1
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Sakuraba Y, Yang M, Yanagisawa S. HASTY-mediated miRNA dynamics modulate nitrogen starvation-induced leaf senescence in Arabidopsis. Nat Commun 2024; 15:7913. [PMID: 39256370 PMCID: PMC11387735 DOI: 10.1038/s41467-024-52339-w] [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: 09/11/2023] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
Nitrogen (N) deficiency responses are essential for plant survival and reproduction. Here, via an expression genome-wide association study (eGWAS), we reveal a mechanism that regulates microRNA (miRNA) dynamics necessary for N deficiency responses in Arabidopsis. Differential expression levels of three NAC transcription factor (TF) genes involved in leaf N deficiency responses among Arabidopsis accessions are most significantly associated with polymorphisms in HASTY (HST), which encodes an importin/exportin family protein responsible for the generation of mature miRNAs. HST acts as a negative regulator of N deficiency-induced leaf senescence, and the disruption and overexpression of HST differently modifies miRNA dynamics in response to N deficiency, altering levels of miRNAs targeting transcripts. Interestingly, N deficiency prevents the interaction of HST with HST-interacting proteins, DCL1 and RAN1, and some miRNAs. This suggests that HST-mediated regulation of miRNA dynamics collectively controls regulations mediated by multiple N deficiency response-associated NAC TFs, thereby being central to the N deficiency response network.
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Affiliation(s)
- Yasuhito Sakuraba
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mailun Yang
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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2
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Zhuo M, Sakuraba Y, Yanagisawa S. Dof1.7 and NIGT1 transcription factors mediate multilayered transcriptional regulation for different expression patterns of NITRATE TRANSPORTER2 genes under nitrogen deficiency stress. THE NEW PHYTOLOGIST 2024; 242:2132-2147. [PMID: 38523242 DOI: 10.1111/nph.19695] [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: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
Elucidating the mechanisms regulating nitrogen (N) deficiency responses in plants is of great agricultural importance. Previous studies revealed that decreased expression of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) transcriptional repressor genes upon N deficiency is involved in N deficiency-inducible gene expression in Arabidopsis thaliana. However, our knowledge of the mechanisms controlling N deficiency-induced changes in gene expression is still limited. Through the identification of Dof1.7 as a direct target of NIGT1 repressors and a novel N deficiency response-related transcriptional activator gene, we here show that NIGT1 and Dof1.7 transcription factors (TFs) differentially regulate N deficiency-inducible expression of three high-affinity nitrate transporter genes, NRT2.1, NRT2.4, and NRT2.5, which are responsible for most of the soil nitrate uptake activity of Arabidopsis plants under N-deficient conditions. Unlike NIGT1 repressors, which directly suppress NRT2.1, NRT2.4, and NRT2.5 under N-sufficient conditions, Dof1.7 directly activated only NRT2.5 but indirectly and moderately activated NRT2.1 and NRT2.4 under N-deficient conditions, probably by indirectly decreasing NIGT1 expression. Thus, Dof1.7 converted passive transcriptional activation into active and potent transcriptional activation, further differentially enhancing the expression of NRT2 genes. These findings clarify the mechanism underlying different expression patterns of NRT2 genes upon N deficiency, suggesting that time-dependent multilayered transcriptional regulation generates complicated expression patterns of N deficiency-inducible genes.
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Affiliation(s)
- Mengna Zhuo
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhito Sakuraba
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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3
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Ohama N, Yanagisawa S. Role of GARP family transcription factors in the regulatory network for nitrogen and phosphorus acquisition. JOURNAL OF PLANT RESEARCH 2024; 137:331-341. [PMID: 38190030 PMCID: PMC11082045 DOI: 10.1007/s10265-023-01513-0] [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: 08/28/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024]
Abstract
The GARP (Golden2, ARR-B, Psr1) family proteins with a conserved DNA-binding domain, called the B-motif, are plant-specific transcription factors involved in the regulation of various physiological processes. The GARP family proteins are divided into members that function as monomeric transcription factors, and members that function as transcription factors in the dimeric form, owing to the presence of a coiled-coil dimerization domain. Recent studies revealed that the dimer-forming GARP family members, which are further divided into the PHR1 and NIGT1 subfamilies, play critical roles in the regulation of phosphorus (P) and nitrogen (N) acquisition. In this review, we present a general overview of the GARP family proteins and discuss how several members of the PHR1 and NIGT1 subfamilies are involved in the coordinated acquisition of P and N in response to changes in environmental nutrient conditions, while mainly focusing on the recent findings that enhance our knowledge of the roles of PHR1 and NIGT1 in phosphate starvation signaling and nitrate signaling.
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Affiliation(s)
- Naohiko Ohama
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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4
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Kanno S, Nussaume L. Update of phosphate transport regulations. JOURNAL OF PLANT RESEARCH 2024; 137:293-295. [PMID: 38700602 DOI: 10.1007/s10265-024-01544-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Affiliation(s)
- Satomi Kanno
- Institute for Advanced Research, Nagoya University, 1‑1‑1, Furocho, Chikusaku, Nagoya, Aichi, 464‑8601, Japan
| | - Laurent Nussaume
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, EBMP, 13115, Saint‑Paul Lez Durance, France.
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5
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Ueda Y, Yanagisawa S. Transcription factor module NLP-NIGT1 fine-tunes NITRATE TRANSPORTER2.1 expression. PLANT PHYSIOLOGY 2023; 193:2865-2879. [PMID: 37595050 PMCID: PMC10663117 DOI: 10.1093/plphys/kiad458] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 07/22/2023] [Indexed: 08/20/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) high-affinity NITRATE TRANSPORTER2.1 (NRT2.1) plays a dominant role in the uptake of nitrate, the most important nitrogen (N) source for most terrestrial plants. The nitrate-inducible expression of NRT2.1 is regulated by NIN-LIKE PROTEIN (NLP) family transcriptional activators and NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) family transcriptional repressors. Phosphorus (P) availability also affects the expression of NRT2.1 because the PHOSPHATE STARVATION RESPONSE1 transcriptional activator activates NIGT1 genes in P-deficient environments. Here, we show a biology-based mathematical understanding of the complex regulation of NRT2.1 expression by multiple transcription factors using 2 different approaches: a microplate-based assay for the real-time measurement of temporal changes in NRT2.1 promoter activity under different nutritional conditions, and an ordinary differential equation (ODE)-based mathematical modeling of the NLP- and NIGT1-regulated expression patterns of NRT2.1. Both approaches consistently reveal that NIGT1 stabilizes the amplitude of NRT2.1 expression under a wide range of nitrate concentrations. Furthermore, the ODE model suggests that parameters such as the synthesis rate of NIGT1 mRNA and NIGT1 proteins and the affinity of NIGT1 proteins for the NRT2.1 promoter substantially influence the temporal expression patterns of NRT2.1 in response to nitrate. These results suggest that the NLP-NIGT1 feedforward loop allows a precise control of nitrate uptake. Hence, this study paves the way for understanding the complex regulation of nutrient acquisition in plants, thus facilitating engineered nutrient uptake and plant response patterns using synthetic biology approaches.
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Affiliation(s)
- Yoshiaki Ueda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Ohwashi 1-1, Tsukuba, Ibaraki 305-8686, Japan
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Shi Y, Liu D, He Y, Tang J, Chen H, Gong P, Luo JS, Zhang Z. CHLORIDE CHANNEL-b mediates vacuolar nitrate efflux to improve low nitrogen adaptation in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:1987-2002. [PMID: 37527482 DOI: 10.1093/plphys/kiad438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/15/2023] [Accepted: 07/02/2023] [Indexed: 08/03/2023]
Abstract
The vacuole is an important organelle for nitrate storage, and the reuse of vacuolar nitrate under nitrate starvation helps plants adapt to low-nitrate environments. CHLORIDE CHANNEL-b (CLC-b) in the vacuolar membrane is a nitrate transporter; however, its regulation and effects on nitrate efflux have not been established. Here, we evaluated CLC-b expression and its effects on physiological parameters under low nitrate conditions. CLC-b expression increased significantly in the roots of wild-type Arabidopsis (Arabidopsis thaliana) Col-0 under nitrate starvation. Under low nitrate, clcb mutants showed reductions in chlorophyll content and xylem sap nitrate concentration, shoot/root nitrate ratios, shoot/root total N ratios, and biomass. CLC-b-overexpression yielded opposite phenotypes and increased nitrogen use efficiency. CLC-b mutants showed elevated chlorate tolerance and an increased proportion of vacuolar nitrate relative to the total protoplast nitrate content as compared to the wild type. Yeast 1-hybrid, EMSA, and chromatin immunoprecipitation (ChIP) experiments showed that HRS1 HOMOLOG2 (HHO2), the expression of which is downregulated under low nitrate, binds directly to the promoter of CLC-b. clcb/hho2 double mutants and HHO2-overexpressing clcb plants had similar phenotypes under low nitrate to those of clcb single mutants. Thus, CLC-b mediates vacuolar nitrate efflux and is negatively regulated by HHO2, providing a theoretical basis for improving plant adaptability to low nitrate.
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Affiliation(s)
- Yujiao Shi
- College of Resources, Hunan Agricultural University, Changsha 410128, China
| | - Dong Liu
- College of Resources, Hunan Agricultural University, Changsha 410128, China
| | - Yiqi He
- College of Resources, Hunan Agricultural University, Changsha 410128, China
| | - Jing Tang
- College of Resources, Hunan Agricultural University, Changsha 410128, China
| | - Haifei Chen
- College of Resources, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha 410128, China
| | - Pan Gong
- College of Resources, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha 410128, China
| | - Jin-Song Luo
- College of Resources, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha 410128, China
| | - Zhenhua Zhang
- College of Resources, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha 410128, China
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Hu Y, Zeng L, Lv X, Guo J, Li X, Zhang X, Wang D, Wang J, Bi J, Julkowska MM, Li B. NIGT1.4 maintains primary root elongation in response to salt stress through induction of ERF1 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:173-186. [PMID: 37366219 DOI: 10.1111/tpj.16369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Plants employ various molecular mechanisms to maintain primary root elongation upon salt stress. Identification of key functional genes, therein, is important for improving crop salt tolerance. Through analyzing natural variation of the primary root length of Arabidopsis natural population under salt stress, we identified NIGT1.4, encoding an MYB transcription factor, as a novel contributor to maintained root growth under salt stress. Using both T-DNA knockout and functional complementation, NIGT1.4 was confirmed to have a role in promoting primary root growth in response to salt stress. The expression of NIGT1.4 in the root was shown induced by NaCl treatments in an ABA-dependent manner. SnRK2.2 and 2.3 were shown to interact with and phosphorylate NIGT1.4 individually. The growth of the primary root of snrk2.2/2.3/2.6 triple mutant was shown sensitive to salt stress, which was similar to nigt1.4 plants. Using DNA affinity purification sequencing, ERF1, a known positive regulator for primary root elongation and salt tolerance, was identified as a target gene for NIGT1.4. The transcriptional induction of ERF1 by salt stress was shown absent in nigt1.4 background. NIGT1.4 was also confirmed to bind to the promoter region of ERF1 by yeast one-hybrid experiment and to induce the expression of ERF1 by dual-luciferase analysis. All data support the notion that salt- and ABA-elicited NIGT1.4 induces the expression of ERF1 to regulate downstream functional genes that contribute to maintained primary root elongation. NIGT1.4-ERF1, therefore, acts as a signaling node linking regulators for stress resilience and root growth, providing new insights for breeding salt-tolerant crops.
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Affiliation(s)
- Yunfei Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Li Zeng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Xiaodong Lv
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Junhua Guo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Xiaoyan Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Xiaohua Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Dan Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Jingya Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | - Jinlong Bi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
| | | | - Bo Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China
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8
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Zhang Y, Zhang Q, Guo M, Wang X, Li T, Wu Q, Li L, Yi K, Ruan W. NIGT1 represses plant growth and mitigates phosphate starvation signaling to balance the growth response tradeoff in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1874-1889. [PMID: 37096648 DOI: 10.1111/jipb.13496] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Inorganic phosphate (Pi) availability is an important factor which affects the growth and yield of crops, thus an appropriate and effective response to Pi fluctuation is critical. However, how crops orchestrate Pi signaling and growth under Pi starvation conditions to optimize the growth defense tradeoff remains unclear. Here we show that a Pi starvation-induced transcription factor NIGT1 (NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1) controls plant growth and prevents a hyper-response to Pi starvation by directly repressing the expression of growth-related and Pi-signaling genes to achieve a balance between growth and response under a varying Pi environment. NIGT1 directly binds to the promoters of Pi starvation signaling marker genes, like IPS1, miR827, and SPX2, under Pi-deficient conditions to mitigate the Pi-starvation responsive (PSR). It also directly represses the expression of vacuolar Pi efflux transporter genes VPE1/2 to regulate plant Pi homeostasis. We further demonstrate that NIGT1 constrains shoot growth by repressing the expression of growth-related regulatory genes, including brassinolide signal transduction master regulator BZR1, cell division regulator CYCB1;1, and DNA replication regulator PSF3. Our findings reveal the function of NIGT1 in orchestrating plant growth and Pi starvation signaling, and also provide evidence that NIGT1 acts as a safeguard to avoid hyper-response during Pi starvation stress in rice.
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Affiliation(s)
- Yuxin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Beijing, 100081, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Qianqian Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Meina Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing, 100083, China
| | - Xueqing Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Tianjie Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Qingyu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Beijing, 100081, China
| | - Keke Yi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
| | - Wenyuan Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Beijing, 100081, China
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Wang F, Wang Y, Ying L, Lu H, Liu Y, Liu Y, Xu J, Wu Y, Mo X, Wu Z, Mao C. Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1164441. [PMID: 37223782 PMCID: PMC10200874 DOI: 10.3389/fpls.2023.1164441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 05/25/2023]
Abstract
Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. We revealed that N and P shortage inhibit rice growth and uptake of other nutrients. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) suggested that N and Pi deficiency stimulate specific different physiological reactions and also some same physiological processes in rice. We established the transcriptional regulatory network between N and P signaling pathways based on all DEGs. We determined that the transcript levels of 763 core genes changed under both N or P starvation conditions. Among these core genes, we focused on the transcription factor gene NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) and show that its encoded protein is a positive regulator of P homeostasis and a negative regulator of N acquisition in rice. NIGT1 promoted Pi uptake but inhibited N absorption, induced the expression of Pi responsive genes PT2 and SPX1 and repressed the N responsive genes NLP1 and NRT2.1. These results provide new clues about the mechanisms underlying the interaction between plant N and P starvation responses.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Luying Ying
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yijian Liu
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhongchang Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
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Ishizaki T, Ueda Y, Takai T, Maruyama K, Tsujimoto Y. In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111627. [PMID: 36737003 DOI: 10.1016/j.plantsci.2023.111627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/04/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Tillering is an important trait in rice productivity. We introduced mutations into the coding region of rice TEOSINTE BRANCHED1 (OsTB1), which is a negative regulator of tillering, using CRISPR/Cas9. The frameshift mutants exhibited substantially enhanced tillering and produced 3.5 times more panicles than the non-mutated plants at maturity. This enhanced tillering resulted in increased spikelet number; however, grain yields did not increase due to substantially reduced filled grain rate and 1,000-grain weight. In contrast, in-frame mutations in OsTB1 had the effect of slightly increasing tiller numbers, and the in-frame mutants had 40% more panicles than non-mutated plants. The grain yield of in-frame mutants also did not increase on nutrient-rich soil; however, under phosphorus-deficient conditions, where tillering is constrained, the in-frame mutants gave a significantly higher grain yield than non-mutated plants due to higher spikelet number and maintained filled grain rate. Rice grassy tiller1 (OsGT1)/OsHox12, which is directly regulated by OsTB1 to suppress tillering, was moderately down-regulated in in-frame mutants, suggesting that OsTB1 with the in-frame mutation shows partial function of intact OsTB1 in regulating OsGT1/OsHox12. We propose that mildly enhanced tillering by in-frame mutation of OsTB1 can improve grain yield under low phosphorus conditions.
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Affiliation(s)
- Takuma Ishizaki
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa 907-0002, Japan.
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Toshiyuki Takai
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Kyonoshin Maruyama
- Biological Resources and Post-harvest Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Yasuhiro Tsujimoto
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
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11
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Shi X, Cui F, Han X, He Y, Zhao L, Zhang N, Zhang H, Zhu H, Liu Z, Ma B, Zheng S, Zhang W, Liu J, Fan X, Si Y, Tian S, Niu J, Wu H, Liu X, Chen Z, Meng D, Wang X, Song L, Sun L, Han J, Zhao H, Ji J, Wang Z, He X, Li R, Chi X, Liang C, Niu B, Xiao J, Li J, Ling HQ. Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204. MOLECULAR PLANT 2022; 15:1440-1456. [PMID: 35864747 DOI: 10.1016/j.molp.2022.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Studying the regulatory mechanisms that drive nitrogen-use efficiency (NUE) in crops is important for sustainable agriculture and environmental protection. In this study, we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism. By comparative analyses, we found that the high-affinity nitrate transporter gene family had expanded in Triticeae. Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility, providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats. To explore the genetic and molecular mechanisms of high NUE, we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204 (KN9204) and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high- and low-nitrogen conditions. Compared with Jing 411, KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds. Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411, whereas this suppression of gene expression was much lower in KN9204. In addition, KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity. Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411, especially at the reproductive stage. The high NUE of KN9204 is an integrated effect controlled at different levels. Taken together, our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.
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Affiliation(s)
- Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai 264025, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilin He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haidong Zhu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhexin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jiajia Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoli Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuemei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Deyuan Meng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoyan Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Liqiang Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Lijing Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jie Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Hui Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jun Ji
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Zhiguo Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuebin Chi
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Junming Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Yazhou Bay Seed Laboratory of Hainan Province, Sanya 572019, China.
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12
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Wen B, Gong X, Deng W, Chen X, Li D, Fu X, Li L, Tan Q. The apple GARP family gene MdHHO3 regulates the nitrate response and leaf senescence. FRONTIERS IN PLANT SCIENCE 2022; 13:932767. [PMID: 36017256 PMCID: PMC9398197 DOI: 10.3389/fpls.2022.932767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The regulation of plant gene expression by nitrate is a complex regulatory process. Here, we identified 90 GARP family genes in apples by genome-wide analysis. As a member of the GARP gene family, the expression of MdHHO3 (Malus domestica HYPERSENSITIVITY TO LOW PHOSPHATE-ELICITED PRIMARY ROOT SHORTENING1 HOMOLOG 3) is upregulated under N (nitrogen) supply. The results of DNA-binding site analysis and electrophoretic mobility shift assays (EMSA) showed that MdHHO3 binds to the motif-containing GAATC. Furthermore, MdHHO3 binds to its promoter sequence and inhibits its activity. In addition, the overexpression of MdHHO3 in apple calli resulted in less accumulation of nitrate in 35S:MdHHO3-GFP calli and downregulated the expression of the nitrate transport-related genes but upregulated the expression of the nitrate assimilation-related genes. Similarly, the expression of the nitrate transport-related genes was downregulated and the expression of the nitrate assimilation-related genes was upregulated in MdHHO3 overexpression Arabidopsis and tobacco plants. Interaction experiments showed that MdHHO3 could bind to the promoter MdNRT2.1 (NITRATE TRANSPORTER 2.1) and negatively regulate its expression. Moreover, the exposure of MdHHO3-overexpressing Arabidopsis and tobacco to nitrate deficiency resulted in an early senescence phenotype as compared to the WT plants. These results show that MdHHO3 can not only negatively regulate nitrate accumulation in response to nitrate but also promote early leaf senescence under nitrate deficiency. This information may be useful to further reveal the mechanism of the nitrate response and demonstrates that nitrate deficiency induces leaf senescence in apples.
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Affiliation(s)
- Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xingyao Gong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Wenpeng Deng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
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13
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Yue C, Chen Q, Hu J, Li C, Luo L, Zeng L. Genome-Wide Identification and Characterization of GARP Transcription Factor Gene Family Members Reveal Their Diverse Functions in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:947072. [PMID: 35845671 PMCID: PMC9280663 DOI: 10.3389/fpls.2022.947072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Golden2, ARR-B, Psr1 (GARP) proteins are plant-specific transcription factors that play vital and diverse roles in plants. However, systematic research on the GARP gene family in plants, including tea plant (Camellia sinensis), is scarce. In this study, a total of 69 GARP genes were identified and characterized from the tea plant genome based on the B-motif sequence signature. The CsGARP genes were clustered into five subfamilies: PHR1/PHL1, KAN, NIGT1/HRS1/HHO, GLK and ARR-B subfamilies. The phylogenetic relationships, gene structures, chromosomal locations, conserved motifs and regulatory cis-acting elements of the CsGARP family members were comprehensively analyzed. The expansion of CsGARP genes occurred via whole-genome duplication/segmental duplication, proximal duplication, and dispersed duplication under purifying selective pressure. The expression patterns of the CsGARP genes were systematically explored from various perspectives: in different tissues during different seasons; in different leaf color stages of tea plant; under aluminum treatment and nitrogen treatment; and in response to abiotic stresses such as cold, drought and salt and to biotic stress caused by Acaphylla theae. The results demonstrate that CsGARP family genes are ubiquitously expressed and play crucial roles in the regulation of growth and development of tea plant and the responses to environmental stimuli. Collectively, these results not only provide valuable information for further functional investigations of CsGARPs in tea plant but also contribute to broadening our knowledge of the functional diversity of GARP family genes in plants.
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Affiliation(s)
- Chuan Yue
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Congcong Li
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liyong Luo
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
| | - Liang Zeng
- College of Food Science, Tea Research Institute, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-built by Sichuan and Chongqing, Southwest University, Chongqing, China
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14
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Zhou Y, Kishchenko O, Stepanenko A, Chen G, Wang W, Zhou J, Pan C, Borisjuk N. The Dynamics of NO3- and NH4+ Uptake in Duckweed Are Coordinated with the Expression of Major Nitrogen Assimilation Genes. PLANTS (BASEL, SWITZERLAND) 2021; 11:11. [PMID: 35009015 PMCID: PMC8747334 DOI: 10.3390/plants11010011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 02/05/2023]
Abstract
Duckweed plants play important roles in aquatic ecosystems worldwide. They rapidly accumulate biomass and have potential uses in bioremediation of water polluted by fertilizer runoff or other chemicals. Here we studied the assimilation of two major sources of inorganic nitrogen, nitrate (NO3- ) and ammonium (NH4+), in six duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna turionifera, Lemna minor, and Wolffia globosa. All six duckweed species preferred NH4+ over NO3- and started using NO3- only when NH4+ was depleted. Using the available genome sequence, we analyzed the molecular structure and expression of eight key nitrogen assimilation genes in S. polyrhiza. The expression of genes encoding nitrate reductase and nitrite reductase increased about 10-fold when NO3- was supplied and decreased when NH4+ was supplied. NO3- and NH4+ induced the glutamine synthetase (GS) genes GS1;2 and the GS2 by 2- to 5-fold, respectively, but repressed GS1;1 and GS1;3. NH4+ and NO3- upregulated the genes encoding ferredoxin- and NADH-dependent glutamate synthases (Fd-GOGAT and NADH-GOGAT). A survey of nitrogen assimilation gene promoters suggested complex regulation, with major roles for NRE-like and GAATC/GATTC cis-elements, TATA-based enhancers, GA/CTn repeats, and G-quadruplex structures. These results will inform efforts to improve bioremediation and nitrogen use efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, West Changjiang Road 111, Huai’an 223000, China; (Y.Z.); (O.K.); (A.S.); (G.C.); (W.W.); (J.Z.); (C.P.)
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15
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Wang H, Hou J, Ye P, Hu L, Huang J, Dai Z, Zhang B, Dai S, Que J, Min H, Chen G, Wang Y, Jiang M, Liang Y, Li L, Zhang X, Lai Z. A teosinte-derived allele of a MYB transcription repressor confers multiple disease resistance in maize. MOLECULAR PLANT 2021; 14:1846-1863. [PMID: 34271176 DOI: 10.1016/j.molp.2021.07.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Natural alleles that control multiple disease resistance (MDR) are valuable for crop breeding. However, only one MDR gene has been cloned in maize, and the molecular mechanisms of MDR remain unclear in maize. In this study, through map-based cloning we cloned a teosinte-derived allele of a resistance gene, Mexicana lesion mimic 1 (ZmMM1), which causes a lesion mimic phenotype and confers resistance to northern leaf blight (NLB), gray leaf spot (GLS), and southern corn rust (SCR) in maize. Strong MDR conferred by the teosinte allele is linked with polymorphisms in the 3' untranslated region of ZmMM1 that cause increased accumulation of ZmMM1 protein. ZmMM1 acts as a transcription repressor and negatively regulates the transcription of specific target genes, including ZmMM1-target gene 3 (ZmMT3), which functions as a negative regulator of plant immunity and associated cell death. The successful isolation of the ZmMM1 resistance gene will help not only in developing broad-spectrum and durable disease resistance but also in understanding the molecular mechanisms underlying MDR.
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Affiliation(s)
- Hongze Wang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Jiabao Hou
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Pei Ye
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Long Hu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Junshi Huang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Zhikang Dai
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Sha Dai
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Jiamin Que
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Haoxuan Min
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Yanbo Wang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Min Jiang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yan Liang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Mexico
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China.
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16
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Ueda Y, Sakuraba Y, Yanagisawa S. Environmental Control of Phosphorus Acquisition: A Piece of the Molecular Framework Underlying Nutritional Homeostasis. PLANT & CELL PHYSIOLOGY 2021; 62:573-581. [PMID: 33508134 DOI: 10.1093/pcp/pcab010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 05/22/2023]
Abstract
Homeostasis of phosphorus (P), an essential macronutrient, is vital for plant growth under diverse environmental conditions. Although plants acquire P from the soil as inorganic phosphate (Pi), its availability is generally limited. Therefore, plants employ mechanisms involving various Pi transporters that facilitate efficient Pi uptake against a steep concentration gradient across the plant-soil interface. Among the different types of Pi transporters in plants, some members of the PHOSPHATE TRANSPORTER 1 (PHT1) family, present in the plasma membrane of root epidermal cells and root hairs, are chiefly responsible for Pi uptake from the rhizosphere. Therefore, accurate regulation of PHT1 expression is crucial for the maintenance of P homeostasis. Previous investigations positioned the Pi-dependent posttranslational regulation of PHOSPHATE STARVATION RESPONSE 1 (PHR1) transcription factor activity at the center of the regulatory mechanism controlling PHT1 expression and P homeostasis; however, recent studies indicate that several other factors also regulate the expression of PHT1 to modulate P acquisition and sustain P homeostasis against environmental fluctuations. Together with PHR1, several transcription factors that mediate the availability of other nutrients (such as nitrogen and zinc), light, and stress signals form an intricate transcriptional network to maintain P homeostasis under highly diverse environments. In this review, we summarize this intricate transcriptional network for the maintenance of P homeostasis under different environmental conditions, with a main focus on the mechanisms identified in Arabidopsis.
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Affiliation(s)
- Yoshiaki Ueda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Ohwashi 1-1, Tsukuba, Ibaraki, 305-8686 Japan
| | - Yasuhito Sakuraba
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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17
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Ludewig U, Vatov E, Hedderich D, Neuhäuser B. Adjusting plant nutrient acquisition to fluctuating availability: transcriptional co-regulation of the nitrate and phosphate deprivation responses in roots. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3500-3503. [PMID: 33948653 PMCID: PMC8096598 DOI: 10.1093/jxb/erab131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on: Safi A, Medici A, Szponarski W, Martin F, Clement-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. 2021. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. Journal of Experimental Botany 72, 3881–3901.
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Affiliation(s)
- Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr., Stuttgart, Germany
| | - Emil Vatov
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr., Stuttgart, Germany
| | - Dominik Hedderich
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr., Stuttgart, Germany
| | - Benjamin Neuhäuser
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr., Stuttgart, Germany
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