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Chang L, Jin X, Rao Y, Zhang X. Predicting abiotic stress-responsive miRNA in plants based on multi-source features fusion and graph neural network. PLANT METHODS 2024; 20:33. [PMID: 38402152 PMCID: PMC10894500 DOI: 10.1186/s13007-024-01158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND More and more studies show that miRNA plays a crucial role in plants' response to different abiotic stresses. However, traditional experimental methods are often expensive and inefficient, so it is important to develop efficient and economical computational methods. Although researchers have developed machine learning-based method, the information of miRNAs and abiotic stresses has not been fully exploited. Therefore, we propose a novel approach based on graph neural networks for predicting potential miRNA-abiotic stress associations. RESULTS In this study, we fully considered the multi-source feature information from miRNAs and abiotic stresses, and calculated and integrated the similarity network of miRNA and abiotic stress from different feature perspectives using multiple similarity measures. Then, the above multi-source similarity network and association information between miRNAs and abiotic stresses are effectively fused through heterogeneous networks. Subsequently, the Restart Random Walk (RWR) algorithm is employed to extract global structural information from heterogeneous networks, providing feature vectors for miRNA and abiotic stress. After that, we utilized the graph autoencoder based on GIN (Graph Isomorphism Networks) to learn and reconstruct a miRNA-abiotic stress association matrix to obtain potential miRNA-abiotic stress associations. The experimental results show that our model is superior to all known methods in predicting potential miRNA-abiotic stress associations, and the AUPR and AUC metrics of our model achieve 98.24% and 97.43%, respectively, under five-fold cross-validation. CONCLUSIONS The robustness and effectiveness of our proposed model position it as a valuable approach for advancing the field of miRNA-abiotic stress association prediction.
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Affiliation(s)
- Liming Chang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Xiu Jin
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Yuan Rao
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaodan Zhang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China.
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Mo Y, Li G, Liu L, Zhang Y, Li J, Yang M, Chen S, Lin Q, Fu G, Zheng D, Ling Y. OsGRF4AA compromises heat tolerance of developing pollen grains in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1121852. [PMID: 36909437 PMCID: PMC9992635 DOI: 10.3389/fpls.2023.1121852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA ), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.
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Affiliation(s)
- Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
| | - Guangyan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Meizhen Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Qiaoling Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Guanfu Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
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Gao H, Yu W, Yang X, Liang J, Sun X, Sun M, Xiao Y, Peng F. Silicon enhances the drought resistance of peach seedlings by regulating hormone, amino acid, and sugar metabolism. BMC PLANT BIOLOGY 2022; 22:422. [PMID: 36045325 PMCID: PMC9434905 DOI: 10.1186/s12870-022-03785-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Drought is one of the main concerns worldwide and restricts the development of agriculture. Silicon improves the drought resistance of plants, but the underlying mechanism remains unclear. RESULTS We sequenced the transcriptomes of both control and silicon-treated peach seedlings under drought stress to identify genes or gene networks that could be managed to increase the drought tolerance of peach seedlings. Peach (Prunus persica) seedlings were used to analyse the effects of silicon on plant growth and physiological indexes related to drought resistance under drought stress. The results showed that silicon addition improved the water use efficiency, antioxidant capacity, and net photosynthetic rate, inhibition of stomatal closure, promoted the development of roots, and further regulated the synthesis of hormones, amino acids and sugars in peach seedlings. A comparative transcriptome analysis identified a total of 2275 genes that respond to silicon under drought stress. These genes were mainly involved in ion transport, hormone and signal transduction, biosynthetic and metabolic processes, stress and defence responses and other processes. We analysed the effects of silicon on the modulation of stress-related hormonal crosstalk and amino acid and sugar metabolism. The results showed that silicon promotes zeatin, gibberellin, and auxin biosynthesis, inhibits the synthesis of abscisic acid, then promote lateral root development and inhibit stomatal closure, and regulates the signal transduction of auxin, cytokinin, gibberellin and salicylic acid. Silicon also regulates the metabolism of various amino acids and promotes the accumulation of sucrose and glucose to improve drought resistance of peach seedlings. CONCLUSIONS Silicon enhanced the drought resistance of peach seedlings by regulating stress-related hormone synthesis and signal transduction, and regulating amino acid and sugar metabolism.
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Affiliation(s)
- Huaifeng Gao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Wenying Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Xiaoqing Yang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Jiahui Liang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Xiwu Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Maoxiang Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China.
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China.
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ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features. Int J Mol Sci 2022; 23:ijms23031612. [PMID: 35163534 PMCID: PMC8835813 DOI: 10.3390/ijms23031612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational method for prediction of miRNAs associated with abiotic stresses. Three types of datasets were used for prediction, i.e., miRNA, Pre-miRNA, and Pre-miRNA + miRNA. The pseudo K-tuple nucleotide compositional features were generated for each sequence to transform the sequence data into numeric feature vectors. Support vector machine (SVM) was employed for prediction. The area under receiver operating characteristics curve (auROC) of 70.21, 69.71, 77.94 and area under precision-recall curve (auPRC) of 69.96, 65.64, 77.32 percentages were obtained for miRNA, Pre-miRNA, and Pre-miRNA + miRNA datasets, respectively. Overall prediction accuracies for the independent test set were 62.33, 64.85, 69.21 percentages, respectively, for the three datasets. The SVM also achieved higher accuracy than other learning methods such as random forest, extreme gradient boosting, and adaptive boosting. To implement our method with ease, an online prediction server “ASRmiRNA” has been developed. The proposed approach is believed to supplement the existing effort for identification of abiotic stress-responsive miRNAs and Pre-miRNAs.
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Ji C, Li J, Jiang C, Zhang L, Shi L, Xu F, Cai H. Zinc and nitrogen synergistic act on root-to-shoot translocation and preferential distribution in rice. J Adv Res 2022; 35:187-198. [PMID: 35003800 PMCID: PMC8721242 DOI: 10.1016/j.jare.2021.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/30/2022] Open
Abstract
Zn promoted translocation and distribution of N into leaves and brown rice. Zn induced the expression levels of N transporter genes in both root and shoot. Zn increased the N assimilation level in leaves. N promoted translocation and distribution of Zn into leaves and brown rice. N up-regulated the expression levels of Zn transporter genes in both root and shoot.
Introduction Multiple studies have shown strong relationships between different nutrients in plants, and the important role of N in Zn acquisition and translocation has been recognized. Objectives The aim of this study was to estimate the effect of Zn on N uptake, translocation, and distribution in rice as well as the corresponding molecular mechanisms. We also aimed to evaluate the impact of N on the Zn content in rice grains which is closely related to the Zn nutrition in humans with rice-based diets. Methods We conducted both field trials and hydroponic cultures of two rice cultivars to analyze the growth and yield, the uptake, translocation, and distribution of N and Zn, as well as the expression of N transport and assimilation genes, and the Zn transporter genes under different combined applications of N and Zn. Results Zn supply promoted the root-to-shoot translocation (12–70% increasing) and distribution of N into the leaves (19–49% increasing) and brown rice (6–9% increasing) and increased the rice biomass (by 14–35%) and yield (by 13–63%). Zn supply induced the expression of OsNRTs and OsAMTs in both roots and shoots, but repressed the expression of OsNiR2, OsGS1;2, and OsFd-GOGAT in roots, whereas it activated the expression of OsNiR2, OsGS1;1, OsGS2, and OsFd-GOGAT in the shoots. Moreover, the enzyme activities of nitrite reductase, nitrate reductase, and glutamine synthetase increased and the free NO3– concentration decreased, but the soluble protein concentration increased significantly in the shoots after Zn supply. Synergistically, N significantly facilitated the root-to-shoot translocation (1.68–11.66 fold) and distribution of Zn into the leaves (1.68–6.37 fold) and brown rice (7–12% increasing) and upregulated the expression levels of Zn transporter genes in both the roots and shoots. Conclusions We propose a working model of the cross-talk between Zn and N in rice plants, which will aid in the appropriate combined application of Zn and N fertilizers in the field to improve both N utilization in plants and Zn nutrition in humans with rice-based diets.
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Key Words
- AMT, ammonium transporter
- Distribution
- GLY, Guangliangyou 35
- GOGAT, glutamate synthase
- GS, glutamine synthetase
- Interaction
- N, nitrogen
- NR, nitrate reductase
- NRT, nitrate transporter
- NiR, nitrite reductase
- Nip, Nipponbare
- Nitrogen
- Rice
- Translocation
- ZIP, ZRT, IRT-like protein
- Zinc
- Zn, Zinc
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Affiliation(s)
- Chenchen Ji
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Li
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author.
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Zhu M, He Y, Zhu M, Ahmad A, Xu S, He Z, Jiang S, Huang J, Li Z, Liu S, Hou X, Zhang Z. ipa1 improves rice drought tolerance at seedling stage mainly through activating abscisic acid pathway. PLANT CELL REPORTS 2022; 41:221-232. [PMID: 34694441 DOI: 10.1007/s00299-021-02804-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE: ipa1 enhances rice drought tolerance mainly through activating the ABA pathway. It endows rice seedlings with a more developed root system, smaller leaf stomata aperture, and enhanced carbon metabolism. Drought is a major abiotic stress to crop production. IPA1 (IDEAL PLANT ARCHITECTURE 1)/OsSPL14 encodes a transcription factor and has been reported to function in both rice ideal plant architecture and biotic resistance. Here, with a pair of IPA1 and ipa1-NILs (Near Iso-genic Lines), we found that ipa1 could significantly improve rice drought tolerance at seedling stage. The ipa1 plants had a better-developed root system and smaller leaf stomatal aperture. Analysis of carbon-nitrogen metabolism-associated enzyme activity, gene expression, and metabolic profile indicated that ipa1 could tip the carbon-nitrogen metabolism balance towards an increased carbon metabolism pattern. In both the control and PEG-treated conditions, ABA content in the ipa1 seedlings was significantly higher than that in the IPA1 seedlings. Expression of the ABA biosynthesis genes was detected to be up-regulated, whereas the expression of ABA catabolism genes was down-regulated in the ipa1 seedlings. In addition, based on yeast one-hybrid assay and dual-luciferase assay, IPA1 was found to directly activate the promoter activity of OsHOX12, a transcription factor promoting ABA biosynthesis, and OsNAC52, a positive regulator of the ABA pathway. The expression of OsHOX12 and OsNAC52 was significantly up-regulated in the ipa1 plants. Combined with the previous studies, our results suggested that ipa1 could improve rice seedling drought tolerance mainly through activating the ABA pathway and that regulation of the ipa1-mediated ABA pathway will be an important strategy for improving drought resistance of rice.
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Affiliation(s)
- Menghao Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Yonggang He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Mingqiang Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ayaz Ahmad
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shuang Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zijun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shan Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinqiu Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shaojia Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Xin Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihong Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China.
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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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Wang D, Xu T, Yin Z, Wu W, Geng H, Li L, Yang M, Cai H, Lian X. Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition. FRONTIERS IN PLANT SCIENCE 2020; 11:369. [PMID: 32351516 PMCID: PMC7174616 DOI: 10.3389/fpls.2020.00369] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/13/2020] [Indexed: 05/10/2023]
Abstract
Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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Alves LC, Llerena JPP, Mazzafera P, Vicentini R. Diel oscillations in cell wall components and soluble sugars as a response to short-day in sugarcane (Saccharum sp.). BMC PLANT BIOLOGY 2019; 19:215. [PMID: 31122198 PMCID: PMC6533765 DOI: 10.1186/s12870-019-1837-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 05/17/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sugarcane is a tropical crop that can accumulate high concentration of sucrose in the stem as a storage carbohydrate. For that reason, sugarcane accounts for approximately 75% of all the sugar produced in the world and has become the main sugar source to produce first-generation bioethanol in Brazil. Daily rhythms cause plants to adapt and coordinate their metabolism to achieve maximum photosynthesis and carbohydrate production throughout the day. Circadian rhythms arise from the interaction of an internal oscillator and external stimuli, whereas diel rhythms occur in response to a light-dark cycle. Diel signalling contributes to synchronizing circadian rhythms to photoperiods, and levels of carbohydrates oscillate in a diel fashion. Under regular photoperiods, they are synthesized during the daytime and consumed throughout the night as an energy reserve. However, short days can induce higher rates of synthesis during daytime and lower rates of consumption in the dark. Cell wall carbohydrates are also diurnally regulated, and it has been shown that celluloses, hemicelluloses and pectin are deposited/degraded at different times of the day. To assess the diel carbohydrate profile in young sugarcane plants, we measured soluble sugars and cell wall components along a time course in plants subjected either to a regular day or short day. RESULTS Short-day influenced sucrose synthesis and cell wall components. In short-day a 44% increase in sucrose concentration was detected in the dark, but was stable during the day. Cellulose, hemicellulose and pectin also fluctuate within a 24 h interval when subjected to a short day. A 38% increase in leaf sheath cellulose was observed from the middle of the day to the first hour of the night. Leaf sheath pectin and hemicellulose also increased from the day to the night, while it decreased in leaves. CONCLUSIONS The presented data show diurnal patterns of soluble sugar metabolism together with temporal regulation of cell wall metabolism for a short day, suggesting that diel signalling has a role in how sugarcane manages sugar accumulation and partitioning. Understanding cell wall synthesis/degradation dynamics may help to improve the yield of sugarcane.
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Affiliation(s)
- Leonardo Cardoso Alves
- Bioinformatics and Systems Biology Laboratory, Department of Genetics and Evolution and Bioagents, University of Campinas, Campinas, SP Brazil
| | | | - Paulo Mazzafera
- Department of Plant Biology, University of Campinas, Campinas, SP Brazil
- Crop Science Department, College of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Renato Vicentini
- Bioinformatics and Systems Biology Laboratory, Department of Genetics and Evolution and Bioagents, University of Campinas, Campinas, SP Brazil
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Sánchez-Retuerta C, Suaréz-López P, Henriques R. Under a New Light: Regulation of Light-Dependent Pathways by Non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2018; 9:962. [PMID: 30140270 PMCID: PMC6095000 DOI: 10.3389/fpls.2018.00962] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/14/2018] [Indexed: 05/18/2023]
Abstract
The biological relevance of non-protein coding RNAs in the regulation of critical plant processes has been firmly established in recent years. This has been mostly achieved with the discovery and functional characterization of small non-coding RNAs, such as small interfering RNAs and microRNAs (miRNAs). However, recent next-generation sequencing techniques have widened our view of the non-coding RNA world, which now includes long non-coding RNAs (lncRNAs). Small and lncRNAs seem to diverge in their biogenesis and mode of action, but growing evidence highlights their relevance in developmental processes and in responses to particular environmental conditions. Light can affect MIRNA gene transcription, miRNA biogenesis, and RNA-induced silencing complex (RISC) activity, thus controlling not only miRNA accumulation but also their biological function. In addition, miRNAs can mediate several light-regulated processes. In the lncRNA world, few reports are available, but they already indicate a role in the regulation of photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering. In this review, we will discuss how light controls MIRNA gene expression and the accumulation of their mature forms, with a particular emphasis on those miRNAs that respond to different light qualities and are conserved among species. We will also address the role of small non-coding RNAs, particularly miRNAs, and lncRNAs in the regulation of light-dependent pathways. We will mainly focus on the recent progress done in understanding the interconnection between these non-coding RNAs and photomorphogenesis, circadian clock function, and photoperiod-dependent flowering.
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Affiliation(s)
| | - Paula Suaréz-López
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Rossana Henriques
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
- *Correspondence: Rossana Henriques,
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Carlsson J, Svennerstam H, Moritz T, Egertsdotter U, Ganeteg U. Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine. PLoS One 2017; 12:e0181785. [PMID: 28837647 PMCID: PMC5570297 DOI: 10.1371/journal.pone.0181785] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/06/2017] [Indexed: 02/06/2023] Open
Abstract
Somatic embryogenesis is an in vitro system employed for plant propagation and the study of embryo development. Nitrogen is essential for plant growth and development and, hence, the production of healthy embryos during somatic embryogenesis. Glutamine has been shown to increase plant biomass in many in vitro applications, including somatic embryogenesis. However, several aspects of nitrogen nutrition during somatic embryogenesis remain unclear. Therefore, we investigated the uptake and assimilation of nitrogen in Norway spruce pro-embryogenic masses to elucidate some of these aspects. In our study, addition of glutamine had a more positive effect on growth than inorganic nitrogen. The nitrogen uptake appeared to be regulated, with a strong preference for glutamine; 67% of the assimilated nitrogen in the free amino acid pool originated from glutamine-nitrogen. Glutamine addition also relieved the apparently limited metabolism (as evidenced by the low concentration of free amino acids) of pro-embryogenic masses grown on inorganic nitrogen only. The unusually high alanine concentration in the presence of glutamine, suggests that alanine biosynthesis was involved in alleviating these constraints. These findings inspire further studies of nitrogen nutrition during the somatic embryogenesis process; identifying the mechanism(s) that govern glutamine enhancement of pro-embryogenic masses growth is especially important in this regard.
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Affiliation(s)
- Johanna Carlsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Svenska Skogsplantor AB, Seed Production, Lagan, Sweden
| | - Henrik Svennerstam
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ulrika Egertsdotter
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, United States of America
| | - Ulrika Ganeteg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Biosensor-Mediated In Situ Imaging Defines the Availability Period of Assimilatory Glutamine in Maize Seedling Leaves Following Nitrogen Fertilization. NITROGEN 2017. [DOI: 10.3390/nitrogen1010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The amino acid glutamine (Gln) is an important assimilatory intermediate between root-derived inorganic nitrogen (N) (i.e., ammonium) and downstream macromolecules, and is a central regulator in plant N physiology. The timing of Gln accumulation after N uptake by roots has been well characterized. However, the duration of availability of accumulated Gln at a sink tissue has not been well defined. Measuring Gln availability would require temporal measurements of both Gln accumulation and its reciprocal depletion. Furthermore, as Gln varies spatially within a tissue, whole-organ in situ visualization would be valuable. Here, the accumulation and subsequent disappearance of Gln in maize seedling leaves (Zea mays L.) was imaged in situ throughout the 48 h after N application to roots of N-deprived plants. Free Gln was imaged by placing leaves onto agar embedded with bacterial biosensor cells (GlnLux) that emit luminescence in the presence of leaf-derived Gln. Seedling leaves 1, 2, and 3 were imaged simultaneously to measure Gln availability across tissues that potentially vary in N sink strength. The results show that following root N fertilization, free Gln accumulates and then disappears with an availability period of up to 24 h following peak accumulation. The availability period of Gln was similar in all seedling leaves, but the amount of accumulation was leaf specific. As Gln is not only a metabolic intermediate, but also a signaling molecule, the potential importance of regulating its temporal availability within plant tissues is discussed.
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