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Buti M, Pasquariello M, Ronga D, Milc JA, Pecchioni N, Ho VT, Pucciariello C, Perata P, Francia E. Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings. Funct Integr Genomics 2018; 18:627-644. [PMID: 29876699 DOI: 10.1007/s10142-018-0615-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/07/2018] [Accepted: 05/23/2018] [Indexed: 12/26/2022]
Abstract
Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively. To thoroughly profile the short-term response of the two cultivars to chilling, RNA-Seq was performed on Thaibonnet and Volano seedlings after 0 (not stressed), 2, and 10 h at 10 °C. Differential expression analysis revealed that the ICE-DREB1/CBF pathway plays a primary role in chilling tolerance, mainly due to some important transcription factors involved (some of which had never been reported before). Moreover, the expression trends of some genes that were radically different between Thaibonnet and Volano (i.e., calcium-dependent protein kinases OsCDPK21 and OsCDPK23, cytochrome P450 monooxygenase CYP76M8, etc.) suggest their involvement in low temperature tolerance too. Density of differentially expressed genes along rice genome was determined and linked to the position of known QTLs: remarkable co-locations were reported, delivering an overview of genomic regions determinant for low temperature response at seedling stage. Our study contributes to a better understanding of the molecular mechanisms underlying rice response to chilling and provides a solid background for development of low temperature-tolerant germplasm.
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Affiliation(s)
- Matteo Buti
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy.
| | | | - Domenico Ronga
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Nicola Pecchioni
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Cereal Research Centre, Council for Agricultural Research and Economics, Foggia, Italy
| | - Viet The Ho
- PlantLab, Scuola Superiore Sant'Anna, Pisa, Italy
- Ho Chi Minh City University of Food Industry, Ho Chi Minh, Vietnam
| | | | | | - Enrico Francia
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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102
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Wang K, Bai ZY, Liang QY, Liu QL, Zhang L, Pan YZ, Liu GL, Jiang BB, Zhang F, Jia Y. Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress. BMC Genomics 2018; 19:319. [PMID: 29720105 PMCID: PMC5930780 DOI: 10.1186/s12864-018-4706-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 04/22/2018] [Indexed: 12/21/2022] Open
Abstract
Background Chrysanthemum is one kind of ornamental plant well-known and widely used in the world. However, its quality and production were severely affected by low temperature conditions in winter and early spring periods. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze chrysanthemum (Dendranthema grandiflorum) transcription response to low temperature. Results Using Illumina sequencing technology, a total of 86,444,237 high-quality clean reads and 93,837 unigenes were generated from four libraries: T01, controls; T02, 4 °C cold acclimation (CA) for 24 h; T03, − 4 °C freezing treatments for 4 h with prior CA; and T04, − 4 °C freezing treatments for 4 h without prior CA. In total, 7583 differentially expressed genes (DEGs) of 36,462 annotated unigenes were identified. We performed GO and KEGG pathway enrichment analyses, and excavated a group of important cold-responsive genes related to low temperature sensing and signal transduction, membrane lipid stability, reactive oxygen species (ROS) scavenging and osmoregulation. These genes encode many key proteins in plant biological processes, such as protein kinases, transcription factors, fatty acid desaturase, lipid-transfer proteins, antifreeze proteins, antioxidase and soluble sugars synthetases. We also verified expression levels of 10 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR). In addition, we performed the determination of physiological indicators of chrysanthemum treated at low temperature, and the results were basically consistent with molecular sequencing results. Conclusion In summary, our study presents a genome-wide transcript profile of Dendranthema grandiflorum var. jinba and provides insights into the molecular mechanisms of D. grandiflorum in response to low temperature. These data contributes to our deeper relevant researches on cold tolerance and further exploring new candidate genes for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-4706-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ke Wang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Zhen-Yu Bai
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qian-Yu Liang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qing-Lin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China.
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuan-Zhi Pan
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Guang-Li Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Bei-Bei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yin Jia
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
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103
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Arora R. Mechanism of freeze-thaw injury and recovery: A cool retrospective and warming up to new ideas. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:301-313. [PMID: 29576084 DOI: 10.1016/j.plantsci.2018.03.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/19/2018] [Accepted: 03/01/2018] [Indexed: 05/20/2023]
Abstract
Understanding cellular mechanism(s) of freeze-thaw injury (FTI) is key to the efforts for improving plant freeze-tolerance by cultural methods or molecular/genetic approaches. However, not much work has been done in the last 25+ years to advance our understanding of the nature and cellular loci of FTI. Currently, two FTI lesions are predominantly implicated: 1) structural and functional perturbations in plasma membrane; 2) ROS-induced oxidative damage. While both have stood the test of time, many questions remain unresolved and other potentially significant lesions need to be investigated. Additionally, molecular mechanism of post-thaw recovery (PTR), a critical component of frost-survival, has not been well investigated. Mechanistic understanding of repair after reversible injury could expand the options for strategies to improve frost-hardiness. In this review, without claiming to be exhaustive, I have attempted to synthesize major discoveries from last several decades on the mechanisms of FTI and the relatively little research conducted thus far on PTR mechanisms. It is followed by proposing of hypotheses for mechanism(s) for irreversible FTI or PTR involving cytosolic calcium and ROS signaling. Perspective is presented on some unresolved questions and research on new ideas to fill the knowledge gaps and advance the field.
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Affiliation(s)
- Rajeev Arora
- Department of Horticulture, Iowa State University, Ames, IA, 50011, USA.
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104
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Singh B, Khurana P, Khurana JP, Singh P. Gene encoding vesicle-associated membrane protein-associated protein from Triticum aestivum (TaVAP) confers tolerance to drought stress. Cell Stress Chaperones 2018; 23:411-428. [PMID: 29116579 PMCID: PMC5904086 DOI: 10.1007/s12192-017-0854-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/08/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022] Open
Abstract
Abiotic stresses like drought, salinity, high and low temperature, and submergence are major factors that limit the crop productivity. Hence, identification of genes associated with stress response in crops is a prerequisite for improving their tolerance to adverse environmental conditions. In an earlier study, we had identified a drought-inducible gene, vesicle-associated membrane protein-associated protein (TaVAP), in developing grains of wheat. In this study, we demonstrate that TaVAP is able to complement yeast and Arabidopsis mutants, which are impaired in their respective orthologs, signifying functional conservation. Constitutive expression of TaVAP in Arabidopsis imparted tolerance to water stress conditions without any apparent yield penalty. Enhanced tolerance to water stress was associated with maintenance of higher relative water content, photosynthetic efficiency, and antioxidant activities. Compared to wild type, the TaVAP-overexpressing plants showed enhanced lateral root proliferation that was attributed to higher endogenous levels of IAA. These studies are the first to demonstrate that TaVAP plays a critical role in growth and development in plants, and is a potential candidate for improving the abiotic stress tolerance in crop plants.
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Affiliation(s)
- Brinderjit Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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105
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Abstract
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
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106
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Sperotto RA, de Araújo Junior AT, Adamski JM, Cargnelutti D, Ricachenevsky FK, de Oliveira BHN, da Cruz RP, Dos Santos RP, da Silva LP, Fett JP. Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage. PLANT CELL REPORTS 2018; 37:347-375. [PMID: 29151156 DOI: 10.1007/s00299-017-2234-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/08/2017] [Indexed: 05/13/2023]
Abstract
Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Differentially expressed genes were identified: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expression in the CT genotype were used in systems biology analyses to identify protein-protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as affected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identified. Quantitative RT-PCR confirmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efficiency and antioxidant capacity, as well as more effective ethylene, Ca2+ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice.
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Affiliation(s)
- Raul Antonio Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari-UNIVATES, Lajeado, RS, Brazil.
| | | | - Janete Mariza Adamski
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Denise Cargnelutti
- Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil
| | | | - Ben-Hur Neves de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Renata Pereira da Cruz
- Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rinaldo Pires Dos Santos
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Leila Picolli da Silva
- Departamento de Zootecnia, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Janette Palma Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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107
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Liu Y, Xu C, Zhu Y, Zhang L, Chen T, Zhou F, Chen H, Lin Y. The calcium-dependent kinase OsCPK24 functions in cold stress responses in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:173-188. [PMID: 29193704 DOI: 10.1111/jipb.12614] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/23/2017] [Indexed: 05/08/2023]
Abstract
Calcium-dependent protein kinases (CPKs) are serine/threonine protein kinases that function in plant stress responses. Although CPKs are recognized as key messengers in signal transduction, the specific roles of CPKs and the molecular mechanisms underlying their activity remain largely unknown. Here, we characterized the function of OsCPK24, a cytosol-localized calcium-dependent protein kinase in rice. OsCPK24 was universally and highly expressed in rice plants and was induced by cold treatment. Whereas OsCPK24 knockdown plants exhibited increased sensitivity to cold compared to wild type (WT), OsCPK24-overexpressing plants exhibited increased cold tolerance. Plants overexpressing OsCPK24 exhibited increased accumulation of proline (an osmoprotectant) and glutathione (an antioxidant) and maintained a higher GSH/GSSG (reduced glutathione to oxidized glutathione) ratio during cold stress compared to WT. In addition to these effects in response to cold stress, we observed the kinase activity of OsCPK24 varied under different calcium concentrations. Further, OsCPK24 phosphorylated OsGrx10, a glutathione-dependent thioltransferase, at rates modulated by changes in calcium concentration. Together, our results support the hypothesis that OsCPK24 functions as a positive regulator of cold stress tolerance in rice, a process mediated by calcium signaling and involving phosphorylation and the inhibition of OsGrx10 to sustain higher glutathione levels.
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Affiliation(s)
- Yu Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China
| | - Yanfen Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lina Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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108
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Gao W, Xu FC, Guo DD, Zhao JR, Liu J, Guo YW, Singh PK, Ma XN, Long L, Botella JR, Song CP. Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress. BMC PLANT BIOLOGY 2018; 18:15. [PMID: 29343239 PMCID: PMC5772696 DOI: 10.1186/s12870-018-1230-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/11/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Soil salinization is one of the major environmental constraints to plant growth and agricultural production worldwide. Signaling components involving calcium (Ca2+) and the downstream calcium-dependent protein kinases (CPKs) play key roles in the perception and transduction of stress signals. However, the study of CPKs in cotton and their functions in response to salt stress remain unexplored. RESULTS A total of 98 predicted CPKs were identified from upland cotton (Gossypium hirsutum L. 'TM-1'), and phylogenetic analyses classified them into four groups. Gene family distribution studies have revealed the substantial impacts of the genome duplication events to the total number of GhCPKs. Transcriptome analyses showed a wide distribution of CPKs' expression among different organs. A total of 19 CPKs were selected for their rapid responses to salt stress at the transcriptional level, most of which were also incduced by the thylene-releasing chemical ethephon, suggesting a partal overlap of the salinity and ethylene responses. Silencing of 4 of the 19 CPKs (GhCPK8, GhCPK38, GhCPK54, and GhCPK55) severely compromised the basal cotton resistance to salt stress. CONCLUSIONS Our genome-wide expression analysis of CPK genes from up-land cotton suggests that CPKs are involved in multiple developmental responses as well as the response to different abiotic stresses. A cluster of the cotton CPKs was shown to participate in the early signaling events in cotton responses to salt stress. Our results provide significant insights on functional analysis of CPKs in cotton, especially in the context of cotton adaptions to salt stress.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Dan-Dan Guo
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Jing-Ruo Zhao
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 People’s Republic of China
| | - Ya-Wei Guo
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Prashant Kumar Singh
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Lu Long
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
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OsMAPK3 Phosphorylates OsbHLH002/OsICE1 and Inhibits Its Ubiquitination to Activate OsTPP1 and Enhances Rice Chilling Tolerance. Dev Cell 2018; 43:731-743.e5. [PMID: 29257952 DOI: 10.1016/j.devcel.2017.11.016] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/17/2017] [Accepted: 11/19/2017] [Indexed: 11/20/2022]
Abstract
Improvement of chilling tolerance is a major target in rice breeding. The signaling pathways regulating chilling consist of complex networks, including key transcription factors and their targets. However, it remains largely unknown how transcription factors are activated by chilling stress. Here, we report that the transcription factor OsbHLH002/OsICE1 is phosphorylated by OsMAPK3 under chilling stress. The osbhlh002-1 knockout mutant and antisense transgenic plants showed chilling hypersensitivity, whereas OsbHLH002-overexpressing plants exhibited enhanced chilling tolerance. OsbHLH002 can directly target OsTPP1, which encodes a key enzyme for trehalose biosynthesis. OsMAPK3 interacts with OsbHLH002 to prevent its ubiquitination by the E3 ligase OsHOS1. Under chilling stress, active OsMAPK3 phosphorylates OsbHLH002, leading to accumulation of phospho-OsbHLH002, which promotes OsTPP1 expression and increases trehalose content and resistance to chilling damage. Taken together, these results indicate that OsbHLH002 is phosphorylated by OsMAPK3, which enhances OsbHLH002 activation to its target OsTPP1 during chilling stress.
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110
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Mittal S, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement. Front Chem 2017; 5:115. [PMID: 29312925 PMCID: PMC5742180 DOI: 10.3389/fchem.2017.00115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022] Open
Abstract
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Atmakuri R. Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR), New Delhi, India
| | - Prashant A. Jain
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, India
| | - Prasanta K. Dash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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111
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Pareek A, Khurana A, Sharma AK, Kumar R. An Overview of Signaling Regulons During Cold Stress Tolerance in Plants. Curr Genomics 2017; 18:498-511. [PMID: 29204079 PMCID: PMC5684653 DOI: 10.2174/1389202918666170228141345] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 10/05/2016] [Indexed: 11/22/2022] Open
Abstract
Plants, being sessile organisms, constantly withstand environmental fluctuations, including low-temperature, also referred as cold stress. Whereas cold poses serious challenges at both physiological and developmental levels to plants growing in tropical or sub-tropical regions, plants from temperate climatic regions can withstand chilling or freezing temperatures. Several cold inducible genes have already been isolated and used in transgenic approach to generate cold tolerant plants. The conventional breeding methods and marker assisted selection have helped in developing plant with improved cold tolerance, however, the development of freezing tolerant plants through cold acclimation remains an unaccomplished task. Therefore, it is essential to have a clear understanding of how low temperature sensing strategies and corresponding signal transduction act during cold acclimation process. Herein, we synthesize the available information on the molecular mechanisms underlying cold sensing and signaling with an aim that the summarized literature will help develop efficient strategies to obtain cold tolerant plants.
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Affiliation(s)
- Amit Pareek
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Ashima Khurana
- Ashima Khurana, Botany Department, Zakir Husain Delhi College, University of Delhi, New Delhi-110002, India
| | - Arun K. Sharma
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Rahul Kumar
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad500046, India
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112
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Wang L, Nick P. Cold sensing in grapevine-Which signals are upstream of the microtubular "thermometer". PLANT, CELL & ENVIRONMENT 2017; 40:2844-2857. [PMID: 28898434 DOI: 10.1111/pce.13066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 05/09/2023]
Abstract
Plants can acquire freezing tolerance in response to cold but non-freezing temperatures. To efficiently activate this cold acclimation, low temperature has to be sensed and processed swiftly, a process that is linked with a transient elimination of microtubules. Here, we address cold-induced microtubules elimination in a grapevine cell line stably expressing a green fluorescent protein fusion of Arabidopsis TuB6, which allows to follow their response in vivo and to quantify this response by quantitative image analysis. We use time-course studies with several specific pharmacological inhibitors and activators to dissect the signalling events acting upstream of microtubules elimination. We find that microtubules disappear within 30 min after the onset of cold stress. We provide evidence for roles of calcium influx, membrane rigidification, and activation of NAD(P)H oxidase as factors in signal susception and amplification. We further conclude that a G-protein in concert with a phospholipase D convey the signal towards microtubules, whereas calmodulin seems to be not involved. Moreover, activation of jasmonate pathway in response to cold is required for an efficient microtubule response. We summarize our findings in a working model on a complex signalling hub at the membrane-cytoskeleton interphase that assembles the susception, perception and early transduction of cold signals.
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Affiliation(s)
- Lixin Wang
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
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113
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Jha SK, Malik S, Sharma M, Pandey A, Pandey GK. Recent Advances in Substrate Identification of Protein Kinases in Plants and Their Role in Stress Management. Curr Genomics 2017; 18:523-541. [PMID: 29204081 PMCID: PMC5684648 DOI: 10.2174/1389202918666170228142703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/13/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation-dephosphorylation is a well-known regulatory mechanism in biological systems and has become one of the significant means of protein function regulation, modulating most of the biological processes. Protein kinases play vital role in numerous cellular processes. Kinases transduce external signal into responses such as growth, immunity and stress tolerance through phosphorylation of their target proteins. In order to understand these cellular processes at the molecular level, one needs to be aware of the different substrates targeted by protein kinases. Advancement in tools and techniques has bestowed practice of multiple approaches that enable target identification of kinases. However, so far none of the methodologies has been proved to be as good as a panacea for the substrate identification. In this review, the recent advances that have been made in the identifications of putative substrates and the implications of these kinases and their substrates in stress management are discussed.
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Affiliation(s)
- Saroj K Jha
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Shikha Malik
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Amita Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi-110021, India
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Hao J, Yang J, Dong J, Fei SZ. Characterization of BdCBF genes and genome-wide transcriptome profiling of BdCBF3-dependent and -independent cold stress responses in Brachypodium distachyon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:52-61. [PMID: 28716420 DOI: 10.1016/j.plantsci.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/02/2017] [Indexed: 05/23/2023]
Abstract
Freezing stress substantially reduces crop yields and limits plant distribution. The identification of genes critical for cold acclimation is thus of great importance. C-repeat binding factors (CBFs) are transcription factors that play key regulatory roles in the cold acclimation process, which dramatically increases freezing tolerance in plants. We report here that B. distachyon can successfully cold acclimate and we identified a CBF gene family consisting of eight genes in a tandem array and are designated as BdCBF1-8. Expression analysis indicated that all the eight BdCBF genes are induced by cold. Freezing tolerance experiments showed that the knockdown of BdCBF3 gene in RNAi cbf3 mutant plants results in a significant reduction in survival after an exposure to freezing temperatures. RNA-seq transcriptomic analysis was conducted using the wild type and cbf3 mutant plants under both normal and cold conditions. We identified 460, 3213, 2839 and 1871 differentially expressed genes exhibiting different expression levels by pairwise comparisons of cbf3 (23°C) vs. WT (23°C), WT (23°C) vs. WT (4°C), cbf3 (23°C) vs. cbf3 (4°C), and cbf3 (4°C) vs. WT (4°C), respectively. These differentially expressed genes were enriched in several biological pathways. Combined analyses of differentially expressed genes in some of the enriched pathways provide insights into mechanisms of plant response to cold in the BdCBF3-dependent, -independent or -compensatory categories.
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Affiliation(s)
- Jingjie Hao
- Interdepartmental Graduate Major in Genetics, Iowa State University, Ames, IA 50011, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Shui-Zhang Fei
- Interdepartmental Graduate Major in Genetics, Iowa State University, Ames, IA 50011, USA; Department of Horticulture, Iowa State University, Ames, IA 50011, USA.
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115
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Khan TA, Fariduddin Q, Yusuf M. Low-temperature stress: is phytohormones application a remedy? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:21574-21590. [PMID: 28831664 DOI: 10.1007/s11356-017-9948-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 08/11/2017] [Indexed: 05/11/2023]
Abstract
Among the various abiotic stresses, low temperature is one of the major environmental constraints that limit the plant development and crop productivity. Plants are able to adapt to low-temperature stress through the changes in membrane composition and activation of reactive oxygen scavenging systems. The genetic pathway induced due to temperature downshift is based on C-repeat-binding factors (CBF) which activate promoters through the C-repeat (CRT) cis-element. Calcium entry is a major signalling event occurring immediately after a downshift in temperature. The increase in the level of cytosolic calcium activates many enzymes, such as phospholipases and calcium dependent-protein kinases. MAP-kinase module has been shown to be involved in the cold response. Ultimately, the activation of these signalling pathways leads to changes in the transcriptome. Several phytohormones, such as abscisic acid, brassinosteroids, auxin, salicylic acid, gibberellic acid, cytokinins and jasmonic acid, have been shown to play key roles in regulating the plant development under low-temperature stress. These phytohormones modulate important events involved in tolerance to low-temperature stress in plants. Better understanding of these events and genes controlling these could open new strategies for improving tolerance mediated by phytohormones.
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Affiliation(s)
- Tanveer Alam Khan
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Qazi Fariduddin
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
| | - Mohammad Yusuf
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
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Wang Y, Tong X, Qiu J, Li Z, Zhao J, Hou Y, Tang L, Zhang J. A phosphoproteomic landscape of rice (Oryza sativa) tissues. PHYSIOLOGIA PLANTARUM 2017; 160:458-475. [PMID: 28382632 DOI: 10.1111/ppl.12574] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differentially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phosphorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regulate the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuxuan Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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117
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Yang Y, Wang Q, Chen Q, Yin X, Qian M, Sun X, Yang Y. Genome-wide survey indicates diverse physiological roles of the barley (Hordeum vulgare L.) calcium-dependent protein kinase genes. Sci Rep 2017; 7:5306. [PMID: 28706292 PMCID: PMC5509701 DOI: 10.1038/s41598-017-05646-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 06/01/2017] [Indexed: 11/23/2022] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are crucial calcium sensors that play important roles in the regulation of plant growth and developmental processes, as well as protective responses to environmental stress. Here, we identified 28 CDPK genes from barley and cloned 5 new, full-length CDPK genes, MLOC_58648a, MLOC_19618a, MLOC_71733a, AK249361a and MLOC_4965a, using their expressed sequence tags. Phylogenetic and gene structural analyses revealed that the CDPK could be divided into four subgroups. Significant site-specific altered constraints and a high evolutionary rate may have contributed to the functional divergences among CDPK gene subfamilies. Expression profiles of different tissues and developmental stages suggested that several CDPK genes are involved in the functional development of plants. Different expression levels under a variety of abiotic stresses also indicated that the CDPK family underwent functional divergence during long-term evolution. Furthermore, several CDPK genes responded to single treatments and individual CDPK genes responded to multiple treatments, suggesting that barley CDPKs may be involved in mediating cross-talk among different signalling pathways. Our data provide an important foundation for the functional and evolutionary analyses of this important gene family in barley.
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Affiliation(s)
- Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qiuli Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qian Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xin Yin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Qian
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xudong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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118
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Almadanim MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA, Oliveira MM. Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. PLANT, CELL & ENVIRONMENT 2017; 40:1197-1213. [PMID: 28102545 DOI: 10.1111/pce.12916] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/15/2017] [Indexed: 05/20/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.
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Affiliation(s)
- M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Margarida T G Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - António E Leitão
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - José C Ramalho
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8024, USA
- MS and Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, 06520-8024, USA
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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119
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Bundó M, Coca M. Calcium-dependent protein kinase OsCPK10 mediates both drought tolerance and blast disease resistance in rice plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2963-2975. [PMID: 28472292 PMCID: PMC5853374 DOI: 10.1093/jxb/erx145] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/05/2017] [Indexed: 05/21/2023]
Abstract
Plant growth and productivity is negatively affected by different stresses. Most stresses trigger calcium signals that initiate acclimation responses in plants. The multigene family of plant calcium-dependent protein kinases (CPKs) functions in multiple stress responses by transducing calcium signals into phosphorylation events. This work reports that the OsCPK10 isoform positively mediates tolerance to different stresses in rice plants by enhancing their antioxidant capacity and protecting them from reactive oxygen species (ROS) damage, with the uncontrolled generation of ROS being a common feature of these stresses. Here, we show that the constitutive accumulation of an HA-tagged OsCPK10 full-length protein enhances the hydrogen peroxide detoxifying capacity of rice plants during desiccation. This is achived by modulating the accumulation of catalase proteins, which reduces the extent of lipid peroxidation and protects the integrity of cell membranes, resulting in drought tolerance. OsCPK10HA accumulation also confers blast disease resistance by interfering with fungal necrotrophic growth via a reduction in the accumulation of hydrogen peroxide. Furthermore, we show by bimolecular complementation assays that OsCPK10 is a plasma membrane protein that physically interacts in vivo with catalase A. OsCPK10 therefore appears to be a good molecular target to improve tolerance to abiotic stresses as well as to blast disease, which limit rice crop productivity.
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Affiliation(s)
| | - María Coca
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus de la UAB, Bellaterra, Barcelona, Spain
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120
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Zhang H, Wei C, Yang X, Chen H, Yang Y, Mo Y, Li H, Zhang Y, Ma J, Yang J, Zhang X. Genome-wide identification and expression analysis of calcium‑dependent protein kinase and its related kinase gene families in melon (Cucumis melo L.). PLoS One 2017; 12:e0176352. [PMID: 28437432 PMCID: PMC5402965 DOI: 10.1371/journal.pone.0176352] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/10/2017] [Indexed: 11/18/2022] Open
Abstract
The calcium-dependent protein kinase (CDPK) is a ser/thr protein kinase that plays vital roles in plant growth, development, and responses to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CDPK genes in melon. Herein, a total of 18 CDPK genes and 7 CDPK-related protein kinases (CRK) genes were identified in the melon genome via bioinformatic analysis, which were unevenly distributed across eleven chromosomes with an apparent exception for chromosome 3. Comparative syntenic analysis between Cucumis melo L. and Arabidopsis thaliana revealed that 13 CmCDPKs and 19 AtCPKs existed in 20 corresponding syntenic blocks. In addition, based on gene structure and phylogenetic analyses, all CmCDPKs were divided into four groups (CDPK I-IV) and CmCRKs clustered into one group (CRK I). Interestingly, group CDPK IV was clearly distinct from the other three CDPK groups, but clustered with CRK I on the phylogenetic tree, implying their origination from a common ancestor. Furthermore, CmCDPKand CmCRK genes were differentially expressed in response to various stimuli, such as biotic stress (Podosphaera xanthii), abiotic stress (salt and cold), and hormone (abscisic acid) treatment. To our knowledge, this is the first report on CDPK and CRK gene families in melon, which provides a basic foundation for functional characterizations of CmCDPK and CmCRK genes in the future.
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Affiliation(s)
- Haifei Zhang
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Chunhua Wei
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Xiaozhen Yang
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Hejie Chen
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Yongchao Yang
- Department of Horticulture, Northwest A&F University, Yangling, China
- Wenshan Academy of Agricultural Sciences, Wenshan, China
| | - Yanling Mo
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Hao Li
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Jianxiang Ma
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Jianqiang Yang
- Department of Horticulture, Northwest A&F University, Yangling, China
| | - Xian Zhang
- Department of Horticulture, Northwest A&F University, Yangling, China
- * E-mail:
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Passamani LZ, Barbosa RR, Reis RS, Heringer AS, Rangel PL, Santa-Catarina C, Grativol C, Veiga CFM, Souza-Filho GA, Silveira V. Salt stress induces changes in the proteomic profile of micropropagated sugarcane shoots. PLoS One 2017; 12:e0176076. [PMID: 28419154 PMCID: PMC5395195 DOI: 10.1371/journal.pone.0176076] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
Salt stress is one of the most common stresses in agricultural regions worldwide. In particular, sugarcane is affected by salt stress conditions, and no sugarcane cultivar presently show high productivity accompanied by a tolerance to salt stress. Proteomic analysis allows elucidation of the important pathways involved in responses to various abiotic stresses at the biochemical and molecular levels. Thus, this study aimed to analyse the proteomic effects of salt stress in micropropagated shoots of two sugarcane cultivars (CB38-22 and RB855536) using a label-free proteomic approach. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075. The RB855536 cultivar is more tolerant to salt stress than CB38-22. A quantitative label-free shotgun proteomic analysis identified 1172 non-redundant proteins, and 1160 of these were observed in both cultivars in the presence or absence of NaCl. Compared with CB38-22, the RB855536 cultivar showed a greater abundance of proteins involved in non-enzymatic antioxidant mechanisms, ion transport, and photosynthesis. Some proteins, such as calcium-dependent protein kinase, photosystem I, phospholipase D, and glyceraldehyde-3-phosphate dehydrogenase, were more abundant in the RB855536 cultivar under salt stress. Our results provide new insights into the response of sugarcane to salt stress, and the changes in the abundance of these proteins might be important for the acquisition of ionic and osmotic homeostasis during exposure to salt stress.
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Affiliation(s)
- Lucas Z. Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Roberta R. Barbosa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Ricardo S. Reis
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Angelo S. Heringer
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Patricia L. Rangel
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | | | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Carlos F. M. Veiga
- Laboratório de Cultura de Tecidos Vegetais (Biofábrica), Universidade Federal Rural do Rio de Janeiro Campus Campos dos Goytacazes, Campos dos Goytacazes, RJ, Brazil
| | - Gonçalo A. Souza-Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
- * E-mail:
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Yu D, Zhang L, Zhao K, Niu R, Zhai H, Zhang J. VaERD15, a Transcription Factor Gene Associated with Cold-Tolerance in Chinese Wild Vitis amurensis. FRONTIERS IN PLANT SCIENCE 2017; 8:297. [PMID: 28326090 PMCID: PMC5339311 DOI: 10.3389/fpls.2017.00297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/17/2017] [Indexed: 05/23/2023]
Abstract
Early responsive to dehydration (ERD) genes can be rapidly induced to counteract abiotic stresses, such as drought, low temperatures or high salinities. Here, we report on an ERD gene (VaERD15) related to cold tolerance from Chinese wild Vitis amurensis accession 'Heilongjiang seedling'. The full-length VaERD15 cDNA is 685 bp, including a 66 bp 5'-untranslated region (UTR), a 196 bp 3'-UTR region and a 423 bp open reading frame encoding 140 amino acids. The VaERD15 protein shares a high amino acid sequence similarity with ERD15 of Arabidopsis thaliana. In our study, VaERD15 was shown to have a nucleic localization function and a transcriptional activation function. Semi-quantitative PCR and Western blot analyses showed that VaERD15 was constitutively expressed in young leaves, stems and roots of V. amurensis accession 'Heilongjiang seedling' plants, and expression levels increased after low-temperature treatment. We also generated a transgenic Arabidopsis Col-0 line that over-expressed VaERD15 and carried out a cold-treatment assay. Real-time quantitative PCR (qRT-PCR) and Western blot analyses showed that as the duration of cold treatment increased, the expression of both gene and protein levels increased continuously in the transgenic plants, while almost no expression was detected in the wild type Arabidopsis. Moreover, the plants that over-expressed VaERD15 showed higher cold tolerance and accumulation of proline, soluble sugars, proteins, malondialdehyde and three antioxidases (superoxide dismutase, peroxidase, and catalase). Lower levels of relative ion leakage also occurred under cold stress. Taken together, our results indicate that the transcription factor VaERD15 was induced by cold stress and was able to enhance cold tolerance.
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Affiliation(s)
- Dongdong Yu
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
| | - Lihua Zhang
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
| | - Kai Zhao
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
| | - Ruxuan Niu
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
| | - Huan Zhai
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
| | - Jianxia Zhang
- College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of AgricultureYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
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Variable salinity responses of 12 alfalfa genotypes and comparative expression analyses of salt-response genes. Sci Rep 2017; 7:42958. [PMID: 28225027 PMCID: PMC5320470 DOI: 10.1038/srep42958] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/17/2017] [Indexed: 01/22/2023] Open
Abstract
Twelve alfalfa genotypes that were selected for biomass under salinity, differences in Na and Cl concentrations in shoots and K/Na ratio were evaluated in this long-term salinity experiment. The selected plants were cloned to reduce genetic variability within each genotype. Salt tolerance (ST) index of the genotypes ranged from 0.39 to 1. The most salt-tolerant genotypes SISA14-1 (G03) and AZ-90ST (G10), the top performers for biomass, exhibited the least effect on shoot number and height. SISA14-1 (G03) accumulated low Na and Cl under salinity. Most genotypes exhibited a net reduction in shoot Ca, Mg, P, Fe, and Cu, while Mn and Zn increased under salinity. Salinity reduced foliar area and stomatal conductance; while net photosynthetic rate and transpiration were not affected. Interestingly, salinity increased chlorophyll and antioxidant capacity in most genotypes; however neither parameter correlated well to ST index. Salt-tolerant genotypes showed upregulation of the SOS1, SOS2, SOS3, HKT1, AKT1, NHX1, P5CS1, HSP90.7, HSP81.2, HSP71.1, HSPC025, OTS1, SGF29 and SAL1 genes. Gene expression analyses allowed us to classify genotypes based on their ability to regulate different components of the salt tolerance mechanism. Pyramiding different components of the salt tolerance mechanism may lead to superior salt-tolerant alfalfa genotypes.
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Vicherová E, Hájek M, Šmilauer P, Hájek T. Sphagnum establishment in alkaline fens: Importance of weather and water chemistry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:1429-1438. [PMID: 28038871 DOI: 10.1016/j.scitotenv.2016.12.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 06/06/2023]
Abstract
Sphagnum expansion to alkaline fens has accelerated during the last decades in Europe, leading to changes in diversity, habitat distributions and carbon storage. The causes are still not clearly understood and involve an interplay between climate change, hydrology, nutrient supply and Sphagnum physiology. We conducted a 4-year field experiment in eight fens in Central European highlands and assessed survival and establishment of individual apical shoot fragments of S. flexuosum, S. warnstorfii and S. squarrosum transplanted along the microtopographical gradient. In a laboratory experiment, we tested combined effects of desiccation and high calcium bicarbonate concentration on Sphagnum survival. We found that in unflooded positions, living shoots of Sphagnum and brown mosses lowered [Ca2+] and pH in their capillary water, in contrast to dead fragments; yet without differences between species. Survival and expansion of Sphagnum fragments, which did not die of acute calcium toxicity during first weeks/months, was negatively affected by dry weather and alkaline water chemistry, reflecting Sphagnum intolerance to desiccation and to combined high [Ca2+] and pH. Shoot fragments expanded to patches only when precipitation was high. Interestingly, non-toxic concentration of calcium bicarbonate reduced desiccation damage in Sphagnum, probably through protection of membranes or other cell components. This mechanism would facilitate Sphagnum survival in elevated, frequently desiccated microhabitats of calcareous fens such as brown-moss hummocks. However, since water-retaining capacity of few Sphagnum shoots is insufficient to change water chemistry in its surroundings, surface acidification may occur only once the environment (e.g. sufficient humidity) enabled expansion to larger mats. Then, the retained rainwater together with hardly decomposable Sphagnum litter would separate mire surface from groundwater, speeding up successional shift towards poor fens. Sphagnum expansion to alkaline fens is therefore more likely in humid regions.
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Affiliation(s)
- Eliška Vicherová
- Institute of Botany, Czech Academy of Sciences, Department of Functional Ecology, Dukelská 135, CZ-379 82 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic.
| | - Michal Hájek
- Faculty of Science, Masaryk University, Department of Botany and Zoology, Kotlářská 2, CZ-611 37 Brno, Czech Republic.
| | - Petr Šmilauer
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic.
| | - Tomáš Hájek
- Institute of Botany, Czech Academy of Sciences, Department of Functional Ecology, Dukelská 135, CZ-379 82 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic.
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Wu P, Wang W, Duan W, Li Y, Hou X. Comprehensive Analysis of the CDPK-SnRK Superfamily Genes in Chinese Cabbage and Its Evolutionary Implications in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:162. [PMID: 28239387 PMCID: PMC5301275 DOI: 10.3389/fpls.2017.00162] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/25/2017] [Indexed: 05/30/2023]
Abstract
The CDPK-SnRK (calcium-dependent protein kinase/Snf1-related protein kinase) gene superfamily plays important roles in signaling pathways for disease resistance and various stress responses, as indicated by emerging evidence. In this study, we constructed comparative analyses of gene structure, retention, expansion, whole-genome duplication (WGD) and expression patterns of CDPK-SnRK genes in Brassica rapa and their evolution in plants. A total of 49 BrCPKs, 14 BrCRKs, 3 BrPPCKs, 5 BrPEPRKs, and 56 BrSnRKs were identified in B. rapa. All BrCDPK-SnRK proteins had highly conserved kinase domains. By statistical analysis of the number of CDPK-SnRK genes in each species, we found that the expansion of the CDPK-SnRK gene family started from angiosperms. Segmental duplication played a predominant role in CDPK-SnRK gene expansion. The analysis showed that PEPRK was more preferentially retained than other subfamilies and that CPK was retained similarly to SnRK. Among the CPKs and SnRKs, CPKIII and SnRK1 genes were more preferentially retained than other groups. CRK was closest to CPK, which may share a common evolutionary origin. In addition, we identified 196 CPK genes and 252 SnRK genes in 6 species, and their different expansion and evolution types were discovered. Furthermore, the expression of BrCDPK-SnRK genes is dynamic in different tissues as well as in response to abiotic stresses, demonstrating their important roles in development in B. rapa. In summary, this study provides genome-wide insight into the evolutionary history and mechanisms of CDPK-SnRK genes following whole-genome triplication in B. rapa.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Wenli Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
- School of Life Science and Food Engineering, Huaiyin Institute of TechnologyHuaian, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China
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Ribaudo CM, Curá JA, Cantore ML. Activation of a calcium-dependent protein kinase involved in the Azospirillum growth promotion in rice. World J Microbiol Biotechnol 2017; 33:22. [DOI: 10.1007/s11274-016-2186-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/01/2016] [Indexed: 01/16/2023]
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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Xiao XH, Yang M, Sui JL, Qi JY, Fang YJ, Hu SN, Tang CR. The calcium-dependent protein kinase (CDPK) and CDPK-related kinase gene families in Hevea brasiliensis-comparison with five other plant species in structure, evolution, and expression. FEBS Open Bio 2016; 7:4-24. [PMID: 28097084 PMCID: PMC5221434 DOI: 10.1002/2211-5463.12163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/06/2016] [Accepted: 11/10/2016] [Indexed: 11/16/2022] Open
Abstract
Calcium‐dependent protein kinases (CDPKs or CPKs) play important roles in various physiological processes of plants, including growth and development, stress responses and hormone signaling. Although the CDPK gene family has been characterized in several model plants, little is known about this gene family in Hevea brasiliensis (the Para rubber tree). Here, we characterize the entire H. brasiliensis CDPK and CDPK‐related kinase (CRK) gene families comprising 30 CDPK genes (HbCPK1 to 30) and nine CRK genes (HbCRK1 to 9). Structure and phylogeny analyses of these CDPK and CRK genes demonstrate evolutionary conservation in these gene families across H. brasiliensis and other plant species. The expression of HbCPK and HbCRK genes was investigated via Solexa sequencing in a range of experimental conditions (different tissues, phases of leaf development, ethylene treatment, and various abiotic stresses). The results suggest that HbCPK and HbCRK genes are important components in growth, development, and stress responses of H. brasiliensis. Parallel studies on the CDPK and CRK gene families were also extended to five other plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Manihot esculenta, and Ricinus communis). The CDPK and CRK genes from different plant species that exhibit similar expression patterns tend to cluster together, suggesting a coevolution of gene structure and expression behavior in higher plants. The results serve as a foundation to further functional studies of these gene families in H. brasiliensis as well as in the whole plant kingdom.
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Affiliation(s)
- Xiao-Hu Xiao
- Key Lab of Rubber Biology, Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Meng Yang
- Beijing Institute of Genomics Chinese Academy of Sciences Beijing China
| | - Jin-Lei Sui
- Key Lab of Rubber Biology, Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China; College of Agriculture Hainan University Haikou Hainan China
| | - Ji-Yan Qi
- Key Lab of Rubber Biology, Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Yong-Jun Fang
- Key Lab of Rubber Biology, Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
| | - Song-Nian Hu
- Beijing Institute of Genomics Chinese Academy of Sciences Beijing China
| | - Chao-Rong Tang
- Key Lab of Rubber Biology, Ministry of Agriculture & Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences Danzhou Hainan China
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Chandran AKN, Yoo YH, Cao P, Sharma R, Sharma M, Dardick C, Ronald PC, Jung KH. Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. RICE (NEW YORK, N.Y.) 2016; 9:40. [PMID: 27540739 PMCID: PMC4991984 DOI: 10.1186/s12284-016-0106-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/08/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Protein kinases catalyze the transfer of a phosphate moiety from a phosphate donor to the substrate molecule, thus playing critical roles in cell signaling and metabolism. Although plant genomes contain more than 1000 genes that encode kinases, knowledge is limited about the function of each of these kinases. A major obstacle that hinders progress towards kinase characterization is functional redundancy. To address this challenge, we previously developed the rice kinase database (RKD) that integrated omics-scale data within a phylogenetics context. RESULTS An updated version of rice kinase database (RKD) that contains metadata derived from NCBI GEO expression datasets has been developed. RKD 2.0 facilitates in-depth transcriptomic analyses of kinase-encoding genes in diverse rice tissues and in response to biotic and abiotic stresses and hormone treatments. We identified 261 kinases specifically expressed in particular tissues, 130 that are significantly up- regulated in response to biotic stress, 296 in response to abiotic stress, and 260 in response to hormones. Based on this update and Pearson correlation coefficient (PCC) analysis, we estimated that 19 out of 26 genes characterized through loss-of-function studies confer dominant functions. These were selected because they either had paralogous members with PCC values of <0.5 or had no paralog. CONCLUSION Compared with the previous version of RKD, RKD 2.0 enables more effective estimations of functional redundancy or dominance because it uses comprehensive expression profiles rather than individual profiles. The integrated analysis of RKD with PCC establishes a single platform for researchers to select rice kinases for functional analyses.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Rita Sharma
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture - Agricultural Research Service, 2217 Wiltshire Road, Kearneysville, WV, 25442, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA.
- The Joint Bioenergy Institute, Emeryville, CA, 95616, USA.
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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130
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Improvement of Salinity Stress Tolerance in Rice: Challenges and Opportunities. AGRONOMY-BASEL 2016. [DOI: 10.3390/agronomy6040054] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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131
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Cieśla A, Mituła F, Misztal L, Fedorowicz-Strońska O, Janicka S, Tajdel-Zielińska M, Marczak M, Janicki M, Ludwików A, Sadowski J. A Role for Barley Calcium-Dependent Protein Kinase CPK2a in the Response to Drought. FRONTIERS IN PLANT SCIENCE 2016; 7:1550. [PMID: 27826303 PMCID: PMC5078816 DOI: 10.3389/fpls.2016.01550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/03/2016] [Indexed: 05/30/2023]
Abstract
Increasing the drought tolerance of crops is one of the most challenging goals in plant breeding. To improve crop productivity during periods of water deficit, it is essential to understand the complex regulatory pathways that adapt plant metabolism to environmental conditions. Among various plant hormones and second messengers, calcium ions are known to be involved in drought stress perception and signaling. Plants have developed specific calcium-dependent protein kinases that convert calcium signals into phosphorylation events. In this study we attempted to elucidate the role of a calcium-dependent protein kinase in the drought stress response of barley (Hordeum vulgare L.), one of the most economically important crops worldwide. The ongoing barley genome project has provided useful information about genes potentially involved in the drought stress response, but information on the role of calcium-dependent kinases is still limited. We found that the gene encoding the calcium-dependent protein kinase HvCPK2a was significantly upregulated in response to drought. To better understand the role of HvCPK2a in drought stress signaling, we generated transgenic Arabidopsis plants that overexpressed the corresponding coding sequence. Overexpressing lines displayed drought sensitivity, reduced nitrogen balance index (NBI), an increase in total chlorophyll content and decreased relative water content. In addition, in vitro kinase assay experiments combined with mass spectrometry allowed HvCPK2a autophosphorylation sites to be identified. Our results suggest that HvCPK2a is a dual-specificity calcium-dependent protein kinase that functions as a negative regulator of the drought stress response in barley.
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Affiliation(s)
- Agata Cieśla
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Filip Mituła
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Lucyna Misztal
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | | | - Sabina Janicka
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | | | - Małgorzata Marczak
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Maciej Janicki
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Agnieszka Ludwików
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Jan Sadowski
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
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Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses. Sci Rep 2016; 6:32717. [PMID: 27596441 PMCID: PMC5011731 DOI: 10.1038/srep32717] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/15/2016] [Indexed: 11/16/2022] Open
Abstract
Soil alkalization severely affects crop growth and agricultural productivity. Alkali salts impose ionic, osmotic, and high pH stresses on plants. The alkali tolerance molecular mechanism in roots from halophyte Puccinellia tenuiflora is still unclear. Here, the changes associated with Na2CO3 tolerance in P. tenuiflora roots were assessed using physiological and iTRAQ-based quantitative proteomic analyses. We set up the first protein dataset in P. tenuiflora roots containing 2,671 non-redundant proteins. Our results showed that Na2CO3 slightly inhibited root growth, caused ROS accumulation, cell membrane damage, and ion imbalance, as well as reduction of transport and protein synthesis/turnover. The Na2CO3-responsive patterns of 72 proteins highlighted specific signaling and metabolic pathways in roots. Ca2+ signaling was activated to transmit alkali stress signals as inferred by the accumulation of calcium-binding proteins. Additionally, the activities of peroxidase and glutathione peroxidase, and the peroxiredoxin abundance were increased for ROS scavenging. Furthermore, ion toxicity was relieved through Na+ influx restriction and compartmentalization, and osmotic homeostasis reestablishment due to glycine betaine accumulation. Importantly, two transcription factors were increased for regulating specific alkali-responsive gene expression. Carbohydrate metabolism-related enzymes were increased for providing energy and carbon skeletons for cellular metabolism. All these provide new insights into alkali-tolerant mechanisms in roots.
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Liu H, Che Z, Zeng X, Zhou X, Sitoe HM, Wang H, Yu D. Genome-wide analysis of calcium-dependent protein kinases and their expression patterns in response to herbivore and wounding stresses in soybean. Funct Integr Genomics 2016; 16:481-93. [PMID: 27179522 DOI: 10.1007/s10142-016-0498-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 04/27/2016] [Accepted: 05/03/2016] [Indexed: 12/20/2022]
Abstract
Calcium-dependent protein kinases (CDPKs) play important roles in various aspects of plant physiology and involve in many cellular processes. However, genome-wide analysis of CDPK family in plant species is limited and few studies have been reported in soybean. In this study, a total of 39 genes encoding CDPKs were identified from the whole-genome sequence of soybean (Glycine max), which were denominated as GmCPK1-GmCPK39. These 39 CDPK genes could be classified into four subfamilies, and most genes showed tissue-specific expression patterns. Eight soybean CDPKs clustered together with the previously reported CDPKs related to pathogen, wounding, or herbivore stress were further analyzed. Differential gene expression analysis of these eight CDPK genes in response to herbivore and wounding stresses helps us identify GmCPK3 and GmCPK31 as the candidate genes for herbivore resistance in soybean, whose relative transcript abundance rapidly increased after wound and herbivore attacks. Sub-cellular localization revealed that GmCPK3 and GmCPK31 were localized in plasma membranes, which is consistent with previously reported plant defense related CDPKs. These results may suggest that GmCPK3 and GmCPK31 play important roles in the plant response to biotic stress. Simultaneously, our study will provide an important foundation for further functional characterization of the soybean CDPK gene family.
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Affiliation(s)
- Hailun Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhijun Che
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuanrui Zeng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqiong Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hélder Manuel Sitoe
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.
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134
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Khan A, Sovero V, Gemenet D. Genome-assisted Breeding For Drought Resistance. Curr Genomics 2016; 17:330-42. [PMID: 27499682 PMCID: PMC4955035 DOI: 10.2174/1389202917999160211101417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 11/30/2022] Open
Abstract
Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant. Drought stress responses can be divided into four broad types: drought escape, drought avoidance, drought tolerance, and drought recovery, each characterized by interacting mechanisms, which may together be referred to as drought resistance mechanisms. The complex nature of drought resistance requires a multi-pronged approach to breed new varieties with stable and enhanced yield under drought stress conditions. High throughput genomics and phenomics allow marker-assisted selection (MAS) and genomic selection (GS), which offer rapid and targeted improvement of populations and identification of parents for rapid genetic gains and improved drought-resistant varieties. Using these approaches together with appropriate genetic diversity, databases, analytical tools, and well-characterized drought stress scenarios, weather and soil data, new varieties with improved drought resistance corresponding to grower preferences can be introduced into target regions rapidly.
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Affiliation(s)
- Awais Khan
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Valpuri Sovero
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Dorcus Gemenet
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
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135
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Zhou L, Liu Z, Liu Y, Kong D, Li T, Yu S, Mei H, Xu X, Liu H, Chen L, Luo L. A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice. Sci Rep 2016; 6:30264. [PMID: 27453463 PMCID: PMC4958981 DOI: 10.1038/srep30264] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 07/04/2016] [Indexed: 12/22/2022] Open
Abstract
A novel gene, OsAHL1, containing an AT-hook motif and a PPC domain was identified through genome-wide profiling and analysis of mRNAs by comparing the microarray of drought-challenged versus normally watered rice. The results indicated OsAHL1 has both drought avoidance and drought tolerance that could greatly improve drought resistance of the rice plant. Overexpression of OsAHL1 enhanced multiple stress tolerances in rice plants during both seedling and panicle development stages. Functional studies revealed that OsAHL1 regulates root development under drought condition to enhance drought avoidance, participates in oxidative stress response and also regulates the content of chlorophyll in rice leaves. OsAHL1 specifically binds to the A/T rich sequence region of promoters or introns, and hence directly regulates the expression of many stress related downstream genes.
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Affiliation(s)
- Liguo Zhou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zaochang Liu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yunhua Liu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xiaoyan Xu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
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136
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Wu YH, Wang T, Wang K, Liang QY, Bai ZY, Liu QL, Pan YZ, Jiang BB, Zhang L. Comparative Analysis of the Chrysanthemum Leaf Transcript Profiling in Response to Salt Stress. PLoS One 2016; 11:e0159721. [PMID: 27447718 PMCID: PMC4957832 DOI: 10.1371/journal.pone.0159721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/07/2016] [Indexed: 11/18/2022] Open
Abstract
Salt stress has some remarkable influence on chrysanthemum growth and productivity. To understand the molecular mechanisms associated with salt stress and identify genes of potential importance in cultivated chrysanthemum, we carried out transcriptome sequencing of chrysanthemum. Two cDNA libraries were generated from the control and salt-treated samples (Sample_0510_control and Sample_0510_treat) of leaves. By using the Illumina Solexa RNA sequencing technology, 94 million high quality sequencing reads and 161,522 unigenes were generated and then we annotated unigenes through comparing these sequences to diverse protein databases. A total of 126,646 differentially expressed transcripts (DETs) were identified in leaf. Plant hormones, amino acid metabolism, photosynthesis and secondary metabolism were all changed under salt stress after the complete list of GO term and KEGG enrichment analysis. The hormone biosynthesis changing and oxidative hurt decreasing appeared to be significantly related to salt tolerance of chrysanthemum. Important protein kinases and major transcription factor families involved in abiotic stress were differentially expressed, such as MAPKs, CDPKs, MYB, WRKY, AP2 and HD-zip. In general, these results can help us to confirm the molecular regulation mechanism and also provide us a comprehensive resource of chrysanthemum under salt stress.
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Affiliation(s)
- Yin-Huan Wu
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tong Wang
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ke Wang
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qian-Yu Liang
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhen-Yu Bai
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing-Lin Liu
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail:
| | - Yuan-Zhi Pan
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bei-Bei Jiang
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lei Zhang
- Department of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
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137
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Fedorowicz-Strońska O, Koczyk G, Kaczmarek M, Krajewski P, Sadowski J. Genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (Hordeum vulgare L.). J Appl Genet 2016; 58:11-22. [PMID: 27447459 PMCID: PMC5243917 DOI: 10.1007/s13353-016-0357-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
In plant cells, calcium-dependent protein kinases (CDPKs) are important sensors of Ca2+ flux resulting from various environmental stresses like cold, drought or salt stress. Previous genome sequence analysis and comparative studies in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) defined a multi-gene family of CDPKs. Here, we identified and characterised the CDPK gene complement of the model plant, barley (Hordeum vulgare L.). Comparative analysis encompassed phylogeny reconstruction based on newly available barley genome sequence, as well as established model genomes (e.g. O. sativa, A. thaliana, Brachypodium distachyon). Functional gene copies possessed characteristic CDPK domain architecture, including a serine/threonine kinase domain and four regulatory EF-hand motifs. In silico verification was followed by measurements of transcript abundance via real-time polymerase chain reaction (PCR). The relative expression of CDPK genes was determined in the vegetative growth stage under intensifying drought stress conditions. The majority of barley CDPK genes showed distinct changes in patterns of expression during exposure to stress. Our study constitutes evidence for involvement of the barley CDPK gene complement in signal transduction pathways relating to adaptation to drought. Our bioinformatics and transcriptomic analyses will provide an important foundation for further functional dissection of the barley CDPK gene family.
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Affiliation(s)
- Olga Fedorowicz-Strońska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland.
| | - Grzegorz Koczyk
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Małgorzata Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Jan Sadowski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
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138
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Bakhshi B, Mohseni Fard E, Nikpay N, Ebrahimi MA, Bihamta MR, Mardi M, Salekdeh GH. MicroRNA Signatures of Drought Signaling in Rice Root. PLoS One 2016; 11:e0156814. [PMID: 27276090 PMCID: PMC4898717 DOI: 10.1371/journal.pone.0156814] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 05/19/2016] [Indexed: 11/21/2022] Open
Abstract
Background Drought stress is one of the most important abiotic stresses and the main constraint to rice agriculture. MicroRNA-mediated post-transcriptional gene regulation is one of the ways to establish drought stress tolerance in plants. MiRNAs are 20–24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses. Methodology/Principal Findings In this study, we applied a partial root drying system as well as a complete root drying system to identify miRNAs involved in conditions of drought stress, drought signaling and wet signaling using high-throughput sequencing. To this end, we produced four small RNA libraries: (1) fully-watered (WW), (2) fully-droughted (WD), and split-root systems where (3) one-half was well watered (SpWW) and (4) the other half was water-deprived (SpWD). Our analysis revealed 10,671 and 783 unique known and novel miRNA reads in all libraries, respectively. We identified, 65 (52 known + 13 novel), 72 (61 known + 11 novel) and 51 (38 known + 13 novel) miRNAs that showed differential expression under conditions of drought stress, drought signaling and wet signaling, respectively. The results of quantitative real-time PCR showed expression patterns similar to the high-throughput sequencing results. Furthermore, our target prediction led to the identification of 244, 341 and 239 unique target genes for drought-stress-, drought-signaling- and wet-signaling-responsive miRNAs, respectively. Conclusions/Significance Our results suggest that miRNAs that are responsive under different conditions could play different roles in the regulation of abscisic acid signaling, calcium signaling, detoxification and lateral root formation.
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Affiliation(s)
- Behnam Bakhshi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Nava Nikpay
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | | | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- * E-mail:
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139
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Xiao R, Wang L, Cao Y, Zhang G. Transcriptome response to temperature stress in the wolf spider Pardosa pseudoannulata (Araneae: Lycosidae). Ecol Evol 2016; 6:3540-3554. [PMID: 27127612 PMCID: PMC4842027 DOI: 10.1002/ece3.2142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/25/2016] [Accepted: 03/27/2016] [Indexed: 12/21/2022] Open
Abstract
The wolf spider Pardosa pseudoannulata is a dominant predator in paddy ecosystem and an important biological control agent of rice pests. Temperature represents a primary factor influencing its biology and behavior, although the underlying molecular mechanisms remain unknown. To understand the response of P. pseudoannulata to temperature stress, we performed comparative transcriptome analyses of spider adults exposed to 10°C and 40°C for 12 h. We obtained 67,725 assembled unigenes, 21,765 of which were annotated in P. pseudoannulata transcriptome libraries, and identified 905 and 834 genes significantly up- or down-regulated by temperature stress. Functional categorization revealed the differential regulation of transcription, signal transduction, and metabolism processes. Calcium signaling pathway and metabolic pathway involving respiratory chain components played important roles in adapting to low temperature, whereas at high temperature, oxidative phosphorylation and amino acid metabolism were critical. Differentially expressed ribosomal protein genes contributed to temperature stress adaptation, and heat shock genes were significantly up-regulated. This study represents the first report of transcriptome identification related to the Araneae species in response to temperature stress. These results will greatly facilitate our understanding of the physiological and biochemical mechanisms of spiders in response to temperature stress.
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Affiliation(s)
- Rong Xiao
- State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Liang Wang
- State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Yingshuai Cao
- State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
| | - Guren Zhang
- State Key Laboratory for BiocontrolSun Yat‐sen UniversityGuangzhouChina
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140
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Bundó M, Coca M. Enhancing blast disease resistance by overexpression of the calcium-dependent protein kinase OsCPK4 in rice. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1357-67. [PMID: 26578239 DOI: 10.1111/pbi.12500] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/04/2015] [Accepted: 10/09/2015] [Indexed: 05/07/2023]
Abstract
Rice is the most important staple food for more than half of the human population, and blast disease is the most serious disease affecting global rice production. In this work, the isoform OsCPK4 of the rice calcium-dependent protein kinase family is reported as a regulator of rice immunity to blast fungal infection. It shows that overexpression of OsCPK4 gene in rice plants enhances resistance to blast disease by preventing fungal penetration. The constitutive accumulation of OsCPK4 protein prepares rice plants for a rapid and potentiated defence response, including the production of reactive oxygen species, callose deposition and defence gene expression. OsCPK4 overexpression leads also to constitutive increased content of the glycosylated salicylic acid hormone in leaves without compromising rice yield. Given that OsCPK4 overexpression was known to confer also salt and drought tolerance in rice, the results reported in this article demonstrate that OsCPK4 acts as a convergence component that positively modulates both biotic and abiotic signalling pathways. Altogether, our findings indicate that OsCPK4 is a potential molecular target to improve not only abiotic stress tolerance, but also blast disease resistance of rice crops.
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Affiliation(s)
- Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB. Edifici CRAG, Bellaterra, Barcelona, Spain
| | - María Coca
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB. Edifici CRAG, Bellaterra, Barcelona, Spain
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141
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Shen L, Yang S, Yang T, Liang J, Cheng W, Wen J, Liu Y, Li J, Shi L, Tang Q, Shi W, Hu J, Liu C, Zhang Y, Mou S, Liu Z, Cai H, He L, Guan D, Wu Y, He S. CaCDPK15 positively regulates pepper responses to Ralstonia solanacearum inoculation and forms a positive-feedback loop with CaWRKY40 to amplify defense signaling. Sci Rep 2016; 6:22439. [PMID: 26928570 PMCID: PMC4772545 DOI: 10.1038/srep22439] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/15/2016] [Indexed: 01/28/2023] Open
Abstract
CaWRKY40 is a positive regulator of pepper (Capsicum annum) response to Ralstonia solanacearum inoculation (RSI), but the underlying mechanism remains largely unknown. Here, we functionally characterize CaCDPK15 in the defense signaling mediated by CaWRKY40. Pathogen-responsive TGA, W, and ERE boxes were identified in the CaCDPK15 promoter (pCaCDPK15), and pCaCDPK15-driven GUS expression was significantly enhanced in response to RSI and exogenously applied salicylic acid, methyl jasmonate, abscisic acid, and ethephon. Virus-induced gene silencing (VIGS) of CaCDPK15 significantly increased the susceptibility of pepper to RSI and downregulated the immunity-associated markers CaNPR1, CaPR1, and CaDEF1. By contrast, transient CaCDPK15 overexpression significantly activated hypersensitive response associated cell death, upregulated the immunity-associated marker genes, upregulated CaWRKY40 expression, and enriched CaWRKY40 at the promoters of its targets genes. Although CaCDPK15 failed to interact with CaWRKY40, the direct binding of CaWRKY40 to pCaCDPK15 was detected by chromatin immunoprecipitation, which was significantly potentiated by RSI in pepper plants. These combined results suggest that RSI in pepper induces CaCDPK15 and indirectly activates downstream CaWRKY40, which in turn potentiates CaCDPK15 expression. This positive-feedback loop would amplify defense signaling against RSI and efficiently activate strong plant immunity.
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Affiliation(s)
- Lei Shen
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Sheng Yang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Tong Yang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiaqi Liang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Cheng
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiayu Wen
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yanyan Liu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiazhi Li
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lanping Shi
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qian Tang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Shi
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiong Hu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Cailing Liu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yangwen Zhang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shaoliang Mou
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Zhiqin Liu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Hanyang Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Li He
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Deyi Guan
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yang Wu
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Shuilin He
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.,College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
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142
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Hettenhausen C, Sun G, He Y, Zhuang H, Sun T, Qi J, Wu J. Genome-wide identification of calcium-dependent protein kinases in soybean and analyses of their transcriptional responses to insect herbivory and drought stress. Sci Rep 2016; 6:18973. [PMID: 26733237 PMCID: PMC4702179 DOI: 10.1038/srep18973] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/02/2015] [Indexed: 01/14/2023] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are plant-specific calcium sensors that play important roles in various aspects of plant physiology. Here, we investigated phylogenic relationships, chromosomal locations, gene structures, and tissue-specific, herbivory- and drought-induced expression profiles of soybean (Glycine max) GmCDPKs. Fifty GmCDPK genes were identified, which phylogenetically grouped into 4 distinct clusters and distributed across 13 sub-clusters. Individual classes of GmCDPKs harbor highly conserved mRNA splicing sites, and their exon numbers and lengths were consistent with the phylogenetic relationships, suggesting that at least 13 ancestral CDPK genes had emerged before the split of monocots and eudicots. Gene expression analysis indicated that several GmCDPKs were tissue-specific expressed. GmCDPKs' transcript levels changed after wounding, exhibited specific expression patterns after simulated Spodoptera exigua feeding or soybean aphid (Aphis glycines) herbivory, and were largely independent of the phytohormones jasmonic acid and salicylic acid. The most pronounced transcriptional responses were detected after drought and abscisic acid treatments with more than half of all GmCDPKs being upregulated, suggesting their important roles during abiotic stress responses in soybean. Our data provide an important foundation for further functional dissection of GmCDPKs, especially in the context of soybean-insect interactions and drought stress adaptation.
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Affiliation(s)
- Christian Hettenhausen
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guiling Sun
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanbiao He
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Huifu Zhuang
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ting Sun
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jinfeng Qi
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianqiang Wu
- Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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143
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Ma X, Xia H, Liu Y, Wei H, Zheng X, Song C, Chen L, Liu H, Luo L. Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1886. [PMID: 28066455 PMCID: PMC5174129 DOI: 10.3389/fpls.2016.01886] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/29/2016] [Indexed: 05/20/2023]
Abstract
In contrast to wild species, drought-tolerance in crops requires a fully functional metabolism during drought (particularly photosynthetic processes). However, the link between drought-tolerance, photosynthetic regulation during drought, and the associated transcript and metabolic foundation, remains largely unknown. For this study, we used two rice cultivars with contrasting drought-tolerance (the drought-intolerant cultivar IRAT109 and the drought-tolerant cultivar IAC1246) to explore transcript and metabolic responses to long-term drought. The drought-tolerant cultivar represented higher osmotic adjustment and antioxidant capacity, as well as higher relative photosynthesis rate under a progressive drought stress occurred in a modified field with shallow soil-layers. A total of 4059 and 2677 differentially expressed genes (DEGs) were identified in IRAT109 and IAC1246 between the drought and well-watered conditions, respectively. A total of 69 and 47 differential metabolites (DMs) were identified between the two treatments in IRAT109 and IAC1246, respectively. Compared to IRAT109, the DEGs of IAC1246 displayed enhanced regulatory amplitude during drought. We found significant correlations between DEGs and the osmolality and total antioxidant capacity (AOC) of both cultivars. During the early stages of drought, we detected up-regulation of DEGs in IAC1246 related to photosynthesis, in accordance with its higher relative photosynthesis rate. The contents of six differential metabolites were correlated with the osmotic potential and AOC. Moreover, they were differently regulated between the two cultivars. Particularly, up-regulations of 4-hydroxycinnamic acid and ferulic acid were consistent with the performance of photosynthesis-related DEGs at the early stages of drought in IAC1246. Therefore, 4-hydroxycinnamic acid and ferulic acid were considered as key metabolites for rice drought-tolerance. DEGs involved in pathways of these metabolites are expected to be good candidate genes to improve drought-tolerance. In conclusion, well-maintained photosynthesis under drought should contribute to improved drought-tolerance in rice. Metabolites play vital roles in protecting photosynthesis under dehydration via osmotic adjustments and/or antioxidant mechanisms. A metabolite-based method was thus an effective way to explore drought candidate genes. Metabolic accompanied by transcript responses to drought stress should be further studied to find more useful metabolites, pathways, and genes.
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Affiliation(s)
- Xiaosong Ma
- Shanghai Agrobiological Gene CenterShanghai, China
- College of Plant Sciences and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Hui Xia
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Yunhua Liu
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Haibin Wei
- Shanghai Agrobiological Gene CenterShanghai, China
| | | | - Congzhi Song
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghai, China
- College of Plant Sciences and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Lijun Luo
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144
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Hu Z, Lv X, Xia X, Zhou J, Shi K, Yu J, Zhou Y. Genome-Wide Identification and Expression Analysis of Calcium-dependent Protein Kinase in Tomato. FRONTIERS IN PLANT SCIENCE 2016; 7:469. [PMID: 27092168 PMCID: PMC4824780 DOI: 10.3389/fpls.2016.00469] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/24/2016] [Indexed: 05/04/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) play critical roles in regulating growth, development and stress response in plants. Information about CDPKs in tomato, however, remains obscure although it is one of the most important model crops in the world. In this study, we performed a bioinformatics analysis of the entire tomato genome and identified 29 CDPK genes. These CDPK genes are found to be located in 12 chromosomes, and could be divided into four groups. Analysis of the gene structure and splicing site reflected high structure conservation within different CDPK gene groups both in the exon-intron pattern and mRNA splicing. Transcripts of most CDPK genes varied with plant organs and developmental stages and their transcripts could be differentially induced by abscisic acid (ABA), brassinosteroids (BRs), methyl jasmonate (MeJA), and salicylic acid (SA), as well as after exposure to heat, cold, and drought, respectively. To our knowledge, this is the first report about the genome-wide analysis of the CDPK gene family in tomato, and the findings obtained offer a clue to the elaborated regulatory role of CDPKs in plant growth, development and stress response in tomato.
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Affiliation(s)
- Zhangjian Hu
- Department of Horticulture, Zhejiang University Hangzhou, China
| | - Xiangzhang Lv
- Department of Horticulture, Zhejiang University Hangzhou, China
| | - Xiaojian Xia
- Department of Horticulture, Zhejiang University Hangzhou, China
| | - Jie Zhou
- Department of Horticulture, Zhejiang University Hangzhou, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University Hangzhou, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang UniversityHangzhou, China; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Yanhong Zhou
- Department of Horticulture, Zhejiang UniversityHangzhou, China; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
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145
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Mohanta TK, Mohanta N, Mohanta YK, Bae H. Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain. FRONTIERS IN PLANT SCIENCE 2015; 6:1146. [PMID: 26734045 PMCID: PMC4690006 DOI: 10.3389/fpls.2015.01146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/02/2015] [Indexed: 05/04/2023]
Abstract
Calcium ions are considered ubiquitous second messengers in eukaryotic signal transduction pathways. Intracellular Ca(2+) concentration are modulated by various signals such as hormones and biotic and abiotic stresses. Modulation of Ca(2+) ion leads to stimulation of calcium dependent protein kinase genes (CPKs), which results in regulation of gene expression and therefore mediates plant growth and development as well as biotic and abiotic stresses. Here, we reported the CPK gene family of 40 different plant species (950 CPK genes) and provided a unified nomenclature system for all of them. In addition, we analyzed their genomic, biochemical and structural conserved features. Multiple sequence alignment revealed that the kinase domain, auto-inhibitory domain and EF-hands regions of regulatory domains are highly conserved in nature. Additionally, the EF-hand domains of higher plants were found to contain four D-x-D and two D-E-L motifs, while lower eukaryotic plants had two D-x-D and one D-x-E motifs in their EF-hands. Phylogenetic analysis showed that CPK genes are clustered into four different groups. By studying the CPK gene family across the plant lineage, we provide the first evidence of the presence of D-x-D motif in the calcium binding EF-hand domain of CPK proteins.
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Affiliation(s)
- Tapan K. Mohanta
- School of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
| | - Nibedita Mohanta
- Department Of Biotechnology, North Orissa UniversityBaripada, India
| | | | - Hanhong Bae
- School of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
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146
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Lei P, Xu Z, Ding Y, Tang B, Zhang Y, Li H, Feng X, Xu H. Effect of Poly(γ-glutamic acid) on the Physiological Responses and Calcium Signaling of Rape Seedlings (Brassica napus L.) under Cold Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10399-10406. [PMID: 26585291 DOI: 10.1021/acs.jafc.5b04523] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cold stress adversely affects plant growth and development. Poly(γ-glutamic acid) (γ-PGA) is a potential plant growth regulator that may be an effective cryoprotectant that prevents crops from damage during cold weather. In this study, the effects of γ-PGA on the physiological responses of rape seedlings subject to cold stress were investigated using hydroponic experiments. We determined that the malondialdehyde content was decreased by 33.4% and the proline content was increased by 62.5% by γ-PGA after 144 h under cold stress. Antioxidant enzymes activities were also evidently enhanced after treatment with γ-PGA. These responses counteracted increases in the fresh weight and chlorophyll content of rape seedlings, which increased by 24.5 and 50.9%, respectively, after 144 h, which meant that growth inhibition caused by cold was mitigated by γ-PGA. Our results also showed that γ-PGA also regulated Ca(2+) concentrations in the cytoplasm and calcium-dependent protein kinases, which are associated with cold resistance. In conclusion, we suggest that the Ca(2+)/CPKs signal pathway is involved in the γ-PGA-mediated enhancement of cold resistance in rape seedlings.
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Affiliation(s)
- Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Zongqi Xu
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Yan Ding
- Nanjing Shineking Biological Technology Company, Ltd., Nanjing 210000, China
| | - Bao Tang
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Yunxia Zhang
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Huashan Li
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Xiaohai Feng
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211816, China
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147
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Chen Y, Hoehenwarter W. Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:3021-33. [PMID: 26471895 PMCID: PMC4677922 DOI: 10.1104/pp.15.01486] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/14/2015] [Indexed: 05/03/2023]
Abstract
Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K(+) and Na(+) transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (Y.C.); andProteomics Unit, Leibniz Institute for Plant Biochemistry, 06120 Halle (Saale), Germany (W.H.)
| | - Wolfgang Hoehenwarter
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (Y.C.); andProteomics Unit, Leibniz Institute for Plant Biochemistry, 06120 Halle (Saale), Germany (W.H.)
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148
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Yu HQ, Yong TM, Li HJ, Liu YP, Zhou SF, Fu FL, Li WC. Overexpression of a phospholipase Dα gene from Ammopiptanthus nanus enhances salt tolerance of phospholipase Dα1-deficient Arabidopsis mutant. PLANTA 2015; 242:1495-509. [PMID: 26318308 DOI: 10.1007/s00425-015-2390-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/21/2015] [Indexed: 05/28/2023]
Abstract
A phospholipase Dα gene ( AnPLDα ) was cloned from xerophytic desert plant Ammopiptanthus nanus and its overexpression enhanced salt tolerance of a PLDα1 deficient Arabidopsis mutant. Phospholipase Dα (PLDα) hydrolyzes phosphatidylcholine to produce phosphatidic acid, and plays crucial role in plant tolerance to abiotic stress. In this study, a phospholipase Dα gene (AnPLDα) was cloned from xerophyte Ammopiptanthus nanus by the methods of homologous cloning and rapid amplification of cDNA ends, and evaluated for its function in stress tolerance. The full-length cDNA was 2832 bp long, containing an open reading frame of 2427 bp that encodes 808 amino acids. The putative protein was predicted to be localized to the cytoplasm and this was confirmed by transient expression of a fluorescent fusion protein. The endogenous expression of the AnPLDα gene was induced by high salt, dehydration, cold and abscisic acid. The heterologous expression of the AnPLDα gene improved salt tolerance of an Arabidopsis pldα1 knocked out mutant, and positively regulated the expression of the AtABI, AtNCED, AtRD29A, AtRD29B and AtADH genes. Therefore, the AnPLDα gene was concluded to be involved in response to abiotic stress. The AnPLDα gene is a hopeful candidate for transgenic application to improve stress tolerance of commercial crops.
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Affiliation(s)
- Hao Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China
| | - Tai Ming Yong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China
| | - Hong Jie Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yan Ping Liu
- Faculty of Plant Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Shu Feng Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China
| | - Feng Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.
| | - Wan Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.
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149
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Xu Y, Li X, Lin J, Wang Z, Yang Q, Chang Y. Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). BMC Genomics 2015; 16:738. [PMID: 26424153 PMCID: PMC4590731 DOI: 10.1186/s12864-015-1887-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/28/2015] [Indexed: 11/17/2022] Open
Abstract
Background Pears (Pyrus spp. L.) are an important genus of trees that produce one of the world’s oldest fruit crops. Salinity stress is a common limiting factor for plant productivity that significantly affects the flavor and nutritional quality of pear fruits. Much research has shown that calcium signaling pathways, mediated by Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs), are closely associated with responses to stresses, including salt. However, little is known about the molecular mechanisms that govern the relationship between salt stress and calcium signaling pathways in pear plants. The available genomic information for pears has promoted much functional genomic analysis and molecular breeding of the genus. This provided an ample foundation for characterizing the transcriptome of pear under salt stress. Results A high-throughput Illumina RNA-seq technology was used to identify a total of 78,695 unigenes that were successfully annotated by BLASTX analysis, using the publicly available protein database. Additionally, 2,855 novel transcripts, 218,167 SNPs, 23,248 indels and 18,322 alternative splicing events occurred. Assembled unique sequences were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, which revealed that the main activated genes in pear are predominately involved in functions such as basic physiological processes, metabolic pathways, operation of cellular components, signal transduction mechanisms, and other molecular activities. Through targeted searches of the annotations, the majority of the genes involved in calcium signaling pathways were identified, among which, four genes were validated by molecular cloning, while 11 were validated by RT-qPCR expression profiles under salt stress treatment. Conclusions These results facilitate a better understanding of the molecular genetics and functional genomic mechanisms of salt stress in pear plants. Furthermore, they provide a valuable foundation for additional research on the molecular biology and functional genomics of pear and related species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1887-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanyuan Xu
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Xiaogang Li
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Jing Lin
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
| | - Zhonghua Wang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Qingsong Yang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Youhong Chang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
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150
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Chen L, Fan J, Hu L, Hu Z, Xie Y, Zhang Y, Lou Y, Nevo E, Fu J. A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance. BMC PLANT BIOLOGY 2015; 15:216. [PMID: 26362029 PMCID: PMC4566850 DOI: 10.1186/s12870-015-0598-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/22/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cold stress is regarded as a key factor limiting widespread use for bermudagrass (Cynodon dactylon). Therefore, to improve cold tolerance for bermudagrass, it is urgent to understand molecular mechanisms of bermudagrass response to cold stress. However, our knowledge about the molecular responses of this species to cold stress is largely unknown. The objective of this study was to characterize the transcriptomic response to low temperature in bermudagrass by using RNA-Seq platform. RESULTS Ten cDNA libraries were generated from RNA samples of leaves from five different treatments in the cold-resistant (R) and the cold-sensitive (S) genotypes, including 4 °C cold acclimation (CA) for 24 h and 48 h, freezing (-5 °C) treatments for 4 h with or without prior CA, and controls. When subjected to cold acclimation, global gene expressions were initiated more quickly in the R genotype than those in the S genotype. The R genotype activated gene expression more effectively in response to freezing temperature after 48 h CA than the S genotype. The differentially expressed genes were identified as low temperature sensing and signaling-related genes, functional proteins and transcription factors, many of which were specifically or predominantly expressed in the R genotype under cold treatments, implying that these genes play important roles in the enhanced cold hardiness of bermudagrass. KEGG pathway enrichment analysis for DEGs revealed that photosynthesis, nitrogen metabolism and carbon fixation pathways play key roles in bermudagrass response to cold stress. CONCLUSIONS The results of this study may contribute to our understanding the molecular mechanism underlying the responses of bermudagrass to cold stress, and also provide important clues for further study and in-depth characterization of cold-resistance breeding candidate genes in bermudagrass.
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Affiliation(s)
- Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
| | - Jibiao Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Longxing Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
| | - Zhengrong Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Yan Xie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Yingzi Zhang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Yanhong Lou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel.
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
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