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Wu Y, Feng J, Zhang Q, Wang Y, Guan Y, Wang R, Shi F, Zeng F, Wang Y, Chen M, Chang J, He G, Yang G, Li Y. Integrative gene duplication and genome-wide analysis as an approach to facilitate wheat reverse genetics: An example in the TaCIPK family. J Adv Res 2024; 61:19-33. [PMID: 37689241 PMCID: PMC11258669 DOI: 10.1016/j.jare.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023] Open
Abstract
INTRODUCTION Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. OBJECTIVE To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. METHODS We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial-temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. RESULTS As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPKs from seven monocot species, established the orthologous relationship of CIPKs between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g., CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBLs and TaCIPKs could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. CONCLUSION The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat.
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Affiliation(s)
- Ya'nan Wu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Jialu Feng
- Hubei Provincial Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qian Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yanbin Guan
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Ruibin Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fu Shi
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fang Zeng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
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Jung WJ, Yoon JS, Seo YW. TaMAPK3 phosphorylates TaCBF and TaICE and plays a negative role in wheat freezing tolerance. JOURNAL OF PLANT PHYSIOLOGY 2024; 296:154233. [PMID: 38554674 DOI: 10.1016/j.jplph.2024.154233] [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: 11/13/2023] [Revised: 02/27/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Abstract
Freezing temperature during overwintering often kills plants; plants have thus, developed a defense mechanism called 'cold acclimation', in which a number of genes are involved in increasing cell protection and gene expression. Mitogen-activated protein kinase (MAPK) controls proteins' activities by phosphorylation and is involved in numerous metabolic pathways. In this study, we identified the protein interaction between TaMAPK3 and the proteins in the cold response pathway, ICE41, ICE87, and CBFIVd-D9. The subcellular localization and bimolecular fluorescence complement (BiFC) assays revealed that these proteins interact in the nucleus or in the plasma membrane. Furthermore, MAPK3-mediated phosphorylation of ICE41, ICE87, and CBFIVd-D9 was verified using an in vitro phosphorylation assay. TaMAPK3-overexpressing transgenic Brachypodium showed a lower survival rate upon freezing stress and lower proline content during cold acclimation, compared to wild-type plants. Furthermore, cold response gene expression analysis revealed that the expression of these genes was suppressed in the transgenic lines under cold treatment. It was further elucidated that MAPK3 mediates the degradation of ICE and CBF proteins, which implies the negative impact of MAPK3 on the freezing tolerance of plants. This study will help to elucidate the molecular mechanisms of cold tolerance and the activity of MAPK3 in wheat.
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Affiliation(s)
- Woo Joo Jung
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Jin Seok Yoon
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, South Korea
| | - Yong Weon Seo
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, South Korea; Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea.
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Qi C, Wang Q, Niu Y, Zhang Y, Liu M, Liu Z, Wang L. Characteristics of ZjCIPKs and ZjbHLH74-ZjCIPK5 regulated cold tolerance in jujube. Int J Biol Macromol 2024; 264:130429. [PMID: 38428762 DOI: 10.1016/j.ijbiomac.2024.130429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
CIPKs are kind of serine/threonine (Ser/Thr) protein kinases which play important roles in response to biotic and abiotic stresses, and in plant growth and development. However, CIPKs in jujube (Ziziphus jujuba Mill.) had limited information, especially regarding their response to cold stress. In the current study, a total of 18 ZjCIPKs were identified in jujube genome which unevenly distributed on seven chromosomes. Conserved motif and gene structural analysis depicted them with conserved DEGLSA and APE motifs and similar structures. Phylogenetic analysis indicated that CIPKs were classified into five subgroups (I-V). In addition, three pairs of ZjCIPKs exhibited tandem duplication while the segmental duplication of ZjCIPKs was not identified. Study on the cis-acting elements indicted that stress or hormone related cis-acting elements were distributed unevenly on ZjCIPKs promoters and most ZjCIPKs were down- or up-regulated by the cold stress. VIGS induced silencing of ZjCIPK5 decreased the cold tolerance of sour jujube. Subcellular location analysis showed ZjCIPK5 located in nucleus. Moreover, transcription factor ZjbHLH74 which was induced at 6 h under cold stress could interact with the promoter of ZjCIPK5 to regulate jujube cold tolerance. These findings provided insights to a molecular basis of CIPK5 in jujube cold tolerance breeding for future.
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Affiliation(s)
- Chaofeng Qi
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Qingfang Wang
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yahong Niu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Zhiguo Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China.
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Djalovic I, Kundu S, Bahuguna RN, Pareek A, Raza A, Singla-Pareek SL, Prasad PVV, Varshney RK. Maize and heat stress: Physiological, genetic, and molecular insights. THE PLANT GENOME 2024; 17:e20378. [PMID: 37587553 DOI: 10.1002/tpg2.20378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/19/2023] [Accepted: 07/29/2023] [Indexed: 08/18/2023]
Abstract
Global mean temperature is increasing at a rapid pace due to the rapid emission of greenhouse gases majorly from anthropogenic practices and predicted to rise up to 1.5°C above the pre-industrial level by the year 2050. The warming climate is affecting global crop production by altering biochemical, physiological, and metabolic processes resulting in poor growth, development, and reduced yield. Maize is susceptible to heat stress, particularly at the reproductive and early grain filling stages. Interestingly, heat stress impact on crops is closely regulated by associated environmental covariables such as humidity, vapor pressure deficit, soil moisture content, and solar radiation. Therefore, heat stress tolerance is considered as a complex trait, which requires multiple levels of regulations in plants. Exploring genetic diversity from landraces and wild accessions of maize is a promising approach to identify novel donors, traits, quantitative trait loci (QTLs), and genes, which can be introgressed into the elite cultivars. Indeed, genome wide association studies (GWAS) for mining of potential QTL(s) and dominant gene(s) is a major route of crop improvement. Conversely, mutation breeding is being utilized for generating variation in existing populations with narrow genetic background. Besides breeding approaches, augmented production of heat shock factors (HSFs) and heat shock proteins (HSPs) have been reported in transgenic maize to provide heat stress tolerance. Recent advancements in molecular techniques including clustered regularly interspaced short palindromic repeats (CRISPR) would expedite the process for developing thermotolerant maize genotypes.
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Affiliation(s)
- Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - Sayanta Kundu
- National Agri-Food Biotechnology Institute, Mohali, India
| | | | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - P V Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, USA
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Li J, Zenda T, Liu S, Dong A, Wang Y, Liu X, Wang N, Duan H. Integrated Transcriptomic and Proteomic Analyses of Low-Nitrogen-Stress Tolerance and Function Analysis of ZmGST42 Gene in Maize. Antioxidants (Basel) 2023; 12:1831. [PMID: 37891910 PMCID: PMC10603844 DOI: 10.3390/antiox12101831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Maize (Zea mays L.) is one of the major staple crops providing human food, animal feed, and raw material support for biofuel production. For its growth and development, maize requires essential macronutrients. In particular, nitrogen (N) plays an important role in determining the final yield and quality of a maize crop. However, the excessive application of N fertilizer is causing serious pollution of land area and water bodies. Therefore, cultivating high-yield and low-N-tolerant maize varieties is crucial for minimizing the nitrate pollution of land and water bodies. Here, based on the analysis of the maize leaf transcriptome and proteome at the grain filling stage, we identified 3957 differentially expressed genes (DEGs) and 329 differentially abundant proteins (DAPs) from the two maize hybrids contrasting in N stress tolerance (low-N-tolerant XY335 and low-N-sensitive HN138) and screened four sets of low-N-responsive genes and proteins through Venn diagram analysis. We identified 761 DEGs (253 up- and 508 down-regulated) specific to XY335, whereas 259 DEGs (198 up- and 61 down-regulated) were specific to HN138, and 59 DEGs (41 up- and 18 down-regulated) were shared between the two cultivars under low-N-stress conditions. Meanwhile, among the low-N-responsive DAPs, thirty were unique to XY335, thirty were specific to HN138, and three DAPs were shared between the two cultivars under low-N treatment. Key among those genes/proteins were leucine-rich repeat protein, DEAD-box ATP-dependent RNA helicase family proteins, copper transport protein, and photosynthesis-related proteins. These genes/proteins were involved in the MAPK signaling pathway, regulating membrane lipid peroxidation, and photosynthesis. Our results may suggest that XY335 better tolerates low-N stress than HN138, possibly through robust low-N-stress sensing and signaling, amplified protein phosphorylation and stress response, and increased photosynthesis efficiency, as well as the down-regulation of 'lavish' or redundant proteins to minimize N demand. Additionally, we screened glutathione transferase 42 (ZmGST42) and performed physiological and biochemical characterizations of the wild-type (B73) and gst42 mutant at the seedling stage. Resultantly, the wild-type exhibited stronger tolerance to low N than the mutant line. Our findings provide a better understanding of the molecular mechanisms underlying low-N tolerance during the maize grain filling stage and reveal key candidate genes for low-N-tolerance breeding in maize.
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Affiliation(s)
- Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Songtao Liu
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou 075000, China;
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (J.L.); (T.Z.); (A.D.); (Y.W.); (X.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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Li J, Zhu Q, Jiao F, Yan Z, Zhang H, Zhang Y, Ding Z, Mu C, Liu X, Li Y, Chen J, Wang M. Research Progress on the Mechanism of Salt Tolerance in Maize: A Classic Field That Needs New Efforts. PLANTS (BASEL, SWITZERLAND) 2023; 12:2356. [PMID: 37375981 DOI: 10.3390/plants12122356] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Maize is the most important cereal crop globally. However, in recent years, maize production faced numerous challenges from environmental factors due to the changing climate. Salt stress is among the major environmental factors that negatively impact crop productivity worldwide. To cope with salt stress, plants developed various strategies, such as producing osmolytes, increasing antioxidant enzyme activity, maintaining reactive oxygen species homeostasis, and regulating ion transport. This review provides an overview of the intricate relationships between salt stress and several plant defense mechanisms, including osmolytes, antioxidant enzymes, reactive oxygen species, plant hormones, and ions (Na+, K+, Cl-), which are critical for salt tolerance in maize. It addresses the regulatory strategies and key factors involved in salt tolerance, aiming to foster a comprehensive understanding of the salt tolerance regulatory networks in maize. These new insights will also pave the way for further investigations into the significance of these regulations in elucidating how maize coordinates its defense system to resist salt stress.
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Affiliation(s)
- Jiawei Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qinglin Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhenwei Yan
- Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Haiyan Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Yumei Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhaohua Ding
- Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Chunhua Mu
- Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Xia Liu
- Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Yan Li
- Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
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Li C, Guo J, Wang D, Chen X, Guan H, Li Y, Zhang D, Liu X, He G, Wang T, Li Y. Genomic insight into changes of root architecture under drought stress in maize. PLANT, CELL & ENVIRONMENT 2023; 46:1860-1872. [PMID: 36785485 DOI: 10.1111/pce.14567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/03/2023] [Accepted: 02/11/2023] [Indexed: 05/04/2023]
Abstract
Drought stress is a central environmental factor that severely limits maize production worldwide. Root architecture plays an important role in drought tolerance and can be targeted in breeding programmes. Here, we conducted phenotyping of root architecture under different water treatments for 373 maize inbred lines, representative germplasm from both China and the United States in different breeding eras. We found that seminal root length in response to drought stress experienced convergent increase during breeding in both countries. Using a genome-wide association study, we identified a total of 221 associated loci underlying 13 root traits under well-watered and water-stressed conditions. These loci harboured many reported root- and abiotic stress-related genes. Furthermore, a total of 75 strong candidate genes were prioritised by integrating candidate genes associated with seminal root length and differentially expressed genes in seminal root. One of high-confidence candidate genes, ZmCIPK3 was functionally characterised and probably plays a role in enhancing drought tolerance through regulating seminal root growth. This study provides valuable information for genetic improvement of root architecture and drought tolerance in maize.
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Affiliation(s)
- Chunhui Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
| | - Dongmei Wang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojing Chen
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghui Guan
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanhua He
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Transcriptome-Wide Identification and Functional Characterization of CIPK Gene Family Members in Actinidia valvata under Salt Stress. Int J Mol Sci 2023; 24:ijms24010805. [PMID: 36614245 PMCID: PMC9821023 DOI: 10.3390/ijms24010805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023] Open
Abstract
Fruit plants are severely constrained by salt stress in the soil due to their sessile nature. Ca2+ sensors, which are known as CBL-interacting protein kinases (CIPKs), transmit abiotic stress signals to plants. Therefore, it is imperative to investigate the molecular regulatory role of CIPKs underlying salt stress tolerance in kiwifruit. In the current study, we have identified 42 CIPK genes from Actinidia. valvata (A.valvata). All the AvCIPKs were divided into four different phylogenetic groups. Moreover, these genes showed different conserved motifs. The expression pattern analysis showed that AvCIPK11 was specifically highly expressed under salt stress. The overexpression of AvCIPK11 in 'Hongyang' (a salt sensitive commercial cultivar from Actinidia chinensis) enhanced salt tolerance by maintaining K+/Na+ homeostasis in the leaf and positively improving the activity of POD. In addition, the salt-related genes AcCBL1 and AcNHX1 had higher expression in overexpression lines. Collectively, our study suggested that AvCIPK11 is involved in the positive regulation of salt tolerance in kiwifruit.
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Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:371-439. [PMID: 36858741 DOI: 10.1016/bs.apcsb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Calcium (Ca2+) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca2+-signature, and are decoded by plethora of Ca2+ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca2+-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca2+ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca2+ sensor protein in plants. Their ability to bind Ca2+, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca2+ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca2+, the Ca2+ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca2+ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca2+ signaling.
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Yang C, Yi-feng J, Yushu W, Yansong G, Qi W, Xue Y. Diverse roles of the CIPK gene family in transcription regulation and various biotic and abiotic stresses: A literature review and bibliometric study. Front Genet 2022; 13:1041078. [PMID: 36457742 PMCID: PMC9705351 DOI: 10.3389/fgene.2022.1041078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/24/2022] [Indexed: 12/10/2023] Open
Abstract
CIPKs are a subclass of serine/threonine (Ser/Thr) protein kinases. CBLs are ubiquitous Ca2+ sensors that interact with CIPK with the aid of secondary Ca2+ messengers for regulation of growth and development and response to stresses faced by plants. The divergent roles of the CIPK-CBL interaction in plants include responding to environmental stresses (salt, cold, drought, pH, ABA signaling, and ion toxicity), ion homeostasis (K+, NH4 +, NO3 -, and microelement homeostasis), biotic stress, and plant development. Each member of this gene family produces distinct proteins that help plants adapt to diverse stresses or stimuli by interacting with calcium ion signals. CIPK consists of two structural domains-an N-terminal domain and a C-terminal domain-connected by a junction domain. The N-terminal domain, the site of phosphorylation, is also called the activation domain and kinase domain. The C-terminal, also known as the regulatory domain of CIPK, further comprises NAF/FISL and PPI. CBL comprises four EF domains and conserved PFPF motifs and is the site of binding with the NAF/FISL domain of CIPK to form a CBL-CIPK complex. In addition, we also performed a bibliometric analysis of the CIPK gene family of data extracted from the WoSCC. A total of 95 documents were retrieved, which had been published by 47 sources. The production over time was zigzagged. The top key terms were gene, CIPK, abiotic stress, and gene expression. Beijing Forestry University was the top affiliation, while The Plant Cell was the top source. The genomics and metabolomics of this gene family require more study.
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Affiliation(s)
- Chen Yang
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory Resistance Gene Engineering, Qiqihar, China
| | - Jin Yi-feng
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory Resistance Gene Engineering, Qiqihar, China
| | - Wang Yushu
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory Resistance Gene Engineering, Qiqihar, China
| | - Gao Yansong
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Wang Qi
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - You Xue
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
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Qiu K, Pan H, Sheng Y, Wang Y, Shi P, Xie Q, Zhang J, Zhou H. The Peach ( Prunus persica) CBL and CIPK Family Genes: Protein Interaction Profiling and Expression Analysis in Response to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3001. [PMID: 36365452 PMCID: PMC9653928 DOI: 10.3390/plants11213001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/01/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The plant calcineurin B-like protein-CBL interacting protein kinase (CBL-CIPK) signaling pathway is a Ca2+-related signaling pathway that responds strongly to both biological and abiotic environmental stimuli. This study identified eight CBL and eighteen CIPK genes from peach for the first time. Their basic properties and gene structure were analyzed, and the CBL and CIPK members from Arabidopsis and apple were combined to study their evolutionary relationships. Using RT-qPCR and RNA-seq data, we detected the expression patterns of PprCBLs and PprCIPKs in different tissues and fruit development stages of peach. Among them, the expression levels of PprCBL1 and PprCIPK18 were stable in various tissues and stages. The expression patterns of other members showed specificity between cultivars and developmental stages. By treating shoots with drought and salt stress simulated using PEG6000 and NaCl, it was found that PprCIPK3, PprCIPK6, PprCIPK15 and PprCIPK16 were strongly responsive to salt stress, and PprCIPK3, PprCIPK4, PprCIPK10, PprCIPK14, PprCIPK15, PprCIPK16 and PprCIPK18 were sensitive to drought stress. Three genes, PprCIPK3, PprCIPK15 and PprCIPK16, were sensitive to both salt and drought stress. We cloned four PprCBL and several PprCIPK genes and detected their interaction by yeast two-hybrid assay (Y2H). The results of Y2H show not only the evolutionary conservation of the interaction network of CBL-CIPK but also the specificity among different species. In conclusion, CBL and CIPK genes are important in peach and play an important role in the response to various abiotic stresses.
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Affiliation(s)
- Keli Qiu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Haifa Pan
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yu Sheng
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yunyun Wang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Pei Shi
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Qingmei Xie
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Jinyun Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Hui Zhou
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, China
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12
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Sequence Characteristics and Expression Analysis of GhCIPK23 Gene in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2022; 23:ijms231912040. [PMID: 36233340 PMCID: PMC9570493 DOI: 10.3390/ijms231912040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
CIPK (calcineurin B-like-interacting protein kinase) is a kind of serine/threonine protein kinase widely existing in plants, and it plays an important role in plant growth and development and stress response. To better understand the biological functions of the GhCIPK23 gene in upland cotton, the coding sequence (CDS) of the GhCIPK23 gene was cloned in upland cotton, and its protein sequence, evolutionary relationship, subcellular localization, expression pattern and cis-acting elements in the promoter region were analyzed. Our results showed that the full-length CDS of GhCIPK23 was 1368 bp, encoding a protein with 455 amino acids. The molecular weight and isoelectric point of this protein were 50.83 KDa and 8.94, respectively. The GhCIPK23 protein contained a conserved N-terminal protein kinase domain and C-terminal regulatory domain of the CIPK gene family member. Phylogenetic tree analysis demonstrated that GhCIPK23 had a close relationship with AtCIPK23, followed by OsCIPK23, and belonged to Group A with AtCIPK23 and OsCIPK23. The subcellular localization experiment indicated that GhCIPK23 was located in the plasma membrane. Tissue expression analysis showed that GhCIPK23 had the highest expression in petals, followed by sepals, and the lowest in fibers. Stress expression analysis showed that the expression of the GhCIPK23 gene was in response to drought, salt, low-temperature and exogenous abscisic acid (ABA) treatment, and had different expression patterns under different stress conditions. Further cis-acting elements analysis showed that the GhCIPK23 promoter region had cis-acting elements in response to abiotic stress, phytohormones and light. These results established a foundation for understanding the function of GhCIPK23 and breeding varieties with high-stress tolerance in cotton.
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Zhou X, Li J, Wang Y, Liang X, Zhang M, Lu M, Guo Y, Qin F, Jiang C. The classical SOS pathway confers natural variation of salt tolerance in maize. THE NEW PHYTOLOGIST 2022; 236:479-494. [PMID: 35633114 DOI: 10.1111/nph.18278] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 05/27/2023]
Abstract
Sodium (Na+ ) is the major cation damaging crops in the salinised farmland. Previous studies have shown that the Salt Overly Sensitive (SOS) pathway is important for salt tolerance in Arabidopsis. Nevertheless, the SOS pathway remains poorly investigated in most crops. This study addresses the function of the SOS pathway and its association with the natural variation of salt tolerance in maize. First, we showed that a naturally occurring 4-bp frame-shifting deletion in ZmSOS1 caused the salt hypersensitive phenotype of the maize inbred line LH65. Accordingly, mutants lacking ZmSOS1 also displayed a salt hypersensitive phenotype, due to an impaired root-to-rhizosphere Na+ efflux and an increased shoot Na+ concentration. We next showed that the maize SOS3/SOS2 complex (ZmCBL4/ZmCIPK24a and ZmCBL8/ZmCIPK24a) phosphorylates ZmSOS1 therefore activating its Na+ -transporting activity, with their loss-of-function mutants displaying salt hypersensitive phenotypes. Moreover, we observed that a LTR/Gypsy insertion decreased the expression of ZmCBL8, thereby increasing shoot Na+ concentration in natural maize population. Taken together, our study demonstrated that the maize SOS pathway confers a conservative salt-tolerant role, and the components of SOS pathway (ZmSOS1 and ZmCBL8) confer the natural variations of Na+ regulation and salt tolerance in maize, therefore providing important gene targets for breeding salt-tolerant maize.
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Affiliation(s)
- Xueyan Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jianfang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Yiqiao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Minhui Lu
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
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Genome-Wide Investigation and Expression Analysis of the Nitraria sibirica Pall. CIPK Gene Family. Int J Mol Sci 2022; 23:ijms231911599. [PMID: 36232901 PMCID: PMC9569540 DOI: 10.3390/ijms231911599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The calcineurin B-like-interacting protein kinase (CIPK) protein family plays a key role in the plant calcium ion-mediated signal transduction pathway, which regulates a plant's response to abiotic stress. Nitraria sibirica pall. (N. sibirica) is a halophyte with a strong tolerance for high salt environments, yet how it is able to deal with salt stress on a molecular level is still unknown. Due to their function as described in other plant species, CIPK genes are prime candidates for a role in salt stress signaling in N. sibirica. In this study, we identified and analyzed the phylogenetic makeup and gene expression of the N. sibirica CIPK gene family. A total of 14 CIPKs were identified from the N. sibirica genome and were clustered into seven groups based on their phylogeny. The promoters of NsCIPK genes contained multiple elements involved in hormonal and stress response. Synteny analysis identified a total of three pairs of synteny relationships between NsCIPK genes. Each gene showed its own specific expression pattern across different tissues, with the overall expression of CIPK6 being the lowest, and that of CIPK20 being the highest. Almost all CIPK genes tended to respond to salt, drought, and cold stress, but with different sensitivity levels. In this study, we have provided a general description of the NsCIPK gene family and its expression, which will be of great significance for further understanding of the NsCIPK gene family function.
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15
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Yu C, Ke Y, Qin J, Huang Y, Zhao Y, Liu Y, Wei H, Liu G, Lian B, Chen Y, Zhong F, Zhang J. Genome-wide identification of calcineurin B-like protein-interacting protein kinase gene family reveals members participating in abiotic stress in the ornamental woody plant Lagerstroemia indica. FRONTIERS IN PLANT SCIENCE 2022; 13:942217. [PMID: 36204074 PMCID: PMC9530917 DOI: 10.3389/fpls.2022.942217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs) play important roles in plant responses to stress. However, their function in the ornamental woody plant Lagerstroemia indica is remains unclear. In this study, the LiCIPK gene family was analyzed at the whole genome level. A total of 37 LiCIPKs, distributed across 17 chromosomes, were identified. Conserved motif analysis indicated that all LiCIPKs possess a protein kinase motif (S_TKc) and C-terminal regulatory motif (NAF), while seven LiCIPKs lack a protein phosphatase interaction (PPI) motif. 3D structure analysis further revealed that the N-terminal and C-terminal 3D-structure of 27 members are situated near to each other, while 4 members have a looser structure, and 6 members lack intact structures. The intra- and interspecies collinearity analysis, synonymous substitution rate (K s ) peaks of duplicated LiCIPKs, revealed that ∼80% of LiCIPKs were retained by the two whole genome duplication (WGD) events that occurred approximately 56.12-61.16 million year ago (MYA) and 16.24-26.34 MYA ago. The promoter of each LiCIPK contains a number of auxin, abscisic acid, gibberellic acid, salicylic acid, and drought, anaerobic, defense, stress, and wound responsive cis-elements. Of the 21 members that were successfully amplified by qPCR, 18 LiCIPKs exhibited different expression patterns under NaCl, mannitol, PEG8000, and ABA treatments. Given that LiCIPK30, the AtSOS2 ortholog, responded to all four types of stress it was selected for functional verification. LiCIPK30 complements the atsos2 phenotype in vivo. 35S:LiCIPK-overexpressing lines exhibit increased leaf area increment, chlorophyll a and b content, reactive oxygen species scavenging enzyme activity, and expression of ABF3 and RD22, while the degree of membrane lipid oxidation decreases under NaCl treatment compared to WT. The evolutionary history, and potential mechanism by which LiCIPK30 may regulate plant tolerance to salt stress were also discussed. In summary, we identified LiCIPK members involved in abiotic stress and found that LiCIPK30 transgenic Arabidopsis exhibits more salt and osmotic stress tolerance than WT. This research provides a theoretical foundation for further investigation into the function of LiCIPKs, and for mining gene resources to facilitate the cultivation and breeding of new L. indica varieties in coastal saline-alkali soil.
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Affiliation(s)
- Chunmei Yu
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Yongchao Ke
- School of Life Sciences, Nantong University, Nantong, China
| | - Jin Qin
- School of Life Sciences, Nantong University, Nantong, China
| | - Yunpeng Huang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yanchun Zhao
- School of Life Sciences, Nantong University, Nantong, China
| | - Yu Liu
- School of Life Sciences, Nantong University, Nantong, China
| | - Hui Wei
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Guoyuan Liu
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Bolin Lian
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Yanhong Chen
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Fei Zhong
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
| | - Jian Zhang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China
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16
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Ren W, Zhang J, He J, Fang J, Wan L. Identification, expression, and association analysis of calcineurin B-like protein–interacting protein kinase genes in peanut. Front Genet 2022; 13:939255. [PMID: 36134030 PMCID: PMC9483126 DOI: 10.3389/fgene.2022.939255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Plants usually respond to the external environment by initiating a series of signal transduction processes mediated by protein kinases, especially calcineurin B-like protein–interacting protein kinases (CIPKs). In this study, 54 CIPKs were identified in the peanut genome, of which 26 were from cultivated species (named AhCIPKs) and 28 from two diploid progenitors (Arachis duranensis—AdCIPKs and Arachis ipaensis—AiCIPKs). Evolution analysis revealed that the 54 CIPKs were composed of two different evolutionary branches. The CIPK members were unevenly distributed at different chromosomes. Synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CIPK. Comparative genomics analysis showed that there was only one common collinear CIPK pairs among peanut, Arabidopsis, rice, grape, and soybean. The prediction results of cis-acting elements showed that AhCIPKs, AdCIPKs, and AiCIPKs contained different proportions of transcription factor binding motifs involved in regulating plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCIPKs had tissue-specific expression patterns. Furthermore, association analysis identified one polymorphic site in AdCIPK12 (AhCIPK11), which was significantly associated with pod length, seed length, hundred seed weight, and shoot root ratio. Our results provide valuable information of CIPKs in peanut and facilitate better understanding of their biological functions.
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Affiliation(s)
- Weifang Ren
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Juncheng Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jie He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Jiahai Fang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Liyun Wan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Liyun Wan,
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Chang Y, Ahlawat YK, Gu T, Sarkhosh A, Liu T. Transcriptional profiling of two muscadine grape cultivars "Carlos" and "Noble" to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:949383. [PMID: 36061784 PMCID: PMC9435441 DOI: 10.3389/fpls.2022.949383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
In commercial fruit production, synchronized ripening and stable shelf life are important properties. The loosely clustered or non-bunching muscadine grape has unrealized potential as a disease-resistant cash crop, but requires repeated hand harvesting due to its unsynchronized or long or heterogeneous maturation period. Genomic research can be used to identify the developmental and environmental factors that control fruit ripening and postharvest quality. This study coupled the morphological, biochemical, and genetic variations between "Carlos" and "Noble" muscadine grape cultivars with RNA-sequencing analysis during berry maturation. The levels of antioxidants, anthocyanins, and titratable acids varied between the two cultivars during the ripening process. We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. These findings may help develop a large-scale database of the genetic factors of muscadine grape ripening and postharvest profiles and allow the discovery of the factors underlying the ripeness heterogeneity at harvest. These genetic resources may allow us to combine applied and basic research methods in breeding to improve table and wine grape ripening uniformity, quality, stress tolerance, and postharvest handling and storage.
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Affiliation(s)
- Yuru Chang
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Yogesh Kumar Ahlawat
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Ali Sarkhosh
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Tie Liu
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
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18
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Xiaolin Z, Baoqiang W, Xian W, Xiaohong W. Identification of the CIPK-CBL family gene and functional characterization of CqCIPK14 gene under drought stress in quinoa. BMC Genomics 2022; 23:447. [PMID: 35710332 PMCID: PMC9204864 DOI: 10.1186/s12864-022-08683-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Background Calcineurin-like Protein (CBL) and CBL interacting protein kinase (CIPK) play a key role in plant signal transduction and response to various environmental stimuli. Quinoa, as an important plant with high nutritional value, can meet the basic nutritional needs of human Cash crop, is also susceptible to abiotic stress. However, CBL-CIPK in quinoa have not been reported. Results In this study, 16 CBL and 41 CIPK genes were identified in quinoa. CBL-CIPK gene shows different intron-exon gene structure and motif, they participate in different biological processes, and form a complex regulatory network between CBL-CIPK proteins. Many cis-regulatory element associated with ABA and drought have been found. The expression patterns of CBL-CIPK showed different expression patterns in various abiotic stresses and tissues. RT-qPCR showed that most members of these two gene families were involved in drought regulation of quinoa, in particular, the expression levels of CqCIPK11, CqCIPK15, CqCIPK37 and CqCBL13 increased significantly under drought stress. Conclusions The structures and functions of the CBL-CIPK family in quinoa were systematically explored. Many CBL-CIPK may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the quinoa CBL-CIPK family and our understanding of the CBL-CIPK family in higher plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08683-6.
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Affiliation(s)
- Zhu Xiaolin
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wang Baoqiang
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wang Xian
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wei Xiaohong
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China. .,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China. .,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
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19
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Wang Q, Zhao K, Gong Y, Yang Y, Yue Y. Genome-Wide Identification and Functional Analysis of the Calcineurin B-like Protein and Calcineurin B-like Protein-Interacting Protein Kinase Gene Families in Chinese Cabbage (Brassica rapa ssp. pekinensis). Genes (Basel) 2022; 13:genes13050795. [PMID: 35627180 PMCID: PMC9140732 DOI: 10.3390/genes13050795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
In plants, calcineurin B-like proteins (CBL) are a unique set of calcium sensors that decode calcium signals by activating a plant-specific protein kinase family called CBL-interacting protein kinases (CIPKs). The CBL–CIPK family and its interacting complexes regulate plant responses to various environmental stimuli. Chinese cabbage (Brassica rapa ssp. pekinensis) is an important vegetable crop in Asia; however, there are no reports on the role of the CBLs–CIPKs’ signaling system in response to abiotic stress during cabbage growth. In this study, 18 CBL genes and 47 CIPK genes were identified from the Chinese cabbage genome. Expansion of the gene families was mainly due to tandem repeats and segmental duplication. An analysis of gene expression patterns showed that different duplicate genes exhibited different expression patterns in response to treatment with Mg2+, K+, and low temperature. In addition, differences in the structural domain sequences of NAF/FISL and interaction profiles in yeast two-hybrid assays suggested a functional divergence of the duplicate genes during the long-term evolution of Chinese cabbage, a result further validated by potassium deficiency treatment using trans-BraCIPK23.1/23.2/23.3 Arabidopsis thaliana. Our results provide a basis for studies related to the functional divergence of duplicate genes and in-depth studies of BraCBL–BraCIPK functions in Chinese cabbage.
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Affiliation(s)
- Qianwen Wang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (K.Z.); (Y.G.)
| | - Kai Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (K.Z.); (Y.G.)
| | - Yuqiang Gong
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (K.Z.); (Y.G.)
| | - Yunqiang Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| | - Yanling Yue
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (K.Z.); (Y.G.)
- Correspondence:
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20
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Schneider HM, Lor VSN, Hanlon MT, Perkins A, Kaeppler SM, Borkar AN, Bhosale R, Zhang X, Rodriguez J, Bucksch A, Bennett MJ, Brown KM, Lynch JP. Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15). PLANT, CELL & ENVIRONMENT 2022; 45:837-853. [PMID: 34169548 PMCID: PMC9544310 DOI: 10.1111/pce.14135] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/05/2021] [Accepted: 06/16/2021] [Indexed: 05/06/2023]
Abstract
Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.
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Affiliation(s)
- Hannah M. Schneider
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Vai Sa Nee Lor
- Department of AgronomyUniversity of WisconsinMadisonWisconsinUSA
| | - Meredith T. Hanlon
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alden Perkins
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Aditi N. Borkar
- School of Veterinary Medicine and ScienceUniversity of NottinghamSutton BoningtonUK
| | - Rahul Bhosale
- Future Food Beacon of Excellence and School of BiosciencesUniversity of NottinghamNottinghamUK
| | - Xia Zhang
- Department of AgronomyUniversity of WisconsinMadisonWisconsinUSA
| | - Jonas Rodriguez
- Department of AgronomyUniversity of WisconsinMadisonWisconsinUSA
| | - Alexander Bucksch
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgiaUSA
- Institute of BioinformaticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Malcolm J. Bennett
- Future Food Beacon of Excellence and School of BiosciencesUniversity of NottinghamNottinghamUK
| | - Kathleen M. Brown
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jonathan P. Lynch
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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21
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New functions of CIPK gene family are continue to emerging. Mol Biol Rep 2022; 49:6647-6658. [PMID: 35229240 DOI: 10.1007/s11033-022-07255-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
Abstract
CIPK protein family is a key protein family in Ca2+ mediated plant signaling pathway, which plays an indispensable role in plant response to stress and development. Every gene in this family encodes specific proteins. They interact with calcium ion signals, make plants to deal with various stress or stimuli. This article mainly reviews the mechanism, positioning and physiological functions of the CIPK family in different species in recent years. According to our team's research, CIPK8 interacts with CBL5 to improve salt tolerance, and CIPK23 interacts with TGA1 to regulate nitrate uptake negatively in chrysanthemum. In addition, we discussed current limitations and future research directions. The article will enhance the understanding of the functional characteristics of the CIPK gene family under different stresses, provide insights for future breeding and the development of new crop varieties with enhanced stress tolerance.
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22
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Gao C, Zhu X, Lu S, Xu J, Zhou R, Lv J, Chen Y, Cao Y. Functional Analysis of OsCIPK17 in Rice Grain Filling. FRONTIERS IN PLANT SCIENCE 2022; 12:808312. [PMID: 35145535 PMCID: PMC8821165 DOI: 10.3389/fpls.2021.808312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
We used mutant cipk17 and Nipponbare in field experiments to analyze agronomic traits, photosynthetic parameters, transcriptome, and gene expression. The results demonstrated cytoplasmic localization of OsCIPK17, while GUS allogeneic (A. thaliana) tissue-staining and quantitative analysis showed the gene was expressed in many organs, including flower buds; furthermore, it was involved in root, stem, and leaf growth. Compared to Nipponbare plants, grain filling rate and final grain weight decreased in plants of the knockout mutant owing to a delay in attainment of maximum grain filling rate. Photosystem II (PSII) efficiency was also reduced. Enrichment analysis showed that the functions of differentially expressed genes (DEGs) focused on nucleoside-, nucleotide-, and lipid-binding, as well as hydrolase, transferase, and phosphorylase activities. Signaling pathways mainly included starch and sucrose metabolism, as well as photosynthesis. Additionally, some DEGs were verified by fluorescence analysis. The results showed that knockout of OsCIPK17 affected photosynthesis and starch-, sucrose-, and amino acid metabolism-related gene expression; furthermore, the mutation reduced PSII utilization efficiency, it blocked the synthesis and metabolism of starch and sucrose, and affected the formation and transport of assimilates, thereby reducing final grain weight.
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Ma R, Liu W, Li S, Zhu X, Yang J, Zhang N, Si H. Genome-Wide Identification, Characterization and Expression Analysis of the CIPK Gene Family in Potato ( Solanum tuberosum L.) and the Role of StCIPK10 in Response to Drought and Osmotic Stress. Int J Mol Sci 2021; 22:ijms222413535. [PMID: 34948331 PMCID: PMC8708990 DOI: 10.3390/ijms222413535] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
The potato (Solanum tuberosum L.), one of the most important food crops worldwide, is sensitive to environmental stresses. Sensor–responder complexes comprising calcineurin B-like (CBL) proteins and CBL-interacting protein kinases (CIPKs) not only modulate plant growth and development but also mediate numerous stress responses. Here, using a Hidden Markov Model and BLAST searches, 27 CIPK genes were identified in potato and divided into five groups by phylogenetic analysis and into two clades (intron-poor and intron-rich) by gene structure analysis. Quantitative reverse-transcription PCR (qRT-PCR) assays revealed that StCIPK genes play important roles in plant growth, development and abiotic stress tolerance. Up-regulated expression of StCIPK10 was significantly induced by drought, PEG6000 and ABA. StCIPK10 enhances both the ability of potato to scavenge reactive oxygen species and the content of corresponding osmoregulation substances, thereby strengthening tolerance to drought and osmotic stress. StCIPK10 is located at the intersection between the abscisic acid and abiotic stress signaling pathways, which control both root growth and stomatal closure in potato. In addition, StCIPK10 interacts with StCBL1, StCBL4, StCBL6, StCBL7, StCBL8, StCBL11 and StCBL12, and is specifically recruited to the plasma membrane by StCBL11.
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Affiliation(s)
- Rui Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Dingxi Academy of Agricultural Sciences, Dingxi 743000, China
| | - Weigang Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Shigui Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xi Zhu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-931-763-1875
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24
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Huang L, Li Z, Fu Q, Liang C, Liu Z, Liu Q, Pu G, Li J. Genome-Wide Identification of CBL-CIPK Gene Family in Honeysuckle ( Lonicera japonica Thunb.) and Their Regulated Expression Under Salt Stress. Front Genet 2021; 12:751040. [PMID: 34795693 PMCID: PMC8593244 DOI: 10.3389/fgene.2021.751040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
In plants, calcineurin B-like proteins (CBLs) are a unique group of Ca2+ sensors that decode Ca2+ signals by activating a family of plant-specific protein kinases known as CBL-interacting protein kinases (CIPKs). CBL-CIPK gene families and their interacting complexes are involved in regulating plant responses to various environmental stimuli. To gain insight into the functional divergence of CBL-CIPK genes in honeysuckle, a total of six LjCBL and 17 LjCIPK genes were identified. The phylogenetic analysis along with the gene structure analysis divided both CBL and CBL-interacting protein kinase genes into four subgroups and validated by the distribution of conserved protein motifs. The 3-D structure prediction of proteins shown that most LjCBLs shared the same Protein Data Bank hit 1uhnA and most LjCIPKs shared the 6c9Da. Analysis of cis-acting elements and gene ontology implied that both LjCBL and LjCIPK genes could be involved in hormone signal responsiveness and stress adaptation. Protein-protein interaction prediction suggested that LjCBL4 is hypothesized to interact with LjCIPK7/9/15/16 and SOS1/NHX1. Gene expression analysis in response to salinity stress revealed that LjCBL2/4, LjCIPK1/15/17 under all treatments gradually increased over time until peak expression at 72 h. These results demonstrated the conservation of salt overly sensitive pathway genes in honeysuckle and a model of Ca2+-LjCBL4/LjSOS3-LjCIPK16/LjSOS2 module-mediated salt stress signaling in honeysuckle is proposed. This study provides insight into the characteristics of the CBL-CIPK gene families involved in honeysuckle salt stress responses, which could serve as a foundation for gene transformation technology, to obtain highly salt-tolerant medicinal plants in the context of the global reduction of cultivated land.
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Affiliation(s)
- Luyao Huang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhuangzhuang Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Qingxia Fu
- Department of Pharmacy, Linyi People's Hospital, Linyi, China
| | - Conglian Liang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhenhua Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qian Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Gaobin Pu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jia Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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25
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Xu M, Li H, Liu ZN, Wang XH, Xu P, Dai SJ, Cao X, Cui XY. The soybean CBL-interacting protein kinase, GmCIPK2, positively regulates drought tolerance and ABA signaling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:980-989. [PMID: 34583133 DOI: 10.1016/j.plaphy.2021.09.026] [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: 07/08/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 05/27/2023]
Abstract
Calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant environmental stress responses. However, the biological functions of the CBL-CIPK signaling pathway in the tolerance of soybean (Glycine max) to drought stress remain elusive. Here, we characterized the GmCIPK2 gene in soybean, and its expression was induced by drought stress and exogenous abscisic acid (ABA) treatments. The overexpression of GmCIPK2 enhanced drought tolerance in transgenic Arabidopsis and soybean hairy roots, whereas downregulation of GmCIPK2 expression in soybean hairy roots by RNA interference resulted in increased drought sensitivity. Further analysis showed that GmCIPK2 was involved in ABA-mediated stomatal closure in plants under drought stress conditions. GmCIPK2 increased the expression of ABA- and drought-responsive genes during drought stress. Additionally, yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays demonstrated that a positive regulator of drought stress, GmCBL1, physically interacted with GmCIPK2 on the plasma membrane. Collectively, our results demonstrated that GmCIPK2 positively regulates drought tolerance and ABA signaling in plants, providing new insights into the underlying mechanisms of how the CBL-CIPK signaling pathway contributes to drought tolerance in soybean.
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Affiliation(s)
- Meng Xu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Hui Li
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Zhen-Ning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Xiao-Hua Wang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Ping Xu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Sheng-Jie Dai
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Xue Cao
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
| | - Xiao-Yu Cui
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, China.
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26
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Zheng Y, Hou P, Zhu L, Song W, Liu H, Huang Y, Wang H, Guo J. Genome-Wide Association Study of Vascular Bundle-Related Traits in Maize Stalk. FRONTIERS IN PLANT SCIENCE 2021; 12:699486. [PMID: 34504506 PMCID: PMC8423097 DOI: 10.3389/fpls.2021.699486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
The vascular bundle plays an important role in nutrient transportation in plants and exerts great influence on crop yield. Maize is widely used for food, feed, and fuel, producing the largest yield in the world. However, genes and molecular mechanism controlling vascular bundle-related traits in maize have largely remained undiscovered. In this study, a natural population containing 248 diverse maize inbred lines genotyped with high-throughput SNP markers was used for genome-wide association study. The results showed that broad variations existed for the vascular bundle-related traits which are subject to genetic structure and it was suitable for association analysis. In this study, we identified 15, 13, 2, 1, and 5 SNPs significantly associated with number of small vascular bundle, number of large vascular bundle, average area of single small vascular bundle, average area of single large vascular bundle, and cross-sectional area, respectively. The 210 candidate genes in the confidence interval can be classified into ten biological processes, three cellular components, and eight molecular functions. As for the Kyoto Encyclopedia of Genes and Genomes analysis of the candidate genes, a total of six pathways were identified. Finally, we found five genes related to vascular development, three genes related to cell wall, and two genes related to the mechanical strength of the stalk. Our results provide the further understanding of the genetic foundation of vascular bundle-related traits in maize stalk.
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Affiliation(s)
- Yunxiao Zheng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Peng Hou
- Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liying Zhu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Han Liu
- State Key Laboratory of Agrobiotechnology, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yaqun Huang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, China
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27
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Meng D, Dong B, Niu L, Song Z, Wang L, Amin R, Cao H, Li H, Yang Q, Fu Y. The pigeon pea CcCIPK14-CcCBL1 pair positively modulates drought tolerance by enhancing flavonoid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1278-1297. [PMID: 33733535 DOI: 10.1111/tpj.15234] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 05/22/2023]
Abstract
Calcineurin B-like (CBL)-interacting protein kinases (CIPKs) play a central role in Ca2+ signalling and promote drought tolerance in plants. The CIPK gene family in pigeon pea (Cajanus cajan L.), a major food crop affected by drought, has not previously been characterised. Here, we identified 28 CIPK genes in the pigeon pea genome. Five CcCIPK genes were strongly upregulated in roots upon drought treatment and were selected for further characterisation. Overexpression of CcCIPK13 and CcCIPK14 increased survival rates by two- to three-fold relative to controls after 14 days of drought. Furthermore, the three major flavonoids, genistin, genistein and apigenin, were significantly upregulated in the same transgenic plants. Using CcCIPK14 as bait, we performed a yeast two-hybrid screen and identified six interactors, including CcCBL1. CcCIPK14 exhibited autophosphorylation and phosphorylation of CcCBL1 in vitro. CcCBL1-overexpressed plants displayed higher survival rates upon drought stress as well as higher expression of flavonoid biosynthetic genes and flavonoid content. CcCIPK14-overexpressed plants in which CcCBL1 transcript levels were reduced by RNA interference had lower survival rates, which indicated CcCBL1 in the same pathway as CcCIPK14. Together, our results demonstrate a role for the CcCIPK14-CcCBL1 complex in drought stress tolerance through the regulation of flavonoid biosynthesis in pigeon pea.
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Affiliation(s)
- Dong Meng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Biying Dong
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Lili Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Zhihua Song
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Litao Wang
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Rohul Amin
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Hongyan Cao
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Hanghang Li
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Qing Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Bejing, China
| | - Yujie Fu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Bejing, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
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28
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Wang C, Abbas F, Zhou Y, Ke Y, Li X, Yue Y, Yu Y, Yu R, Fan Y. Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium. PeerJ 2021; 9:e10883. [PMID: 33854831 PMCID: PMC7955670 DOI: 10.7717/peerj.10883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022] Open
Abstract
The SnRK (Snf1-Related protein Kinase) gene family plays crucial roles in various plant signaling pathways and stress-adaptive responses including biotic and abiotic stresses via activating protein phosphorylation pathways. However, there is no information available on the role of the SnRK gene family in Hedychium coronarium. H. coronarium is an important crop widely cultivated as an ornamental plant, herb, spice, or condiment. In this study, 60 HcSnRK genes were identified from the H. coronarium genomic and transcriptome data. Phylogenetic and gene structure analysis showed that the HcSnRK genes were divided into three groups (HcSnRK1, HcSnRK2 and HcSnRK3) and among them HcSnRK3 subfamily was further subdivided into two clades according to the number of introns. Chromosome localization analysis showed that HcSnRK genes were unevenly mapped onto all chromosomes, and the Ka/Ks ratio of 24 paralogues includes four tandems and 20 segmental duplications indicated that the HcSnRK gene family underwent a purifying selection. Cis-regulatory elements analysis suggested that the HcSnRK genes respond to multiple hormones and other stresses. The responsiveness of HcSnRK genes to several hormones was analyzed by quantitative real-time PCR. Based on the different transcriptome data, two candidates HcSnRK genes (HcSnRK2.2 and HcSnRK2.9) were screened out for further characterization . The subcellular localization experiment revealed that both genes were located in the nucleus and cytoplasm. Moreover, virus-induced gene silencing (VIGS) of HcSnRK2.2 and HcSnRK2.9 significantly reduced the floral volatile contents by suppressing the expression of terpene synthase genes (HcTPS1, HcTPS3, and HcTPS5), indicating that HcSnRK2.2 and HcSnRK2.9 genes play an important role in the regulatory mechanism of floral aroma. These results will provide novel insights into the functional dissection of H. coronarium SnRK gene family.
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Affiliation(s)
- Chutian Wang
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Yiwei Zhou
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Yanguo Ke
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
- College of Economics and Management, Kunming university, Kunming, China
| | - Xinyue Li
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Yuechong Yue
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Yunyi Yu
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangdong, China
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, China
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29
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Shi S, An L, Mao J, Aluko OO, Ullah Z, Xu F, Liu G, Liu H, Wang Q. The CBL-Interacting Protein Kinase NtCIPK23 Positively Regulates Seed Germination and Early Seedling Development in Tobacco ( Nicotiana tabacum L.). PLANTS 2021; 10:plants10020323. [PMID: 33567573 PMCID: PMC7915007 DOI: 10.3390/plants10020323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/31/2022]
Abstract
CBL-interacting protein kinase (CIPK) family is a unique group of serine/threonine protein kinase family identified in plants. Among this family, AtCIPK23 and its homologs in some plants are taken as a notable group for their importance in ions transport and stress responses. However, there are limited reports on their roles in seedling growth and development, especially in Solanaceae plants. In this study, NtCIPK23, a homolog of AtCIPK23 was cloned from Nicotiana tabacum. Expression analysis showed that NtCIPK23 is mainly expressed in the radicle, hypocotyl, and cotyledons of young tobacco seedlings. The transcriptional level of NtCIPK23 changes rapidly and spatiotemporally during seed germination and early seedling growth. To study the biological function of NtCIPK23 at these stages, the overexpressing and CRISPR/Cas9-mediated knock-out (ntcipk23) tobacco lines were generated. Phenotype analysis indicated that knock-out of NtCIPK23 significantly delays seed germination and the appearance of green cotyledon of young tobacco seedling. Overexpression of NtCIPK23 promotes cotyledon expansion and hypocotyl elongation of young tobacco seedlings. The expression of NtCIPK23 in hypocotyl is strongly upregulated by darkness and inhibited under light, suggesting that a regulatory mechanism of light might underlie. Consistently, a more obvious difference in hypocotyl length among different tobacco materials was observed in the dark, compared to that under the light, indicating that the upregulation of NtCIPK23 contributes greatly to the hypocotyl elongation. Taken together, NtCIPK23 not only enhances tobacco seed germination, but also accelerate early seedling growth by promoting cotyledon greening rate, cotyledon expansion and hypocotyl elongation of young tobacco seedlings.
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Affiliation(s)
- Sujuan Shi
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Technology Center, Shanghai Tobacco Co., Ltd., Beijing 101121, China
| | - Lulu An
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jingjing Mao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Oluwaseun Olayemi Aluko
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zia Ullah
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Fangzheng Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Graduate School of Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
| | - Haobao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Correspondence: (H.L.); (Q.W.); Tel.: +86-0532-8870-1031 (H.L. & Q.W.)
| | - Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (S.S.); (L.A.); (J.M.); (O.O.A.); (Z.U.); (F.X.); (G.L.)
- Correspondence: (H.L.); (Q.W.); Tel.: +86-0532-8870-1031 (H.L. & Q.W.)
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Chen X, Chen G, Li J, Hao X, Tuerxun Z, Chang X, Gao S, Huang Q. A maize calcineurin B-like interacting protein kinase ZmCIPK42 confers salt stress tolerance. PHYSIOLOGIA PLANTARUM 2021; 171:161-172. [PMID: 33064336 DOI: 10.1111/ppl.13244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 05/06/2023]
Abstract
Calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) play a crucial role in biotic and abiotic stress responses. However, the roles of different CIPKs in biotic and abiotic stress responses are less well characterized. In this study, we identified a mutation leading to an early protein termination of the maize CIPK gene ZmCIPK42 that undergoes a G to A mutation at the coding region via searching for genes involved in salt stress tolerance and ion homeostasis from maize with querying the EMS mutant library of maize B73. The mutant zmcipk42 plants have less branched tassel and impaired salt stress tolerance at the seedling stage. Quantitative real-time PCR analysis revealed that ZmCIPK42was expressed in diverse tissues and was induced by NaCl stress. A yeast two-hybrid screen identified a proteinase inhibitor (ZmMPI) as well as calcineurin B-like protein 1 and protein 4 (ZmCBL1, ZmCBL4) as interaction partners of ZmCIPK42. These interactions were further confirmed by bimolecular fluorescence complementation in plant cells. Moreover, over-expressing ZmCIPK42 resulted in enhanced tolerance to high salinity in both maize and Arabidopsis. These findings suggest that ZmCIPK42 is a positive regulator of salt stress tolerance and is a promising candidate gene to improve salt stress tolerance in maize through genetic manipulation.
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Affiliation(s)
- Xunji Chen
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Guo Chen
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Jianping Li
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Xiaoyan Hao
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Zumuremu Tuerxun
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Xiaochun Chang
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Shengqi Gao
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
| | - Quansheng Huang
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- Xinjiang Key Laboratory of Crop Biotechnology, Urumqi, China
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Su W, Ren Y, Wang D, Huang L, Fu X, Ling H, Su Y, Huang N, Tang H, Xu L, Que Y. New insights into the evolution and functional divergence of the CIPK gene family in Saccharum. BMC Genomics 2020; 21:868. [PMID: 33287700 PMCID: PMC7720545 DOI: 10.1186/s12864-020-07264-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
Background Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Results In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections. Conclusions In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07264-9.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueqin Fu
- Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanchen Tang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wu DC, Zhu JF, Shu ZZ, Wang W, Yan C, Xu SB, Wu DX, Wang CY, Dong ZR, Sun G. Physiological and transcriptional response to heat stress in heat-resistant and heat-sensitive maize (Zea mays L.) inbred lines at seedling stage. PROTOPLASMA 2020; 257:1615-1637. [PMID: 32728849 DOI: 10.1007/s00709-020-01538-5] [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: 05/02/2020] [Accepted: 07/24/2020] [Indexed: 05/21/2023]
Abstract
To understand the molecular and physiological mechanism underlying the heat stress in maize, transcriptional and physiological response to heat stress in the heat-resistant Huangzaosi (HZS) and heat-sensitive Lv-9-Kuan (L9K) inbred lines at seedling stage were analyzed and compared at seedling stage. Our results indicated that MDA content of the two inbred lines increased significantly under heat stress; the values of MDA in L9K was significantly higher than that in HZS. The level of SOD, CAT, and POD enzyme activities in HZS was higher than those in L9K for both the heat-treated group and controls. The values of Fv/Fm, qP, and ФPSII reduced by heat stress in L9K were higher than the respective values in HZS. RNA-seq data showed that heat stress induced more heat stress-related genes in HZS (257 heat stress-related genes) than in L9K (224 heat stress-related genes). GO and KEGG enrichment analyses indicated that HZS and L9K changed their physiological and biochemical mechanisms in response to heat stress through different molecular mechanisms. Weighted Gene Co-expression Network Analysis showed that HZS might obtain stronger heat resistance than L9K through a unique transcriptional regulatory network. Our findings provide insights into the molecular networks that mediate the tolerance of maize heat stress and also help us to mine key heat stress-related genes.
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Affiliation(s)
- De-Chuan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Jia-Fei Zhu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhong-Ze Shu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Wei Wang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Cheng Yan
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Shan-Bin Xu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - De-Xiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Cheng-Yu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhao-Rong Dong
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, Canada.
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Lu L, Chen X, Zhu L, Li M, Zhang J, Yang X, Wang P, Lu Y, Cheng T, Shi J, Yi Y, Chen J. NtCIPK9: A Calcineurin B-Like Protein-Interacting Protein Kinase From the Halophyte Nitraria tangutorum, Enhances Arabidopsis Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:1112. [PMID: 32973820 PMCID: PMC7472804 DOI: 10.3389/fpls.2020.01112] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 07/06/2020] [Indexed: 05/20/2023]
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs) play essential roles in plant abiotic stress response. In order to better understand salt tolerance, we cloned and analyzed the NtCIPK9 gene from the halophyte Nitraria tangutorum. Phylogenetic analysis shows that NtCIPK9 belongs to a sister clade with the Arabidopsis AtCIPK9 gene and is thought to localize to the plasma membrane. NtCIPK9 shows the highest expression level in the Nitraria tangutorum root under normal growth conditions, whereas after NaCl treatment, the highest expression was found in the blade. NtCIPK9-overexpressing Arabidopsis plants have a higher seed germination rate, longer root length, and displayed higher salt tolerance than wild type seedlings under salt stress conditions. Furthermore, NtCIPK9 overexpression might enhance the expression of genes related to K+ transportation after NaCl treatment. Thus, we conclude that NtCIPK9 increases transgenic plant salt tolerance and reduces damage associated with salt stress by promoting the expression of genes controlling ion homeostasis. Our results suggest that NtCIPK9 could serve as an ideal candidate gene to genetically engineer salt-tolerant plants.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinying Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mengjuan Li
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, China
| | - Xiuyan Yang
- Research Center of Saline and Alkali Land of National Forestry and Grassland Administration, China Academy of Forestry, Beijing, China
| | - Pengkai Wang
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yin Yi
- State Forestry Administration Key Laboratory of Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
- Guizhou Provincial Key Laboratory of Plant Physiology and Developmental Regulation, Guizhou Normal University, Guiyang, China
| | - Jinhui Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Long S, Yan F, Yang L, Sun Z, Wei S. Responses of Manila Grass (Zoysia matrella) to chilling stress: From transcriptomics to physiology. PLoS One 2020; 15:e0235972. [PMID: 32687533 PMCID: PMC7371177 DOI: 10.1371/journal.pone.0235972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Manila grass (Zoysia matrella), a warm-season turfgrass, usually wilts and browns by late autumn because of low temperature. To elucidate the molecular mechanisms regarding Manila grass responses to cold stress, we performed transcriptome sequencing of leaves exposed to 4°C for 0 (CK), 2h (2h_CT) and 72h (72h_CT) by Illumina technology. Approximately 250 million paired-end reads were obtained and de novo assembled into 82,605 unigenes. A total of 34,879 unigenes were annotated by comparing their sequence to public protein databases. At the 2h- and 72h-cold time points, 324 and 5,851 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) and metabolism pathway (KEGG) enrichment analyses of DEGs indicated that auxin, gibberellins, ethylene and calcium took part in the cold signal transduction in the early period. And in the late cold period, electron transport activities, photosynthetic machinery and activity, carbohydrate and nitrogen metabolism, redox equilibrium and hormone metabolism were disturbed. Low temperature stress triggered high light, drought and oxidative stress. At the physiological level, cold stress induced a decrease in water content, an increase in levels of total soluble sugar, free proline and MDA, and changes in bioactive gibberellins levels, which supported the changes in gene expression. The results provided a large set of sequence data of Manila grass as well as molecular mechanisms of the grass in response to cold stress. This information will be helpful for future study of molecular breeding and turf management.
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Affiliation(s)
- Sixin Long
- College of Life & Environmental Science, Minzu University of China, Beijing, PR China
| | - Fengying Yan
- College of Life & Environmental Science, Minzu University of China, Beijing, PR China
| | - Lin Yang
- College of Life & Environmental Science, Minzu University of China, Beijing, PR China
| | - Zhenyuan Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail: (ZS); (SW)
| | - Shanjun Wei
- College of Life & Environmental Science, Minzu University of China, Beijing, PR China
- * E-mail: (ZS); (SW)
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Cui Y, Su Y, Wang J, Jia B, Wu M, Pei W, Zhang J, Yu J. Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6. Int J Mol Sci 2020; 21:E863. [PMID: 32013234 PMCID: PMC7037685 DOI: 10.3390/ijms21030863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.
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Affiliation(s)
- Yupeng Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Ying Su
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China;
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
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Aliniaeifard S, Shomali A, Seifikalhor M, Lastochkina O. Calcium Signaling in Plants Under Drought. SALT AND DROUGHT STRESS TOLERANCE IN PLANTS 2020:259-298. [DOI: 10.1007/978-3-030-40277-8_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
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37
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Zhang Y, Zhou X, Liu S, Yu A, Yang C, Chen X, Liu J, Wang A. Identification and Functional Analysis of Tomato CIPK Gene Family. Int J Mol Sci 2019; 21:E110. [PMID: 31877938 PMCID: PMC6981861 DOI: 10.3390/ijms21010110] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022] Open
Abstract
The calcineurin B-like interacting protein kinase (CIPK) protein family is a critical protein family in plant signaling pathways mediated by Ca2+, playing a pivotal role in plant stress response and growth. However, to the best of our knowledge, no study of the tomato CIPK gene family in response to abiotic stress has been reported. In this study, 22 members of the tomato CIPK gene family were successfully identified by using a combination of bioinformatics techniques and molecular analyses. The expression level of each member of tomato CIPK gene family under abiotic stress (low temperature, high salt, drought treatment) was determined by qRT-PCR. Results indicated that tomato CIPK demonstrated different degrees of responding to various abiotic stresses, and changes in SlCIPK1 and SlCIPK8 expression level were relatively apparent. The results of qRT-PCR showed that expression levels of SlCIPK1 increased significantly in early stages of cold stress, and the expression level of SlCIPK8 increased significantly during the three treatments at different time points, implicating Solanum lycopersicum CIPK1(SlCIPK1) and Solanum lycopersicum CIPK8 (SlCIPK8) involvement in abiotic stress response. SlCIPK1 and SlCIPK8 were silenced using Virus-induced gene silencing (VIGS), and physiological indexes were detected by low temperature, drought, and high salt treatment. The results showed that plants silenced by SlCIPK1 and SlCIPK8 at the later stage of cold stress were significantly less resistant to cold than wild-type plants. SlCIPK1 and SlCIPK8 silenced plants had poor drought resistance, indicating a relationship between SlCIPK1 and SlCIPK8 with response to low temperature and drought resistance. This is the first study to uncover the nucleotide sequence for tomato CIPK family members and systematically study the changes of tomato CIPK family members under abiotic stress. Here, we investigate the CIPK family's response under abiotic stress providing understanding into the signal transduction pathway. This study provides a theoretical basis for elucidating the function of tomato CIPK at low temperature and its molecular mechanism of regulating low temperatures.
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Affiliation(s)
- Yao Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (X.Z.); (A.Y.)
| | - Xi’nan Zhou
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (X.Z.); (A.Y.)
| | - Siyuan Liu
- College of Plant Protection, China Agricultural University, Beijing 100000, China;
| | - Anzhou Yu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (X.Z.); (A.Y.)
| | - Chuanming Yang
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China;
| | - Jiayin Liu
- College of Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Aoxue Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (X.Z.); (A.Y.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China;
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Zhao J, Yu A, Du Y, Wang G, Li Y, Zhao G, Wang X, Zhang W, Cheng K, Liu X, Wang Z, Wang Y. Foxtail millet (Setaria italica (L.) P. Beauv) CIPKs are responsive to ABA and abiotic stresses. PLoS One 2019; 14:e0225091. [PMID: 31714948 PMCID: PMC6850536 DOI: 10.1371/journal.pone.0225091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/29/2019] [Indexed: 11/18/2022] Open
Abstract
CBL-interacting protein kinases (CIPKs) have been shown to regulate a variety of environmental stress-related signalling pathways in plants. Foxtail millet (Setaria italica (L.) P. Beauv) is known worldwide as a relatively stress-tolerant C4 crop species. Although the foxtail millet genome sequence has been released, little is known about the functions of CIPKs in foxtail millet. Therefore, a systematic genome-wide analysis of CIPK genes in foxtail millet was performed. In total, 35 CIPK members were identified in foxtail millet and divided into four subgroups (I to IV) on the basis of their phylogenetic relationships. Phylogenetic and gene structure analyses clearly divided all SiCIPKs into intron-poor and intron-rich clades. Cis-element analysis subsequently indicated that these SiCIPKs may be involved in responses to abiotic stimuli, hormones, and light signalling during plant growth and development, and stress-induced expression profile analysis revealed that all the SiCIPKs are involved in various stress signalling pathways. These results suggest that the CIPK genes in foxtail millet exhibit the basic characteristics of CIPK family members and play important roles in response to abiotic stresses. The results of this study will contribute to future functional characterization of abiotic stress responses mediated by CIPKs in foxtail millet.
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Affiliation(s)
- Jinfeng Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
- * E-mail: (AY); (JZ)
| | - Aili Yu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
- * E-mail: (AY); (JZ)
| | - Yanwei Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Gaohong Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Yanfang Li
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Genyou Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Xiangdong Wang
- Tangshan Academy of Agricultural Sciences, Tangshan, Hebei, People's Republic of China
| | - Wenzhong Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Kai Cheng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Xin Liu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Zhenhua Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Yuwen Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
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Wang X, Zhu B, Jiang Z, Wang S. Calcium-mediation of jasmonate biosynthesis and signaling in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110192. [PMID: 31481228 DOI: 10.1016/j.plantsci.2019.110192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/24/2019] [Accepted: 07/15/2019] [Indexed: 05/22/2023]
Abstract
Jasmonates (JAs) play vital roles in regulating a range of plant growth and development processes including seed germination, seedling development, reproduction, formation and development of storage organs, and senescence. JAs are also involved in the regulation of plant responses to environmental stimuli. The biosynthesis of JAs takes place in three different subcellular compartments, namely, the chloroplast, peroxisome, and cytoplasm. JAs activate the expression of JA-responsive genes by degrading jasmonate zinc-finger-inflorescence meristem (Zim) domain (JAZ) repressors via the E3 ubiquitin-ligase Skp/Cullin/F-box protein CORONATINE INSENSITIVE1 (COI1) complex (SCFCOI1) by using 26S proteasome. Calcium, reactive oxygen species (ROS), mitogen-activated protein kinase (MAPK), and nitric oxide (NO) are involved in the regulation of the biosynthesis and signaling of JAs in plants. Among these signaling molecules, calcium is one of the most important within plant cells. In plants, intracellular calcium levels change in response to JAs, resulting in calcium signatures with temporal and spatial features. Calcium channels are involved in the generation of calcium signatures. Calcium sensors, including calmodulins (CaMs), CaM-like proteins (CMLs), calcineurin B-like proteins (CBLs), and calcium-dependent protein kinases (CDPKs), can act to regulate the biosynthesis and signaling of JAs.
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Affiliation(s)
- Xiaoping Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Biping Zhu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhonghao Jiang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China; College of Life Science, Linyi University, Linyi, 276000, China.
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40
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Liu H, Wang YX, Li H, Teng RM, Wang Y, Zhuang J. Genome-Wide Identification and Expression Analysis of Calcineurin B-Like Protein and Calcineurin B-Like Protein-Interacting Protein Kinase Family Genes in Tea Plant. DNA Cell Biol 2019; 38:824-839. [DOI: 10.1089/dna.2019.4697] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Hao Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Rui-Min Teng
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yu Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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41
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Aslam M, Fakher B, Jakada BH, Zhao L, Cao S, Cheng Y, Qin Y. Genome-Wide Identification and Expression Profiling of CBL-CIPK Gene Family in Pineapple ( Ananas comosus) and the Role of AcCBL1 in Abiotic and Biotic Stress Response. Biomolecules 2019; 9:biom9070293. [PMID: 31330847 PMCID: PMC6681290 DOI: 10.3390/biom9070293] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/06/2023] Open
Abstract
Ca2+ serves as a ubiquitous second messenger regulating several aspects of plant growth and development. A group of unique calcium sensor proteins, calcineurin B-like (CBL), interact with CBL-interacting protein kinases (CIPKs) to decode the Ca2+ signature inside the cell. Although CBL-CIPK signaling toolkit has been shown to play significant roles in the responses to numerous stresses in different plants, the information about pineapple CBL-CIPK remains obscure. In the present study, a total of eight AcCBL and 21 AcCIPK genes were identified genome-wide in pineapple. The identified genes were renamed on the basis of gene ID in ascending order and phylogenetic analysis divided into five groups. Transcriptomic data analysis showed that AcCBL and AcCIPK genes were expressed differentially in different tissues. Further, the expression analysis of AcCBL1 in different tissues showed significant changes under various abiotic stimuli. Additionally, the ectopic expression of AcCBL1 in Arabidopsis resulted in enhanced tolerance to salinity, osmotic, and fungal stress. The present study revealed the crucial contribution of the CBL-CIPK gene in various biological and physiological processes in pineapple.
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Affiliation(s)
- Mohammad Aslam
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Beenish Fakher
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Bello Hassan Jakada
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Life Science College, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lihua Zhao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shijiang Cao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yan Cheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuan Qin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
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42
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Wang Y, Yan H, Qiu Z, Hu B, Zeng B, Zhong C, Fan C. Comprehensive Analysis of SnRK Gene Family and their Responses to Salt Stress in Eucalyptus grandis. Int J Mol Sci 2019; 20:E2786. [PMID: 31174407 PMCID: PMC6600528 DOI: 10.3390/ijms20112786] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 11/17/2022] Open
Abstract
The sucrose non-fermentation-related protein kinase (SnRK) is a kind of Ser/Thr protein kinase, which plays a crucial role in plant stress response by phosphorylating the target protein to regulate the interconnection of various signaling pathways. However, little is known about the SnRK family in Eucalyptus grandis. Thirty-four putative SnRK sequences were identified in E. grandis and divided into three subgroups (SnRK1, SnRK2 and SnRK3) based on phylogenetic analysis and the type of domain. Chromosome localization showed that SnRK family members are unevenly distributed in the remaining 10 chromosomes, with the notable exception of chromosome 11. Gene structure analysis reveal that 10 of the 24 SnRK3 genes contained no introns. Moreover, conserved motif analyses showed that SnRK sequences belonged to the same subgroup that contained the same motif type of motif. The Ka/Ks ratio of 17 paralogues suggested that the EgrSnRK gene family underwent a purifying selection. The upstream region of EgrSnRK genes enriched with different type and numbers of cis-elements indicated that EgrSnRK genes are likely to play a role in the response to diverse stresses. Quantitative real-time PCR showed that the majority of the SnRK genes were induced by salt treatment. Genome-wide analyses and expression pattern analyses provided further understanding on the function of the SnRK family in the stress response to different environmental salt concentrations.
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Affiliation(s)
- Yujiao Wang
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
- .Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Huifang Yan
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Zhenfei Qiu
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Bing Hu
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Bingshan Zeng
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Chonglu Zhong
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Chunjie Fan
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
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43
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Li P, Zheng T, Li L, Zhuo X, Jiang L, Wang J, Cheng T, Zhang Q. Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume. PeerJ 2019; 7:e6847. [PMID: 31106064 PMCID: PMC6499057 DOI: 10.7717/peerj.6847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/25/2019] [Indexed: 11/20/2022] Open
Abstract
Prunus mume is an important ornamental woody plant that grows in tropical and subtropical regions. Freezing stress can adversely impact plant productivity and limit the expansion of geographical locations. Understanding cold-responsive genes could potentially bring about the development of new ways to enhance plant freezing tolerance. Members of the serine/threonine protein kinase (CIPK) gene family play important roles in abiotic stress. However, the function of CIPK genes in P. mume remains poorly defined. A total of 16 CIPK genes were first identified in P. mume. A systematic phylogenetic analysis was conducted in which 253 CIPK genes from 12 species were divided into three groups. Furthermore, we analysed the chromosomal locations, molecular structures, motifs and domains of CIPK genes in P. mume. All of the CIPK sequences had NAF domains and promoter regions containing cis-acting regulatory elements of the related stress response. Three PmCIPK genes were identified as Pmu-miR172/167-targeted sites. Transcriptome data showed that most PmCIPK genes presented tissue-specific and time-specific expression profiles. Nine genes were highly expressed in flower buds in December and January, and 12 genes were up-regulated in stems in winter. The expression levels of 12 PmCIPK genes were up-regulated during cold stress treatment confirmed by qRT-PCR. Our study improves understanding of the role of the PmCIPK gene family in the low temperature response in woody plants and provides key candidate genes and a theoretical basis for cold resistance molecular-assisted breeding technology in P. mume.
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Affiliation(s)
- Ping Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Lulu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Xiaokang Zhuo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Liangbao Jiang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.,Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Hasan MMU, Ma F, Islam F, Sajid M, Prodhan ZH, Li F, Shen H, Chen Y, Wang X. Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton ( Gossypium spp.) Species Under Drought Stress. Int J Mol Sci 2019; 20:E2076. [PMID: 31035558 PMCID: PMC6539811 DOI: 10.3390/ijms20092076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 01/16/2023] Open
Abstract
Drought is one of the most important abiotic stresses that seriously affects cotton growth, development, and production worldwide. However, the molecular mechanism, key pathway, and responsible genes for drought tolerance incotton have not been stated clearly. In this research, high-throughput next generation sequencing technique was utilized to investigate gene expression profiles of three cotton species (Gossypium hirsutum, Gossypium arboreum, and Gossypium barbadense L.) under drought stress. A total of 6968 differentially expressed genes (DEGs) were identified, where 2053, 742, and 4173 genes were tested as statistically significant; 648, 320, and 1998 genes were up-regulated, and 1405, 422, and 2175 were down-regulated in TM-1, Zhongmian-16, and Pima4-S, respectively. Total DEGs were annotated and classified into functional groups under gene ontology analysis. The biological process was present only in tolerant species(TM-1), indicating drought tolerance condition. The Kyoto encyclopedia of genes and genomes showed the involvement of plant hormone signal transduction and metabolic pathways enrichment under drought stress. Several transcription factors associated with ethylene-responsive genes (ICE1, MYB44, FAMA, etc.) were identified as playing key roles in acclimatizing to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to abscisic acid (ABA) responses (NCED, PYL, PP2C, and SRK2E), reactive oxygen species (ROS) related in small heat shock protein and 18.1 kDa I heat shock protein, YLS3, and ODORANT1 genes. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in cotton.
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Affiliation(s)
- Md Mosfeq-Ul Hasan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
- Examination Controller Section, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh.
| | - Fanglu Ma
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Faisal Islam
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Muhammad Sajid
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Zakaria H Prodhan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Feng Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Hao Shen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Yadong Chen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
| | - Xuede Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Wan X, Zou LH, Zheng BQ, Wang Y. Circadian Regulation of Alternative Splicing of Drought-Associated CIPK Genes in Dendrobium catenatum (Orchidaceae). Int J Mol Sci 2019; 20:E688. [PMID: 30764546 PMCID: PMC6386984 DOI: 10.3390/ijms20030688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 01/23/2023] Open
Abstract
Dendrobium catenatum, an epiphytic and lithophytic species, suffers frequently from perennial shortage of water in the wild. The molecular mechanisms of this orchid's tolerance to abiotic stress, especially drought, remain largely unknown. It is well-known that CBL-interacting protein kinase (CIPKs) proteins play important roles in plant developmental processes, signal transduction, and responses to abiotic stress. To study the CIPKs' functions for D. catenatum, we first identified 24 CIPK genes from it. We divided them into three subgroups, with varying intron numbers and protein motifs, based on phylogeny analysis. Expression patterns of CIPK family genes in different tissues and in response to either drought or cold stresses suggested DcaCIPK11 may be associated with signal transduction and energy metabolism. DcaCIPK9, -14, and -16 are predicted to play critical roles during drought treatment specifically. Furthermore, transcript expression abundances of DcaCIPK16 showed polar opposites during day and night. Whether under drought treatment or not, DcaCIPK16 tended to emphatically express transcript1 during the day and transcript3 at night. This implied that expression of the transcripts might be regulated by circadian rhythm. qRT-PCR analysis also indicated that DcaCIPK3, -8, and -20 were strongly influenced by circadian rhythmicity. In contrast with previous studies, for the first time to our knowledge, our study revealed that the major CIPK gene transcript expressed was not always the same and was affected by the biological clock, providing a different perspective on alternative splicing preference.
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Affiliation(s)
- Xiao Wan
- Research Institute of Forestry; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Long-Hai Zou
- Research Institute of Forestry; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Bao-Qiang Zheng
- Research Institute of Forestry; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Yan Wang
- Research Institute of Forestry; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
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Pan W, Shen J, Zheng Z, Yan X, Shou J, Wang W, Jiang L, Pan J. Overexpression of the Tibetan Plateau annual wild barley (Hordeum spontaneum) HsCIPKs enhances rice tolerance to heavy metal toxicities and other abiotic stresses. RICE (NEW YORK, N.Y.) 2018; 11:51. [PMID: 30209684 PMCID: PMC6135728 DOI: 10.1186/s12284-018-0242-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) signaling system plays a key regulatory role in plant stress signaling. The roles of plant-specific CIPKs, essential for CBL-CIPK functions, in the response to various abiotic stresses have been extensively studied so far. However, until now, the possible roles of the CIPKs in the plant response to heavy metal toxicities are largely unknown. RESULTS In this study, we used bioinformatic and molecular strategies to isolate 12 HsCIPK genes in Tibetan Plateau annual wild barley (Hordeum spontaneum C. Koch) and subsequently identified their functional roles in the response to heavy metal toxicities. The results showed that multiple HsCIPKs were transcriptionally regulated by heavy metal toxicities (e.g., Hg, Cd, Cr, Pb, and Cu) and other abiotic stresses (e.g., salt, drought, aluminum, low and high temperature, and abscisic acid). Furthermore, the ectopic overexpression of each HsCIPK in rice (Oryza sativa L. cv Nipponbare) showed that transgenic plants of multiple HsCIPKs displayed enhanced tolerance of root growth to heavy metal toxicities (Hg, Cd, Cr, and Cu), salt and drought stresses. These results suggest that HsCIPKs are involved in the response to heavy metal toxicities and other abiotic stresses. CONCLUSIONS Tibetan Plateau annual wild barley HsCIPKs possess broad applications in genetically engineering of rice with tolerance to heavy metal toxicities and other abiotic stresses.
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Affiliation(s)
- Weihuai Pan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- College of Life Sciences, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Jinqiu Shen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Zhongzhong Zheng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Xu Yan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jianxin Shou
- College of Life Sciences, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Wenxiang Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Lixi Jiang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jianwei Pan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Genome-Wide Identification and Characterization of CIPK Family and Analysis Responses to Various Stresses in Apple ( Malus domestica). Int J Mol Sci 2018; 19:ijms19072131. [PMID: 30037137 PMCID: PMC6073193 DOI: 10.3390/ijms19072131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022] Open
Abstract
In the CIPK family, the CBL-interacting protein kinases have shown crucial roles in hormone signaling transduction, and response to abiotic stress in plant developmental processes. The CIPK family is characterized by conserved NAF/FISL (Asn-Ala-Phe) and PPI (protein-phosphatase interaction) domains in the C-terminus. However, little data has been reported about the CIPK family in apple. A total of 34 MdCIPK genes were identified from the apple genome in this study and were later divided into two groups according to the CIPK domains, characterized by gene structure and chromosomal distribution, and then mapped onto 17 chromosomes. All MdCIPK genes were expressed in the four apple tissues (leaf, root, flower, and fruit). In addition, the MdCIPK gene expression profile showed that five members among them revealed enhanced expression during the pollen tube growth stages. The MdCIPK4 was the most expressive during the entire fruit development stages. Under stress conditions 21 MdCIPK genes transcript levels were up-regulated in response to fungal and salt treatments. This suggested the possible features of these genes’ response to stresses in apples. Our findings provide a new insight about the roles of CIPK genes in apples, which could contribute to the cloning and functional analysis of CIPK genes in the future.
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Yan Y, He X, Hu W, Liu G, Wang P, He C, Shi H. Functional analysis of MeCIPK23 and MeCBL1/9 in cassava defense response against Xanthomonas axonopodis pv. manihotis. PLANT CELL REPORTS 2018; 37:887-900. [PMID: 29523964 DOI: 10.1007/s00299-018-2276-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/05/2018] [Indexed: 12/17/2023]
Abstract
KEY MESSAGE MeCIPK23 interacts with MeCBL1/9, and they confer improved defense response, providing potential genes for further genetic breeding in cassava. Cassava (Manihot esculenta) is an important food crop in tropical area, but its production is largely affected by cassava bacterial blight. However, the information of defense-related genes in cassava is very limited. Calcium ions play essential roles in plant development and stress signaling pathways. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) are crucial components of calcium signals. In this study, systematic expression profile of 25MeCIPKs in response to Xanthomonas axonopodis pv. manihotis (Xam) infection was examined, by which seven candidate MeCIPKs were chosen for functional investigation. Through transient expression in Nicotiana benthamiana leaves, we found that six MeCIPKs (MeCIPK5, MeCIPK8, MeCIPK12, MeCIPK22, MeCIPK23 and MeCIPK24) conferred improved defense response, via regulating the transcripts of several defense-related genes. Notably, we found that MeCIPK23 interacted with MeCBL1 and MeCBL9, and overexpression of these genes conferred improved defense response. On the contrary, virus-induced gene silencing of either MeCIPK23 or MeCBL1/9 or both genes resulted in disease sensitive in cassava. To our knowledge, this is the first study identifying MeCIPK23 as well as MeCBL1 and MeCBL9 that confer enhanced defense response against Xam.
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Affiliation(s)
- Yu Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Xinyi He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, Hainan Province, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Peng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
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Mo C, Wan S, Xia Y, Ren N, Zhou Y, Jiang X. Expression Patterns and Identified Protein-Protein Interactions Suggest That Cassava CBL-CIPK Signal Networks Function in Responses to Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2018; 9:269. [PMID: 29552024 PMCID: PMC5841119 DOI: 10.3389/fpls.2018.00269] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/14/2018] [Indexed: 05/30/2023]
Abstract
Cassava is an energy crop that is tolerant of multiple abiotic stresses. It has been reported that the interaction between Calcineurin B-like (CBL) protein and CBL-interacting protein kinase (CIPK) is implicated in plant development and responses to various stresses. However, little is known about their functions in cassava. Herein, 8 CBL (MeCBL) and 26 CIPK (MeCIPK) genes were isolated from cassava by genome searching and cloning of cDNA sequences of Arabidopsis CBLs and CIPKs. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed that the expression levels of MeCBL and MeCIPK genes were different in different tissues throughout the life cycle. The expression patterns of 7 CBL and 26 CIPK genes in response to NaCl, PEG, heat and cold stresses were analyzed by quantitative real-time PCR (qRT-PCR), and it was found that the expression of each was induced by multiple stimuli. Furthermore, we found that many pairs of CBLs and CIPKs could interact with each other via investigating the interactions between 8 CBL and 25 CIPK proteins using a yeast two-hybrid system. Yeast cells co-transformed with cassava MeCIPK24, MeCBL10, and Na+/H+ antiporter MeSOS1 genes exhibited higher salt tolerance compared to those with one or two genes. These results suggest that the cassava CBL-CIPK signal network might play key roles in response to abiotic stresses.
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Revisiting paradigms of Ca2+ signaling protein kinase regulation in plants. Biochem J 2018; 475:207-223. [DOI: 10.1042/bcj20170022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/15/2022]
Abstract
Calcium (Ca2+) serves as a universal second messenger in eukaryotic signal transduction. Understanding the Ca2+ activation kinetics of Ca2+ sensors is critical to understanding the cellular signaling mechanisms involved. In this review, we discuss the regulatory properties of two sensor classes: the Ca2+-dependent protein kinases (CPKs/CDPKs) and the calcineurin B-like (CBL) proteins that control the activity of CBL-interacting protein kinases (CIPKs) and identify emerging topics and some foundational points that are not well established experimentally. Most plant CPKs are activated by physiologically relevant Ca2+ concentrations except for those with degenerate EF hands, and new results suggest that the Ca2+-dependence of kinase activation may be modulated by both protein–protein interactions and CPK autophosphorylation. Early results indicated that activation of plant CPKs by Ca2+ occurred by relief of autoinhibition. However, recent studies of protist CDPKs suggest that intramolecular interactions between CDPK domains contribute allosteric control to CDPK activation. Further studies are required to elucidate the mechanisms regulating plant CPKs. With CBL–CIPKs, the two major activation mechanisms are thought to be (i) binding of Ca2+-bound CBL to the CIPK and (ii) phosphorylation of residues in the CIPK activation loop. However, the relative importance of these two mechanisms in regulating CIPK activity is unclear. Furthermore, information detailing activation by physiologically relevant [Ca2+] is lacking, such that the paradigm of CBLs as Ca2+ sensors still requires critical, experimental validation. Developing models of CPK and CIPK regulation is essential to understand how these kinases mediate Ca2+ signaling and to the design of experiments to test function in vivo.
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