analyzed by proteome analysis after 6 days of N- and K-deficient treatments and 3 days of P-deficient treatment using MALDI-TOF/TOF mass spectrometry and 32, 27 and 51 differential proteins were obtained, respectively. These proteins were involved in photosynthesis, protein destination and storage, energy metabolism, primary metabolism, disease/defense, signal transduction, cell structure, transcription, secondary metabolism and protein synthesis. Ramie responded to NPK stress by enhancing secondary metabolism and reducing photosynthesis and energy metabolism to increase endurance. Specifically, ramie adapted to NPK deficiency by increasing signal transduction pathways, enhancing the connection between glycolysis and photosynthesis, promoting the intracellular flow of carbon and N; promoting the synthesis cysteine and related hormones and upregulating actin protein to promote growth of the root system. The experimental results provide important information for further study on the high-efficiency NPK utilization mechanism of ramie.
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Affiliation(s)
- Gang Deng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Ghashghaie J, Badeck FW. Opposite carbon isotope discrimination during dark respiration in leaves versus roots - a review. THE NEW PHYTOLOGIST 2014; 201:751-769. [PMID: 24251924 DOI: 10.1111/nph.12563] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/15/2013] [Indexed: 05/13/2023]
Abstract
In general, leaves are (13) C-depleted compared with all other organs (e.g. roots, stem/trunk and fruits). Different hypotheses are formulated in the literature to explain this difference. One of these states that CO2 respired by leaves in the dark is (13) C-enriched compared with leaf organic matter, while it is (13) C-depleted in the case of root respiration. The opposite respiratory fractionation between leaves and roots was invoked as an explanation for the widespread between-organ isotopic differences. After summarizing the basics of photosynthetic and post-photosynthetic discrimination, we mainly review the recent findings on the isotopic composition of CO2 respired by leaves (autotrophic organs) and roots (heterotrophic organs) compared with respective plant material (i.e. apparent respiratory fractionation) as well as its metabolic origin. The potential impact of such fractionation on the isotopic signal of organic matter (OM) is discussed. Some perspectives for future studies are also proposed .
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Affiliation(s)
- Jaleh Ghashghaie
- Laboratoire d'Ecologie, Systématique et Evolution (ESE), CNRS UMR8079, Bâtiment 362, Université de Paris-Sud (XI), F-91405, Orsay Cedex, France
| | - Franz W Badeck
- Consiglio per la Ricerca e la sperimentazione in Agricoltura, Genomics research centre (CRA - GPG), Via San Protaso, 302, 29017, Fiorenzuola d'Arda (PC), Italy
- Potsdam Institute for Climate Impact Research (PIK), PF 60 12 03, 14412, Potsdam, Germany
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Wang X, Tang D, Huang D. Proteomic analysis of pakchoi leaves and roots under glycine-nitrogen conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 75:96-104. [PMID: 24429133 DOI: 10.1016/j.plaphy.2013.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
The physiological and differential proteomic responses of pakchoi leaves and roots to glycine-nitrogen (Gly-N) treatments were determined. Two pakchoi (Brassica campestris ssp. chinensis L. Makino. var. communis Tsen et Lee) cultivars, 'Huawang' and 'Wuyueman', were grown under sterile hydroponic conditions with different N forms (Gly-N and nitrate-N). Gly-N-treated pakchoi exhibited decreased fresh weights, total N uptake, leaf areas, and net photosynthetic rates than those treated with nitrate-N. Differentially regulated proteins were selected after image analysis and identified using MALDI-TOF MS. A total of 23 proteins was up- or down-regulated following Gly-N treatment. These spots are involved in several processes, such as energy synthesis, N metabolism, photosynthesis, and active antioxidant defense mechanisms, that could enhance plant adaptation to Gly-N. The superior Gly tolerance of 'Huawang' was predominantly associated with a less severe down-regulation of proteins that are involved in the electron transport chain and N metabolism. Other factors could include less ribulose-1,5-bisphosphate carboxylase/oxygenase turnover or a higher up-regulation of stress defense proteins. These characteristics demonstrated that maintaining ATP synthesis, N metabolism, photosynthesis, and active defense mechanisms play a critical role in pakchoi adaptation to Gly-N.
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Affiliation(s)
- Xiaoli Wang
- Department of Horticulture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, PR China
| | - Dongmei Tang
- Department of Horticulture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, PR China
| | - Danfeng Huang
- Department of Horticulture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, PR China.
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Wang R, Gao F, Guo BQ, Huang JC, Wang L, Zhou YJ. Short-term chromium-stress-induced alterations in the maize leaf proteome. Int J Mol Sci 2013; 14:11125-44. [PMID: 23712354 PMCID: PMC3709723 DOI: 10.3390/ijms140611125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/25/2013] [Accepted: 05/15/2013] [Indexed: 11/16/2022] Open
Abstract
Soil contamination by chromium (Cr) has become an increasing problem worldwide as a result of extensive industrial activities. Chromium, especially hexavalent Cr, impairs the growth and productivity of plants. Although it has been proposed that plants could modify their metabolism to adapt to Cr stress by reprogramming the expression of genes, especially those related to the antioxidant system, damage response, and electron transport chain, evidence at the protein expression level is lacking. To better understand the precise mechanisms underlying Cr phytoxicity and the plant response to Cr exposure, the time-course of changes in the protein expression profile induced by short-term hexavalent Cr exposure (1, 6 and 24 h) were analyzed in maize leaves. Among the over 1200 protein spots detected reproducibly by two-dimensional electrophoresis (2-DE), 60 were found to be differentially accumulated during Cr stress treatment. Of the Cr-regulated proteins, 58 were identified using tandem mass spectrometry (MS/MS). The Cr-regulated proteins identified were mainly involved in ROS detoxification and defense responses (26%), photosynthesis and chloroplast organization (22%), post-transcriptional processing of mRNA and rRNA (12%), protein synthesis and folding (10%), the DNA damage response (5%), and the cytoskeleton (3%). The possible involvement of these Cr stress-responsive proteins in Cr phytoxicity and the plant response to Cr exposure in maize is discussed, taking into consideration the information available from other plant models. Our results provide preliminary evidence that will facilitate understanding the molecular mechanisms underlying Cr toxicity in maize.
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Affiliation(s)
- Rong Wang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing-Qian Guo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
| | - Ji-Chang Huang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Lei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
| | - Yi-Jun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
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50
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Shane MW, Fedosejevs ET, Plaxton WC. Reciprocal control of anaplerotic phosphoenolpyruvate carboxylase by in vivo monoubiquitination and phosphorylation in developing proteoid roots of phosphate-deficient harsh hakea. PLANT PHYSIOLOGY 2013; 161:1634-44. [PMID: 23407057 PMCID: PMC3613444 DOI: 10.1104/pp.112.213496] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 02/12/2013] [Indexed: 05/08/2023]
Abstract
Accumulating evidence indicates important functions for phosphoenolpyruvate (PEP) carboxylase (PEPC) in inorganic phosphate (Pi)-starved plants. This includes controlling the production of organic acid anions (malate, citrate) that are excreted in copious amounts by proteoid roots of nonmycorrhizal species such as harsh hakea (Hakea prostrata). This, in turn, enhances the bioavailability of mineral-bound Pi by solubilizing Al(3+), Fe(3+), and Ca(2+) phosphates in the rhizosphere. Harsh hakea thrives in the nutrient-impoverished, ancient soils of southwestern Australia. Proteoid roots from Pi-starved harsh hakea were analyzed over 20 d of development to correlate changes in malate and citrate exudation with PEPC activity, posttranslational modifications (inhibitory monoubiquitination versus activatory phosphorylation), and kinetic/allosteric properties. Immature proteoid roots contained an equivalent ratio of monoubiquitinated 110-kD and phosphorylated 107-kD PEPC polypeptides (p110 and p107, respectively). PEPC purification, immunoblotting, and mass spectrometry indicated that p110 and p107 are subunits of a 430-kD heterotetramer and that they both originate from the same plant-type PEPC gene. Incubation with a deubiquitinating enzyme converted the p110:p107 PEPC heterotetramer of immature proteoid roots into a p107 homotetramer while significantly increasing the enzyme's activity under suboptimal but physiologically relevant assay conditions. Proteoid root maturation was paralleled by PEPC activation (e.g. reduced Km [PEP] coupled with elevated I50 [malate and Asp] values) via in vivo deubiquitination of p110 to p107, and subsequent phosphorylation of the deubiquitinated subunits. This novel mechanism of posttranslational control is hypothesized to contribute to the massive synthesis and excretion of organic acid anions that dominates the carbon metabolism of the mature proteoid roots.
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Affiliation(s)
- Michael W Shane
- School of Plant Biology, Faculty of Science, University of Western Australia, Crawley, Western Australia 6009, Australia.
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