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Bo C, Liu M, You Q, Liu X, Zhu Y, Duan Y, Wang D, Xue T, Xue J. Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings. BMC Genomics 2024; 25:398. [PMID: 38654150 DOI: 10.1186/s12864-024-10318-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata that differed between heat-stress and room-temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, and catalytic and binding activities. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed between the two test conditions. According to the analysis, genes and miRNAs associated with the regulation of transcription, DNA template, transcription factor activity, and sequence-specific DNA binding pathways may play a major role in the resistance to heat stress in P. ternata. Integrated analysis of the transcriptome and miRNAome expression data revealed 41 high-confidence miRNA-mRNA pairs, forming 25 modules. MYB-like proteins and calcium-responsive transcription coactivators may play an integral role in heat-stress resistance in P. ternata. Additionally, the candidate genes and miRNAs were subjected to quantitative real-time polymerase chain reaction to validate their expression patterns. These results offer a foundation for future studies exploring the mechanisms and critical genes involved in heat-stress resistance in P. ternata.
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Affiliation(s)
- Chen Bo
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Mengmeng Liu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Qian You
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Xiao Liu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yanfang Zhu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yongbo Duan
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Dexin Wang
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, China.
| | - Tao Xue
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Jianping Xue
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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2
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Kawakatsu Y, Okada R, Hara M, Tsutsui H, Yanagisawa N, Higashiyama T, Arima A, Baba Y, Kurotani KI, Notaguchi M. Microfluidic Device for Simple Diagnosis of Plant Growth Condition by Detecting miRNAs from Filtered Plant Extracts. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0162. [PMID: 38572468 PMCID: PMC10988387 DOI: 10.34133/plantphenomics.0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Plants are exposed to a variety of environmental stress, and starvation of inorganic phosphorus can be a major constraint in crop production. In plants, in response to phosphate deficiency in soil, miR399, a type of microRNA (miRNA), is up-regulated. By detecting miR399, the early diagnosis of phosphorus deficiency stress in plants can be accomplished. However, general miRNA detection methods require complicated experimental manipulations. Therefore, simple and rapid miRNA detection methods are required for early plant nutritional diagnosis. For the simple detection of miR399, microfluidic technology is suitable for point-of-care applications because of its ability to detect target molecules in small amounts in a short time and with simple manipulation. In this study, we developed a microfluidic device to detect miRNAs from filtered plant extracts for the easy diagnosis of plant growth conditions. To fabricate the microfluidic device, verification of the amine-terminated glass as the basis of the device and the DNA probe immobilization method on the glass was conducted. In this device, the target miRNAs were detected by fluorescence of sandwich hybridization in a microfluidic channel. For plant stress diagnostics using a microfluidic device, we developed a protocol for miRNA detection by validating the sample preparation buffer, filtering, and signal amplification. Using this system, endogenous sly-miR399 in tomatoes, which is expressed in response to phosphorus deficiency, was detected before the appearance of stress symptoms. This early diagnosis system of plant growth conditions has a potential to improve food production and sustainability through cultivation management.
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Affiliation(s)
- Yaichi Kawakatsu
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Ryo Okada
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mitsuo Hara
- Department of Molecular and Macromolecular Chemistry,
Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiroki Tsutsui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Naoki Yanagisawa
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules,
Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules,
Nagoya University, Nagoya 464-8601, Japan
- Department of Biological Sciences,
Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering,
Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Botany,
Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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3
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Liu J, Ren Y, Sun Y, Yin Y, Han B, Zhang L, Song Y, Zhang Z, Xu Y, Fan D, Li J, Liu H, Ma C. Identification and Analysis of the MIR399 Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress. Int J Mol Sci 2024; 25:2979. [PMID: 38474225 PMCID: PMC10931670 DOI: 10.3390/ijms25052979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem-loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding.
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Affiliation(s)
- Jingjing Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yi Ren
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Yan Sun
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Yonggang Yin
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Bin Han
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Lipeng Zhang
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junpeng Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaifeng Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Pacheco R, Estrada-Navarrete G, Solis-Miranda J, Nava N, Juárez-Verdayes MA, Ortega-Ortega Y, Quinto C. A comprehensive, improved protocol for generating common bean (Phaseolus vulgaris L.) transgenic hairy roots and their use in reverse-genetics studies. PLoS One 2024; 19:e0294425. [PMID: 38381734 PMCID: PMC10880956 DOI: 10.1371/journal.pone.0294425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/23/2023] [Indexed: 02/23/2024] Open
Abstract
Generating transgenic hairy roots has been the preferred strategy for molecular studies in common bean (Phaseolus vulgaris L.), since generating stable knockout lines in this species is challenging. However, the number of plants producing hairy roots following the original protocol published in 2007 is usually low, which has impeded progress. Since its initial publication, the original protocol has been extensively modified, but these modifications have not been adequately or systematically reported, making it difficult to assess the reproducibility of the method. The protocol presented here is an update and expansion of the original method. Importantly, it includes new, critical steps for generating transgenic hairy roots and using them in molecular analyses based on reverse-genetics approaches. Using this protocol, the expression of two different genes, used as an example, was significantly increased or decreased in approximately 30% of the transformed plants. In addition, the promoter activity of a given gene was observed, and the infection process of rhizobia in transgenic hairy roots was monitored successfully. Thus, this improved protocol can be used to upregulate, downregulate, and perform promoter activity analysis of various genes in common bean transgenic hairy roots as well as to track rhizobia infection.
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Affiliation(s)
- Ronal Pacheco
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Georgina Estrada-Navarrete
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Solis-Miranda
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - MA Juárez-Verdayes
- Departamento de Ciencias Básica, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, México
| | - Yolanda Ortega-Ortega
- Departamento de Biociencias y Agrotecnología, Centro de Investigación Química Aplicada, Saltillo, Coahuila, México
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Ding Y, Li H, Liu X, Cheng X, Chen W, Wu M, Chen L, He J, Chao H, Jia H, Fu C, Li M. Multi-Omics Analysis Revealed the AGR-FC.C3 Locus of Brassica napus as a Novel Candidate for Controlling Petal Color. PLANTS (BASEL, SWITZERLAND) 2024; 13:507. [PMID: 38498487 PMCID: PMC10892695 DOI: 10.3390/plants13040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Variations in the petal color of Brassica napus are crucial for ornamental value, but the controlled loci for breeding remain to be unraveled. Here, we report a candidate locus, AGR-FC.C3, having conducted a bulked segregant analysis on a segregating population with different petal colors. Our results showed that the locus covers 9.46 Mb of the genome, harboring 951 genes. BnaC03.MYB4, BnaC03.MYB85, BnaC03.MYB73, BnaC03.MYB98, and BnaC03.MYB102 belonging to MYB TFs families that might regulate the petal color were observed. Next, a bulk RNA sequencing of white and orange-yellow petals on three development stages was performed to further identify the possible governed genes. The results revealed a total of 51 genes by overlapping the transcriptome data and the bulked segregant analysis data, and it was found that the expression of BnaC03.CCD4 was significantly up-regulated in the white petals at three development stages. Then, several novel candidate genes such as BnaC03.ENDO3, BnaC03.T22F8.180, BnaC03.F15C21.8, BnaC03.Q8GSI6, BnaC03.LSD1, BnaC03.MAP1Da, BnaC03.MAP1Db, and BnaC03G0739700ZS putative to controlling the petal color were identified through deeper analysis. Furthermo re, we have developed two molecular markers for the reported functional gene BnaC03.CCD4 to discriminate the white and orange-yellow petal colors. Our results provided a novel locus for breeding rapeseed with multi-color petals.
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Affiliation(s)
- Yiran Ding
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Xinmin Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Xin Cheng
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Wang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Mingli Wu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Liurong Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Haibo Jia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (Y.D.); (H.L.); (X.L.); (X.C.); (W.C.); (M.W.); (L.C.); (J.H.); (H.J.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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Zhou XW, Yao XD, He DX, Sun HX, Xie FT. Comparative physiological and transcriptomic analysis of two salt-tolerant soybean germplasms response to low phosphorus stress: role of phosphorus uptake and antioxidant capacity. BMC PLANT BIOLOGY 2023; 23:662. [PMID: 38124037 PMCID: PMC10731862 DOI: 10.1186/s12870-023-04677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Phosphorus (P) and salt stress are common abiotic stressors that limit crop growth and development, but the response mechanism of soybean to low phosphorus (LP) and salt (S) combined stress remains unclear. RESULTS In this study, two soybean germplasms with similar salt tolerance but contrasting P-efficiency, A74 (salt-tolerant and P-efficient) and A6 (salt-tolerant and P-inefficient), were selected as materials. By combining physiochemical and transcriptional analysis, we aimed to elucidate the mechanism by which soybean maintains high P-efficiency under salt stress. In total, 14,075 differentially expressed genes were identified through pairwise comparison. PageMan analysis subsequently revealed several significantly enriched categories in the LP vs. control (CK) or low phosphorus + salt (LPS) vs. S comparative combination when compared to A6, in the case of A74. These categories included genes involved in mitochondrial electron transport, secondary metabolism, stress, misc, transcription factors and transport. Additionally, weighted correlation network analysis identified two modules that were highly correlated with acid phosphatase and antioxidant enzyme activity. Citrate synthase gene (CS), acyl-coenzyme A oxidase4 gene (ACX), cytokinin dehydrogenase 7 gene (CKXs), and two-component response regulator ARR2 gene (ARR2) were identified as the most central hub genes in these two modules. CONCLUSION In summary, we have pinpointed the gene categories responsible for the LP response variations between the two salt-tolerant germplasms, which are mainly related to antioxidant, and P uptake process. Further, the discovery of the hub genes layed the foundation for further exploration of the molecular mechanism of salt-tolerant and P-efficient in soybean.
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Affiliation(s)
- Xiu-Wen Zhou
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xing-Dong Yao
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - De-Xin He
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - He-Xiang Sun
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Fu-Ti Xie
- Soybean Research Institute, Shenyang Agricultural University, Shenyang, China.
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7
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Parra-Aguilar TJ, Sarmiento-López LG, Santana O, Olivares JE, Pascual-Morales E, Jiménez-Jiménez S, Quero-Hostos A, Palacios-Martínez J, Chávez-Martínez AI, Cárdenas L. TETRASPANIN 8-1 from Phaseolus vulgaris plays a key role during mutualistic interactions. FRONTIERS IN PLANT SCIENCE 2023; 14:1152493. [PMID: 37465390 PMCID: PMC10352089 DOI: 10.3389/fpls.2023.1152493] [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: 01/27/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi and rhizobia form two of the most important plant-microbe associations for the assimilation of phosphorus (P) and nitrogen (N). Symbiont-derived signals are able to coordinate the infection process by triggering multiple responses in the plant root, such as calcium influxes and oscillations, increased reactive oxygen species (ROS), cytoskeletal rearrangements and altered gene expression. An examination was made of the role of tetraspanins, which are transmembrane proteins that self-organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking, and ROS generation. In plant cells, tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, plasmodesmata and hormonal regulation. Some plant tetraspanins, such as Arabidopsis thaliana TETRASPANIN 8 and TETRASPANIN 9 (AtTET8 and AtTET9) are associated with exosomes during inter-kingdom communication. In this study, a homolog of AtTET8, PvTET8-1, in common bean (Phaseolus vulgaris L. var. Negro Jamapa) was examined in roots during interactions with Rhizobium tropici and Rhizophagus irregularis. The promoter of PvTET8-1 contained several cis-acting regulatory DNA elements potentially related to mutualistic interactions, and PvTET8-1 was transcriptionally activated during AM fungal and rhizobial associations. Silencing it decreased the size and number of nodules, nitrogen fixation, and mycorrhizal arbuscule formation, whereas overexpressing it increased the size and number of nodules, and mycorrhizal arbuscule formation but decreased nitrogen fixation. PvTET8-1 appears to be an important element in both of these mutualistic interactions, perhaps through its interaction with NADPH oxidase and the generation of ROS during the infection processes.
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Affiliation(s)
- Thelma J. Parra-Aguilar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis G. Sarmiento-López
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Sinaloa-Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan Elías Olivares
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Pascual-Morales
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Saul Jiménez-Jiménez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Andrea Quero-Hostos
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Janet Palacios-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ana I. Chávez-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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8
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Gu P, Tao W, Tao J, Sun H, Hu R, Wang D, Zong G, Xie X, Ruan W, Xu G, Yi K, Zhang Y. The D14-SDEL1-SPX4 cascade integrates the strigolactone and phosphate signalling networks in rice. THE NEW PHYTOLOGIST 2023; 239:673-686. [PMID: 37194447 DOI: 10.1111/nph.18963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/12/2023] [Indexed: 05/18/2023]
Abstract
Modern agriculture needs large quantities of phosphate (Pi) fertilisers to obtain high yields. Information on how plants sense and adapt to Pi is required to enhance phosphorus-use efficiency (PUE) and thereby promote agricultural sustainability. Here, we show that strigolactones (SLs) regulate rice root developmental and metabolic adaptations to low Pi, by promoting efficient Pi uptake and translocation from roots to shoots. Low Pi stress triggers the synthesis of SLs, which dissociate the Pi central signalling module of SPX domain-containing protein (SPX4) and PHOSPHATE STARVATION RESPONSE protein (PHR2), leading to the release of PHR2 into the nucleus and activating the expression of Pi-starvation-induced genes including Pi transporters. The SL synthetic analogue GR24 enhances the interaction between the SL receptor DWARF 14 (D14) and a RING-finger ubiquitin E3 ligase (SDEL1). The sdel mutants have a reduced response to Pi starvation relative to wild-type plants, leading to insensitive root adaptation to Pi. Also, SLs induce the degradation of SPX4 via forming the D14-SDEL1-SPX4 complex. Our findings reveal a novel mechanism underlying crosstalk between the SL and Pi signalling networks in response to Pi fluctuations, which will enable breeding of high-PUE crop plants.
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Affiliation(s)
- Pengyuan Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wenqing Tao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jinyuan Tao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Huwei Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 450002, Zhengzhou, China
| | - Ripeng Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Daojian Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Guoxinan Zong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiaonan Xie
- Utsunomiya University, 321-8505, Utsunomiya, Japan
| | - Wenyuan Ruan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, 210095, Nanjing, China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yali Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, 210095, Nanjing, China
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9
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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10
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Solís-Miranda J, Juárez-Verdayes MA, Nava N, Rosas P, Leija-Salas A, Cárdenas L, Quinto C. The Phaseolus vulgaris Receptor-Like Kinase PvFER1 and the Small Peptides PvRALF1 and PvRALF6 Regulate Nodule Number as a Function of Nitrate Availability. Int J Mol Sci 2023; 24:ijms24065230. [PMID: 36982308 PMCID: PMC10049175 DOI: 10.3390/ijms24065230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
Legumes associate with Gram-negative soil bacteria called rhizobia, resulting in the formation of a nitrogen-fixing organ, the nodule. Nodules are an important sink for photosynthates for legumes, so these plants have developed a systemic regulation mechanism that controls their optimal number of nodules, the so-called autoregulation of nodulation (AON) pathway, to balance energy costs with the benefits of nitrogen fixation. In addition, soil nitrate inhibits nodulation in a dose-dependent manner, through systemic and local mechanisms. The CLE family of peptides and their receptors are key to tightly controlling these inhibitory responses. In the present study, a functional analysis revealed that PvFER1, PvRALF1, and PvRALF6 act as positive regulators of the nodule number in growth medium containing 0 mM of nitrate but as negative regulators in medium with 2 and 5 mM of nitrate. Furthermore, the effect on nodule number was found to be consistent with changes in the expression levels of genes associated with the AON pathway and with the nitrate-mediated regulation of nodulation (NRN). Collectively, these data suggest that PvFER1, PvRALF1, and PvRALF6 regulate the optimal number of nodules as a function of nitrate availability.
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Affiliation(s)
- Jorge Solís-Miranda
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Marco A. Juárez-Verdayes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
- Departamento de Docencia, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila 25315, Mexico
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Rosas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Alfonso Leija-Salas
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
- Correspondence:
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11
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Wang Z, Zheng Z, Zhu Y, Kong S, Liu D. PHOSPHATE RESPONSE 1 family members act distinctly to regulate transcriptional responses to phosphate starvation. PLANT PHYSIOLOGY 2023; 191:1324-1343. [PMID: 36417239 PMCID: PMC9922430 DOI: 10.1093/plphys/kiac521] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 11/18/2022] [Indexed: 06/01/2023]
Abstract
To sustain growth when facing phosphate (Pi) starvation, plants trigger an array of adaptive responses that are largely controlled at transcriptional levels. In Arabidopsis (Arabidopsis thaliana), the four transcription factors of the PHOSPHATE RESPONSE 1 (PHR1) family, PHR1 and its homologs PHR1-like 1 (PHL1), PHL2, and PHL3 form the central regulatory system that controls the expression of Pi starvation-responsive (PSR) genes. However, how each of these four proteins function in regulating the transcription of PSR genes remains largely unknown. In this work, we performed comparative phenotypic and transcriptomic analyses using Arabidopsis mutants with various combinations of mutations in these four genes. The results showed that PHR1/PHL1 and PHL2/PHL3 do not physically interact with each other and function as two distinct modules in regulating plant development and transcriptional responses to Pi starvation. In the PHR1/PHL1 module, PHR1 plays a dominant role, whereas, in the PHL2/PHL3 module, PHL2 and PHL3 contribute similarly to the regulation of PSR gene transcription. By analyzing their common and specific targets, we showed that these PHR proteins could function as both positive and negative regulators of PSR gene expression depending on their targets. Some interactions between PHR1 and PHL2/PHL3 in regulating PSR gene expression were also observed. In addition, we identified a large set of defense-related genes whose expression is not affected in wild-type plants but is altered in the mutant plants under Pi starvation. These results increase our understanding of the molecular mechanism underlying plant transcriptional responses to Pi starvation.
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Affiliation(s)
- Zhen Wang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zai Zheng
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuyao Kong
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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12
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Chen Z, Wang L, Cardoso JA, Zhu S, Liu G, Rao IM, Lin Y. Improving phosphorus acquisition efficiency through modification of root growth responses to phosphate starvation in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1094157. [PMID: 36844096 PMCID: PMC9950756 DOI: 10.3389/fpls.2023.1094157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Phosphorus (P) is one of the essential macronutrients for plant growth and development, and it is an integral part of the major organic components, including nucleic acids, proteins and phospholipids. Although total P is abundant in most soils, a large amount of P is not easily absorbed by plants. Inorganic phosphate (Pi) is the plant-available P, which is generally immobile and of low availability in soils. Hence, Pi starvation is a major constraint limiting plant growth and productivity. Enhancing plant P efficiency can be achieved by improving P acquisition efficiency (PAE) through modification of morpho-physiological and biochemical alteration in root traits that enable greater acquisition of external Pi from soils. Major advances have been made to dissect the mechanisms underlying plant adaptation to P deficiency, especially for legumes, which are considered important dietary sources for humans and livestock. This review aims to describe how legume root growth responds to Pi starvation, such as changes in the growth of primary root, lateral roots, root hairs and cluster roots. In particular, it summarizes the various strategies of legumes to confront P deficiency by regulating root traits that contribute towards improving PAE. Within these complex responses, a large number of Pi starvation-induced (PSI) genes and regulators involved in the developmental and biochemical alteration of root traits are highlighted. The involvement of key functional genes and regulators in remodeling root traits provides new opportunities for developing legume varieties with maximum PAE needed for regenerative agriculture.
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Affiliation(s)
- Zhijian Chen
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Linjie Wang
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Shengnan Zhu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Guodao Liu
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Idupulapati M. Rao
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Yan Lin
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
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13
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Lu G, Tian Z, Hao Y, Xu M, Lin Y, Wei J, Zhao Y. Overexpression of soybean microRNA156b enhanced tolerance to phosphorus deficiency and seed yield in Arabidopsis. Sci Rep 2023; 13:652. [PMID: 36635356 PMCID: PMC9837069 DOI: 10.1038/s41598-023-27847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
microRNAs (miRNAs) are endogenous small RNAs that are key regulatory factors participating in various biological activities such as the signaling of phosphorus deficiency in the plant. Previous studies have shown that miR156 expression was modulated by phosphorus starvation in Arabidopsis and soybean. However, it is not clear whether the over-expression of soybean miR156b (GmmiR156b) can improve a plant's tolerance to phosphorus deficiency and affect yield component traits. In this study, we generated Arabidopsis transgenic lines overexpressing GmmiR156b and investigated the plant's response to phosphorus deficiency. Compared with the wild type, the transgenic Arabidopsis seedlings had longer primary roots and higher phosphorus contents in roots under phosphorus-deficit conditions, but lower fresh weight root/shoot ratios under either phosphorus-deficient or sufficient conditions. Moreover, the GmmiR156b overexpression transgenic lines had higher phosphorus content in shoots of adult plants and grew better than the wide type under phosphorus-deficient conditions, and exhibited increased seed yields as well as strong pleiotropic developmental morphology such as dwarfness, prolonged growth period, bushy shoot/branching, and shorter silique length, suggesting that the transgenic lines were more tolerant to phosphorus deficiency. In addition, the expression level of four SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes (i.e., AtSPL4/5/6/15) were markedly suppressed in transgenic plants, indicating that they were the main targets negatively regulated by GmmiR156b (especially AtSPL15) and that the enhanced tolerance to phosphorus deficiency and seed yield is conferred mainly by the miR156-mediated downregulation of AtSPL15.
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Affiliation(s)
- Guangyuan Lu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Zhitao Tian
- grid.35155.370000 0004 1790 4137College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430062 People’s Republic of China
| | - Yifan Hao
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Meihua Xu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongxin Lin
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Jinxing Wei
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, People's Republic of China.
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14
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Ojeda-Rivera JO, Alejo-Jacuinde G, Nájera-González HR, López-Arredondo D. Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4125-4150. [PMID: 35524816 PMCID: PMC9729153 DOI: 10.1007/s00122-022-04095-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/31/2022] [Indexed: 05/04/2023]
Abstract
Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.
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Affiliation(s)
- Jonathan Odilón Ojeda-Rivera
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA.
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15
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Li Y, Pei Y, Shen Y, Zhang R, Kang M, Ma Y, Li D, Chen Y. Progress in the Self-Regulation System in Legume Nodule Development-AON (Autoregulation of Nodulation). Int J Mol Sci 2022; 23:ijms23126676. [PMID: 35743118 PMCID: PMC9224500 DOI: 10.3390/ijms23126676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
The formation and development of legumes nodules requires a lot of energy. Legumes must strictly control the number and activity of nodules to ensure efficient energy distribution. The AON system can limit the number of rhizobia infections and nodule numbers through the systemic signal pathway network that the aboveground and belowground parts participate in together. It can also promote the formation of nodules when plants are deficient in nitrogen. The currently known AON pathway includes four parts: soil NO3− signal and Rhizobium signal recognition and transmission, CLE-SUNN is the negative regulation pathway, CEP-CRA2 is the positive regulation pathway and the miR2111/TML module regulates nodule formation and development. In order to ensure the biological function of this important approach, plants use a variety of plant hormones, polypeptides, receptor kinases, transcription factors and miRNAs for signal transmission and transcriptional regulation. This review summarizes and discusses the research progress of the AON pathway in Legume nodule development.
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16
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Miller SS, Dornbusch MR, Farmer AD, Huertas R, Gutierrez-Gonzalez JJ, Young ND, Samac DA, Curtin SJ. Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate. G3 (BETHESDA, MD.) 2022; 12:jkac096. [PMID: 35471600 PMCID: PMC9157135 DOI: 10.1093/g3journal/jkac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
In this article, we describe a set of novel alfalfa (Medicago sativa L.) plants that hyper-accumulate Phosphate ion (Pi) at levels 3- to 6-fold higher than wild-type. This alfalfa germplasm will have practical applications reclaiming Pi from contaminated or enriched soil or be used in conservation buffer strips to protect waterways from Pi run-off. Hyper-accumulating alfalfa plants were generated by targeted mutagenesis of PHOSPHATE2 (PHO2) using newly created CRISPR/Cas9 reagents and an improved mutant screening strategy. PHO2 encodes a ubiquitin conjugating E2 enzyme (UBC24) previously characterized in Arabidopsis thaliana, Medicago truncatula, and Oryza sativa. Mutations of PHO2 disrupt Pi homeostasis resulting in Pi hyper-accumulation. Successful CRISPR/Cas9 editing of PHO2 demonstrates that this is an efficient mutagenesis tool in alfalfa despite its complex autotetraploid genome structure. Arabidopsis and M. truncatula ortholog genes were used to identify PHO2 haplotypes in outcrossing tetraploid M. sativa with the aim of generating heritable mutations in both PHO2-like genes (PHO2-B and PHO2-C). After delivery of the reagent and regeneration from transformed leaf explants, plants with mutations in all haplotypes of PHO2-B and PHO2-C were identified. These plants were evaluated for morphology, Pi accumulation, heritable transmission of targeted mutations, segregation of mutant haplotypes and removal of T-DNA(s). The Agrobacterium-mediated transformation assay and gene editing reagents reported here were also evaluated for further optimization for future alfalfa functional genomic studies.
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Affiliation(s)
- Susan S Miller
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Melinda R Dornbusch
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | - Juan J Gutierrez-Gonzalez
- Facultad de Ciencias Biológicas y Ambientales, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
- Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Deborah A Samac
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
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17
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Wang Q, Du W, Zhang S, Yu W, Wang J, Zhang C, Zhang H, Huang F, Cheng H, Yu D. Functional study and elite haplotype identification of soybean phosphate starvation response transcription factors GmPHR14 and GmPHR32. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:29. [PMID: 37309533 PMCID: PMC10248592 DOI: 10.1007/s11032-022-01301-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/22/2022] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) is one of the important mineral elements required for plant growth and development. However, because of the low mobility in soil, P deficiency has been an important factor limiting soybean production. Here, we identified 14 PHR (phosphate starvation response) genes in soybean genome and verified that two previously unreported GmPHR members, GmPHR14 and GmPHR32, were involved in low-P stress tolerance in soybean. GmPHR14 and GmPHR32 were present in two diverged branches of the phylogenic tree. Both genes were highly expressed in roots and root nodules and were induced by P deficiency. GmPHR14 and GmPHR32 both were expressed in the nucleus. The 211 amino acids in the N terminus of GmPHR32 were found to be required for the transcriptional activity. Overexpressing GmPHR14 or GmPHR32 in soybean hairy roots significantly increased roots and shoots dry weight under low-P condition, and overexpressing GmPHR14 additionally significantly increased roots P concentration under low-P condition. GmPHR14 and GmPHR32 were polymorphic in soybean population and the elite haplotype2 (Hap2) for both genes was preferentially present in improved cultivars and showed significantly higher shoots dry weight under low-P condition than the other two haplotypes. These results suggested GmPHR14 and GmPHR32 both positively regulated low-P responses in soybean, and would shed light on the molecular mechanism of low-P stress tolerance. Furthermore, the identified elite haplotypes would be useful in P-efficient soybean breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01301-z.
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Affiliation(s)
- Qing Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenkai Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shixi Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenqing Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Cankui Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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18
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Tao Y, Huang J, Jing HK, Shen RF, Zhu XF. Jasmonic acid is involved in root cell wall phosphorus remobilization through the nitric oxide dependent pathway in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2618-2630. [PMID: 35084463 DOI: 10.1093/jxb/erac023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Jasmonic acid (JA) is involved in phosphorus (P) stress in plants, but its underlying molecular mechanisms are still elusive. In this study, we found root endogenous JA content in rice increased under P deficiency (-P), suggesting that JA might participate in P homeostasis in plants. This hypothesis was further confirmed through the addition of exogenous JA (+JA), as this could increase both the root and shoot soluble P content through regulating root cell wall P reutilization. In addition, -P+JA treatment significantly induced the expression of P transporter gene OsPT2, together with increased xylem P content, implying that JA is also important for P translocation from the root to the shoot in P-deficient rice. Furthermore, the accumulation of the molecular signal nitric oxide (NO) was enhanced under -P+JA treatment when compared with -P treatment alone, while the addition of c-PTIO, a scavenger of NO, could reverse the P-deficient phenotype alleviated by JA. Taken together, our results reveal a JA-NO-cell wall P reutilization pathway under P deficiency in rice.
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Affiliation(s)
- Ye Tao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huai Kang Jing
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Fang Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Gu BJ, Tong YK, Wang YY, Zhang ML, Ma GJ, Wu XQ, Zhang JF, Xu F, Li J, Ren F. Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp. PeerJ 2022; 10:e12882. [PMID: 35237467 PMCID: PMC8884064 DOI: 10.7717/peerj.12882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant's adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
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Affiliation(s)
- Bin-Jie Gu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - You-Yi Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Guang-Jing Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Qin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Fan Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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Metallothionein1A Regulates Rhizobial Infection and Nodulation in Phaseolus vulgaris. Int J Mol Sci 2022; 23:ijms23031491. [PMID: 35163415 PMCID: PMC8836284 DOI: 10.3390/ijms23031491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Metallothioneins (MTs) constitute a heterogeneous family of ubiquitous metal ion-binding proteins. In plants, MTs participate in the regulation of cell growth and proliferation, protection against heavy metal stress, oxidative stress responses, and responses to pathogen attack. Despite their wide variety of functions, the role of MTs in symbiotic associations, specifically nodule-fabacean symbiosis, is poorly understood. Here, we analyzed the role of the PvMT1A gene in Phaseolus vulgaris-Rhizobium tropici symbiosis using bioinformatics and reverse genetics approaches. Using in silico analysis, we identified six genes encoding MTs in P. vulgaris, which were clustered into three of the four classes described in plants. PvMT1A transcript levels were significantly higher in roots inoculated with R. tropici at 7 and 30 days post inoculation (dpi) than in non-inoculated roots. Functional analysis showed that downregulating PvMT1A by RNA interference (RNAi) reduced the number of infection events at 7 and 10 dpi and the number of nodules at 14 and 21 dpi. In addition, nodule development was negatively affected in PvMT1A:RNAi transgenic roots, and these nodules displayed a reduced nitrogen fixation rate at 21 dpi. These results strongly suggest that PvMT1A plays an important role in the infection process and nodule development in P. vulgaris during rhizobial symbiosis.
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21
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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22
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Chen Z, Song J, Li X, Arango J, Cardoso JA, Rao I, Schultze-Kraft R, Peters M, Mo X, Liu G. Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency. BMC PLANT BIOLOGY 2021; 21:466. [PMID: 34645406 PMCID: PMC8513372 DOI: 10.1186/s12870-021-03249-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/06/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phosphorus (P) is an essential macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency limits crop growth and yield. Although Stylosanthes guianensis (stylo) is an important tropical legume that displays adaptation to low phosphate (Pi) availability, its adaptive mechanisms remain largely unknown. RESULTS In this study, differences in low-P stress tolerance were investigated using two stylo cultivars ('RY2' and 'RY5') that were grown in hydroponics. Results showed that cultivar RY2 was better adapted to Pi starvation than RY5, as reflected by lower values of relative decrease rates of growth parameters than RY5 at low-P stress, especially for the reduction of shoot and root dry weight. Furthermore, RY2 exhibited higher P acquisition efficiency than RY5 under the same P treatment, although P utilization efficiency was similar between the two cultivars. In addition, better root growth performance and higher leaf and root APase activities were observed with RY2 compared to RY5. Subsequent RNA-seq analysis revealed 8,348 genes that were differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and Pi homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), and multidrug and toxin extrusion (MATE). Furthermore, a variety of genes related to transcription factors and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY and the SYG1/PHO81/XPR1 (SPX) domain, were also regulated by P deficiency in stylo roots. CONCLUSIONS This study reveals the possible mechanisms underlying the adaptation of stylo to P deficiency. The low-P tolerance in stylo is probably manifested through regulation of root growth, Pi acquisition and cellular Pi homeostasis as well as Pi signaling pathway. The identified genes involved in low-P tolerance can be potentially used to design the breeding strategy for developing P-efficient stylo cultivars to grow on acid soils in the tropics.
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Affiliation(s)
- Zhijian Chen
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Jianling Song
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570110, P.R. China
| | - Xinyong Li
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China
| | - Jacobo Arango
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Juan Andres Cardoso
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Idupulapati Rao
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Rainer Schultze-Kraft
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Michael Peters
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Xiaohui Mo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, P.R. China.
| | - Guodao Liu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P.R. China.
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23
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Ayra L, Reyero-Saavedra MDR, Isidra-Arellano MC, Lozano L, Ramírez M, Leija A, Fuentes SI, Girard L, Valdés-López O, Hernández G. Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors. FRONTIERS IN PLANT SCIENCE 2021; 12:679463. [PMID: 34163511 PMCID: PMC8216239 DOI: 10.3389/fpls.2021.679463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/25/2023]
Abstract
Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.
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Affiliation(s)
- Litzy Ayra
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María del Rocio Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Luis Lozano
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara-Isabel Fuentes
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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24
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Ángel Martín-Rodríguez J, Ariani A, Leija A, Elizondo A, Fuentes SI, Ramirez M, Gepts P, Hernández G, Formey D. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1521-1533. [PMID: 33300202 DOI: 10.1111/tpj.15129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 05/28/2023]
Abstract
The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.
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Affiliation(s)
| | - Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Elizondo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara I Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramirez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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25
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Cai J, Cai W, Huang X, Yang S, Wen J, Xia X, Yang F, Shi Y, Guan D, He S. Ca14-3-3 Interacts With CaWRKY58 to Positively Modulate Pepper Response to Low-Phosphorus Starvation. FRONTIERS IN PLANT SCIENCE 2021; 11:607878. [PMID: 33519860 PMCID: PMC7840522 DOI: 10.3389/fpls.2020.607878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Low-phosphorus stress (LPS) and pathogen attack are two important stresses frequently experienced by plants in their natural habitats, but how plant respond to them coordinately remains under-investigated. Here, we demonstrate that CaWRKY58, a known negative regulator of the pepper (Capsicum annuum) response to attack by Ralstonia solanacearum, is upregulated by LPS. Virus-induced gene silencing (VIGS) and overexpression of CaWRKY58 in Nicotiana benthamiana plants in combination with chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA) demonstrated that CaWRKY58 positively regulates the response of pepper to LPS by directly targeting and regulating genes related to phosphorus-deficiency tolerance, including PHOSPHATE STARVATION RESPONSE1 (PHR1). Yeast two-hybrid assays revealed that CaWRKY58 interacts with a 14-3-3 protein (Ca14-3-3); this interaction was confirmed by pull-down, bimolecular fluorescence complementation (BiFC), and microscale thermophoresis (MST) assays. The interaction between Ca14-3-3 and CaWRKY58 enhanced the activation of PHR1 expression by CaWRKY58, but did not affect the expression of the immunity-related genes CaNPR1 and CaDEF1, which are negatively regulated by CaWRKY58 in pepper upon Ralstonia solanacearum inoculation. Collectively, our data indicate that CaWRKY58 negatively regulates immunity against Ralstonia solanacearum, but positively regulates tolerance to LPS and that Ca14-3-3 transcriptionally activates CaWRKY58 in response to LPS.
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Affiliation(s)
- Jinsen Cai
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiwei Cai
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueying Huang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayu Wen
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoqin Xia
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Shi
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyi Guan
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuilin He
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, China
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Parreira JR, Cappuccio M, Balestrazzi A, Fevereiro P, Araújo SDS. MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L. HORTICULTURE RESEARCH 2021; 8:18. [PMID: 33436559 PMCID: PMC7804330 DOI: 10.1038/s41438-020-00448-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 05/04/2023]
Abstract
The knowledge on post-transcriptional regulation mechanisms implicated in seed development (SD) is still limited, particularly in one of the most consumed grain legumes, Phaseolus vulgaris L. We explore for the first time the miRNA expression dynamics in P. vulgaris developing seeds. Seventy-two known and 39 new miRNAs were found expressed in P. vulgaris developing seeds. Most of the miRNAs identified were more abundant at 10 and 40 days after anthesis, suggesting that late embryogenesis/early filling and desiccation were SD stages in which miRNA action is more pronounced. Degradome analysis and target prediction identified targets for 77 expressed miRNAs. While several known miRNAs were predicted to target HD-ZIP, ARF, SPL, and NF-Y transcription factors families, most of the predicted targets for new miRNAs encode for functional proteins. MiRNAs-targets expression profiles evidenced that these miRNAs could tune distinct seed developmental stages. MiRNAs more accumulated at early SD stages were implicated in regulating the end of embryogenesis, postponing the seed maturation program, storage compound synthesis and allocation. MiRNAs more accumulated at late SD stages could be implicated in seed quiescence, desiccation tolerance, and longevity with still uncovered roles in germination. The miRNAs herein described represent novel P. vulgaris resources with potential application in future biotechnological approaches to modulate the expression of genes implicated in legume seed traits with impact in horticultural production systems.
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Affiliation(s)
- José Ricardo Parreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michela Cappuccio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Pedro Fevereiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
- InnovPlantProtect Collaborative Laboratory, Estrada de Gil Vaz, 7351-901, Elvas, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- Association BLC3-Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155, Oliveira do Hospital, Portugal.
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27
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Molecular Manipulation of the miR399/ PHO2 Expression Module Alters the Salt Stress Response of Arabidopsis thaliana. PLANTS 2020; 10:plants10010073. [PMID: 33396498 PMCID: PMC7824465 DOI: 10.3390/plants10010073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
In Arabidopsis thaliana (Arabidopsis), the microRNA399 (miR399)/PHOSPHATE2 (PHO2) expression module is central to the response of Arabidopsis to phosphate (PO4) stress. In addition, miR399 has been demonstrated to also alter in abundance in response to salt stress. We therefore used a molecular modification approach to alter miR399 abundance to investigate the requirement of altered miR399 abundance in Arabidopsis in response to salt stress. The generated transformant lines, MIM399 and MIR399 plants, with reduced and elevated miR399 abundance respectively, displayed differences in their phenotypic and physiological response to those of wild-type Arabidopsis (Col-0) plants following exposure to a 7-day period of salt stress. However, at the molecular level, elevated miR399 abundance, and therefore, altered PHO2 target gene expression in salt-stressed Col-0, MIM399 and MIR399 plants, resulted in significant changes to the expression level of the two PO4 transporter genes, PHOSPHATE TRANSPORTER1;4 (PHT1;4) and PHT1;9. Elevated PHT1;4 and PHT1;9 PO4 transporter levels in salt stressed Arabidopsis would enhance PO4 translocation from the root to the shoot tissue which would supply additional levels of this precious cellular resource that could be utilized by the aerial tissues of salt stressed Arabidopsis to either maintain essential biological processes or to mount an adaptive response to salt stress.
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28
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Murakami H, Kakutani N, Kuroyanagi Y, Iwai M, Hori K, Shimojima M, Ohta H. MYB-like transcription factor NoPSR1 is crucial for membrane lipid remodeling under phosphate starvation in the oleaginous microalga Nannochloropsis oceanica. FEBS Lett 2020; 594:3384-3394. [PMID: 32770739 DOI: 10.1002/1873-3468.13902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 11/07/2022]
Abstract
Membrane lipid remodeling under phosphate (Pi) limitation, a process that replaces structural membrane phospholipids with nonphosphorus lipids, is a widely observed adaptive response in plants and algae. Here, we identified the transcription factor phosphorus starvation response 1 (NoPSR1) as an indispensable player for regulating membrane lipid conversion during Pi starvation in the microalga Nannochloropsis oceanica. Knocking out NoPSR1 scarcely perturbed membrane lipid composition under Pi-sufficient conditions but significantly impaired dynamic alteration in membrane lipids during Pi starvation. In contrast, the absence of NoPSR1 led to no obvious change in cell proliferation or storage lipid accumulation under either nutrient-sufficient or Pi-deficient conditions. Our results demonstrate a key factor controlling the membrane lipid profile during the Pi starvation response in N. oceanica.
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Affiliation(s)
- Hiroki Murakami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Natsue Kakutani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yunato Kuroyanagi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masako Iwai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Koichi Hori
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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29
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Isidra-Arellano MC, Pozas-Rodríguez EA, Del Rocío Reyero-Saavedra M, Arroyo-Canales J, Ferrer-Orgaz S, Del Socorro Sánchez-Correa M, Cardenas L, Covarrubias AA, Valdés-López O. Inhibition of legume nodulation by Pi deficiency is dependent on the autoregulation of nodulation (AON) pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1125-1139. [PMID: 32344464 DOI: 10.1111/tpj.14789] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Inhibition of nodule development is one of the main adverse effects of phosphate (Pi) deficiency in legumes. Despite all of the efforts made over the last decades to understand how root nodules cope with Pi deficiency, the molecular mechanisms leading to the reduction in nodule number under Pi deficiency remain elusive. In the present study, we provide experimental evidence indicating that Pi deficiency activates the autoregulation of nodulation (AON) pathway, leading to a reduction in nodule numbers in both common bean and soybean. A transcriptional profile analysis revealed that the expression of the AON-related genes PvNIN, PvRIC1, PvRIC2, and PvTML is upregulated under Pi deficiency conditions. The downregulation of the MYB transcription factor PvPHR1 in common bean roots significantly reduced the expression of these four AON-related genes. Physiological analyses indicated that Pi deficiency does not affect the establishment of the root nodule symbiosis in the supernodulation mutant lines Pvnark and Gmnark. Reciprocal grafting and split-roots analyses determined that the activation of the AON pathway was required for the inhibitory effect of Pi deficiency. Altogether, these data improve our understanding of the genetic mechanisms controlling the establishment of the root nodule symbiosis under Pi deficiency.
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Affiliation(s)
- Mariel C Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autonoma de Mexico, Coyoacan, Mexico City, 04510, Mexico
| | - Eithan A Pozas-Rodríguez
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - María Del Rocío Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Jazmin Arroyo-Canales
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Susana Ferrer-Orgaz
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - María Del Socorro Sánchez-Correa
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Luis Cardenas
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
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30
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Ortega-Ortega Y, Carrasco-Castilla J, Juárez-Verdayes MA, Toscano-Morales R, Fonseca-García C, Nava N, Cárdenas L, Quinto C. Actin Depolymerizing Factor Modulates Rhizobial Infection and Nodule Organogenesis in Common Bean. Int J Mol Sci 2020; 21:ijms21061970. [PMID: 32183068 PMCID: PMC7139724 DOI: 10.3390/ijms21061970] [Citation(s) in RCA: 10] [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: 02/22/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/28/2022] Open
Abstract
Actin plays a critical role in the rhizobium-legume symbiosis. Cytoskeletal rearrangements and changes in actin occur in response to Nod factors secreted by rhizobia during symbiotic interactions with legumes. These cytoskeletal rearrangements are mediated by diverse actin-binding proteins, such as actin depolymerization factors (ADFs). We examined the function of an ADF in the Phaseolus vulgaris-rhizobia symbiotic interaction (PvADFE). PvADFE was preferentially expressed in rhizobia-inoculated roots and nodules. PvADFE promoter activity was associated with root hairs harbouring growing infection threads, cortical cell divisions beneath root hairs, and vascular bundles in mature nodules. Silencing of PvADFE using RNA interference increased the number of infection threads in the transgenic roots, resulting in increased nodule number, nitrogen fixation activity, and average nodule diameter. Conversely, overexpression of PvADFE reduced the nodule number, nitrogen fixation activity, average nodule diameter, as well as NODULE INCEPTION (NIN) and EARLY NODULIN2 (ENOD2) transcript accumulation. Hence, changes in ADFE transcript levels affect rhizobial infection and nodulation, suggesting that ADFE is fine-tuning these processes.
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Affiliation(s)
- Yolanda Ortega-Ortega
- Departamento de Biociencias y Agrobiotecnología, Centro de Investigación en Química Aplicada-CONACYT, Saltillo 25294, Coahuila, Mexico;
| | - Janet Carrasco-Castilla
- Instituto Politécnico Nacional, Centro de Estudios Científicos y Tecnológicos 17 León, León 37358, Guanajuato, Mexico;
| | - Marco A. Juárez-Verdayes
- Departamento de Docencia, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Coahuila, Mexico;
| | - Roberto Toscano-Morales
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA;
| | - Citlali Fonseca-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Cuernavaca 62210, Morelos, Mexico; (C.F.-G.); (N.N.); (L.C.)
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Cuernavaca 62210, Morelos, Mexico; (C.F.-G.); (N.N.); (L.C.)
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Cuernavaca 62210, Morelos, Mexico; (C.F.-G.); (N.N.); (L.C.)
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Cuernavaca 62210, Morelos, Mexico; (C.F.-G.); (N.N.); (L.C.)
- Correspondence:
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31
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Dong J, Ma G, Sui L, Wei M, Satheesh V, Zhang R, Ge S, Li J, Zhang TE, Wittwer C, Jessen HJ, Zhang H, An GY, Chao DY, Liu D, Lei M. Inositol Pyrophosphate InsP 8 Acts as an Intracellular Phosphate Signal in Arabidopsis. MOLECULAR PLANT 2019; 12:1463-1473. [PMID: 31419530 DOI: 10.1016/j.molp.2019.08.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
The maintenance of cellular phosphate (Pi) homeostasis is of great importance in living organisms. The SPX domain-containing protein 1 (SPX1) proteins from both Arabidopsis and rice have been proposed to act as sensors of Pi status. The molecular signal indicating the cellular Pi status and regulating Pi homeostasis in plants, however, remains to be identified, as Pi itself does not bind to the SPX domain. Here, we report the identification of the inositol pyrophosphate InsP8 as a signaling molecule that regulates Pi homeostasis in Arabidopsis. Polyacrylamide gel electrophoresis profiling of InsPs revealed that InsP8 level positively correlates with cellular Pi concentration. We demonstrated that the homologs of diphosphoinositol pentakisphosphate kinase (PPIP5K), VIH1 and VIH2, function redundantly to synthesize InsP8, and that the vih1 vih2 double mutant overaccumulates Pi. SPX1 directly interacts with PHR1, the central regulator of Pi starvation responses, to inhibit its function under Pi-replete conditions. However, this interaction is compromised in the vih1 vih2 double mutant, resulting in the constitutive induction of Pi starvation-induced genes, indicating that plant cells cannot sense cellular Pi status without InsP8. Furthermore, we showed that InsP8 could directly bind to the SPX domain of SPX1 and is essential for the interaction between SPX1 and PHR1. Collectively, our study suggests that InsP8 is the intracellular Pi signaling molecule serving as the ligand of SPX1 for controlling Pi homeostasis in plants.
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Affiliation(s)
- Jinsong Dong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guojie Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academic of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqian Sui
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mengwei Wei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ruyue Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenghong Ge
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinkai Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-En Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Christopher Wittwer
- Institute of Organic Chemistry, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guo-Yong An
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academic of Sciences, Shanghai 200032, China
| | - Dong Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.
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Ruan W, Guo M, Wang X, Guo Z, Xu Z, Xu L, Zhao H, Sun H, Yan C, Yi K. Two RING-Finger Ubiquitin E3 Ligases Regulate the Degradation of SPX4, An Internal Phosphate Sensor, for Phosphate Homeostasis and Signaling in Rice. MOLECULAR PLANT 2019; 12:1060-1074. [PMID: 31002982 DOI: 10.1016/j.molp.2019.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 05/13/2023]
Abstract
SPX-domain-containing proteins (SPXs) play an important role in inorganic phosphate (Pi) sensing, signaling, and transport in eukaryotes. In plants, SPXs are known to integrate cellular Pi status and negatively regulate the activity of Pi central regulators, the PHOSPATE STARVATION RESPONSE proteins (PHRs). The stability of SPXs, such as SPX4, is reduced under Pi-deficient conditions. However, the mechanisms by which SPXs are degraded remain unclear. In this study, using a yeast-two-hybrid screen we identified two RING-finger ubiquitin E3 ligases regulating SPX4 degradation, designated SDEL1 and SDEL2, which were post-transcriptionally induced by Pi starvation. We found that both SDELs were located in the nucleus and cytoplasm, had ubiquitin E3 ligase activity, and directly ubiquitinated the K213 and K299 lysine residues in SPX4 to regulate its stability. Furthermore, we found that PHR2, a Pi central regulator in rice, could compete with SDELs by interacting with SPX4 under Pi-sufficient conditions, which protected SPX4 from ubiquitination and degradation. Consistent with the biochemical function of SDEL1 and SDEL2, overexpression of SDEL1 or SDEL2 resulted in Pi overaccumulation and induced Pi-starvation signaling even under Pi-sufficient conditions. Conversely, their loss-of-function mutants displayed decreased Pi accumulation and reduced Pi-starvation signaling. Collectively, our study revealed that SDEL1 and SDEL2 facilitate the degradation of SPX4 to modulate PHR2 activity and regulate Pi homeostasis and Pi signaling in response to external Pi availability in rice.
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Affiliation(s)
- Wenyuan Ruan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meina Guo
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueqing Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenhui Guo
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuang Xu
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Xu
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongyu Zhao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiji Sun
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Chengqi Yan
- Ningbo Academy of Agriculture Sciences, 19 Dehou Street, Ningbo City 315000, China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Rodríguez-López J, López AH, Estrada-Navarrete G, Sánchez F, Díaz-Camino C. The Noncanonical Heat Shock Protein PvNod22 Is Essential for Infection Thread Progression During Rhizobial Endosymbiosis in Common Bean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:939-948. [PMID: 30893001 DOI: 10.1094/mpmi-02-19-0041-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the establishment of plant-rhizobial symbiosis, the plant hosts express nodulin proteins during root nodule organogenesis. A limited number of nodulins have been characterized, and these perform essential functions in root nodule development and metabolism. Most nodulins are expressed in the nodule and at lower levels in other plant tissues. Previously, we isolated Nodulin 22 (PvNod22) from a common bean (Phaseolus vulgaris L.) cDNA library derived from Rhizobium-infected roots. PvNod22 is a noncanonical, endoplasmic reticulum (ER)-localized, small heat shock protein that confers protection against oxidative stress when overexpressed in Escherichia coli. Virus-induced gene silencing of PvNod22 resulted in necrotic lesions in the aerial organs of P. vulgaris plants cultivated under optimal conditions, activation of the ER-unfolded protein response (UPR), and, finally, plant death. Here, we examined the expression of PvNod22 in common bean plants during the establishment of rhizobial endosymbiosis and its relationship with two cellular processes associated with plant immunity, the UPR and autophagy. In the RNA interference lines, numerous infection threads stopped their progression before reaching the cortex cell layer of the root, and nodules contained fewer nitrogen-fixing bacteroids. Collectively, our results suggest that PvNod22 has a nonredundant function during legume-rhizobia symbiosis associated with infection thread elongation, likely by sustaining protein homeostasis in the ER.
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Affiliation(s)
- Jonathan Rodríguez-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Alejandrina Hernández López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Georgina Estrada-Navarrete
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Federico Sánchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Claudia Díaz-Camino
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
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Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa. Funct Integr Genomics 2019; 19:953-972. [PMID: 31177404 DOI: 10.1007/s10142-019-00692-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 11/02/2018] [Accepted: 05/17/2019] [Indexed: 12/16/2022]
Abstract
miRNAs (microRNAs) are ~ 21-nt non-coding small RNAs (sRNAs) that play crucial regulatory roles in plant biotic and abiotic stress responses. Phosphorus (Pi) deficiency constrains plant growth and reduces yields worldwide. To identify tree miRNAs and evaluate their functions in the response to low Pi, we identified 261 known and 31 candidate novel miRNA families from three sRNA libraries constructed from Populus tomentosa subjected to sufficient or Pi deficiency condition or to restoration of a sufficient Pi level after Pi deficiency. Pi deficiency resulted in significant changes in the abundance of TPM (transcript per million) of 65 known and 3 novel miRNAs. Interestingly, four miRNAs responsive to low N-miR167, miR394, miR171, and miR857-were found to be involved in the response to low Pi. Thirty-five known and one novel miRNAs responded dynamically to Pi fluctuations, suggesting their involvement in the response to Pi deficiency. miRNA clusters comprising 36 miRNAs were identified in 10 chromosomes. Intriguingly, nine pairs of sense and antisense miRNAs transcribed from the same loci were detected in P. tomentosa, which is the first such report in woody plants. Moreover, target genes of the known miRNAs and novel miRNA candidates with significantly changed abundance were predicted, and their functions were annotated. Degradome sequencing supported the identified targets of miRNAs in P. tomentosa. These findings will enhance our understanding of universal and specific molecular regulatory mechanisms of trees under nutrition stress and may facilitate improvement of the Pi utilization efficiency of woody plants.
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Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang Q, Wang Q, Yang W, Wu Y. Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1. FEBS J 2019; 286:2809-2821. [PMID: 30974511 DOI: 10.1111/febs.14846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/18/2019] [Accepted: 04/09/2019] [Indexed: 11/26/2022]
Abstract
The phosphate starvation response 1 (PHR1) protein has a central role in mediating the response to phosphate starvation in plants. PHR1 is composed of a number of domains including a MYB domain involved with DNA binding and a coiled-coil domain proposed to be involved with dimer formation. PHR1 binds to the promoter of phosphate starvation-induced genes to control the levels of phosphate required for nutrition. Previous studies have shown that both the MYB domain and the coiled-coil domain of PHR1 are required for binding the target DNA. Here, we describe the crystal structure of the PHR1 MYB domain and two structures of its complex with the PHR1-binding DNA sequence (P1BS). Structural and isothermal titration calorimetry has been carried out showing that the MYB domain of PHR1 alone is sufficient for target DNA recognition and binding. Two copies of the PHR1 MYB domain bind to the same major groove of the P1BS DNA with few direct interactions between the individual MYB domains. In addition, the PHR1 MYB-P1BS DNA complex structures reveal amino acid residues involved in DNA recognition and binding. Mutagenesis of these residues results in lost or impaired ability of PHR1 MYB to bind to its target DNA. The results presented reveal the structural basis for DNA recognition by the PHR1 MYB domain and demonstrate that two PHR1 MYB domains attach to their P1BS DNA targeting sequence. DATABASE: Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 6J4K (PHR1 MYB), 6J4R (PHR1 MYB-R-P1BS), 6J5B (MYB-CC-R2-P1BS).
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Affiliation(s)
- Meiqin Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK
| | | | - Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qin Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
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Wang Y, Zhang F, Cui W, Chen K, Zhao R, Zhang Z. The FvPHR1 transcription factor control phosphate homeostasis by transcriptionally regulating miR399a in woodland strawberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:258-268. [PMID: 30824004 DOI: 10.1016/j.plantsci.2018.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 05/26/2023]
Abstract
Plants have evolved phosphate (Pi) starvation response to adapt the low-Pi environment. The regulation of adaptive responses to phosphorus deficiency by the PHR1-miR399-PHO2 module has been well studied in Arabidopsis thaliana but not in strawberry. Transcription factor PHR1 as the central regulator in the Pi starvation signaling has been revealed in a few plant species. However, the function of PHR1 homologues in strawberry is still unknown. In this study, a total of 13 MYB-CC genes were identified in the woodland strawberry (Fragaria vesca) genome and the FvPHR1 gene was characterized. FvPHR1 contains MYB domain and coiled-coil (CC) domain and is localized in the nucleus. FvPHR1 also exhibits trans-activation ability. Furthermore, the P content in leaves of FvPHR1-overexpressing woodland strawberries was significantly increased by 1.38-fold to 1.78-fold compared with that in the wild type. FvPHR1 was also demonstrated to directly bind to the FvMIR399a promoter and positively regulate the expression of FvmiR399a in woodland strawberry. These results showed that PHR1-miR399 module is involved in the regulation of phosphate-signaling pathway and phosphate homeostasis in woodland strawberry.
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Affiliation(s)
- Yan Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Feng Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Weixu Cui
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Keqin Chen
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Rui Zhao
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
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Hernández-López A, Díaz M, Rodríguez-López J, Guillén G, Sánchez F, Díaz-Camino C. Uncovering Bax inhibitor-1 dual role in the legume-rhizobia symbiosis in common bean roots. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1049-1061. [PMID: 30462254 PMCID: PMC6363093 DOI: 10.1093/jxb/ery417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/13/2018] [Indexed: 05/23/2023]
Abstract
Bax-inhibitor 1 (BI-1) is a cell death suppressor conserved in all eukaryotes that modulates cell death in response to abiotic stress and pathogen attack in plants. However, little is known about its role in the establishment of symbiotic interactions. Here, we demonstrate the functional relevance of an Arabidopsis thaliana BI-1 homolog (PvBI-1a) to symbiosis between the common bean (Phaseolus vulgaris) and Rhizobium tropici. We show that the changes in expression of PvBI-1a observed during early symbiosis resemble those of some defence response-related proteins. By using gain- and loss-of-function approaches, we demonstrate that the overexpression of PvBI-1a in the roots of common bean increases the number of rhizobial infection events (and therefore the final number of nodules per root), but induces the premature death of nodule cells, affecting their nitrogen fixation efficiency. Nodule morphological alterations are known to be associated with changes in the expression of genes tied to defence, autophagy, and vesicular trafficking. Results obtained in the present work suggest that BI-1 has a dual role in the regulation of programmed cell death during symbiosis, extending our understanding of its critical function in the modulation of host immunity while responding to beneficial microbes.
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Affiliation(s)
- Alejandrina Hernández-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Mauricio Díaz
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Jonathan Rodríguez-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Gabriel Guillén
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Federico Sánchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
| | - Claudia Díaz-Camino
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
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Formey D, Martín-Rodríguez JÁ, Hernández G. Functional Analysis of Root microRNAs by a Constitutive Overexpression Approach in a Composite Plant System. Methods Mol Biol 2019; 1932:215-226. [PMID: 30701503 DOI: 10.1007/978-1-4939-9042-9_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Agrobacterium-mediated transformation is a fast and efficient method for genome modification in plants. In this protocol, we apply this technique for the analysis of root microRNA functionality. The induction of hairy roots constitutively overexpressing a given microRNA precursor allows us, in a simple way, to modify the accumulation of specific mature microRNA and analyze the consequence of this alteration on a phenotype of interest. This method generates ready-to-phenotype "composite plants" with untransformed aerial part and microRNA-overexpressing root system, in about 20 days.
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Affiliation(s)
- Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico.
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Patwa N, Nithin C, Bahadur RP, Basak J. Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction. Genomics 2018; 111:1333-1342. [PMID: 30237075 DOI: 10.1016/j.ygeno.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/17/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023]
Abstract
Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.
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Affiliation(s)
- Nisha Patwa
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India.
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Martín-Rodríguez JÁ, Leija A, Formey D, Hernández G. The MicroRNA319d/TCP10 Node Regulates the Common Bean - Rhizobia Nitrogen-Fixing Symbiosis. FRONTIERS IN PLANT SCIENCE 2018; 9:1175. [PMID: 30147704 PMCID: PMC6095992 DOI: 10.3389/fpls.2018.01175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/23/2018] [Indexed: 05/30/2023]
Abstract
Micro-RNAs from legume plants are emerging as relevant regulators of the rhizobia nitrogen-fixing symbiosis. In this work we functionally characterized the role of the node conformed by micro-RNA319 (miR319) - TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factor in the common bean (Phaseolus vulgaris) - Rhizobium tropici symbiosis. The miR319d, one of nine miR319 isoforms from common bean, was highly expressed in root and nodules from inoculated plants as compared to roots from fertilized plants. The miR319d targets TCP10 (Phvul.005G067950), identified by degradome analysis, whose expression showed a negative correlation with miR319d expression. The phenotypic analysis of R. tropici-inoculated composite plants with transgenic roots/nodules overexpressing or silencing the function of miR319d demonstrated the relevant role of the miR319d/TCP10 node in the common bean rhizobia symbiosis. Increased miR319d resulted in reduced root length/width ratio, increased rhizobial infection evidenced by more deformed root hairs and infection threads, and decreased nodule formation and nitrogenase activity per plant. In addition, these plants with lower TCP10 levels showed decreased expression level of the jasmonic acid (JA) biosynthetic gene: LOX2. The transcription of LOX2 by TCPs has been demonstrated for Arabidopsis and in several plants LOX2 level and JA content have been associate with TCP levels. On this basis, we propose that in roots/nodules of inoculated common bean plants TCP10 could be the transcriptional regulator of LOX2 and the miR319d/TCP10 node could affect nodulation through JA signaling. However, given the complexity of nodulation, the participation of other signaling pathways in the phenotypes observed cannot be ruled out.
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Zhong Y, Wang Y, Guo J, Zhu X, Shi J, He Q, Liu Y, Wu Y, Zhang L, Lv Q, Mao C. Rice SPX6 negatively regulates the phosphate starvation response through suppression of the transcription factor PHR2. THE NEW PHYTOLOGIST 2018; 219:135-148. [PMID: 29658119 DOI: 10.1111/nph.15155] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth and development, but the molecular mechanism determining how plants sense external inorganic phosphate (Pi) levels and reprogram transcriptional and adaptive responses is incompletely understood. In this study, we investigated the function of OsSPX6 (hereafter SPX6), an uncharacterized member of SPX domain (SYG1, Pho81 and XPR1)-containing proteins in rice, using reverse genetics and biochemical approaches. Transgenic plants overexpressing SPX6 exhibited decreased Pi concentrations and suppression of phosphate starvation-induced (PSI) genes. By contrast, transgenic lines with decreased SPX6 transcript levels or spx6 mutant showed significant Pi accumulation in the leaf and upregulation of PSI genes. Overexpression of SPX6 genetically suppressed the overexpression of PHOSPHATE STARVATION RESPONSE REGULATOR 2 (PHR2) in terms of the accumulation of high Pi content. Moreover, direct interaction of SPX6 with PHR2 impeded PHR2 translocation into the nucleus, and inhibited PHR2 binding to the P1BS (PHR1 binding sequence) element. SPX6 protein was degraded in leaves under Pi-deficient conditions, whereas it accumulated in roots. We conclude that rice SPX6 is another important negative regulator in Pi starvation signaling through the interaction with PHR2. SPX6 shows different responses to Pi starvation in shoot and root, which differ from those of other SPX proteins.
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Affiliation(s)
- Yongjia Zhong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Yuguang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiangfan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Xinlu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Qiuju He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Li Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Qundan Lv
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
- Chemical Biology Center, Lishui Institute of Agricultural Science, Lishui, Zhejiang, 323000, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, China
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Curtin SJ, Xiong Y, Michno J, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM. CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1125-1137. [PMID: 29087011 PMCID: PMC5978873 DOI: 10.1111/pbi.12857] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 05/14/2023]
Abstract
Processing of double-stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL-effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi-allelic double mutant for the two soya bean paralogous Double-stranded RNA-binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9-generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ-line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer-like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer-like3 gene and the GmHen1a gene was observed in the T0 generation, but these mutations failed to transmit to the T1 generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole-genome sequencing to reveal a spectrum of non-germ-line-targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.
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Affiliation(s)
- Shaun J. Curtin
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Present address:
Plant Science Research UnitAgricultural Research ServiceUnited States Department of AgricultureSt PaulMNUSA
| | - Yer Xiong
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Jean‐Michel Michno
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
| | | | - Adrian O. Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Tomas Čermák
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Present address:
Agricultural Research ServiceInari Agriculture, Inc.CambridgeMAUSA
| | - Colby Starker
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & DevelopmentCenter for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Andrew L. Eamens
- School of Environmental and Life SciencesThe University of NewcastleCallaghanNew South WalesAustralia
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of MinnesotaMinneapolisMNUSA
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Robert G, Muñoz N, Alvarado-Affantranger X, Saavedra L, Davidenco V, Rodríguez-Kessler M, Estrada-Navarrete G, Sánchez F, Lascano R. Phosphatidylinositol 3-kinase function at very early symbiont perception: a local nodulation control under stress conditions? JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2037-2048. [PMID: 29394394 DOI: 10.1093/jxb/ery030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/24/2018] [Indexed: 05/12/2023]
Abstract
Root hair curling is an early and essential morphological change required for the success of the symbiotic interaction between legumes and rhizobia. At this stage rhizobia grow as an infection thread within root hairs and are internalized into the plant cells by endocytosis, where the PI3K enzyme plays important roles. Previous observations show that stress conditions affect early stages of the symbiotic interaction, from 2 to 30 min post-inoculation, which we term as very early host responses, and affect symbiosis establishment. Herein, we demonstrated the relevance of the very early host responses for the symbiotic interaction. PI3K and the NADPH oxidase complex are found to have key roles in the microsymbiont recognition response, modulating the apoplastic and intracellular/endosomal ROS induction in root hairs. Interestingly, compared with soybean mutant plants that do not perceive the symbiont, we demonstrated that the very early symbiont perception under sublethal saline stress conditions induced root hair death. Together, these results highlight not only the importance of the very early host-responses on later stages of the symbiont interaction, but also suggest that they act as a mechanism for local control of nodulation capacity, prior to the abortion of the infection thread, preventing the allocation of resources/energy for nodule formation under unfavorable environmental conditions.
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Affiliation(s)
- Germán Robert
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, de Septiembre, X5020ICA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
| | - Nacira Muñoz
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, de Septiembre, X5020ICA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
| | - Xochitl Alvarado-Affantranger
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Laura Saavedra
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
| | - Vanina Davidenco
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, de Septiembre, X5020ICA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Margarita Rodríguez-Kessler
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Georgina Estrada-Navarrete
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Federico Sánchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ramiro Lascano
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield, Córdoba, Argentina
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Yang WT, Baek D, Yun DJ, Lee KS, Hong SY, Bae KD, Chung YS, Kwon YS, Kim DH, Jung KH, Kim DH. Rice OsMYB5P improves plant phosphate acquisition by regulation of phosphate transporter. PLoS One 2018; 13:e0194628. [PMID: 29566032 PMCID: PMC5864048 DOI: 10.1371/journal.pone.0194628] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
Myeloblastosis (MYB) transcription factors play central roles in plant developmental processes and in responses to nutrient deficiency. In this study, OsMYB5P, an R2R3-MYB transcription factor, was isolated and identified from rice (Oryza sativa L. 'Dongjin') under inorganic phosphate (Pi)-deficient conditions. OsMYB5P protein is localized to the nucleus and functions as a transcription activator in plant development. Overexpression of OsMYB5P in rice and Arabidopsis (Arabidopsis thaliana Col-0) increases tolerance to phosphate starvation, whereas OsMYB5P knock-out through RNA interference increases sensitivity to Pi depletion in rice. Furthermore, shoots and roots of transgenic rice plants overexpressing OsMYB5P were longer than those of wild plants under both normal and Pi-deficient conditions. These results indicate that OsMYB5P is associated with the regulation of shoot development and root- system architecture. Overexpression of OsMYB5P led to increased Pi accumulation in shoots and roots. Interestingly, OsMYB5P directly bound to MBS (MYB binding site) motifs on the OsPT5 promoter and induced transcription of OsPT5 in rice. In addition, overexpression of OsMYB5P in Arabidopsis triggered increased expression of AtPht1;3, an Arabidopsis Pi transporter, in shoots and roots under normal and Pi-deficient conditions. Together, these results demonstrate that overexpression of OsMYB5P increases tolerance to Pi deficiency in plants by modulating Pi transporters at the transcriptional level in monocots and dicots.
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Affiliation(s)
- Won Tae Yang
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21 PLUS), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Kwang Sik Lee
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - So Yeon Hong
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Ki Deuk Bae
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Young Soo Chung
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Yong Sham Kwon
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Du Hyun Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Ki Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Doh Hoon Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
- * E-mail:
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In BPS1 Downregulated Roots, the BYPASS1 Signal Disrupts the Induction of Cortical Cell Divisions in Bean-Rhizobium Symbiosis. Genes (Basel) 2018; 9:genes9010011. [PMID: 29301366 PMCID: PMC5793164 DOI: 10.3390/genes9010011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/23/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022] Open
Abstract
BYPASS1 (BPS1), which is a well-conserved gene in plants, is required for normal root and shoot development. In the absence of BPS1 gene function, Arabidopsis overproduces a mobile signalling compound (the BPS1 signal) in roots, and this transmissible signal arrests shoot growth and causes abnormal root development. In addition to the shoot and root meristem activities, the legumes also possess transient meristematic activity in root cortical cells during Rhizobium symbiosis. We explored the role of Phaseolus vulgaris BPS1 during nodule primordium development using an RNA-interference (RNAi) silencing approach. Our results show that upon Rhizobium infection, the PvBPS1-RNAi transgenic roots failed to induce cortical cell divisions without affecting the rhizobia-induced root hair curling and infection thread formation. The transcript accumulation of early nodulin genes, cell cyclins, and cyclin-dependent kinase genes was affected in RNAi lines. Interestingly, the PvBPS1-RNAi root nodule phenotype was partially rescued by exogenous application of fluridone, a carotenoid biosynthesis inhibitor, which was used because the carotenoids are precursors of BPS1 signalling molecules. Furthermore, we show that the PvBPS1 promoter was active in the nodule primordia. Together, our data show that PvBPS1 plays a vital role in the induction of meristematic activity in root cortical cells and in the establishment of nodule primordia during Phaseolus-Rhizobium symbiosis.
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Liu A, Contador CA, Fan K, Lam HM. Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes. FRONTIERS IN PLANT SCIENCE 2018; 9:1860. [PMID: 30619423 PMCID: PMC6305480 DOI: 10.3389/fpls.2018.01860] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
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Affiliation(s)
- Ailin Liu
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carolina A. Contador
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kejing Fan
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Hon-Ming Lam,
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Saroha M, Singroha G, Sharma M, Mehta G, Gupta OP, Sharma P. sRNA and epigenetic mediated abiotic stress tolerance in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0330-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis. Genes (Basel) 2017; 8:genes8120352. [PMID: 29182547 PMCID: PMC5748670 DOI: 10.3390/genes8120352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022] Open
Abstract
The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.
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Arthikala MK, Montiel J, Sánchez-López R, Nava N, Cárdenas L, Quinto C. Respiratory Burst Oxidase Homolog Gene A Is Crucial for Rhizobium Infection and Nodule Maturation and Function in Common Bean. FRONTIERS IN PLANT SCIENCE 2017; 8:2003. [PMID: 29218056 PMCID: PMC5703732 DOI: 10.3389/fpls.2017.02003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/09/2017] [Indexed: 05/23/2023]
Abstract
Reactive oxygen species (ROS) produced by respiratory burst oxidase homologs (RBOHs) regulate numerous plant cell processes, including the symbiosis between legumes and nitrogen-fixing bacteria. Rapid and transient ROS production was reported after Phaseolus vulgaris root hairs were treated with Nod factors, indicating the presence of a ROS-associated molecular signature in the symbiosis signaling pathway. Rboh is a multigene family containing nine members (RbohA-I) in P. vulgaris. RNA interference of RbohB suppresses ROS production and attenuates rhizobial infection thread (IT) progression in P. vulgaris root hairs. However, the roles of other Rboh members in symbiotic interactions are largely unknown. In this study, we characterized the role of the NADPH oxidase-encoding gene RbohA (Phvulv091020621) in the P. vulgaris-Rhizobium tropici symbiosis. The spatiotemporal activity of the RbohA promoter colocalized with growing ITs and was associated with vascular bundles in developing nodules. Subcellular localization studies indicated that RBOHA was localized in the plasma membrane of P. vulgaris root hairs. After rhizobial inoculation, PvRBOHA was mainly distributed in the infection pocket and, to a lesser extent, throughout the IT. In PvRbohA RNAi lines, the rhizobial infection events were significantly reduced and, in successful infections, IT progression was arrested within the root hair, but did not impede cortical cell division. PvRbohA-RNAi nodules failed to fix nitrogen, since the infected cells in the few nodules formed were empty. RbohA-dependent ROS production and upregulation of several antioxidant enzymes was attenuated in rhizobia-inoculated PvRbohA-RNAi roots. These combined results indicate that PvRbohA is crucial for effective Rhizobium infection and its release into the nodule cells. This oxidase is partially or indirectly required to promote nodule organogenesis, altering the expression of auxin- and cyclin-related genes and genes involved in cell growth and division.
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Affiliation(s)
- Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Mexico
| | - Jesús Montiel
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rosana Sánchez-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Xue YB, Xiao BX, Zhu SN, Mo XH, Liang CY, Tian J, Liao H. GmPHR25, a GmPHR member up-regulated by phosphate starvation, controls phosphate homeostasis in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4951-4967. [PMID: 28992334 PMCID: PMC5853305 DOI: 10.1093/jxb/erx292] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 05/22/2023]
Abstract
As an essential nutrient element, phosphorus (P) plays an important role in plant growth and development. Low P availability is a limiting factor for crop production, especially for legume crops (e.g. soybean), which require additional P to sustain nitrogen fixation through symbiotic associations with rhizobia. Although PHOSPHATE STARVATION RESPONSE 1 (PHR1) or PHR1-like is considered as a central regulator of phosphate (Pi) homeostasis in several plant species, it remains undefined in soybean. In this study, 35 GmPHR members were cloned from the soybean genome and expression patterns in soybean were assayed under nitrogen (N) and P deficiency conditions. GmPHR25, which is up-regulated in response to Pi starvation, was then overexpressed in soybean hairy roots in vitro and in vivo to investigate its functions. The results showed that overexpressing GmPHR25 increased Pi concentration in transgenic soybean hairy roots under normal conditions, accompanied with a significant decrease in hairy root growth. Furthermore, transcripts of 11 out of 14 high-affinity Pi transporter (GmPT) members as well as five other Pi starvation-responsive genes were significantly increased in soybean hairy roots with GmPHR25 overexpression. Taken together, this study suggests that GmPHR25 is a vital regulator in the P signaling network, and controls Pi homeostasis in soybean.
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Affiliation(s)
- Ying-Bin Xue
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Bi-Xian Xiao
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Sheng-Nan Zhu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Xiao-Hui Mo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Cui-Yue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
| | - Hong Liao
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P.R. China
- Root Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China
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