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Kwiatkowski M, Wong A, Fiderewicz A, Gehring C, Jaworski K. A SNF1-related protein kinase regulatory subunit functions as a molecular tuner. PHYTOCHEMISTRY 2024; 224:114146. [PMID: 38763313 DOI: 10.1016/j.phytochem.2024.114146] [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: 02/10/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/21/2024]
Abstract
Metabolic processes in prokaryotic and eukaryotic organisms are often modulated by kinases which are in turn, dependent on Ca2+ and the cyclic mononucleotides cAMP and cGMP. It has been established that some proteins have both kinase and cyclase activities and that active cyclases can be embedded within the kinase domains. Here, we identified phosphodiesterase (PDE) sites, enzymes that hydrolyse cAMP and cGMP, to AMP and GMP, respectively, in some of these proteins in addition to their kinase/cyclase twin-architecture. As an example, we tested the Arabidopsis thaliana KINγ, a subunit of the SnRK2 kinase, to demonstrate that all three enzymatic centres, adenylate cyclase (AC), guanylate cyclase (GC) and PDE, are catalytically active, capable of generating and hydrolysing cAMP and cGMP. These data imply that the signal output of the KINγ subunit modulates SnRK2, consequently affecting the downstream kinome. Finally, we propose a model where a single protein subunit, KINγ, is capable of regulating cyclic mononucleotide homeostasis, thereby tuning stimulus specific signal output.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland.
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou, 325060, Zhejiang Province, China; Research Center for Integrative Plant Sciences, Wenzhou-Kean University, 88 Daxue Road, Wenzhou, 325060, Zhejiang Province, China.
| | - Adam Fiderewicz
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy.
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100, Toruń, Poland.
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Sun J, Liu H, Blanford JK, Cai Y, Zhai Z, Shanklin J. GRIK phosphorylates and activates KIN10 which also promotes its degradation. FRONTIERS IN PLANT SCIENCE 2024; 15:1375471. [PMID: 38590740 PMCID: PMC10999582 DOI: 10.3389/fpls.2024.1375471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
The sensor kinase Sucrose Non-fermenting-1-Related Kinase 1 (SnRK1) plays a central role in energy and metabolic homeostasis. KIN10 is a major catalytic (α) kinase subunit of SnRK1 regulated by transcription, posttranslational modification, targeted protein degradation, and its subcellular localization. Geminivirus Rep Interacting Kinase 1 and 2 (GRIK1 and 2) are immediate upstream kinases of KIN10. In the transient protein expression assays carried out in Nicotiana benthamiana (N. benthamiana) leaves, GRIK1 not only phosphorylates KIN10 but also simultaneously initiates its degradation. Posttranslational GRIK-mediated KIN10 degradation is dependent on both GRIK kinase activity and phosphorylation of the KIN10 T-loop. KIN10 proteins are significantly enriched in the grik1-1 grik2-1 double mutant, consistent with the transient assays in N. benthamiana. Interestingly. Among the enriched KIN10 proteins from grik1-1 grik2-1, is a longer isoform, putatively derived by alternative splicing which is barely detectable in wild-type plants. The reduced stability of KIN10 upon phosphorylation and activation by GRIK represents a mechanism that enables the KIN10 activity to be rapidly reduced when the levels of intracellular sugar/energy are restored to their set point, representing an important homeostatic control that prevents a metabolic overreaction to low-sugar conditions. Since GRIKs are activating kinases of KIN10, KIN10s in the grik1 grik2 double null mutant background remain un-phosphorylated, with only their basal level of activity, are more stable, and therefore increase in abundance, which also explains the longer isoform KIN10L which is a minor isoform in wild type is clearly detected in the grik1 grik2 double mutant.
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Zhang XQ, Liang YJ, Zhang BQ, Yan MX, Wang ZP, Huang DM, Huang YX, Lei JC, Song XP, Huang DL. Screening of Sugarcane Proteins Associated with Defense against Leifsonia xyli subsp. xyli, Agent of Ratoon Stunting Disease. PLANTS (BASEL, SWITZERLAND) 2024; 13:448. [PMID: 38337981 PMCID: PMC10857455 DOI: 10.3390/plants13030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Sugarcane is the most important sugar crop and one of the leading energy-producing crops in the world. Ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli, poses a huge threat to ratoon crops, causing a significant yield loss in sugarcane. Breeding resistant varieties is considered the most effective and fundamental approach to control RSD in sugarcane. The exploration of resistance genes forms the foundation for breeding resistant varieties through molecular technology. The pglA gene is a pathogenicity gene in L. xyli subsp. xyli, encoding an endopolygalacturonase. In this study, the pglA gene from L. xyli subsp. xyli and related microorganisms was analyzed. Then, a non-toxic, non-autoactivating pglA bait was successfully expressed in yeast cells. Simultaneously the yeast two-hybrid library was generated using RNA from the L. xyli subsp. xyli-infected sugarcane. Screening the library with the pglA bait uncovered proteins that interacted with pglA, primarily associated with ABA pathways and the plant immune system, suggesting that sugarcane employs these pathways to respond to L. xyli subsp. xyli, triggering pathogenicity or resistance. The expression of genes encoding these proteins was also investigated in L. xyli subsp. xyli-infected sugarcane, suggesting multiple layers of regulatory mechanisms in the interaction between sugarcane and L. xyli subsp. xyli. This work promotes the understanding of plant-pathogen interaction and provides target proteins/genes for molecular breeding to improve sugarcane resistance to L. xyli subsp. xyli.
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Affiliation(s)
- Xiao-Qiu Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Yong-Jian Liang
- Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo 532415, China;
| | - Bao-Qing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Mei-Xin Yan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Ze-Ping Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Dong-Mei Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Yu-Xin Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Jing-Chao Lei
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.-Q.Z.); (B.-Q.Z.); (M.-X.Y.); (Z.-P.W.); (D.-M.H.); (Y.-X.H.); (J.-C.L.)
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Yang YY, An XH, Rui L, Liu GD, Tian Y, You CX, Wang XF. MdSnRK1.1 interacts with MdGLK1 to regulate abscisic acid-mediated chlorophyll accumulation in apple. HORTICULTURE RESEARCH 2024; 11:uhad288. [PMID: 38371633 PMCID: PMC10873579 DOI: 10.1093/hr/uhad288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/17/2023] [Indexed: 02/20/2024]
Abstract
Abscisic acid (ABA), as a plant hormone, plays a positive role in leaf chlorosis; however, the underlying molecular mechanism is less known. Our findings provide ABA treatment reduced the chlorophyll accumulation in apple, and Malus × domestica Sucrose Non-fermenting 1-Related Protein Kinase 1.1 (MdSnRK1.1) participates in the process. MdSnRK1.1 interacts with MdGLK1, a GOLDEN2-like transcription factor that orchestrates development of the chloroplast. Furthermore, MdSnRK1.1 affects MdGLK1 protein stability through phosphorylation. We found that Ser468 of MdGLK1 is target site of MdSnRK1.1 phosphorylation. MdSnRK1.1-mediated phosphorylation was critical for MdGLK1 binding to the target gene MdHEMA1 promoters. Collectively, our results demonstrate that ABA activates MdSnRK1.1 to degrade MdGLK1 and inhibit the accumulation of chlorophyll. These findings extend our understanding on how MdSnRK1.1 balances normal growth and hormone response.
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Affiliation(s)
- Yu-Ying Yang
- State Key Laboratory of Crop Biology, Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultral Science, Enshi 445000, China
| | - Xiu-Hong An
- National Engineering Research Center for Agriculture in Northern Mountainous Areas, Agricultural Technology Innovation Center in Mountainous Areas of Hebei Province, Hebei Agricultural University, Baoding 071000, Hebei, China
| | - Lin Rui
- State Key Laboratory of Crop Biology, Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Guo-Dong Liu
- State Key Laboratory of Crop Biology, Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Yi Tian
- National Engineering Research Center for Agriculture in Northern Mountainous Areas, Agricultural Technology Innovation Center in Mountainous Areas of Hebei Province, Hebei Agricultural University, Baoding 071000, Hebei, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
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Fox H, Ben-Dor S, Doron-Faigenboim A, Goldsmith M, Klein T, David-Schwartz R. Carbohydrate dynamics in Populus trees under drought: An expression atlas of genes related to sensing, translocation, and metabolism across organs. PHYSIOLOGIA PLANTARUM 2023; 175:e14001. [PMID: 37882295 DOI: 10.1111/ppl.14001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 10/27/2023]
Abstract
In trees, nonstructural carbohydrates (NSCs) serve as long-term carbon storage and long-distance carbon transport from source to sink. NSC management in response to drought stress is key to our understanding of drought acclimation. However, the molecular mechanisms underlying these processes remain unclear. By combining a transcriptomic approach with NSC quantification in the leaves, stems, and roots of Populus alba under drought stress, we analyzed genes from 29 gene families related to NSC signaling, translocation, and metabolism. We found starch depletion across organs and accumulation of soluble sugars (SS) in the leaves. Activation of the trehalose-6-phosphate/SNF1-related protein kinase (SnRK1) signaling pathway across organs via the suppression of class I TREHALOSE-PHOSPHATE SYNTHASE (TPS) and the expression of class II TPS genes suggested an active response to drought. The expression of SnRK1α and β subunits, and SUCROSE SYNTHASE6 supported SS accumulation in leaves. The upregulation of active transporters and the downregulation of most passive transporters implied a shift toward active sugar transport and enhanced regulation over partitioning. SS accumulation in vacuoles supports osmoregulation in leaves. The increased expression of sucrose synthesis genes and reduced expression of sucrose degradation genes in the roots did not coincide with sucrose levels, implying local sucrose production for energy. Moreover, the downregulation of invertases in the roots suggests limited sucrose allocation from the aboveground organs. This study provides an expression atlas of NSC-related genes that respond to drought in poplar trees, and can be tested in tree improvement programs for adaptation to drought conditions.
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Affiliation(s)
- Hagar Fox
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Shifra Ben-Dor
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tamir Klein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rakefet David-Schwartz
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
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Yue Q, Yang X, Cheng P, He J, Shen W, Li Y, Ma F, Niu C, Guan Q. Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2848. [PMID: 37571003 PMCID: PMC10421076 DOI: 10.3390/plants12152848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
Fruit ripening is governed by a complex regulatory network, and ethylene plays an important role in this process. MdKING1 is a γ subunit of SNF1-related protein kinases (SnRKs), but the function was unclear. Here, we characterized the role of MdKING1 during fruit ripening, which can promote fruit ripening through the ethylene pathway. Our findings reveal that MdKING1 has higher expression in early-ripening cultivars than late-ripening during the early stage of apple fruit development, and its transcription level significantly increased during apple fruit ripening. Overexpression of MdKING1 (MdKING1 OE) in tomatoes could promote early ripening of fruits, with the increase in ethylene content and the loss of fruit firmness. Ethylene inhibitor treatment could delay the fruit ripening of both MdKING1 OE and WT fruits. However, MdKING1 OE fruits turned fruit ripe faster, with an increase in carotenoid content compared with WT. In addition, the expression of genes involved in ethylene biosynthesis (SlACO1, SlACS2, and SlACS4), carotenoid biosynthesis (SlPSY1 and SlGgpps2a), and fruit firmness regulation (SlPG2a, SlPL, and SlCEL2) was also increased in the fruits of MdKING1 OE plants. In conclusion, our results suggest that MdKING1 plays a key role in promoting tomato fruit ripening, thus providing a theoretical basis for apple fruit quality improvement by genetic engineering in the future.
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Affiliation(s)
- Qianyu Yue
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Xinyue Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Pengda Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Yixuan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Chundong Niu
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
| | - Qingmei Guan
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China;
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.Y.); (P.C.); (J.H.); (W.S.); (Y.L.); (F.M.)
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Yang C, Li X, Yang L, Chen S, Liao J, Li K, Zhou J, Shen W, Zhuang X, Bai M, Bassham DC, Gao C. A positive feedback regulation of SnRK1 signaling by autophagy in plants. MOLECULAR PLANT 2023; 16:1192-1211. [PMID: 37408307 DOI: 10.1016/j.molp.2023.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/02/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.
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Affiliation(s)
- Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China; Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xibao Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lianming Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shunquan Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Kailin Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Zhou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Mingyi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Liu H, Wang Q, Xie L, Xu K, Zhang F, Ruan X, Li L, Tan G. Genome-wide identification of cystathionine beta synthase genes in wheat and its relationship with anther male sterility under heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1061472. [PMID: 36589045 PMCID: PMC9795209 DOI: 10.3389/fpls.2022.1061472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Cystathionine beta synthase (CBS) domains containing proteins (CDCPs) plays an important role in plant development through regulation of the thioredoxin system, as well as its ability to respond to biotic and abiotic stress conditions. Despite this, no systematic study has examined the wheat CBS gene family and its relation to high temperature-induced male sterility. In this study, 66 CBS family members were identified in the wheat genome, and their gene or protein sequences were used for subsequent analysis. The TaCBS gene family was found to be unevenly distributed on 21 chromosomes, and they were classified into four subgroups according to their gene structure and phylogeny. The results of collinearity analysis showed that there were 25 shared orthologous genes between wheat, rice and Brachypodium distachyon, and one shared orthologous gene between wheat, millet and barley. The cis-regulatory elements of the TaCBS were related to JA, IAA, MYB, etc. GO and KEGG pathway analysis identified these TaCBS genes to be associated with pollination, reproduction, and signaling and cellular processes, respectively. A heatmap of wheat plants based on transcriptome data showed that TaCBS genes were expressed to a higher extent in spikelets relative to other tissues. In addition, 29 putative tae-miRNAs were identified, targeting 41 TaCBS genes. Moreover, qRT-PCR validation of six TaCBS genes indicated their critical role in anther development, as five of them were expressed at lower levels in heat-stressed male sterile anthers than in Normal anthers. Together with anther phenotypes, paraffin sections, starch potassium iodide staining, and qRT-PCR data, we hypothesized that the TaCBS gene has a very important connection with the heat-stressed sterility process in wheat, and these data provide a basis for further insight into their relationship.
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Affiliation(s)
- Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qi Wang
- School of Network Engineering, Zhoukou Normal University, Zhoukou, Henan, China
| | - Liuyong Xie
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Institute of Plant Protection and Edible Mushrooms, Zhoukou Academy of Agricultural Sciences, Zhoukou, Henan, China
| | - Xianle Ruan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
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9
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Gutierrez-Beltran E, Crespo JL. Compartmentalization, a key mechanism controlling the multitasking role of the SnRK1 complex. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7055-7067. [PMID: 35861169 PMCID: PMC9664234 DOI: 10.1093/jxb/erac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
SNF1-related protein kinase 1 (SnRK1), the plant ortholog of mammalian AMP-activated protein kinase/fungal (yeast) Sucrose Non-Fermenting 1 (AMPK/SNF1), plays a central role in metabolic responses to reduced energy levels in response to nutritional and environmental stresses. SnRK1 functions as a heterotrimeric complex composed of a catalytic α- and regulatory β- and βγ-subunits. SnRK1 is a multitasking protein involved in regulating various cellular functions, including growth, autophagy, stress response, stomatal development, pollen maturation, hormone signaling, and gene expression. However, little is known about the mechanism whereby SnRK1 ensures differential execution of downstream functions. Compartmentalization has been recently proposed as a new key mechanism for regulating SnRK1 signaling in response to stimuli. In this review, we discuss the multitasking role of SnRK1 signaling associated with different subcellular compartments.
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Affiliation(s)
| | - Jose L Crespo
- Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, Sevilla, Spain
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10
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Van Leene J, Eeckhout D, Gadeyne A, Matthijs C, Han C, De Winne N, Persiau G, Van De Slijke E, Persyn F, Mertens T, Smagghe W, Crepin N, Broucke E, Van Damme D, Pleskot R, Rolland F, De Jaeger G. Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins. NATURE PLANTS 2022; 8:1245-1261. [PMID: 36376753 DOI: 10.1038/s41477-022-01269-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kinases as SnRK1, corroborating the relation of SnRK1 with metabolic enzymes and transcriptional regulators, while also pointing to SnRK1 control of intracellular trafficking. Next, we integrated affinity purification, proximity labelling and crosslinking mass spectrometry to map the protein interaction landscape, composition and structure of the SnRK1 heterotrimer, providing insight in its plant-specific regulation. At the intersection of this multi-dimensional interactome, we discovered a strong association of SnRK1 with class II T6P synthase (TPS)-like proteins. Biochemical and cellular assays show that TPS-like proteins function as negative regulators of SnRK1. Next to stable interactions with the TPS-like proteins, similar intricate connections were found with known regulators, suggesting that plants utilize an extended kinase complex to fine-tune SnRK1 activity for optimal responses to metabolic stress.
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Affiliation(s)
- Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Astrid Gadeyne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Caroline Matthijs
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Han
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Nancy De Winne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Persiau
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Eveline Van De Slijke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Freya Persyn
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Toon Mertens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smagghe
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Ellen Broucke
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Daniël Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Roman Pleskot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Heverlee-Leuven, Belgium
- KU Leuven Plant Institute-LPI, Heverlee-Leuven, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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11
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Baudry K, Barbut F, Domenichini S, Guillaumot D, Thy MP, Vanacker H, Majeran W, Krieger-Liszkay A, Issakidis-Bourguet E, Lurin C. Adenylates regulate Arabidopsis plastidial thioredoxin activities through the binding of a CBS domain protein. PLANT PHYSIOLOGY 2022; 189:2298-2314. [PMID: 35736508 PMCID: PMC9342986 DOI: 10.1093/plphys/kiac199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Cystathionine-β-synthase (CBS) domains are found in proteins of all living organisms and have been proposed to play a role as energy sensors regulating protein activities through their adenosyl ligand binding capacity. In plants, members of the CBSX protein family carry a stand-alone pair of CBS domains. In Arabidopsis (Arabidopsis thaliana), CBSX1 and CBSX2 are targeted to plastids where they have been proposed to regulate thioredoxins (TRXs). TRXs are ubiquitous cysteine thiol oxido-reductases involved in the redox-based regulation of numerous enzymatic activities as well as in the regeneration of thiol-dependent peroxidases. In Arabidopsis, 10 TRX isoforms have been identified in plastids and divided into five sub-types. Here, we show that CBSX2 specifically inhibits the activities of m-type TRXs toward two chloroplast TRX-related targets. By testing activation of NADP-malate dehydrogenase and reduction of 2-Cys peroxiredoxin, we found that TRXm1/2 inhibition by CBSX2 was alleviated in the presence of AMP or ATP. We also determined, by pull-down assays, a direct interaction of CBSX2 with reduced TRXm1 and m2 that was abolished in the presence of adenosyl ligands. In addition, we report that, compared with wild-type plants, the Arabidopsis T-DNA double mutant cbsx1 cbsx2 exhibits growth and chlorophyll accumulation defects in cold conditions, suggesting a function of plastidial CBSX proteins in plant stress adaptation. Together, our results show an energy-sensing regulation of plastid TRX m activities by CBSX, possibly allowing a feedback regulation of ATP homeostasis via activation of cyclic electron flow in the chloroplast, to maintain a high energy level for optimal growth.
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Affiliation(s)
- Kevin Baudry
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Félix Barbut
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | | | - Damien Guillaumot
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Mai Pham Thy
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Hélène Vanacker
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Wojciech Majeran
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Anja Krieger-Liszkay
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | | | - Claire Lurin
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
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12
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Zacharaki V, Ponnu J, Crepin N, Langenecker T, Hagmann J, Skorzinski N, Musialak‐Lange M, Wahl V, Rolland F, Schmid M. Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant. THE NEW PHYTOLOGIST 2022; 235:220-233. [PMID: 35306666 PMCID: PMC9320823 DOI: 10.1111/nph.18104] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/09/2022] [Indexed: 05/19/2023]
Abstract
Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.
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Affiliation(s)
- Vasiliki Zacharaki
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
| | - Jathish Ponnu
- Department of Molecular BiologyMax Planck Institute for Developmental BiologySpemannstr. 3572076TübingenGermany
- Institute for Plant SciencesCologne BiocenterUniversität zu KölnZülpicher Straße 47b50674KölnGermany
| | - Nathalie Crepin
- Laboratory for Molecular Plant BiologyBiology DepartmentUniversity of Leuven–KU LeuvenKasteelpark Arenberg 313001Heverlee‐LeuvenBelgium
- KU Leuven Plant Institute (LPI)3001Heverlee‐LeuvenBelgium
| | - Tobias Langenecker
- Department of Molecular BiologyMax Planck Institute for Developmental BiologySpemannstr. 3572076TübingenGermany
| | - Jörg Hagmann
- Department of Molecular BiologyMax Planck Institute for Developmental BiologySpemannstr. 3572076TübingenGermany
| | - Noemi Skorzinski
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
- Department of Molecular BiologyMax Planck Institute for Developmental BiologySpemannstr. 3572076TübingenGermany
| | - Magdalena Musialak‐Lange
- Department of Plant Reproductive Biology and EpigeneticsMax Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476PotsdamGermany
| | - Vanessa Wahl
- Department of Plant Reproductive Biology and EpigeneticsMax Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476PotsdamGermany
| | - Filip Rolland
- Laboratory for Molecular Plant BiologyBiology DepartmentUniversity of Leuven–KU LeuvenKasteelpark Arenberg 313001Heverlee‐LeuvenBelgium
- KU Leuven Plant Institute (LPI)3001Heverlee‐LeuvenBelgium
| | - Markus Schmid
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
- Department of Molecular BiologyMax Planck Institute for Developmental BiologySpemannstr. 3572076TübingenGermany
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13
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Upadhyaya HD, Wang L, Prakash CS, Liu Y, Gao L, Meng R, Seetharam K, Gowda CLL, Ganesamurthy K, Singh SK, Kumar R, Li J, Wang YH. Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3584-3596. [PMID: 35290448 DOI: 10.1093/jxb/erac110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.
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Affiliation(s)
- Hari D Upadhyaya
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | | | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Li Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Ruirui Meng
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Kaliyamoorthy Seetharam
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | - C L Laxmipathi Gowda
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | | | - Shailesh Kumar Singh
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | - Rajendra Kumar
- Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
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14
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Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
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15
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Ali F, Li Y, Li F, Wang Z. Genome-wide characterization and expression analysis of cystathionine β-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.). Int J Biol Macromol 2021; 193:823-837. [PMID: 34687765 DOI: 10.1016/j.ijbiomac.2021.10.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Cystathionine β-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.
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Affiliation(s)
- Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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16
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Tan Q, Li S, Zhang Y, Chen M, Wen B, Jiang S, Chen X, Fu X, Li D, Wu H, Wang Y, Xiao W, Li L. Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach. HORTICULTURE RESEARCH 2021; 8:213. [PMID: 34593767 PMCID: PMC8484544 DOI: 10.1038/s41438-021-00648-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/18/2021] [Accepted: 06/13/2021] [Indexed: 05/09/2023]
Abstract
Prunus species include many important perennial fruit crops, such as peach, plum, apricot, and related wild species. Here, we report de novo genome assemblies for five species, including the cultivated species peach (Prunus persica), plum (Prunus salicina), and apricot (Prunus armeniaca), and the wild peach species Tibetan peach (Prunus mira) and Chinese wild peach (Prunus davidiana). The genomes ranged from 240 to 276 Mb in size, with contig N50 values of 2.27-8.30 Mb and 25,333-27,826 protein-coding gene models. As the phylogenetic tree shows, plum diverged from its common ancestor with peach, wild peach species, and apricot ~7 million years ago (MYA). We analyzed whole-genome resequencing data of 417 peach accessions, called 3,749,618 high-quality SNPs, 577,154 small indels, 31,800 deletions, duplications, and inversions, and 32,338 insertions, and performed a structural variant-based genome-wide association study (GWAS) of key agricultural traits. From our GWAS data, we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor, where a large inversion event correlates with higher OVATE expression in flat-shaped accessions. Furthermore, a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions. We also identified a locus encoding microRNA172d, where insertion of a transposable element into its promoter was found in double-flower accessions. Thus, our efforts have suggested roles for OVATE, a NAC transcription factor, and microRNA172d in fruit shape, fruit development period, and floral morphology, respectively, that can be connected to traits in other crops, thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species. In general, these genomic resources will facilitate functional genomics, evolutionary research, and agronomic improvement of these five and other Prunus species. We believe that structural variant-based GWASs can also be used in other plants, animal species, and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.
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Affiliation(s)
- Qiuping Tan
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Sen Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Yuzheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Min Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, People's Republic of China
| | - Binbin Wen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Shan Jiang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Xiude Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Xiling Fu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Dongmei Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China
| | - Hongyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Yong Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Wei Xiao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China.
| | - Ling Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Tai'an, 271018, People's Republic of China.
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17
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Jamsheer K M, Kumar M, Srivastava V. SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6042-6065. [PMID: 33693699 DOI: 10.1093/jxb/erab079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Manoj Kumar
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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18
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Abstract
Nutrients are vital to life through intertwined sensing, signaling, and metabolic processes. Emerging research focuses on how distinct nutrient signaling networks integrate and coordinate gene expression, metabolism, growth, and survival. We review the multifaceted roles of sugars, nitrate, and phosphate as essential plant nutrients in controlling complex molecular and cellular mechanisms of dynamic signaling networks. Key advances in central sugar and energy signaling mechanisms mediated by the evolutionarily conserved master regulators HEXOKINASE1 (HXK1), TARGET OF RAPAMYCIN (TOR), and SNF1-RELATED PROTEIN KINASE1 (SNRK1) are discussed. Significant progress in primary nitrate sensing, calcium signaling, transcriptome analysis, and root-shoot communication to shape plant biomass and architecture are elaborated. Discoveries on intracellular and extracellular phosphate signaling and the intimate connections with nitrate and sugar signaling are examined. This review highlights the dynamic nutrient, energy, growth, and stress signaling networks that orchestrate systemwide transcriptional, translational, and metabolic reprogramming, modulate growth and developmental programs, and respond to environmental cues. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
| | - Kun-Hsiang Liu
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; , .,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, and Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA; ,
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19
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Yu W, Peng F, Wang W, Liang J, Xiao Y, Yuan X. SnRK1 phosphorylation of SDH positively regulates sorbitol metabolism and promotes sugar accumulation in peach fruit. TREE PHYSIOLOGY 2021; 41:1077-1086. [PMID: 33576402 PMCID: PMC8190949 DOI: 10.1093/treephys/tpaa163] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/11/2020] [Indexed: 05/07/2023]
Abstract
Fruit quality depends largely on the type and amount of sugar accumulated in the fruit. In peach [Prunus persica (L.) Batsch], sorbitol is the main photosynthetic product and plays a crucial role in sugar metabolism. As a conserved energy sensor, SNF1-related kinase 1 (SnRK1) is involved in the regulation of carbon metabolism. In this study, SnRK1 was able to respond to induction by treatment with exogenous trehalose and sorbitol on 'Ruipan 17' peach fruit. After treatment with 100-mM trehalose for 3 h, the SnRK1 activity decreased by 18% and the activities of sorbitol dehydrogenase (SDH) and sucrose synthase (SS) also decreased significantly, but sucrose phosphate synthase (SPS) activity increased significantly; whereas sorbitol treatment under the same conditions resulted in a 12.6% increase in SnRK1 activity and the activities of SDH and SS synthase also increased significantly, compared with the control. The contents of glucose, fructose and sucrose in peach fruit increased significantly after 3 h of sorbitol treatment. In addition, the interactions between PpSnRK1α and enzymes PpSDH and PpSPS were confirmed by yeast two-hybrid method and the phosphorylation of PpSnRK1α and PpSDH was detected in vitro. Taken together, these results suggest that SnRK1 promotes sorbitol metabolism by activating SDH and it also regulates the activities of SS and SPS that enhance sucrose accumulation in peach fruit. SnRK1 protein kinase is involved in sugar metabolism and has the potential to be used for improving fruit quality.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Biology and Molecular Biology in University of Shandong, College of Biological and Agricultural Engineering, Weifang University, Weifang, Shandong 261061, China
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong 271000, China
| | | | - Wenru Wang
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong 271000, China
| | - Jiahui Liang
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong 271000, China
| | | | - Xuefeng Yuan
- College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271000, China
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20
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Fichtner F, Dissanayake IM, Lacombe B, Barbier F. Sugar and Nitrate Sensing: A Multi-Billion-Year Story. TRENDS IN PLANT SCIENCE 2021; 26:352-374. [PMID: 33281060 DOI: 10.1016/j.tplants.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 05/03/2023]
Abstract
Sugars and nitrate play a major role in providing carbon and nitrogen in plants. Understanding how plants sense these nutrients is crucial, most notably for crop improvement. The mechanisms underlying sugar and nitrate sensing are complex and involve moonlighting proteins such as the nitrate transporter NRT1.1/NFP6.3 or the glycolytic enzyme HXK1. Major components of nutrient signaling, such as SnRK1, TOR, and HXK1, are relatively well conserved across eukaryotes, and the diversification of components such as the NRT1 family and the SWEET sugar transporters correlates with plant terrestrialization. In plants, Tre6P plays a hormone-like role in plant development. In addition, nutrient signaling has evolved to interact with the more recent hormone signaling, allowing fine-tuning of physiological and developmental responses.
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Affiliation(s)
- Franziska Fichtner
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Benoit Lacombe
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Francois Barbier
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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21
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Guo J, Cao K, Yao JL, Deng C, Li Y, Zhu G, Fang W, Chen C, Wang X, Wu J, Guo W, Wang L. Reduced expression of a subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1βγ, confers flat fruit abortion in peach by regulating sugar and starch metabolism. BMC PLANT BIOLOGY 2021; 21:88. [PMID: 33568056 PMCID: PMC7877075 DOI: 10.1186/s12870-021-02850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Fruit abortion is a major limiting factor for fruit production. In flat peach, fruit abortion is present in the whole tree of some accessions during early fruit development. However, the physiological factors and genetic mechanism underlying flat fruit abortion remain largely elusive. RESULTS In this study, we have revealed that the fertilization process was accomplished and the reduction of sucrose and starch contents might result in flat fruit abortion. By combining association and gene expression analysis, a key candidate gene, PpSnRK1βγ, was identified. A 1.67-Mb inversion co-segregated with flat fruit shape altered the promoter activity of PpSnRK1βγ, resulting in much lower expression in aborting flat peach. Ectopic transformation in tomato and transient overexpression in peach fruit have shown that PpSnRK1βγ could increase sugar and starch contents. Comparative transcriptome analysis further confirmed that PpSnRK1βγ participated in carbohydrate metabolism. Subcellular localization found that PpSnRK1βγ was located in nucleus. CONCLUSIONS This study provides a possible reason for flat fruit abortion and identified a critical candidate gene, PpSnRK1βγ, that might be responsible for flat fruit abortion in peach. The results will provide great help in peach breeding and facilitate gene identification for fruit abortion in other plant species.
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Affiliation(s)
- Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jinlong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenwu Guo
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
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22
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Zhai Z, Keereetaweep J, Liu H, Xu C, Shanklin J. The Role of Sugar Signaling in Regulating Plant Fatty Acid Synthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:643843. [PMID: 33828577 PMCID: PMC8020596 DOI: 10.3389/fpls.2021.643843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/17/2021] [Indexed: 05/07/2023]
Abstract
Photosynthates such as glucose, sucrose, and some of their derivatives play dual roles as metabolic intermediates and signaling molecules that influence plant cell metabolism. Such sugars provide substrates for de novo fatty acid (FA) biosynthesis. However, compared with the well-defined examples of sugar signaling in starch and anthocyanin synthesis, until recently relatively little was known about the role of signaling in regulating FA and lipid biosynthesis. Recent research progress shows that trehalose 6-phosphate and 2-oxoglutarate (2-OG) play direct signaling roles in the regulation of FA biosynthesis by modulating transcription factor stability and enzymatic activities involved in FA biosynthesis. Specifically, mechanistic links between sucrose non-fermenting-1-related protein kinase 1 (SnRK1)-mediated trehalose 6-phosphate (T6P) sensing and its regulation by phosphorylation of WRI1 stability, diacylglycerol acyltransferase 1 (DGAT1) enzyme activity, and of 2-OG-mediated relief of inhibition of acetyl-CoA carboxylase (ACCase) activity by protein PII are exemplified in detail in this review.
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23
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Li M, Sun X, Di D, Zhang A, Qing L, Zhou T, Miao H, Fan Z. Maize AKINβγ Proteins Interact with P8 of Rice Black Streaked Dwarf Virus and Inhibit Viral Infection. Viruses 2020; 12:v12121387. [PMID: 33291518 PMCID: PMC7761811 DOI: 10.3390/v12121387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 01/23/2023] Open
Abstract
Rice black streaked dwarf virus (RBSDV) is an important agent causing maize rough dwarf disease, whereas the host factors responding to RBSDV infection are poorly understood. To uncover the molecular interactions between RBSDV and maize, a yeast two-hybrid screen of a maize cDNA library was carried out using the viral P8 protein as a bait. ZmAKINβγ-1 and ZmAKINβγ-2 (βγ subunit of Arabidopsis SNF1 kinase homolog in maize) possessing high sequence similarities (encoded by two gene copies) were identified as interaction partners. Their interactions with P8 were confirmed in both Nicotiana benthamiana cells and maize protoplasts by bimolecular fluorescence complementation assay. The accumulation levels of ZmAKINβγ mRNAs were upregulated at the stage of the viral symptoms beginning to appear and then downregulated. ZmAKINβγs are putative regulatory subunits of the SnRK1 complex, a core regulator for energy homeostasis. Knockdown of ZmAKINβγs in maize regulated the expression levels of the genes involved in sugar synthesis or degradation, and also the contents of both glucose and sucrose. Importantly, downregulation of ZmAKINβγs expressions facilitated the accumulation of RBSDV in maize. These results implicate a role of ZmAKINβγs in the regulation of primary carbohydrate metabolism, and in the defense against RBSDV infection.
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Affiliation(s)
- Mingjun Li
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China; (X.S.); (T.Z.)
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China;
- Correspondence: (M.L.); (Z.F.); Tel.: +86-10-62732771 (Z.F.)
| | - Xi Sun
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China; (X.S.); (T.Z.)
| | - Dianping Di
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China; (D.D.); (A.Z.); (H.M.)
| | - Aihong Zhang
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China; (D.D.); (A.Z.); (H.M.)
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China;
| | - Tao Zhou
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China; (X.S.); (T.Z.)
| | - Hongqin Miao
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China; (D.D.); (A.Z.); (H.M.)
| | - Zaifeng Fan
- State Key Laboratory of Agro-Biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, China; (X.S.); (T.Z.)
- Correspondence: (M.L.); (Z.F.); Tel.: +86-10-62732771 (Z.F.)
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24
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Carianopol CS, Chan AL, Dong S, Provart NJ, Lumba S, Gazzarrini S. An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response. Commun Biol 2020; 3:145. [PMID: 32218501 PMCID: PMC7099082 DOI: 10.1038/s42003-020-0866-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022] Open
Abstract
Yeast Snf1 (Sucrose non-fermenting1), mammalian AMPK (5′ AMP-activated protein kinase) and plant SnRK1 (Snf1-Related Kinase1) are conserved heterotrimeric kinase complexes that re-establish energy homeostasis following stress. The hormone abscisic acid (ABA) plays a crucial role in plant stress response. Activation of SnRK1 or ABA signaling results in overlapping transcriptional changes, suggesting these stress pathways share common targets. To investigate how SnRK1 and ABA interact during stress response in Arabidopsis thaliana, we screened the SnRK1 complex by yeast two-hybrid against a library of proteins encoded by 258 ABA-regulated genes. Here, we identify 125 SnRK1- interacting proteins (SnIPs). Network analysis indicates that a subset of SnIPs form signaling modules in response to abiotic stress. Functional studies show the involvement of SnRK1 and select SnIPs in abiotic stress responses. This targeted study uncovers the largest set of SnRK1 interactors, which can be used to further characterize SnRK1 role in plant survival under stress. Carianopol et al. construct a detailed protein interaction network for the SnRK1 kinase complex to investigate the interaction of SnRK1 and ABA during stress response. They identify 125 proteins that interact with SnRK1, which can be used further to characterise the role of SnRK1 in plant survival under stress.
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Affiliation(s)
- Carina Steliana Carianopol
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.,Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aaron Lorheed Chan
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.,Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Shaowei Dong
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Centre for the Analysis of Genome Evolution and Function, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada. .,Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.
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25
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Martínez-Barajas E, Coello P. Review: How do SnRK1 protein kinases truly work? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110330. [PMID: 31928656 DOI: 10.1016/j.plantsci.2019.110330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
The AMPK/SNF1/SnRK1 family of protein kinases is involved in cellular responses to energy stress. They also interact with molecules of other signaling pathways to regulate many aspects of growth and development. The biochemical, genetic and molecular knowledge of SnRK1 in plants lags behind that of AMPK and SNF1 and is freely extrapolated such that, in many cases, it is assumed that plant enzymes behave in the same way as homologs in other organisms. In this review, we present data that support the evidence that the structural characteristics of the SnRK1 subunits determine the functional properties of the complex. We also discuss results suggesting that the SnRK1 subunits participate in the assembly of different complexes and that not all combinations are equally important. The activity of SnRK1 is dependent on the phosphorylation of SnRK1αThr175 found in the activation loop of the catalytic domain. However, we propose that the phosphorylation of sites close to SnRK1αThr175 might contribute to the fine-tuned regulation of SnRK1 activity and thus requires further evaluation. Finally, we also call attention to the interaction of the SnRK1α with regulatory proteins that are not typically identified as putative substrates. The additional functions of the SnRK1 subunits, in addition to those of the active complex, may be necessary for the cell to respond to the complicated conditions presented by energy stress.
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Affiliation(s)
- Eleazar Martínez-Barajas
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, 04510, Mexico
| | - Patricia Coello
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, 04510, Mexico.
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26
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Rodriguez M, Parola R, Andreola S, Pereyra C, Martínez-Noël G. TOR and SnRK1 signaling pathways in plant response to abiotic stresses: Do they always act according to the "yin-yang" model? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110220. [PMID: 31521220 DOI: 10.1016/j.plantsci.2019.110220] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
Plants are sessile photo-autotrophic organisms continuously exposed to a variety of environmental stresses. Monitoring the sugar level and energy status is essential, since this knowledge allows the integration of external and internal cues required for plant physiological and developmental plasticity. Most abiotic stresses induce severe metabolic alterations and entail a great energy cost, restricting plant growth and producing important crop losses. Therefore, balancing energy requirements with supplies is a major challenge for plants under unfavorable conditions. The conserved kinases target of rapamycin (TOR) and sucrose-non-fermenting-related protein kinase-1 (SnRK1) play central roles during plant growth and development, and in response to environmental stresses; these kinases affect cellular processes and metabolic reprogramming, which has physiological and phenotypic consequences. The "yin-yang" model postulates that TOR and SnRK1 act in opposite ways in the regulation of metabolic-driven processes. In this review, we describe and discuss the current knowledge about the complex and intricate regulation of TOR and SnRK1 under abiotic stresses. We especially focus on the physiological perspective that, under certain circumstances during the plant stress response, the TOR and SnRK1 kinases could be modulated differently from what is postulated by the "yin-yang" concept.
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Affiliation(s)
- Marianela Rodriguez
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Rodrigo Parola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Sofia Andreola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Cintia Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
| | - Giselle Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
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Crepin N, Rolland F. SnRK1 activation, signaling, and networking for energy homeostasis. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:29-36. [PMID: 31030062 DOI: 10.1016/j.pbi.2019.03.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 05/25/2023]
Abstract
The SnRK1 kinases are key regulators of the plant energy balance, but how their activity is regulated by metabolic status is still unclear. While the heterotrimeric kinase complex is well conserved among plants, fungi, and animals, plants appear to have modified its regulation to better fit their unique physiology and lifestyle. The SnRK1 kinases control metabolism, growth, and development, and stress tolerance by direct phosphorylation of metabolic enzymes and regulatory proteins and by extensive transcriptional regulation. Diverse types of transcription factors have already been implicated, with a well-studied role for the heterodimerizing group C and group S1 bZIPs. SnRK1 is also part of a more elaborate metabolic and stress signaling network, which includes the TOR kinase and the ABA-signaling SnRK2 kinases.
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Affiliation(s)
- Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium.
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28
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Chapman K, Taleski M, Ogilvie HA, Imin N, Djordjevic MA. CEP-CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3955-3967. [PMID: 31056646 PMCID: PMC6685651 DOI: 10.1093/jxb/erz207] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/29/2019] [Indexed: 05/22/2023]
Abstract
Lateral root (LR) proliferation is a major determinant of soil nutrient uptake. How resource allocation controls the extent of LR growth remains unresolved. We used genetic, physiological, transcriptomic, and grafting approaches to define a role for C-TERMINALLY ENCODED PEPTIDE RECEPTOR 1 (CEPR1) in controlling sucrose-dependent LR growth. CEPR1 inhibited LR growth in response to applied sucrose, other metabolizable sugars, and elevated light intensity. Pathways through CEPR1 restricted LR growth by reducing LR meristem size and the length of mature LR cells. RNA-sequencing of wild-type (WT) and cepr1-1 roots with or without sucrose treatment revealed an intersection of CEP-CEPR1 signalling with the sucrose transcriptional response. Sucrose up-regulated several CEP genes, supporting a specific role for CEP-CEPR1 in the response to sucrose. Moreover, genes with basally perturbed expression in cepr1-1 overlap with WT sucrose-responsive genes significantly. We found that exogenous CEP inhibited LR growth via CEPR1 by reducing LR meristem size and mature cell length. This result is consistent with CEP-CEPR1 acting to curtail the extent of sucrose-dependent LR growth. Reciprocal grafting indicates that LR growth inhibition requires CEPR1 in both the roots and shoots. Our results reveal a new role for CEP-CEPR1 signalling in controlling LR growth in response to sucrose.
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Affiliation(s)
- Kelly Chapman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Michael Taleski
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Huw A Ogilvie
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- Present address: Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Nijat Imin
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- Present address: School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- Correspondence:
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29
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Ramon M, Dang TVT, Broeckx T, Hulsmans S, Crepin N, Sheen J, Rolland F. Default Activation and Nuclear Translocation of the Plant Cellular Energy Sensor SnRK1 Regulate Metabolic Stress Responses and Development. THE PLANT CELL 2019; 31:1614-1632. [PMID: 31123051 PMCID: PMC6635846 DOI: 10.1105/tpc.18.00500] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/12/2019] [Accepted: 05/06/2019] [Indexed: 05/18/2023]
Abstract
Energy homeostasis is vital to all living organisms. In eukaryotes, this process is controlled by fuel gauging protein kinases: AMP-activated kinase in mammals, Sucrose Non-Fermenting1 (SNF1) in yeast (Saccharomyces cerevisiae), and SNF1-related kinase1 (SnRK1) in plants. These kinases are highly conserved in structure and function and (according to this paradigm) operate as heterotrimeric complexes of catalytic-α and regulatory β- and γ-subunits, responding to low cellular nucleotide charge. Here, we determined that the Arabidopsis (Arabidopsis thaliana) SnRK1 catalytic α-subunit has regulatory subunit-independent activity, which is consistent with default activation (and thus controlled repression), a strategy more generally used by plants. Low energy stress (caused by darkness, inhibited photosynthesis, or hypoxia) also triggers SnRK1α nuclear translocation, thereby controlling induced but not repressed target gene expression to replenish cellular energy for plant survival. The myristoylated and membrane-associated regulatory β-subunits restrict nuclear localization and inhibit target gene induction. Transgenic plants with forced SnRK1α-subunit localization consistently were affected in metabolic stress responses, but their analysis also revealed key roles for nuclear SnRK1 in leaf and root growth and development. Our findings suggest that plants have modified the ancient, highly conserved eukaryotic energy sensor to better fit their unique lifestyle and to more effectively cope with changing environmental conditions.
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Affiliation(s)
- Matthew Ramon
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Tuong Vi T Dang
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
| | - Tom Broeckx
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
| | - Sander Hulsmans
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
| | - Nathalie Crepin
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven, Belgium
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30
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Bruns AN, Li S, Mohannath G, Bisaro DM. Phosphorylation of Arabidopsis eIF4E and eIFiso4E by SnRK1 inhibits translation. FEBS J 2019; 286:3778-3796. [PMID: 31120171 DOI: 10.1111/febs.14935] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 05/21/2019] [Indexed: 01/01/2023]
Abstract
Regulation of protein synthesis is critical for maintaining cellular homeostasis. In mammalian systems, translational regulatory networks have been elucidated in considerable detail. In plants, however, regulation occurs through different mechanisms that remain largely elusive. In this study, we present evidence that the Arabidopsis thaliana energy sensing kinase SnRK1, a homologue of mammalian AMP-activated kinase and yeast sucrose non-fermenting 1 (SNF1), inhibits translation by phosphorylating the cap binding proteins eIF4E and eIFiso4E. We establish that eIF4E and eIFiso4E contain two deeply conserved SnRK1 consensus target sites and that both interact with SnRK1 in vivo. We then demonstrate that SnRK1 phosphorylation inhibits the ability of Arabidopsis eIF4E and eIFiso4E to complement a yeast strain lacking endogenous eIF4E, and that inhibition correlates with repression of polysome formation. Finally, we show that SnRK1 over-expression in Nicotiana benthamiana plants reduces polysome formation, and that this effect can be counteracted by transient expression of eIF4E or mutant eIF4E containing non-phosphorylatable SnRK1 target residues, but not by a phosphomimic eIF4E. Together, these studies elucidate a novel and direct pathway for translational control in plant cells. In light of previous findings that SnRK1 conditions an innate antiviral defense and is inhibited by geminivirus pathogenicity factors, we speculate that phosphorylation of cap binding proteins may be a component of the resistance mechanism.
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Affiliation(s)
- Aaron N Bruns
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Sizhun Li
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Gireesha Mohannath
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
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31
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Jamsheer K M, Jindal S, Laxmi A. Evolution of TOR-SnRK dynamics in green plants and its integration with phytohormone signaling networks. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2239-2259. [PMID: 30870564 DOI: 10.1093/jxb/erz107] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/26/2019] [Indexed: 05/07/2023]
Abstract
The target of rapamycin (TOR)-sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) signaling is an ancient regulatory mechanism that originated in eukaryotes to regulate nutrient-dependent growth. Although the TOR-SnRK1 signaling cascade shows highly conserved functions among eukaryotes, studies in the past two decades have identified many important plant-specific innovations in this pathway. Plants also possess SnRK2 and SnRK3 kinases, which originated from the ancient SnRK1-related kinases and have specialized roles in controlling growth, stress responses and nutrient homeostasis in plants. Recently, an integrative picture has started to emerge in which different SnRKs and TOR kinase are highly interconnected to control nutrient and stress responses of plants. Further, these kinases are intimately involved with phytohormone signaling networks that originated at different stages of plant evolution. In this review, we highlight the evolution and divergence of TOR-SnRK signaling components in plants and their communication with each other as well as phytohormone signaling to fine-tune growth and stress responses in plants.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Noida, India
| | - Sunita Jindal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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32
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Margalha L, Confraria A, Baena-González E. SnRK1 and TOR: modulating growth-defense trade-offs in plant stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2261-2274. [PMID: 30793201 DOI: 10.1093/jxb/erz066] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/07/2019] [Indexed: 05/11/2023]
Abstract
The evolutionarily conserved protein kinase complexes SnRK1 and TOR are central metabolic regulators essential for plant growth, development, and stress responses. They are activated by opposite signals, and the outcome of their activation is, in global terms, antagonistic. Similarly to their yeast and animal counterparts, SnRK1 is activated by the energy deficit often associated with stress to restore homeostasis, while TOR is activated in nutrient-rich conditions to promote growth. Recent evidence suggests that SnRK1 represses TOR in plants, revealing evolutionary conservation also in their crosstalk. Given their importance for integrating environmental information into growth and developmental programs, these signaling pathways hold great promise for reducing the growth penalties caused by stress. Here we review the literature connecting SnRK1 and TOR to plant stress responses. Although SnRK1 and TOR emerge mostly as positive regulators of defense and growth, respectively, the outcome of their activities in plant growth and performance is not always straightforward. Manipulation of both pathways under similar experimental setups, as well as further biochemical and genetic analyses of their molecular and functional interaction, is essential to fully understand the mechanisms through which these two metabolic pathways contribute to stress responses, growth, and development.
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Affiliation(s)
- Leonor Margalha
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
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Zúñiga-Sánchez E, Rodríguez-Sotres R, Coello P, Martínez-Barajas E. Effect of catalytic subunit phosphorylation on the properties of SnRK1 from Phaseolus vulgaris embryos. PHYSIOLOGIA PLANTARUM 2019; 165:632-643. [PMID: 29766514 DOI: 10.1111/ppl.12761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Legume seed development represents a high demand for energy and metabolic resources to support the massive synthesis of starch and proteins. However, embryo growth occurs in an environment with reduced O2 that forces the plant to adapt its metabolic activities to maximize efficient energy use. SNF1-related protein kinase1 (SnRK1) is a master metabolic regulator needed for cells adaptation to conditions that reduce energy availability, and its activity is needed for the successful development of seeds. In bean embryo extracts, SnRK1 can be separated by anion exchange chromatography into two pools: one where the catalytic subunit is phosphorylated (SnRK1-p) and another with reduced phosphorylation (SnRK1-np). The phosphorylation of the catalytic subunit produces a large increase in SnRK1 activity but has a minor effect in determining its sensitivity to metabolic inhibitors such as trehalose 6-P (T6P), ADP-glucose (ADPG), glucose 1-P (G1P) and glucose 6-P (G6P). In Arabidopsis thaliana, upstream activating kinases (SnAK) phosphorylate the SnRK1 catalytic subunit at T175/176, promoting and enhancing its activity. Recombinant Phaseolus vulgaris homologous to SnAK proteins (PvSnAK), can phosphorylate and activate the catalytic domains of the α-subunits of Arabidopsis, as well as the SnRK1-np pool purified from bean embryos. While the phosphorylation process is extremely efficient for catalytic domains, the phosphorylation of the SnRK1-np complex was less effective but produced a significant increase in activity. The presence of SnRK1-np could contribute to a quick response to unexpected adverse conditions. However, in addition to PvSnAK kinases, other factors might contribute to regulating the activation of SnRK1.
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Affiliation(s)
- Esther Zúñiga-Sánchez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México, DF, 04510, Mexico
| | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México, DF, 04510, Mexico
| | - Patricia Coello
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México, DF, 04510, Mexico
| | - Eleazar Martínez-Barajas
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México, DF, 04510, Mexico
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Janse van Rensburg HC, Van den Ende W, Signorelli S. Autophagy in Plants: Both a Puppet and a Puppet Master of Sugars. FRONTIERS IN PLANT SCIENCE 2019; 10:14. [PMID: 30723485 PMCID: PMC6349728 DOI: 10.3389/fpls.2019.00014] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
Autophagy is a major pathway that recycles cellular components in eukaryotic cells both under stressed and non-stressed conditions. Sugars participate both metabolically and as signaling molecules in development and response to various environmental and nutritional conditions. It is therefore essential to maintain metabolic homeostasis of sugars during non-stressed conditions in cells, not only to provide energy, but also to ensure effective signaling when exposed to stress. In both plants and animals, autophagy is activated by the energy sensor SnRK1/AMPK and inhibited by TOR kinase. SnRK1/AMPK and TOR kinases are both important regulators of cellular metabolism and are controlled to a large extent by the availability of sugars and sugar-phosphates in plants whereas in animals AMP/ATP indirectly translate sugar status. In plants, during nutrient and sugar deficiency, SnRK1 is activated, and TOR is inhibited to allow activation of autophagy which in turn recycles cellular components in an attempt to provide stress relief. Autophagy is thus indirectly regulated by the nutrient/sugar status of cells, but also regulates the level of nutrients/sugars by recycling cellular components. In both plants and animals sugars such as trehalose induce autophagy and in animals this is independent of the TOR pathway. The glucose-activated G-protein signaling pathway has also been demonstrated to activate autophagy, although the exact mechanism is not completely clear. This mini-review will focus on the interplay between sugar signaling and autophagy.
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Affiliation(s)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
| | - Santiago Signorelli
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
- Departamento de Biologiía Vegetal, Facultad de Agronomía, Universidad de la Repuíblica, Montevideo, Uruguay
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35
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Van Dingenen J, Vermeersch M, De Milde L, Hulsmans S, De Winne N, Van Leene J, Gonzalez N, Dhondt S, De Jaeger G, Rolland F, Inzé D. The role of HEXOKINASE1 in Arabidopsis leaf growth. PLANT MOLECULAR BIOLOGY 2019; 99:79-93. [PMID: 30511331 DOI: 10.1007/s11103-018-0803-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Here, we used a hxk1 mutant in the Col-0 background. We demonstrated that HXK1 regulates cell proliferation and expansion early during leaf development, and that HXK1 is involved in sucrose-induced leaf growth stimulation independent of GPT2. Furthermore, we identified KINγ as a novel HXK1-interacting protein. In the last decade, extensive efforts have been made to unravel the underlying mechanisms of plant growth control through sugar availability. Signaling by the conserved glucose sensor HEXOKINASE1 (HXK1) has been shown to exert both growth-promoting and growth-inhibitory effects depending on the sugar levels, the environmental conditions and the plant species. Here, we used a hxk1 mutant in the Col-0 background to investigate the role of HXK1 during leaf growth in more detail and show that it is affected in both cell proliferation and cell expansion early during leaf development. Furthermore, the hxk1 mutant is less sensitive to sucrose-induced cell proliferation with no significant increase in final leaf growth after transfer to sucrose. Early during leaf development, transfer to sucrose stimulates expression of GLUCOSE-6-PHOSPHATE/PHOSPHATE TRANSPORTER2 (GPT2) and represses chloroplast differentiation. However, in the hxk1 mutant GPT2 expression was still upregulated by transfer to sucrose although chloroplast differentiation was not affected, suggesting that GPT2 is not involved in HXK1-dependent regulation of leaf growth. Finally, using tandem affinity purification of protein complexes from cell cultures, we identified KINγ, a protein containing four cystathionine β-synthase domains, as an interacting protein of HXK1.
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Affiliation(s)
- Judith Van Dingenen
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Mattias Vermeersch
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Liesbeth De Milde
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Sander Hulsmans
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Nancy De Winne
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Jelle Van Leene
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Stijn Dhondt
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Geert De Jaeger
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 927, 9052, Gent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
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36
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Jamsheer K M, Shukla BN, Jindal S, Gopan N, Mannully CT, Laxmi A. The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions. J Biol Chem 2018; 293:13134-13150. [PMID: 29945970 DOI: 10.1074/jbc.ra118.002073] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/05/2018] [Indexed: 11/06/2022] Open
Abstract
The SNF1-related protein kinase 1 (SnRK1) is a heterotrimeric eukaryotic kinase that interacts with diverse proteins and regulates their activity in response to starvation and stress signals. Recently, the FCS-like zinc finger (FLZ) proteins were identified as a potential scaffold for SnRK1 in plants. However, the evolutionary and mechanistic aspect of this complex formation is currently unknown. Here, in silico analyses predicted that FLZ proteins possess conserved intrinsically disordered regions (IDRs) with a propensity for protein binding in the N and C termini across the plant lineage. We observed that the Arabidopsis FLZ proteins promiscuously interact with SnRK1 subunits, which formed different isoenzyme complexes. The FLZ domain was essential for mediating the interaction with SnRK1α subunits, whereas the IDRs in the N termini facilitated interactions with the β and βγ subunits of SnRK1. Furthermore, the IDRs in the N termini were important for mediating dimerization of different FLZ proteins. Of note, the interaction of FLZ with SnRK1 was confined to cytoplasmic foci, which colocalized with the endoplasmic reticulum. An evolutionary analysis revealed that in general, the IDR-rich regions are under more relaxed selection than the FLZ domain. In summary, the findings in our study reveal the structural details, origin, and evolution of a land plant-specific scaffold of SnRK1 formed by the coordinated actions of IDRs and structured regions in the FLZ proteins. We propose that the FLZ protein complex might be involved in providing flexibility, thus enhancing the binding repertoire of the SnRK1 hub in land plants.
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Affiliation(s)
- Muhammed Jamsheer K
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Brihaspati N Shukla
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Sunita Jindal
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
| | - Nandu Gopan
- the Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru-560064, India
| | | | - Ashverya Laxmi
- From the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067 and
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37
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Coenen H, Viaene T, Vandenbussche M, Geuten K. TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms. BMC PLANT BIOLOGY 2018; 18:129. [PMID: 29929474 PMCID: PMC6013966 DOI: 10.1186/s12870-018-1349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants. RESULTS We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events. Through knock-down of NbTM8 by virus induced gene silencing in Nicotiana benthamiana, we show that NbTM8 represses miR172 together with another MADS-box gene, SHORT VEGETATIVE PHASE (NbSVP). In the closely related species Petunia hybrida, PhTM8 is not expressed under the conditions we investigated and consistent with this, a knock-out mutant did not show a phenotype. Finally, we generated transgenic tomato plants in which TM8 was silenced or ectopically expressed, but these plants did not display a clear phenotype. Therefore, no clear function could be confirmed for Solanum lycopersium. CONCLUSIONS While the presence of TM8 is generally conserved, it remains difficult to propose a general function in angiosperms. Based on all the available data to date, supplemented with our own results, TM8 function seems to have diversified quickly throughout angiosperms and acts as repressor of miR172 in Nicotiana benthamiana, together with NbSVP.
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Affiliation(s)
- Heleen Coenen
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Tom Viaene
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes, University Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Koen Geuten
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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The UBA domain of SnRK1 promotes activation and maintains catalytic activity. Biochem Biophys Res Commun 2018; 497:127-132. [PMID: 29428737 DOI: 10.1016/j.bbrc.2018.02.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/05/2018] [Indexed: 12/28/2022]
Abstract
Sucrose non-fermenting 1-related protein kinase 1 (SnRK1) is a central metabolic regulator and the plant orthologue of the mammalian AMP-activated protein kinase (AMPK); both are energy-sensing heterotrimeric enzymes comprising a catalytic α- and regulatory β- and γ-subunits. α-Subunits contain a serine/threonine kinase domain (KD) at their N-terminus that is immediately followed by a small regulatory domain termed the auto-inhibitory domain (AID) in AMPK and the ubiquitin-associated domain (UBA) in SnRK1. Association of the AID with the AMPK KD inhibits activating phosphorylation of the KD by upstream kinases and promotes dephosphorylation, as well as inhibiting AMPK catalytic activity. Despite these mechanistic insights regarding the AMPK AID, the SnRK1 UBA regulatory implications have not been investigated. Using recombinant protein comprising either the KD-only or KD-AID/KD-UBA, we found that the UBA of SnRK1 acts in a distinct regulatory manner to its orthologous AID of AMPK. Firstly, the plant upstream kinase GRIK2 preferentially phosphorylates the SnRK1 KD-UBA. Secondly, the SnRK1 KD in the absence of the UBA shows near identical initial catalytic activity to the KD-UBA, but in comparison a rapid loss of catalytic activity is observed. Our findings indicate that the role of the UBA in SnRK1 regulation may be more akin to that of the UBA in the mammalian AMPK-related kinases rather than its immediate functional orthologue, AMPK. This study adds to a growing body of work demonstrating the divergent regulatory mechanisms of the orthologous plant SnRK1 and mammalian AMPK.
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Nietzsche M, Guerra T, Alseekh S, Wiermer M, Sonnewald S, Fernie AR, Börnke F. STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) Interacts with Protein Kinase SnRK1. PLANT PHYSIOLOGY 2018; 176:1773-1792. [PMID: 29192025 PMCID: PMC5813543 DOI: 10.1104/pp.17.01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/27/2017] [Indexed: 05/19/2023]
Abstract
Sucrose nonfermenting related kinase1 (SnRK1) is a conserved energy sensor kinase that regulates cellular adaptation to energy deficit in plants. Activation of SnRK1 leads to the down-regulation of ATP-consuming biosynthetic processes and the stimulation of energy-generating catabolic reactions by transcriptional reprogramming and posttranslational modifications. Although considerable progress has been made during the last years in understanding the SnRK1 signaling pathway, many of its components remain unidentified. Here, we show that the catalytic α-subunits KIN10 and KIN11 of the Arabidopsis (Arabidopsis thaliana) SnRK1 complex interact with the STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) inside the plant cell nucleus. Overexpression of STKR1 in transgenic Arabidopsis plants led to reduced growth, a delay in flowering, and strongly attenuated senescence. Metabolite profiling revealed that the transgenic lines exhausted their carbohydrates during the dark period to a greater extent than the wild type and accumulated a range of amino acids. At the global transcriptome level, genes affected by STKR1 overexpression were broadly associated with systemic acquired resistance, and transgenic plants showed enhanced resistance toward a virulent strain of the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. We discuss a possible connection of STKR1 function, SnRK1 signaling, and plant immunity.
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Affiliation(s)
- Madlen Nietzsche
- Plant Metabolism Group, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany
| | - Tiziana Guerra
- Plant Metabolism Group, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Marcel Wiermer
- University of Goettingen, Albrecht-von-Haller Institute for Plant Sciences, RG Molecular Biology of Plant-Microbe Interactions, 37077 Goettingen, Germany
| | - Sophia Sonnewald
- Friedrich-Alexander-Universität, Department of Biology, Division of Biochemistry, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Frederik Börnke
- Plant Metabolism Group, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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Yu W, Peng F, Xiao Y, Wang G, Luo J. Overexpression of PpSnRK1α in Tomato Promotes Fruit Ripening by Enhancing RIPENING INHIBITOR Regulation Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:1856. [PMID: 30619421 PMCID: PMC6304366 DOI: 10.3389/fpls.2018.01856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/30/2018] [Indexed: 05/14/2023]
Abstract
As a conserved kinase complex, sucrose non-fermenting-1-related protein kinase 1 (SnRK1) is a major regulator of plant growth and development. In our previous study, overexpression of MhSnRK1 in tomato (Solanum lycopersicum L.) modified fruit maturation: the transgenic fruit ripened earlier than the wild type (WT). However, the mechanism by which fruit maturation is regulated by SnRK1 is not clear; therefore, the test materials used were the transgenic tomato lines (OE-1, OE-3, and OE-4) overexpressing the coding gene of peach [Prunus persica (L.) Batsch] SNF1-related kinase α subunit (PpSnRK1α). The activity of SnRK1 kinase in transgenic tomato lines OE-1, OE-3, and OE-4 was higher than that in the WT at different periods of fruit development; in the pink coloring period the SnRK1 kinase activity increased the most, with 23.5, 28.8, and 21.4% increases, respectively. The content of starch and soluble sugars in red ripe transgenic fruit significantly increased, while the soluble protein and titratable acid content decreased significantly. We also found that the tomatoes overexpressing PpSnRK1α matured approximately 10 days earlier than the WT. Moreover, the yeast-two-hybrid assay showed that PpSnRK1α interacted with the MADS-box transcription factor (TF) SIRIN, which acts as an essential regulator of tomato fruit ripening. The BiFC technology further validated the location of the PpSnRK1α interaction sites within the nucleus. The quantitative real-time PCR analysis showed that RIN expression was up-regulated by PpSnRK1α overexpression; the expression of RIN-targeted TF genes NOR and FUL1 increased during different stages of fruit development. The expression of key genes, ACS2, ACS4, and E8, in ethylene synthesis also changed accordingly, and the ethylene emitted by the red ripe fruit increased by 36.1-43.9% compared with the WT. These results suggest that PpSnRK1α interacts with SIRIN, increasing the expression of RIN, thereby regulating the expression of downstream ripening-related genes, finally promoting fruit ripening.
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Affiliation(s)
- Wen Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- *Correspondence: Futian Peng, Yuansong Xiao,
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- *Correspondence: Futian Peng, Yuansong Xiao,
| | | | - Jingjing Luo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
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Kumar R, Subba A, Kaur C, Ariyadasa TU, Sharan A, Pareek A, Sopory SK, Singla-Pareek SL. OsCBSCBSPB4 is a Two Cystathionine-β-Synthase Domain-containing Protein from Rice that Functions in Abiotic Stress Tolerance. Curr Genomics 2017; 19:50-59. [PMID: 29491732 PMCID: PMC5817877 DOI: 10.2174/1389202918666170228141706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/05/2016] [Accepted: 10/20/2016] [Indexed: 01/08/2023] Open
Abstract
Cystathionine β-synthase (CBS) domains have been identified in a wide range of proteins of unrelated functions such as, metabolic enzymes, kinases and channels, and usually occur as tandem re-peats, often in combination with other domains. In plants, CBS Domain-Containing Proteins (CDCPs) form a multi-gene family and only a few are so far been reported to have a role in development via regu-lation of thioredoxin system as well as in abiotic and biotic stress response. However, the function of majority of CDCPs still remains to be elucidated in plants. Here, we report the cloning, characterization and functional validation of a CBS domain containing protein, OsCBSCBSPB4 from rice, which pos-sesses two CBS domains and one PB1 domain. We show that OsCBSCBSPB4 encodes a nucleo-cytoplasmic protein whose expression is induced in response to various abiotic stress conditions in salt-sensitive IR64 and salt-tolerant Pokkali rice cultivars. Further, heterologous expression of OsCBSCB-SPB4 in E. coli and tobacco confers marked tolerance against various abiotic stresses. Transgenic tobac-co seedlings over-expressing OsCBSCBSPB4 were found to exhibit better growth in terms of delayed leaf senescence, profuse root growth and increased biomass in contrast to the wild-type seedlings when subjected to salinity, dehydration, oxidative and extreme temperature treatments. Yeast-two hybrid stud-ies revealed that OsCBSCBSPB4 interacts with various proteins. Of these, some are known to be in-volved in abiotic stress tolerance. Our results suggest that OsCBSCBSPB4 is involved in abiotic stress response and is a potential candidate for raising multiple abiotic stress tolerant plants.
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Affiliation(s)
- Ritesh Kumar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Thilini U Ariyadasa
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashutosh Sharan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudhir K Sopory
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Maya-Bernal JL, Ávila A, Ruiz-Gayosso A, Trejo-Fregoso R, Pulido N, Sosa-Peinado A, Zúñiga-Sánchez E, Martínez-Barajas E, Rodríguez-Sotres R, Coello P. Expression of recombinant SnRK1 in E. coli. Characterization of adenine nucleotide binding to the SnRK1.1/AKINβγ-β3 complex. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:116-125. [PMID: 28818366 DOI: 10.1016/j.plantsci.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
The SnRK1 complexes in plants belong to the family of AMPK/SNF1 kinases, which have been associated with the control of energy balance, in addition to being involved in the regulation of other aspects of plant growth and development. Analysis of complex formation indicates that increased activity is achieved when the catalytic subunit is phosphorylated and bound to regulatory subunits. SnRK1.1 subunit activity is higher than that of SnRK1.2, which also exhibits reduced activation due to the regulatory subunits. The catalytic phosphomimetic subunits (T175/176D) do not exhibit high activity levels, which indicate that the amino acid change does not produce the same effect as phosphorylation. Based on the mammalian AMPK X-ray structure, the plant SnRK1.1/AKINβγ-β3 was modeled by homology modeling and Molecular Dynamics simulations (MD). The model predicted an intimate and extensive contact between a hydrophobic region of AKINβγ and the β3 subunit. While the AKINβγ prediction retains the 4 CBS domain organization of the mammalian enzyme, significant differences are found in the putative nucleotide binding pockets. Docking and MD studies identified two sites between CBS 3 and 4 which may bind adenine nucleotides, but only one appears to be functional, as judging from the predicted binding energies. The recombinant AKINβγ-βs complexes were found to bind adenine nucleotides with dissociation constant (Kd) in the range of the AMP low affinity site in AMPK. The saturation binding data was consistent with a one-site model, in agreement with the in silico calculations. As has been suggested previously, the effect of AMP was found to slow down dephosphorylation but did not influence activity.
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Affiliation(s)
- José Luis Maya-Bernal
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Alejandra Ávila
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Ana Ruiz-Gayosso
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Ricardo Trejo-Fregoso
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Nancy Pulido
- Centro de Investigaciones Químicas, UAEM, Morelos, 62210, Mexico
| | | | - Esther Zúñiga-Sánchez
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | | | | | - Patricia Coello
- Departamento de Bioquímica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico.
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Li DD, Guan H, Li F, Liu CZ, Dong YX, Zhang XS, Gao XQ. Arabidopsis shaker pollen inward K + channel SPIK functions in SnRK1 complex-regulated pollen hydration on the stigma. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:604-611. [PMID: 28636077 DOI: 10.1111/jipb.12563] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 05/21/2023]
Abstract
Pollen hydration is a critical step that determines pollen germination on the stigma. KINβγ is a plant-specific subunit of the SNF1-related protein kinase 1 complex (SnRK1 complex). In pollen of the Arabidopsis kinβγ mutant, the levels of reactive oxygen species were decreased which lead to compromised hydration of the mutant pollen on the stigma. In this study, we analyzed gene expression in kinβγ mutant pollen by RNA-seq and found the expression of inward shaker K+ channel SPIK was down-regulated in the kinβγ pollen. Furthermore, we showed that the pollen hydration of the Arabidopsis spik mutant was defective on the wild-type stigma, although the mutant pollen demonstrated normal hydration in vitro. Additionally, the defective hydration of spik mutant pollen could not be rescued by the wild-type pollen on the stigma, indicating that the spik mutation deprived the capability of pollen absorption on the stigma. Our results suggest that the Arabidopsis SnRK1 complex regulates SPIK expression, which functions in determining pollen hydration on the stigma.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Huan Guan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Fei Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Chang-Zhen Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yu-Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Xian-Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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Soto-Burgos J, Bassham DC. SnRK1 activates autophagy via the TOR signaling pathway in Arabidopsis thaliana. PLoS One 2017; 12:e0182591. [PMID: 28783755 PMCID: PMC5544219 DOI: 10.1371/journal.pone.0182591] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/20/2017] [Indexed: 12/26/2022] Open
Abstract
Autophagy is a degradation process in which cells break down and recycle their cytoplasmic contents when subjected to environmental stress or during cellular remodeling. The Arabidopsis thaliana SnRK1 complex is a protein kinase that senses changes in energy levels and triggers downstream responses to enable survival. Its mammalian ortholog, AMPK, and yeast ortholog, Snf-1, activate autophagy in response to low energy conditions. We therefore hypothesized that SnRK1 may play a role in the regulation of autophagy in response to nutrient or energy deficiency in Arabidopsis. To test this hypothesis, we determined the effect of overexpression or knockout of the SnRK1 catalytic subunit KIN10 on autophagy activation by abiotic stresses, including nutrient deficiency, salt, osmotic, oxidative, and ER stress. While wild-type plants had low basal autophagy activity in control conditions, KIN10 overexpression lines had increased autophagy under these conditions, indicating activation of autophagy by SnRK1. A kin10 mutant had a basal level of autophagy under control conditions similar to wild-type plants, but activation of autophagy by most abiotic stresses was blocked, indicating that SnRK1 is required for autophagy induction by a wide variety of stress conditions. In mammals, TOR is a negative regulator of autophagy, and AMPK acts to activate autophagy both upstream of TOR, by inhibiting its activity, and in a parallel pathway. Inhibition of Arabidopsis TOR leads to activation of autophagy; inhibition of SnRK1 did not block this activation. Furthermore, an increase in SnRK1 activity was unable to induce autophagy when TOR was also activated. These results demonstrate that SnRK1 acts upstream of TOR in the activation of autophagy in Arabidopsis.
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Affiliation(s)
- Junmarie Soto-Burgos
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Plant Sciences Institute, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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Liu XJ, An XH, Liu X, Hu DG, Wang XF, You CX, Hao YJ. MdSnRK1.1 interacts with MdJAZ18 to regulate sucrose-induced anthocyanin and proanthocyanidin accumulation in apple. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2977-2990. [PMID: 28549152 PMCID: PMC5853841 DOI: 10.1093/jxb/erx150] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/09/2017] [Indexed: 05/19/2023]
Abstract
Sugars induce anthocyanin biosynthesis in plants. As a conserved energy sensor, SnRK1 (SNF1-related kinase 1) is involved in sucrose-induced anthocyanin accumulation. However, the exact molecular mechanism by which SnRK1 regulates the biosynthesis of anthocyanins and proanthocyanidins (PAs) in response to sucrose in plants is not clear. In this study, it was found that MdSnRK1.1 interacted with MdJAZ18 protein which acts as a repressor in the jasmonate (JA) signaling pathway. MdSnRK1.1 then phosphorylated MdJAZ18 to facilitate its 26S proteasome-mediated degradation, which released MdbHLH3 thereby activating the expression of the regulatory and structural genes, thus finally promoting the biosynthesis of anthocyanins and PAs. Taken together, these results demonstrate the involvement of MdSnRK1.1 in sucrose-induced accumulation of anthocyanins and PAs. For the first time, our findings shed light on the molecular mechanism by which the crosstalk of sucrose and JA signaling regulates flavonoid biosynthesis.
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Affiliation(s)
- Xiao-Juan Liu
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xiu-Hong An
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
- Research Institute of Pomology, CAAS, Xingcheng, China
| | - Xin Liu
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Da-Gang Hu
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
- Correspondence:
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Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network. Sci Rep 2017; 7:44948. [PMID: 28337996 PMCID: PMC5364480 DOI: 10.1038/srep44948] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/16/2017] [Indexed: 12/27/2022] Open
Abstract
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event. By swapping SEPALLATA3 and its ancestors between dimeric networks of different ages, we found that the protein lost the capacity of promiscuous interaction and acquired specificity in evolution. This was accompanied with constraints on conformations through proline residue accumulation, which made the protein less flexible. SHORT VEGETATIVE PHASE on the other hand (non-hub) was able to gain protein-protein interactions due to a C-terminal domain insertion, allowing for a larger interaction interface. These findings illustrate that protein interaction evolution occurs at the level of conformational dynamics, when the binding mechanism concerns an induced fit or conformational selection. Proteins can evolve towards increased specificity with reduced flexibility when the complexity of the protein interaction network requires specificity.
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Baena-González E, Hanson J. Shaping plant development through the SnRK1-TOR metabolic regulators. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:152-157. [PMID: 28027512 DOI: 10.1016/j.pbi.2016.12.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 05/20/2023]
Abstract
SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.
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Affiliation(s)
- Elena Baena-González
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 90187 Umeå, Sweden.
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Broeckx T, Hulsmans S, Rolland F. The plant energy sensor: evolutionary conservation and divergence of SnRK1 structure, regulation, and function. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6215-6252. [PMID: 27856705 DOI: 10.1093/jxb/erw416] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The SnRK1 (SNF1-related kinase 1) kinases are the plant cellular fuel gauges, activated in response to energy-depleting stress conditions to maintain energy homeostasis while also gatekeeping important developmental transitions for optimal growth and survival. Similar to their opisthokont counterparts (animal AMP-activated kinase, AMPK, and yeast Sucrose Non-Fermenting 1, SNF), they function as heterotrimeric complexes with a catalytic (kinase) α subunit and regulatory β and γ subunits. Although the overall configuration of the kinase complexes is well conserved, plant-specific structural modifications (including a unique hybrid βγ subunit) and associated differences in regulation reflect evolutionary divergence in response to fundamentally different lifestyles. While AMP is the key metabolic signal activating AMPK in animals, the plant kinases appear to be allosterically inhibited by sugar-phosphates. Their function is further fine-tuned by differential subunit expression, localization, and diverse post-translational modifications. The SnRK1 kinases act by direct phosphorylation of key metabolic enzymes and regulatory proteins, extensive transcriptional regulation (e.g. through bZIP transcription factors), and down-regulation of TOR (target of rapamycin) kinase signaling. Significant progress has been made in recent years. New tools and more directed approaches will help answer important fundamental questions regarding their structure, regulation, and function, as well as explore their potential as targets for selection and modification for improved plant performance in a changing environment.
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Affiliation(s)
- Tom Broeckx
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Sander Hulsmans
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
| | - Filip Rolland
- Laboratory for Molecular Plant Biology, Biology Department, University of Leuven-KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee-Leuven, Belgium
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49
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Li L, Sheen J. Dynamic and diverse sugar signaling. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:116-125. [PMID: 27423125 PMCID: PMC5050104 DOI: 10.1016/j.pbi.2016.06.018] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 05/18/2023]
Abstract
Sugars fuel life and exert numerous regulatory actions that are fundamental to all life forms. There are two principal mechanisms underlie sugar 'perception and signal transduction' in biological systems. Direct sensing and signaling is triggered via sugar-binding sensors with a broad range of affinity and specificity, whereas sugar-derived bioenergetic molecules and metabolites modulate signaling proteins and indirectly relay sugar signals. This review discusses the emerging sugar signals and potential sugar sensors discovered in plant systems. The findings leading to informative understanding of physiological regulation by sugars are considered and assessed. Comparative transcriptome analyses highlight the primary and dynamic sugar responses and reveal the convergent and specific regulators of key biological processes in the sugar-signaling network.
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Affiliation(s)
- Lei Li
- Department of Genetics, Harvard Medical School, USA; Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, MA 02114, USA
| | - Jen Sheen
- Department of Genetics, Harvard Medical School, USA; Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, MA 02114, USA.
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Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M. Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1955-81. [PMID: 27075884 DOI: 10.1111/pce.12754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 05/06/2023]
Abstract
Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of 10 core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 h photoperiods revealed 1-4 h earlier peak times under short photoperiods and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 h photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, light signalling and changes in carbon availability at night as a result of clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis and underpins the response of metabolism and growth to photoperiod.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, NUIG, Galway, Ireland
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Magda Liput
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Christin Abel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
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