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Wang J, Zhang Q, Cui F, Hou L, Zhao S, Xia H, Qiu J, Li T, Zhang Y, Wang X, Zhao C. Genome-Wide Analysis of Gene Expression Provides New Insights into Cold Responses in Thellungiella salsuginea. FRONTIERS IN PLANT SCIENCE 2017; 8:713. [PMID: 28533787 PMCID: PMC5420556 DOI: 10.3389/fpls.2017.00713] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/18/2017] [Indexed: 05/21/2023]
Abstract
Low temperature is one of the major environmental stresses that affects plant growth and development, and leads to decrease in crop yield and quality. Thellungiella salsuginea (salt cress) exhibits high tolerance to chilling, is an appropriate model to investigate the molecular mechanisms of cold tolerance. Here, we compared transcription changes in the roots and leaves of T. salsuginea under cold stress using RNA-seq. We identified 2,782 and 1,430 differentially expressed genes (DEGs) in leaves and roots upon cold treatment, respectively. The expression levels of some genes were validated by quantitative real-time-PCR (qRT-PCR). Among these DEGs, 159 (11.1%) genes in roots and 232 (8.3%) genes in leaves were annotated as various types of transcription factors. We found that five aquaporin genes (three TIPs, one PIPs, and one NIPs) responded to cold treatment. In addition, the expression of COR47, ICE1, and CBF1 genes of DREB1/CBF-dependent cold signaling pathway genes altered in response to low temperature. KEGG pathway analysis indicated that these cold regulated genes were enriched in metabolism, photosynthesis, circadian rhythm, and transcriptional regulation. Our findings provided a complete picture of the regulatory network of cold stress response in T. salsuginea. These cold-responsive genes could be targeted for detail functional study and utilization in crop cold tolerance improvement.
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Affiliation(s)
- Jiangshan Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- Yantai Institute of China Agricultural UniversityYantai, China
| | - Quan Zhang
- College of Life Sciences, Shandong Normal UniversityJinan, China
| | - Feng Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Jingjing Qiu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
| | - Tingting Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
- *Correspondence: Chuanzhi Zhao,
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202
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Jha UC, Bohra A, Jha R. Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. PLANT CELL REPORTS 2017; 36:1-35. [PMID: 27878342 DOI: 10.1007/s00299-016-2073-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/04/2016] [Indexed: 05/11/2023]
Abstract
Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Abhishek Bohra
- Indian Institute of Pulses Research, Kanpur, 208024, India.
| | - Rintu Jha
- Indian Institute of Pulses Research, Kanpur, 208024, India
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203
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Li A, Zhou M, Wei D, Chen H, You C, Lin J. Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors. FRONTIERS IN PLANT SCIENCE 2017; 8:1647. [PMID: 28983312 PMCID: PMC5613223 DOI: 10.3389/fpls.2017.01647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/07/2017] [Indexed: 05/18/2023]
Abstract
C-repeat binding factors (CBF) are a subfamily of AP2 transcription factors that play critical roles in the regulation of plant cold tolerance and growth in low temperature. In the present work, we sought to perform a detailed investigation into global transcriptional regulation of plant hormone signaling associated genes in transgenic plants engineered with CBF genes. RNA samples from Arabidopsis thaliana plants overexpressing two CBF genes, CBF2 and CBF3, were subjected to Illumina HiSeq 2000 RNA sequencing (RNA-Seq). Our results showed that more than half of the hormone associated genes that were differentially expressed in CBF2 or CBF3 transgenic plants were related to auxin signal transduction and metabolism. Most of these alterations in gene expression could lead to repression of auxin signaling. Accordingly, the IAA content was significantly decreased in young tissues of plants overexpressing CBF2 and CBF3 compared with wild type. In addition, genes associated with the biosynthesis of Jasmonate (JA) and Salicylic acid (SA), as well as the signal sensing of Brassinolide (BR) and SA, were down-regulated, while genes associated with Gibberellin (GA) deactivation were up-regulated. In general, overexpression of CBF2 and CBF3 negatively affects multiple plant hormone signaling pathways in Arabidopsis. The transcriptome analysis using CBF2 and CBF3 transgenic plants provides novel and integrated insights into the interaction between CBFs and plant hormones, particularly the modulation of auxin signaling, which may contribute to the improvement of crop yields under abiotic stress via molecular engineering using CBF genes.
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204
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Fu J, Miao Y, Shao L, Hu T, Yang P. De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress. BMC Genomics 2016; 17:870. [PMID: 27814694 PMCID: PMC5097361 DOI: 10.1186/s12864-016-3222-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/27/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Elymus nutans Griseb., is an important alpine perennial forage of Pooideae subfamily with strong inherited cold tolerance. To get a deeper insight into its molecular mechanisms of cold tolerance, we compared the transcriptome profiling by RNA-Seq in two genotypes of Elymus nutans Griseb. the tolerant Damxung (DX) and the sensitive Gannan (GN) under cold stress. RESULTS The new E. nutans transcriptomes were assembled and comprised 200,520 and 181,331 transcripts in DX and GN, respectively. Among them, 5436 and 4323 genes were differentially expressed in DX and GN, with 170 genes commonly expressed over time. Early cold responses involved numerous genes encoding transcription factors and signal transduction in both genotypes. The AP2/EREBP famliy of transcription factors was predominantly expressed in both genotypes. The most significant transcriptomic changes in the later phases of cold stress are associated with oxidative stress, primary and secondary metabolism, and photosynthesis. Higher fold expressions of fructan, trehalose, and alpha-linolenic acid metabolism-related genes were detected in DX. The DX-specific dehydrins may be promising candidates to improve cold tolerance. Twenty-six hub genes played a central role in both genotypes under cold stress. qRT-PCR analysis of 26 genes confirmed the RNA-Seq results. CONCLUSIONS The stronger transcriptional differentiation during cold stress in DX explains its better cold tolerance compared to GN. The identified fructan biosynthesis, alpha-linolenic acid metabolism, and DX-specific dehydrin-related genes may provide genetic resources for the improvement of cold-tolerant characters in DX. Our findings provide important clues for further studies of the molecular mechanisms underlying cold stress responses in plants.
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Affiliation(s)
- Juanjuan Fu
- Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanjun Miao
- College of Plant Science, Agriculture and Animal Husbandry College of Tibet University, Linzhi, Tibet, 860000, China
| | - Linhui Shao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100101, China
| | - Tianming Hu
- Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Peizhi Yang
- Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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205
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Figueroa-Yañez L, Pereira-Santana A, Arroyo-Herrera A, Rodriguez-Corona U, Sanchez-Teyer F, Espadas-Alcocer J, Espadas-Gil F, Barredo-Pool F, Castaño E, Rodriguez-Zapata LC. RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PLoS One 2016; 11:e0165030. [PMID: 27764197 PMCID: PMC5072549 DOI: 10.1371/journal.pone.0165030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/05/2016] [Indexed: 11/18/2022] Open
Abstract
Plants respond to stress through metabolic and morphological changes that increase their ability to survive and grow. To this end, several transcription factor families are responsible for transmitting the signals that are required for these changes. Here, we studied the transcription factor superfamily AP2/ERF, particularly, RAP2.4 from Carica papaya cv. Maradol. We isolated four genes (CpRap2.4a, CpRAap2.4b, CpRap2.1 and CpRap2.10), and an in silico analysis showed that the four genes encode proteins that contain a conserved APETALA2 (AP2) domain located within group I and II transcription factors of the AP2/ERF superfamily. Semiquantitative PCR experiments indicated that each CpRap2 gene is differentially expressed under stress conditions, such as extreme temperatures. Moreover, genetic transformants of tobacco plants overexpressing CpRap2.4a and CpRap2.4b genes show a high level of tolerance to cold and heat stress compared to non-transformed plants. Confocal microscopy analysis of tobacco transgenic plants showed that CpRAP2.4a and CpRAP2.4b proteins were mainly localized to the nuclei of cells from the leaves and roots and also in the sieve elements. Moreover, the movement of CpRap2.4a RNA in tobacco grafting was analyzed. Our results indicate that CpRap2.4a and CpRap2.4b RNA in the papaya tree have a functional role in the response to stress conditions such as exposure to extreme temperatures via direct translation outside the parental RNA cell.
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Affiliation(s)
- Luis Figueroa-Yañez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | | - Ana Arroyo-Herrera
- Laboratorio de Farmacología, Facultad de Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Felipe Sanchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Jorge Espadas-Alcocer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Francisco Espadas-Gil
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Felipe Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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206
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Figueroa-Yañez L, Pereira-Santana A, Arroyo-Herrera A, Rodriguez-Corona U, Sanchez-Teyer F, Espadas-Alcocer J, Espadas-Gil F, Barredo-Pool F, Castaño E, Rodriguez-Zapata LC. RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PLoS One 2016; 11:e0165030. [DOI: https:/doi.org/10.1371/journal.pone.0165030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
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207
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Smith AR, Zhao D. Sterility Caused by Floral Organ Degeneration and Abiotic Stresses in Arabidopsis and Cereal Grains. FRONTIERS IN PLANT SCIENCE 2016; 7:1503. [PMID: 27790226 PMCID: PMC5064672 DOI: 10.3389/fpls.2016.01503] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Natural floral organ degeneration or abortion results in unisexual or fully sterile flowers, while abiotic stresses lead to sterility after initiation of floral reproductive organs. Since normal flower development is essential for plant sexual reproduction and crop yield, it is imperative to have a better understanding of plant sterility under regular and stress conditions. Here, we review the functions of ABC genes together with their downstream genes in floral organ degeneration and the formation of unisexual flowers in Arabidopsis and several agriculturally significant cereal grains. We further explore the roles of hormones, including auxin, brassinosteroids, jasmonic acid, gibberellic acid, and ethylene, in floral organ formation and fertility. We show that alterations in genes affecting hormone biosynthesis, hormone transport and perception cause loss of stamens/carpels, abnormal floral organ development, poor pollen production, which consequently result in unisexual flowers and male/female sterility. Moreover, abiotic stresses, such as heat, cold, and drought, commonly affect floral organ development and fertility. Sterility is induced by abiotic stresses mostly in male floral organ development, particularly during meiosis, tapetum development, anthesis, dehiscence, and fertilization. A variety of genes including those involved in heat shock, hormone signaling, cold tolerance, metabolisms of starch and sucrose, meiosis, and tapetum development are essential for plants to maintain normal fertility under abiotic stress conditions. Further elucidation of cellular, biochemical, and molecular mechanisms about regulation of fertility will improve yield and quality for many agriculturally valuable crops.
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Affiliation(s)
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, MilwaukeeWI, USA
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208
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Kudo T, Sasaki Y, Terashima S, Matsuda-Imai N, Takano T, Saito M, Kanno M, Ozaki S, Suwabe K, Suzuki G, Watanabe M, Matsuoka M, Takayama S, Yano K. Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants. Genes Genet Syst 2016; 91:111-125. [PMID: 27040147 DOI: 10.1266/ggs.15-00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.
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Affiliation(s)
- Toru Kudo
- School of Agriculture, Meiji University
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209
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Liu W, Wang H, Chen Y, Zhu S, Chen M, Lan X, Chen G, Liao Z. Cold stress improves the production of artemisinin depending on the increase in endogenous jasmonate. Biotechnol Appl Biochem 2016; 64:305-314. [DOI: 10.1002/bab.1493] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Wanhong Liu
- Key Laboratory of Biorheological Science and Technology (Ministry of Education) College of Bioengineering; Chongqing University; Chongqing People's Republic of China
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education); SWU-TAAHC Medicinal Plant Joint R&D Centre; School of Life Sciences; Southwest University; Chongqing People's Republic of China
- School of Chemistry and Chemical Engineering; Chongqing University of Science and Technology; Chongqing People's Republic of China
| | - Huanyan Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education); SWU-TAAHC Medicinal Plant Joint R&D Centre; School of Life Sciences; Southwest University; Chongqing People's Republic of China
| | - Yupei Chen
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education); SWU-TAAHC Medicinal Plant Joint R&D Centre; School of Life Sciences; Southwest University; Chongqing People's Republic of China
| | - Shunqin Zhu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education); SWU-TAAHC Medicinal Plant Joint R&D Centre; School of Life Sciences; Southwest University; Chongqing People's Republic of China
| | - Min Chen
- SWU-TAAHC Medicinal Plant Joint R&D Centre; College of Pharmaceutical Sciences; Southwest University; Chongqing People's Republic of China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre; Agricultural and Animal Husbandry College; Tibet University; Nyingchi of Tibe People's Republic of China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology (Ministry of Education) College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Zhihua Liao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education); SWU-TAAHC Medicinal Plant Joint R&D Centre; School of Life Sciences; Southwest University; Chongqing People's Republic of China
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210
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Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. Proc Natl Acad Sci U S A 2016; 113:E5982-E5991. [PMID: 27655893 DOI: 10.1073/pnas.1611477113] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix-loop-helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation.
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211
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Chen M, Thelen JJ. Acyl-lipid desaturase 1 primes cold acclimation response in Arabidopsis. PHYSIOLOGIA PLANTARUM 2016; 158:11-22. [PMID: 27062193 DOI: 10.1111/ppl.12448] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 06/05/2023]
Abstract
Membrane fluidity change has long been suggested as the primary mechanism by which, plants adapt to cold stress, but the underlying molecular mechanisms are not completely established. In this study, we found that a knockout of acyl-lipid/CoA desaturase 1 gene (ADS1; EC 1.14.99) enhances freezing tolerance after cold acclimation (CA). Fatty acid composition analysis demonstrated that 18:1 content in ads1 mutant plants was 20% lower than in wild-type (WT) grown at 23°C. Lipidomics revealed that 34C-species of monogalactosyl diacylglycerol (MGDG) content in ads1 mutants were 3.3-14.9% lower than in WT. Lipid positional analysis identified 10% lower 18:1 fatty acid content at the sn-2 position of MGDG. The cytosolic calcium content in ads1 mutant plants was also approximately two-times higher than that of WT in response to cold shock. Each of these biochemical differences between WT and ads1 mutant disappeared after CA. Subcellular localization of C- and N-terminal enhanced-fluorescence-fusion proteins indicated that ADS1 localized exclusively to chloroplasts. These observations suggest that ADS1-mediated alteration of chloroplast membrane fluidity is required to prime a CA response, and is the upstream event of cytosolic calcium signaling.
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Affiliation(s)
- Mingjie Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jay J Thelen
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
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212
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Kanjana W, Suzuki T, Ishii K, Kozaki T, Iigo M, Yamane K. Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch). BMC Genomics 2016; 17:575. [PMID: 27501791 PMCID: PMC4977653 DOI: 10.1186/s12864-016-2973-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/28/2016] [Indexed: 11/24/2022] Open
Abstract
Background Ornamental peaches cv. ‘Yaguchi’ (Prunus persica (L.) Batsch) can be propagated via seeds. The establishment of efficient seed treatments for early germination and seedling growth is required to shorten nursery and breeding periods. It is important, therefore, to identify potential candidate genes responsible for the effects of rinsing and chilling on seed germination. We hypothesized that longer rinsing combined with chilling of seeds can alter the genes expression in related to dormancy and then raise the germination rate in the peach. To date, most molecular studies in peaches have involved structural genomics, and few transcriptome studies of seed germination have been conducted. In this study, we investigated the function of key seed dormancy-related genes using next-generation sequencing to profile the transcriptomes involved in seed dormancy in peaches. De novo assembly and analysis of the transcriptome identified differentially expressed and unique genes present in this fruit. Results De novo RNA-sequencing of peach was performed using the Illumina Miseq 2000 system. Paired-end sequence from mRNAs generated high quality sequence reads (9,049,964, 10,026,362 and 10,101,918 reads) from ‘Yaguchi’ peach seeds before rinsed (BR) and after rinsed for 2 or 7 days with a chilling period of 4 weeks (termed 2D4W and 7D4W), respectively. The germination rate of 7D4W was significantly higher than that of 2D4W. In total, we obtained 51,366 unique sequences. Differential expression analysis identified 7752, 8469 and 506 differentially expressed genes from BR vs 2D4W, BR vs 7D4W and 2D4W vs 7D4W libraries respectively, filtered based on p-value and an adjusted false discovery rate of less than 0.05. This study identified genes associated with the rinsing and chilling process that included those associated with phytohormones, the stress response and transcription factors. 7D4W treatment downregulated genes involved in ABA synthesis, catabolism and signaling pathways, which eventually suppressed abscisic acid activity and consequently promoted germination and seedling growth. Stress response genes were also downregulated by the 7D4W treatment, suggesting that this treatment released seeds from endodormancy. Transcription factors were upregulated by the BR and 2D4W treatment, suggesting that they play important roles in maintaining seed dormancy. Conclusions This work indicated that longer rinsing combined with chilling affects gene expression and germination rate, and identified potential candidate genes responsible for dormancy progression in seeds of ‘Yaguchi’ peach. The results could be used to develop breeding programs and will aid future functional genomic research in peaches and other fruit trees. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2973-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Worarad Kanjana
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.,Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Tomohiro Suzuki
- Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Kazuo Ishii
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Toshinori Kozaki
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Masayuki Iigo
- Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.,Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Kenji Yamane
- Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan. .,Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
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Jeon J, Cho C, Lee MR, Van Binh N, Kim J. CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root Development in Response to Cold Stress in Arabidopsis. THE PLANT CELL 2016; 28:1828-43. [PMID: 27432872 PMCID: PMC5006697 DOI: 10.1105/tpc.15.00909] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 05/24/2016] [Accepted: 07/14/2016] [Indexed: 05/18/2023]
Abstract
Lateral roots (LRs) are a major determinant of the root system architecture in plants, and developmental plasticity of LR formation is critical for the survival of plants in changing environmental conditions. In Arabidopsis thaliana, genetic pathways have been identified that regulate LR branching in response to numerous environmental cues, including some nutrients, salt, and gravity. However, it is not known how genetic components are involved in the LR adaptation response to cold. Here, we demonstrate that CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3, encoding APETALA2 transcription factors, play an important role in regulating Arabidopsis LR initiation under cold stress. Analysis of LR developmental kinetics demonstrated that both CRF2 and CRF3 regulate LR initiation. crf2 and crf3 single mutants exhibited decreased LR initiation under cold stress compared with the wild type, and the crf2 crf3 double mutants showed additively decreased LR densities compared with the single mutants. Conversely, CRF2 or CRF3 overexpression caused increased LR densities. CRF2 was induced by cold via a subset of the cytokinin two-component signaling (TCS) pathway, whereas CRF3 was upregulated by cold via TCS-independent pathways. Our results suggest that CRF2 and CRF3 respond to cold via TCS-dependent and TCS-independent pathways and control LR initiation and development, contributing to LR adaptation to cold stress.
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Affiliation(s)
- Jin Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
| | - Mi Rha Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
| | - Nguyen Van Binh
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
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214
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Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK. Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis. PLANT PHYSIOLOGY 2016. [PMID: 27252305 DOI: 10.1104/pp.16.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The three tandemly arranged CBF genes, CBF1, CBF2, and CBF3, are involved in cold acclimation. Due to the lack of stable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants deficient in all three CBF genes, it is still unclear whether the CBF genes are essential for freezing tolerance and whether they may have other functions besides cold acclimation. In this study, we used the CRISPR/Cas9 system to generate cbf single, double, and triple mutants. Compared to the wild type, the cbf triple mutants are extremely sensitive to freezing after cold acclimation, demonstrating that the three CBF genes are essential for cold acclimation. Our results show that the three CBF genes also contribute to basal freezing tolerance. Unexpectedly, we found that the cbf triple mutants are defective in seedling development and salt stress tolerance. Transcript profiling revealed that the CBF genes regulate 414 cold-responsive (COR) genes, of which 346 are CBF-activated genes and 68 are CBF-repressed genes. The analysis suggested that CBF proteins are extensively involved in the regulation of carbohydrate and lipid metabolism, cell wall modification, and gene transcription. Interestingly, like the triple mutants, cbf2 cbf3 double mutants are more sensitive to freezing after cold acclimation compared to the wild type, but cbf1 cbf3 double mutants are more resistant, suggesting that CBF2 is more important than CBF1 and CBF3 in cold acclimation-dependent freezing tolerance. Our results not only demonstrate that the three CBF genes together are required for cold acclimation and freezing tolerance, but also reveal that they are important for salt tolerance and seedling development.
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Affiliation(s)
- Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Shaojun Xie
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Tong Si
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Yuanya Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
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Ben Daniel BH, Cattan E, Wachtel C, Avrahami D, Glick Y, Malichy A, Gerber D, Miller G. Identification of novel transcriptional regulators of Zat12 using comprehensive yeast one-hybrid screens. PHYSIOLOGIA PLANTARUM 2016; 157:422-441. [PMID: 26923089 DOI: 10.1111/ppl.12439] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
To appropriately acclimate to environmental stresses, plants have to rapidly activate a specific transcriptional program. Yet, the identity and function of many of the transcriptional regulators that mediate early responses to abiotic stress stimuli is still unknown. In this work we employed the promoter of the multi-stress-responsive zinc-finger protein Zat12 in yeast one-hybrid (Y1H) screens to identify early abiotic stress-responsive transcriptional regulators. Analysis of Zat12 promoter fragments fused to luciferase underlined an approximately 200 bp fragment responsive to NaCl and to reactive oxygen species (ROS). Using these segments and others as baits against Y1H control or stress Arabidopsis prey libraries, we identified 15 potential Zat12 transcriptional regulators. Among the prominent proteins identified were known transcription factors including bZIP29 and ANAC91 as well as unknown function proteins such as a homolog of the human USB1, a U6 small nuclear RNA (snRNA) processing protein, and dormancy/auxin-associated family protein 2 (DRM2). Altered expression of Zat12 during high light stress in the knockout mutants further indicated the involvement of these proteins in the regulation of Zat12. Using a state of the art microfluidic approach we showed that AtUSB1 and DRM2 can specifically bind dsDNA and were able to identify the preferred DNA-binding motif of all four proteins. Overall, the proteins identified in this work provide an important start point for charting the earliest signaling network of Zat12 and of other genes required for acclimation to abiotic stresses.
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Affiliation(s)
- Bat-Hen Ben Daniel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Esther Cattan
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Chaim Wachtel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorit Avrahami
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yair Glick
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Asaf Malichy
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Doron Gerber
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Gad Miller
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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216
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Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK. Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis. PLANT PHYSIOLOGY 2016; 171:2744-59. [PMID: 27252305 PMCID: PMC4972280 DOI: 10.1104/pp.16.00533] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/30/2016] [Indexed: 05/12/2023]
Abstract
The three tandemly arranged CBF genes, CBF1, CBF2, and CBF3, are involved in cold acclimation. Due to the lack of stable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants deficient in all three CBF genes, it is still unclear whether the CBF genes are essential for freezing tolerance and whether they may have other functions besides cold acclimation. In this study, we used the CRISPR/Cas9 system to generate cbf single, double, and triple mutants. Compared to the wild type, the cbf triple mutants are extremely sensitive to freezing after cold acclimation, demonstrating that the three CBF genes are essential for cold acclimation. Our results show that the three CBF genes also contribute to basal freezing tolerance. Unexpectedly, we found that the cbf triple mutants are defective in seedling development and salt stress tolerance. Transcript profiling revealed that the CBF genes regulate 414 cold-responsive (COR) genes, of which 346 are CBF-activated genes and 68 are CBF-repressed genes. The analysis suggested that CBF proteins are extensively involved in the regulation of carbohydrate and lipid metabolism, cell wall modification, and gene transcription. Interestingly, like the triple mutants, cbf2 cbf3 double mutants are more sensitive to freezing after cold acclimation compared to the wild type, but cbf1 cbf3 double mutants are more resistant, suggesting that CBF2 is more important than CBF1 and CBF3 in cold acclimation-dependent freezing tolerance. Our results not only demonstrate that the three CBF genes together are required for cold acclimation and freezing tolerance, but also reveal that they are important for salt tolerance and seedling development.
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Affiliation(s)
- Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Shaojun Xie
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Tong Si
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Yuanya Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (C.Z., Z.Z., S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (C.Z., S.X., T.S., Y.L., J.-K.Z.);Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China (T.S.); andCollege of Life Science, Yunnan University, Kunming 650091, China (Y.L.)
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217
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van Buer J, Cvetkovic J, Baier M. Cold regulation of plastid ascorbate peroxidases serves as a priming hub controlling ROS signaling in Arabidopsis thaliana. BMC PLANT BIOLOGY 2016; 16:163. [PMID: 27439459 PMCID: PMC4955218 DOI: 10.1186/s12870-016-0856-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/15/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Short cold periods comprise a challenge to plant growth and development. Series of cold stresses improve plant performance upon a future cold stress. This effect could be provoked by priming, training or acclimation dependent hardening. Here, we compared the effect of 24 h (short priming stimulus) and of 2 week long cold-pretreatment (long priming stimulus) on the response of Arabidopsis thaliana to a single 24 h cold stimulus (triggering) after a 5 day long lag-phase, to test Arabidopsis for cold primability. RESULTS Three types of pretreatment dependent responses were observed: (1) The CBF-regulon controlled gene COR15A was stronger activated only after long-term cold pretreatment. (2) The non-chloroplast specific stress markers PAL1 and CHS were more induced by cold after long-term and slightly stronger expressed after short-term cold priming. (3) The chloroplast ROS signaling marker genes ZAT10 and BAP1 were less activated by the triggering stimulus in primed plants. The effects on ZAT10 and BAP1 were more pronounced in 24 h cold-primed plants than in 14 day long cold-primed ones demonstrating independence of priming from induction and persistence of primary cold acclimation responses. Transcript and protein abundance analysis and studies in specific knock-out lines linked the priming-specific regulation of ZAT10 and BAP1 induction to the priming-induced long-term regulation of stromal and thylakoid-bound ascorbate peroxidase (sAPX and tAPX) expression. CONCLUSION The plastid antioxidant system, especially, plastid ascorbate peroxidase regulation, transmits information on a previous cold stress over time without the requirement of establishing cold-acclimation. We hypothesize that the plastid antioxidant system serves as a priming hub and that priming-dependent regulation of chloroplast-to-nucleus ROS signaling is a strategy to prepare plants under unstable environmental conditions against unpredictable stresses by supporting extra-plastidic stress protection.
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Affiliation(s)
- Jörn van Buer
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Jelena Cvetkovic
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Margarete Baier
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
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218
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The OsCYP19-4 Gene Is Expressed as Multiple Alternatively Spliced Transcripts Encoding Isoforms with Distinct Cellular Localizations and PPIase Activities under Cold Stress. Int J Mol Sci 2016; 17:ijms17071154. [PMID: 27447607 PMCID: PMC4964526 DOI: 10.3390/ijms17071154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing (AS) is an important molecular mechanism by which single genes can generate multiple mRNA isoforms. We reported previously that, in Oryza sativa, the cyclophilin 19-4 (OsCYP19-4.1) transcript was significantly upregulated in response to cold stress, and that transgenic plants were cold tolerant. Here we show that, under cold stress, OsCYP19-4 produces eight transcript variants by intron retention and exon skipping, resulting in production of four distinct protein isoforms. The OsCYP19-4 AS isoforms exhibited different cellular localizations in the epidermal cells: in contrast to OsCYP19-4.1, the OsCYP19-4.2 and OsCYP19-4.3 proteins were primarily targeted to guard and subsidiary cells, whereas OsCYP19-4.5, which consists largely of an endoplasmic reticulum (ER) targeting signal, was co-localized with the RFP-BiP marker in the ER. In OsCYP19-4.2, the key residues of the PPIase domain are altered; consistent with this, recombinant OsCYP19-4.2 had significantly lower PPIase activity than OsCYP19-4.1 in vitro. Specific protein-protein interactions between OsCYP19-4.2/3 and AtRCN1 were verified in yeast two-hybrid (Y2H) and bimolecular fluoresence complementation (BiFC assays), although the OsCYP19-4 isoforms could not bind each other. Based on these results, we propose that two OsCYP19-4 AS isoforms, OsCYP19-4.2 and OsCYP19-4.3, play roles linking auxin transport and cold stress via interactions with RCN1.
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219
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Li SG, Hou J, Liu XH, Cui BS, Bai JH. Morphological and transcriptional responses of Lycopersicon esculentum to hexavalent chromium in agricultural soil. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:1751-1758. [PMID: 26627465 DOI: 10.1002/etc.3315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The carcinogenic, teratogenic, and mutagenic effects of hexavalent chromium (Cr[VI]) on living organisms through the food chain raise the immediate need to assess the potential toxicological impacts of Cr(VI) on human health. Therefore, the concentration-dependent responses of 12 Cr(VI)-responsive genes selected from a high-throughput Lycopersicon esculentum complementary DNA microarray were examined at different Cr concentrations. The results indicated that most of the genes were differentially expressed from 0.1 mg Cr/kg soil, whereas the lowest-observable-adverse-effect concentrations of Cr(VI) were 1.6 mg Cr/kg soil, 6.4 mg Cr/kg soil, 3.2 mg Cr/kg soil, and 0.4 mg Cr/kg soil for seed germination, root elongation, root biomass, and root morphology, respectively, implying that the transcriptional method was more sensitive than the traditional method in detecting Cr(VI) toxicity. Dose-dependent responses were observed for the relative expression of expansin (p = 0.778), probable chalcone-flavonone isomerase 3 (p = -0.496), and 12S seed storage protein CRD (p = -0.614); therefore, the authors propose the 3 genes as putative biomarkers in Cr(VI)-contaminated soil. Environ Toxicol Chem 2016;35:1751-1758. © 2015 SETAC.
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Affiliation(s)
- Shi-Guo Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Hou
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
- Department of Environmental and Chemical Engineering, North China Electric Power University, Beijing, China
| | - Xin-Hui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Bao-Shan Cui
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Jun-Hong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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220
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Zhang Y, Li X, Goodrich J, Wu C, Wei H, Yang S, Feng X. Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through. PLANT MOLECULAR BIOLOGY 2016; 91:549-61. [PMID: 27164978 DOI: 10.1007/s11103-016-0487-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/27/2016] [Indexed: 05/08/2023]
Abstract
T-DNA insertion mutants have been widely used to investigate plant gene functions. Unexpectedly, in several reported cases, the phenotype of T-DNA insertion mutations can be suppressed because of trans T-DNA interactions associated with epigenetic modification, which indicates that caution is needed when T-DNA mutants are used. In the present study, we characterized a novel process suppressing a T-DNA mutation. The spz2 (suppressor of zou 2) mutant was isolated as a suppressor of the phenotype of the zou-4 mutant caused by a T-DNA insertion in the first intron. The spz2 mutation partially recovered the native ZOU gene expression in the zou-4 background, but not in two other zou alleles, zou-2 and zou-3, with T-DNAs inserted in the exon and intron, respectively. The suppressed phenotype was inherited in a Mendelian fashion and is not associated with epigenetic modification. The recovery of the native ZOU gene expression in the spz2 zou-4 double mutant is caused by transcriptional read-through of the intronic T-DNA as a result of decreased proximal polyadenylation. SPZ2 encodes an RNA-binding protein, FPA, which is known to regulate polyadenylation site selection. This is the first example of FPA rescuing a T-DNA insertion mutation by affecting the polyadenylation site selection.
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MESH Headings
- Alleles
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Cloning, Molecular
- DNA, Bacterial/genetics
- Drug Resistance, Microbial/genetics
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genes, Plant
- Genes, Suppressor
- Introns/genetics
- Mutagenesis, Insertional/genetics
- Mutation
- Phenotype
- Polyadenylation/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/metabolism
- Seeds/genetics
- Seeds/growth & development
- Transcription, Genetic
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Affiliation(s)
- Yaohua Zhang
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, People's Republic of China
| | - Xin Li
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, People's Republic of China
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Chunxia Wu
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Haichao Wei
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, People's Republic of China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, People's Republic of China.
| | - Xianzhong Feng
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China.
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, People's Republic of China.
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Firtzlaff V, Oberländer J, Geiselhardt S, Hilker M, Kunze R. Pre-exposure of Arabidopsis to the abiotic or biotic environmental stimuli "chilling" or "insect eggs" exhibits different transcriptomic responses to herbivory. Sci Rep 2016; 6:28544. [PMID: 27329974 PMCID: PMC4916510 DOI: 10.1038/srep28544] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/03/2016] [Indexed: 12/28/2022] Open
Abstract
Plants can retain information about environmental stress and thus, prepare themselves for impending stress. In nature, it happens that environmental stimuli like ‘cold’ and ‘insect egg deposition’ precede insect herbivory. Both these stimuli are known to elicit transcriptomic changes in Arabidposis thaliana. It is unknown, however, whether they affect the plant’s anti-herbivore defence and feeding-induced transcriptome when they end prior to herbivory. Here we investigated the transcriptomic response of Arabidopsis to feeding by Pieris brassicae larvae after prior exposure to cold or oviposition. The transcriptome of plants that experienced a five-day-chilling period (4 °C) was not fully reset to the pre-chilling state after deacclimation (20 °C) for one day and responded differently to herbivory than that of chilling-inexperienced plants. In contrast, when after a five-day-lasting oviposition period the eggs were removed, one day later the transcriptome and, consistently, also its response to herbivory resembled that of egg-free plants. Larval performance was unaffected by previous exposure of plants to cold and to eggs, thus indicating P. brassicae tolerance to cold-mediated plant transcriptomic changes. Our results show strong differences in the persistence of the plant’s transcriptomic state after removal of different environmental cues, and consequently differential effects on the transcriptomic response to later herbivory.
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Affiliation(s)
- Vivien Firtzlaff
- Institute of Biology-Applied Zoology/Animal Ecology, Freie Universität Berlin, Haderslebener Str. 9, D-12163 Berlin, Germany
| | - Jana Oberländer
- Institute of Biology-Applied Genetics/Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany
| | - Sven Geiselhardt
- Institute of Biology-Applied Zoology/Animal Ecology, Freie Universität Berlin, Haderslebener Str. 9, D-12163 Berlin, Germany
| | - Monika Hilker
- Institute of Biology-Applied Zoology/Animal Ecology, Freie Universität Berlin, Haderslebener Str. 9, D-12163 Berlin, Germany
| | - Reinhard Kunze
- Institute of Biology-Applied Genetics/Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany
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222
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Nosenko T, Böndel KB, Kumpfmüller G, Stephan W. Adaptation to low temperatures in the wild tomato species Solanum chilense. Mol Ecol 2016; 25:2853-69. [PMID: 27037798 DOI: 10.1111/mec.13637] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022]
Abstract
Molecular adaptation to abiotic stresses in plants is a complex process based mainly on the modifications of gene transcriptional activity and the alteration of protein-protein interactions. We used a combination of population genetic, comparative transcriptomic and plant physiology approaches to investigate the mechanisms of adaptation to low temperatures in Solanum chilense populations distributed along Andean altitudinal gradients. We found that plants from all populations have high chilling tolerance, which does not correlate with temperatures in their native habitats. In contrast, tolerance to freezing shows a significant association with altitude and temperature variables. We also observed the differences in expression patterns of cold-response genes between plants from high- and low-altitude populations. These results suggest that genetic adaptations to low temperatures evolved in high-altitude populations of S. chilense. At the transcriptional level, these adaptations may include high levels of constitutive expression of the genes encoding ICE1, the key transcription factor of the cold signalling pathway, and chloroplast ω-3 fatty acid desaturase FAD7. At the sequence level, a signature of selection associated with the adaptation to high altitudes was detected at the C-terminal part of ICE1 encoding the ACT regulatory domain.
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Affiliation(s)
- Tetyana Nosenko
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Katharina B Böndel
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9, 3FL, UK
| | - Gabriele Kumpfmüller
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, Planegg-Martinsried, 82152, Germany.,Museum für Naturkunde Berlin, Invalidenstr. 4, Berlin, 10115, Germany
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223
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Kloth KJ, Wiegers GL, Busscher-Lange J, van Haarst JC, Kruijer W, Bouwmeester HJ, Dicke M, Jongsma MA. AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3383-96. [PMID: 27107291 PMCID: PMC4892728 DOI: 10.1093/jxb/erw159] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aphids induce many transcriptional perturbations in their host plants, but the signalling cascades responsible and the effects on plant resistance are largely unknown. Through a genome-wide association (GWA) mapping study in Arabidopsis thaliana, we identified WRKY22 as a candidate gene associated with feeding behaviour of the green peach aphid, Myzus persicae The transcription factor WRKY22 is known to be involved in pathogen-triggered immunity, and WRKY22 gene expression has been shown to be induced by aphids. Assessment of aphid population development and feeding behaviour on knockout mutants and overexpression lines showed that WRKY22 increases susceptibility to M. persicae via a mesophyll-located mechanism. mRNA sequencing analysis of aphid-infested wrky22 knockout plants revealed the up-regulation of genes involved in salicylic acid (SA) signalling and down-regulation of genes involved in plant growth and cell-wall loosening. In addition, mechanostimulation of knockout plants by clip cages up-regulated jasmonic acid (JA)-responsive genes, resulting in substantial negative JA-SA crosstalk. Based on this and previous studies, WRKY22 is considered to modulate the interplay between the SA and JA pathways in response to a wide range of biotic and abiotic stimuli. Its induction by aphids and its role in suppressing SA and JA signalling make WRKY22 a potential target for aphids to manipulate host plant defences.
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Affiliation(s)
- Karen J Kloth
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Gerrie L Wiegers
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Biointeractions & Plant Health, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Jacqueline Busscher-Lange
- Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Jan C van Haarst
- Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Maarten A Jongsma
- Plant Research International, Business Unit Bioscience, Wageningen University and Research Centre, PO Box 16, 6700 AA Wageningen, The Netherlands
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224
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Yamasaki Y, Randall SK. Functionality of soybean CBF/DREB1 transcription factors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 246:80-90. [PMID: 26993238 DOI: 10.1016/j.plantsci.2016.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/02/2016] [Accepted: 02/06/2016] [Indexed: 05/18/2023]
Abstract
Soybean (Glycine max) is considered to be cold intolerant and is not able to significantly acclimate to cold/freezing stress. In most cold tolerant plants, the C-repeat/DRE Binding Factors (CBF/DREBs) are critical contributors to successful cold-responses; rapidly increasing following cold treatment and regulating the induction of many cold responsive genes. In soybean vegetative tissue, we found strong, transient accumulation of CBF transcripts in response to cold stress; however, the soybean transcripts of typical cold responsive genes (homologues to Arabidopsis genes such as dehydrins, ADH1, RAP2.1, and LEA14) were not significantly altered. Soybean CBFs were found to be functional, as when expressed constitutively in Arabidopsis they increased the levels of AtCOR47 and AtRD29a transcripts and increased freezing tolerance as measured by a decrease in leaf freezing damage and ion leakage. Furthermore the constitutive expression of GmDREB1A;2 and GmDREB1B;1 in Arabidopsis led to stronger up-regulation of downstream genes and more freezing tolerance than GmDREB1A;1, the gene whose transcript is the major contributor to total CBF/DREB1 transcripts in soybean. The inability for the soybean CBFs to significantly up regulate the soybean genes that contribute to cold tolerance is consistent with poor acclimation capability and the cold intolerance of soybean.
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Affiliation(s)
- Yuji Yamasaki
- Biology Department, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, United States.
| | - Stephen K Randall
- Biology Department, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, United States.
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225
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Imadi SR, Kazi AG, Ahanger MA, Gucel S, Ahmad P. Plant transcriptomics and responses to environmental stress: an overview. J Genet 2016; 94:525-37. [PMID: 26440096 DOI: 10.1007/s12041-015-0545-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Different stresses include nutrient deficiency, pathogen attack, exposure to toxic chemicals etc. Transcriptomic studies have been mainly applied to only a few plant species including the model plant, Arabidopsis thaliana. These studies have provided valuable insights into the genetic networks of plant stress responses. Transcriptomics applied to cash crops including barley, rice, sugarcane, wheat and maize have further helped in understanding physiological and molecular responses in terms of genome sequence, gene regulation, gene differentiation, posttranscriptional modifications and gene splicing. On the other hand, comparative transcriptomics has provided more information about plant's response to diverse stresses. Thus, transcriptomics, together with other biotechnological approaches helps in development of stress tolerance in crops against the climate change.
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Affiliation(s)
- Sameen Ruqia Imadi
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, H-12 Campus, Islamabad 25000,
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226
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Gardiner B, Berry P, Moulia B. Review: Wind impacts on plant growth, mechanics and damage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:94-118. [PMID: 26940495 DOI: 10.1016/j.plantsci.2016.01.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 05/08/2023]
Abstract
Land plants have adapted to survive under a range of wind climates and this involve changes in chemical composition, physical structure and morphology at all scales from the cell to the whole plant. Under strong winds plants can re-orientate themselves, reconfigure their canopies, or shed needles, leaves and branches in order to reduce the drag. If the wind is too strong the plants oscillate until the roots or stem fail. The mechanisms of root and stem failure are very similar in different plants although the exact details of the failure may be different. Cereals and other herbaceous crops can often recover after wind damage and even woody plants can partially recovery if there is sufficient access to water and nutrients. Wind damage can have major economic impacts on crops, forests and urban trees. This can be reduced by management that is sensitive to the local site and climatic conditions and accounts for the ability of plants to acclimate to their local wind climate. Wind is also a major disturbance in many plant ecosystems and can play a crucial role in plant regeneration and the change of successional stage.
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Affiliation(s)
- Barry Gardiner
- INRA, UMR 1391 ISPA, F-33140 Villenave D'Ornon, France; Bordeaux Sciences Agro, UMR 1391 ISPA, F-33170, Gradignan, France; Forest Research, Northern Research Station, Roslin, EH25 9SY, Scotland, UK.
| | - Peter Berry
- ADAS High Mowthorpe, Duggleby, Malton, North Yorkshire YO17 8BP, UK
| | - Bruno Moulia
- INRA, UMR 547 PIAF, F-63100 Clermont-Ferrand, France; Clermont Université, Université Blaise Pascal, UMR 547 PIAF, F-63100 Clermont-Ferrand, France
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227
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Ye YJ, Xiao YY, Han YC, Shan W, Fan ZQ, Xu QG, Kuang JF, Lu WJ, Lakshmanan P, Chen JY. Banana fruit VQ motif-containing protein5 represses cold-responsive transcription factor MaWRKY26 involved in the regulation of JA biosynthetic genes. Sci Rep 2016; 6:23632. [PMID: 27004441 PMCID: PMC4804309 DOI: 10.1038/srep23632] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/11/2016] [Indexed: 11/09/2022] Open
Abstract
Most harvested fruits and vegetables are stored at low temperature but many of them are highly sensitive to chilling injury. Jasmonic acid (JA), a plant hormone associated with various stress responses, is known to reduce chilling injury in fruits. However, little is known about the transcriptional regulation of JA biosynthesis in relation to cold response of fruits. Here, we show the involvement of a Group I WRKY transcription factor (TF) from banana fruit, MaWRKY26, in regulating JA biosynthesis. MaWRKY26 was found to be nuclear-localized with transcriptional activation property. MaWRKY26 was induced by cold stress or by methyl jasmonate (MeJA), which enhances cold tolerance in banana fruit. More importantly, MaWRKY26 transactivated JA biosynthetic genes MaLOX2, MaAOS3 and MaOPR3 via binding to their promoters. Further, MaWRKY26 physically interacted with a VQ motif-containing protein MaVQ5, and the interaction attenuated MaWRKY26-induced transactivation of JA biosynthetic genes. These results strongly suggest that MaVQ5 might act as a repressor of MaWRKY26 in activating JA biosynthesis. Taken together, our findings provide new insights into the transcriptional regulation of JA biosynthesis in response to cold stress and a better understanding of the molecular aspects of chilling injury in banana fruit.
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Affiliation(s)
- Yu-Jie Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Yun-Yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Qun-Gang Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Prakash Lakshmanan
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, Brisbane 4068, Queensland, Australia
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
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228
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Tan H, Huang H, Tie M, Tang Y, Lai Y, Li H. Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress. PLoS One 2016; 11:e0151105. [PMID: 26954786 PMCID: PMC4783050 DOI: 10.1371/journal.pone.0151105] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/22/2016] [Indexed: 11/29/2022] Open
Abstract
Cowpea (V. unguiculata L. Walp.) is an important tropical grain legume. Asparagus bean (V. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea, which is considered one of the top ten Asian vegetables. It can be adapted to a wide range of environmental stimuli such as drought and heat. Nevertheless, it is an extremely cold-sensitive tropical species. Improvement of chilling tolerance in asparagus bean may significantly increase its production and prolong its supply. However, gene regulation and signaling pathways related to cold response in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in response to chilling stress in two asparagus bean cultivars—“Dubai bean” and “Ningjiang-3”, which are tolerant and sensitive to chilling, respectively—were investigated. More than 1.8 million clean reads were obtained from each sample. After de novo assembly, 88,869 unigenes were finally generated with a mean length of 635 bp. Of these unigenes, 41,925 (47.18%) had functional annotations when aligned to public protein databases. Further, we identified 3,510 differentially expressed genes (DEGs) in Dubai bean, including 2,103 up-regulated genes and 1,407 down-regulated genes. While in Ningjiang-3, we found 2,868 DEGs, 1,786 of which were increasing and the others were decreasing. 1,744 DEGs were commonly regulated in two cultivars, suggesting that some genes play fundamental roles in asparagus bean during cold stress. Functional classification of the DEGs in two cultivars using Mercator pipeline indicated that RNA, protein, signaling, stress and hormone metabolism were five major groups. In RNA group, analysis of TFs in DREB subfamily showed that ICE1-CBF3-COR cold responsive cascade may also exist in asparagus bean. Our study is the first to provide the transcriptome sequence resource for asparagus bean, which will accelerate breeding cold resistant asparagus bean varieties through genetic engineering, and advance our knowledge of the genes involved in the complex regulatory networks of this plant under cold stress.
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Affiliation(s)
- Huaqiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haitao Huang
- Mianyang Institute of Agricultural Sciences, Mianyang, Sichuan, China
| | - Manman Tie
- Dazhou Institute of Agricultural Sciences, Dazhou, Sichuan, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunsong Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail:
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229
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Chen N, Su M, Chi X, Zhang Z, Pan L, Chen M, Wang T, Wang M, Yang Z, Yu S. Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of peanut (Arachis hypogaea L.). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0395-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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230
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Song JB, Gao S, Wang Y, Li BW, Zhang YL, Yang ZM. miR394 and its target gene LCR are involved in cold stress response in Arabidopsis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2015.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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231
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Chan Z, Wang Y, Cao M, Gong Y, Mu Z, Wang H, Hu Y, Deng X, He XJ, Zhu JK. RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. THE NEW PHYTOLOGIST 2016; 209:1527-39. [PMID: 26522658 PMCID: PMC5515388 DOI: 10.1111/nph.13727] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood. In this study, we characterized cold tolerance of null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA-directed DNA methylation (RdDM) in Arabidopsis. The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold-induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3. We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanping Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Minjie Cao
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuehua Gong
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Science and Food Engineering, Yibin University, Yibin, Sichuan 644000, China
| | - Zixin Mu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Science, Northwest A&F University, Yangling, Shaan’xi 712100, China
| | - Haiqing Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
| | - Yuanlei Hu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Deng
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
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232
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Zwack PJ, Compton MA, Adams CI, Rashotte AM. Cytokinin response factor 4 (CRF4) is induced by cold and involved in freezing tolerance. PLANT CELL REPORTS 2016; 35:573-84. [PMID: 26650835 DOI: 10.1007/s00299-015-1904-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/11/2015] [Accepted: 11/17/2015] [Indexed: 05/19/2023]
Abstract
Cytokinin response factor 4 (CRF4) shows a short-term induction by cold (4 °C) that appears to play a role in non-acclimated freezing tolerance as seen in mutant and overexpression lines. Responses to abiotic stresses, such as cold stress, are critical to plant growth and optimal production. Examination of Arabidopsis cytokinin response factors (CRFs) showed transcriptional induction after exposure to cold (4 °C). In particular, CRF4 was strongly induced in both root and shoot tissues. As CRF4 is one of several CRFs not transcriptionally regulated by cytokinin, we further investigated its response to cold. Peak CRF4 induction occurred 6 h post cold exposure, after which expression was maintained at moderately elevated levels during extended cold and subsequent treatment recovery. Examination of CRF4 mutant and overexpression lines under standard (non-cold) conditions revealed little difference from WT. One exception was a small, but significant increase in primary root growth of overexpression plants (CRF4OX). Under cold conditions, the only phenotype observed was a reduction in the rate of germination of CRF4OX seeds. The pattern of CRF4 expression along with the lack of strong phenotype at 4 °C led us to hypothesize that cold induction of CRF4 could play a role in short-term cold acclimation leading to increased freeze tolerance. Examination of CRF4OX and crf4 plants exposed to freezing temperatures revealed mutants lacking expression of CRF4 were more sensitive to freezing, while CRF4OXs with increased levels CRF4 levels were more tolerant. Altered transcript expression of CBF and COR15a cold signaling pathway genes in crf4 mutant and overexpression lines suggest that CRF4 may be potentially connected to this pathway. Overall this indicates that CRF4 plays an important role in both cold response and freezing stress.
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Affiliation(s)
- Paul J Zwack
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Margaret A Compton
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Cami I Adams
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Aaron M Rashotte
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA.
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Song Y, Ci D, Tian M, Zhang D. Stable methylation of a non-coding RNA gene regulates gene expression in response to abiotic stress in Populus simonii. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1477-92. [PMID: 26712827 DOI: 10.1093/jxb/erv543] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA methylation plays important roles in responses to environmental stimuli. However, in perennial plants, the roles of DNA methylation in stress-specific adaptions to different abiotic stresses remain unclear. Here, we present a systematic, comparative analysis of the methylome and gene expression in poplar under cold, osmotic, heat, and salt stress conditions from 3h to 24h. Comparison of the stress responses revealed different patterns of cytosine methylation in response to the four abiotic stresses. We isolated and sequenced 1376 stress-specific differentially methylated regions (SDMRs); annotation revealed that these SDMRs represent 1123 genes encoding proteins, 16 miRNA genes, and 17 long non-coding RNA (lncRNA) genes. The SDMR162 region, consisting of Psi-MIR396e and PsiLNCRNA00268512, is regulated by epigenetic pathways and we speculate that PsiLNCRNA00268512 regulates miR396e levels by acting as a target mimic. The ratios of methylated cytosine declined to ~35.1% after 1 month of recovery from abiotic stress and to ~15.3% after 6 months. Among methylated miRNA genes, only expression of the methylation-regulated gene MIRNA6445a showed long-term stability. Our data provide a strong basis for future work and improve our understanding of the effect of epigenetic regulation of non-coding RNA expression, which will enable in-depth functional analysis.
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Affiliation(s)
- Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Min Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
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234
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Zhang W, Zhang H, Ning L, Li B, Bao M. Quantitative Proteomic Analysis Provides Novel Insights into Cold Stress Responses in Petunia Seedlings. FRONTIERS IN PLANT SCIENCE 2016; 7:136. [PMID: 26941746 PMCID: PMC4766708 DOI: 10.3389/fpls.2016.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 01/26/2016] [Indexed: 05/17/2023]
Abstract
Low temperature is a major adverse environmental factor that impairs petunia growth and development. To better understand the molecular mechanisms of cold stress adaptation of petunia plants, a quantitative proteomic analysis using iTRAQ technology was performed to detect the effects of cold stress on protein expression profiles in petunia seedlings which had been subjected to 2°C for 5 days. Of the 2430 proteins whose levels were quantitated, a total of 117 proteins were discovered to be differentially expressed under low temperature stress in comparison to unstressed controls. As an initial study, 44 proteins including well known and novel cold-responsive proteins were successfully annotated. By integrating the results of two independent Gene Ontology (GO) enrichment analyses, seven common GO terms were found of which "oxidation-reduction process" was the most notable for the cold-responsive proteins. By using the subcellular localization tool Plant-mPLoc predictor, as much as 40.2% of the cold-responsive protein group was found to be located within chloroplasts, suggesting that the chloroplast proteome is particularly affected by cold stress. Gene expression analyses of 11 cold-responsive proteins by real time PCR demonstrated that the mRNA levels were not strongly correlated with the respective protein levels. Further activity assay of anti-oxidative enzymes showed different alterations in cold treated petunia seedlings. Our investigation has highlighted the role of antioxidation mechanisms and also epigenetic factors in the regulation of cold stress responses. Our work has provided novel insights into the plant response to cold stress and should facilitate further studies regarding the molecular mechanisms which determine how plant cells cope with environmental perturbation. The data have been deposited to the ProteomeXchange with identifier PXD002189.
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Affiliation(s)
- Wei Zhang
- College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Huilin Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Luyun Ning
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Bei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
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235
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Niu J, Wang J, Hu H, Chen Y, An J, Cai J, Sun R, Sheng Z, Liu X, Lin S. Cross-talk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets by miR475b promoter in Populus suaveolens. Sci Rep 2016; 6:20648. [PMID: 26853706 PMCID: PMC4745078 DOI: 10.1038/srep20648] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/07/2016] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play important roles in post-transcriptional regulation of their target genes, yet the transcriptional regulation of plant miRNAs by promoter is poorly understood. Here, we firstly clone pri-miR475b cDNA and its native promoter from P. suaveolens, and characterize Psu-MIR475b as class-II gene transcribed by RNA polymerase II. By 5′ deletion analysis of Psu-miR475b promoter in a series of promoter-GUS chimeric vectors, we functionally identify three positive regulatory regions and multiple cis-acting elements responsible for Psu-miR475b promoter activity in response to freezing stress and exogenous hormone treatment. Moreover, the Psu-miR475b promoter activity displays a tissue-specific manner, negatively regulated by freezing stress and positively by MeJA, SA or GA treatment. Importantly, we comparatively analyze the time-course transcriptional profiles of Psu-miR475b and its targets in Psu-miR475b over-expression transgenic plants controlled by Psu-miR475b-specific promoter or CaMV 35S constitutive promoter, and explore the regulatory mechanism of Psu-miR475b promoter controlling transcriptional expressions of Psu-MIR475b and its targets in response to freezing stress and exogenous hormone treatment. Our results reveal that Psu-miR475b promoter-mediated transcriptions of Psu-MIR475b and its targets in response to freezing stress may be involved in a cross-talk between freezing response and stress signaling process.
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Affiliation(s)
- Jun Niu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jia Wang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Huiwen Hu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Yinlei Chen
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jiyong An
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jian Cai
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Runze Sun
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Zhongting Sheng
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Xieping Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Shanzhi Lin
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
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236
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Comparative analysis of gene expression in response to cold stress in diverse rice genotypes. Biochem Biophys Res Commun 2016; 471:253-9. [PMID: 26855133 DOI: 10.1016/j.bbrc.2016.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Abstract
Cold stress is a major factor affecting rice (Oryza sativa) growth and productivity, limiting its distribution worldwide. Rice production is affected primarily due to its vulnerability to cold stress at seedling stage, as well as reproductive stage leading to spikelet sterility. We report here the analysis of 21 diverse rice genotypes from the USDA mini-core collection for cold tolerance and categorized their tolerance levels on the basis of reduction in growth measured by root and shoot length. The screening identified 12 cold tolerant genotypes from which six tolerant genotypes were characterized at the vegetative stage for cold tolerance and gas-exchange parameters. Two tolerant and two sensitive genotypes were used further for gene expression analysis. Lipid Transfer Protein (LTP) genes showed a clear difference in expression between cold tolerant and sensitive genotypes suggesting that they are good candidates for engineering cold tolerance in rice. Nipponbare was identified as a cold tolerant genotype with stress tolerance mechanism potentially operating via both ABA dependent and independent pathways.
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237
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Eremina M, Rozhon W, Poppenberger B. Hormonal control of cold stress responses in plants. Cell Mol Life Sci 2016; 73:797-810. [PMID: 26598281 PMCID: PMC11108489 DOI: 10.1007/s00018-015-2089-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/20/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Cold stress responses in plants are highly sophisticated events that alter the biochemical composition of cells for protection from damage caused by low temperatures. In addition, cold stress has a profound impact on plant morphologies, causing growth repression and reduced yields. Complex signalling cascades are utilised to induce changes in cold-responsive gene expression that enable plants to withstand chilling or even freezing temperatures. These cascades are governed by the activity of plant hormones, and recent research has provided a better understanding of how cold stress responses are integrated with developmental pathways that modulate growth and initiate other events that increase cold tolerance. Information on the hormonal control of cold stress signalling is summarised to highlight the significant progress that has been made and indicate gaps that still exist in our understanding.
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Affiliation(s)
- Marina Eremina
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany.
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238
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Li P, Zhang G, Gonzales N, Guo Y, Hu H, Park S, Zhao J. Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:377-92. [PMID: 26296956 DOI: 10.1111/pce.12620] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/09/2015] [Accepted: 07/30/2015] [Indexed: 05/21/2023]
Abstract
Calcium (Ca(2+) ) is vital for plant growth, development, hormone response and adaptation to environmental stresses, yet the mechanisms regulating plant cytosolic Ca(2+) homeostasis are not fully understood. Here, we characterize an Arabidopsis Ca(2+) -regulated Na(+) /Ca(2+) exchanger AtNCL that regulates Ca(2+) and multiple physiological processes. AtNCL was localized to the tonoplast in yeast and plant cells. AtNCL appeared to mediate sodium (Na(+) ) vacuolar sequestration and meanwhile Ca(2+) release. The EF-hand domains within AtNCL regulated Ca(2+) binding and transport of Ca(2+) and Na(+) . Plants with diminished AtNCL expression were more tolerant to high CaCl2 but more sensitive to both NaCl and auxin; heightened expression of AtNCL rendered plants more sensitive to CaCl2 but tolerant to NaCl. AtNCL expression appeared to be regulated by the diurnal rhythm and suppressed by auxin. DR5::GUS expression and root responses to auxin were altered in AtNCL mutants. The auxin-induced suppression of AtNCL was attenuated in SLR/IAA14 and ARF6/8 mutants. The mutants with altered AtNCL expression also altered flowering time and FT and CO expression; FT may mediate AtNCL-regulated flowering time change. Therefore, AtNCL is a vacuolar Ca(2+) -regulated Na(+) /Ca(2+) exchanger that regulates auxin responses and flowering time.
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Affiliation(s)
- Penghui Li
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Gaoyang Zhang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Naomi Gonzales
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yingqing Guo
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Honghong Hu
- College of Life Science and technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Sunghun Park
- Department of Horticulture, Forestry and Recreation Resources, Kansas State University, Manhattan, KS, 66506, USA
| | - Jian Zhao
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
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239
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Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing. G3-GENES GENOMES GENETICS 2016; 6:755-65. [PMID: 26801649 PMCID: PMC4777136 DOI: 10.1534/g3.115.025981] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (-8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants.
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240
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Hu R, Zhu X, Xiang S, Zhan Y, Zhu M, Yin H, Zhou Q, Zhu L, Zhang X, Liu Z. Comparative transcriptome analysis revealed the genotype specific cold response mechanism in tobacco. Biochem Biophys Res Commun 2016; 469:535-41. [PMID: 26692485 DOI: 10.1016/j.bbrc.2015.12.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 12/22/2022]
Abstract
Cold stress is a major adverse environmental factor that affects plant growth, development, productivity and quality. In the present study, comparative genome-wide transcriptome analysis on two tobacco (Nicotiana tobacum L.) cultivars, cold-tolerant NC567 and cold-sensitive Taiyan8, was performed using RNA-seq technology. After the first assembly, total length of unigenes is from 101,308,644 to 123,781,795 bp, the N50 length is from 1357 to 1475 bp, and 152,688 unigenes in NC567 and 144,160 unigenes in Taiyan8 were identified, respectively. Functional classification of cold-responsive (COR) genes showed that the genes involved in cell wall metabolism, transcription factors, ubiquitin-proteasome system (UPS) and signaling are over-represented, and the COR genes are specifically induced during cold stress in NC567. Pathway analysis revealed the significant enrichment of the COR genes in plant circadian clock. Taken together, the present study suggested the positive roles of the highly induced expression of the COR genes and the conserved mechanism of circadian clock related genes in tobacco response to cold stress, and provided some valuable genes for crop improvement to cope with cold stress.
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Affiliation(s)
- Risheng Hu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China
| | - Xianxin Zhu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shipeng Xiang
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Youguo Zhan
- Kunming Municipal Tobacco Company, Kunming, 650000, China
| | - Mingdong Zhu
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Hanqi Yin
- Shanghai Biotechnology Corporation, Shanghai, 201203, China
| | - Qingming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lieshu Zhu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xianwen Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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241
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Huo C, Zhang B, Wang H, Wang F, Liu M, Gao Y, Zhang W, Deng Z, Sun D, Tang W. Comparative Study of Early Cold-Regulated Proteins by Two-Dimensional Difference Gel Electrophoresis Reveals a Key Role for Phospholipase Dα1 in Mediating Cold Acclimation Signaling Pathway in Rice. Mol Cell Proteomics 2016; 15:1397-411. [PMID: 26747563 DOI: 10.1074/mcp.m115.049759] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Indexed: 11/06/2022] Open
Abstract
To understand the early signaling steps that regulate cold responses in rice, two-dimensional difference gel electrophoresis (2-D DIGE)(1)was used to study early cold-regulated proteins in rice seedlings. Using mass spectrometry, 32 spots, which represent 26 unique proteins that showed an altered expression level within 5 min of cold treatment were identified. Among these proteins, Western blot analyses confirmed that the cellular phospholipase D α1 (OsPLDα1) protein level was increased as early as 1 min after cold treatment. Genetic studies showed that reducing the expression ofOsPLDα1makes rice plants more sensitive to chilling stress as well as cold acclimation increased freezing tolerance. Correspondingly, cold-regulated proteomic changes and the expression of the cold-responsive C repeat/dehydration-responsive element binding 1 (OsDREB1) family of transcription factors were inhibited in thepldα1mutant. We also found that the expression ofOsPLDα1is directly regulated by OsDREB1A. This transcriptional regulation ofOsPLDα1could provide positive feedback regulation of the cold signal transduction pathway in rice. OsPLDα1 hydrolyzes phosphatidylcholine to produce the signal molecule phosphatidic acid (PA). By lipid-overlay assay, we demonstrated that the rice cold signaling proteins, MAP kinase 6 (OsMPK6) and OsSIZ1, bind directly to PA. Taken together, our results suggest that OsPLDα1 plays a key role in transducing cold signaling in rice by producing PA and regulatingOsDREB1s' expression by OsMPK6, OsSIZ1, and possibly other PA-binding proteins.
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Affiliation(s)
- Chenmin Huo
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China; ‖College of Biology Science & Engineering, Hebei University of Economics & Business, Shijiazhuang, Hebei 050061, China
| | - Baowen Zhang
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
| | - Hui Wang
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
| | - Fawei Wang
- §State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Meng Liu
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
| | - Yingjie Gao
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
| | - Wenhua Zhang
- §State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiping Deng
- ¶State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Daye Sun
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
| | - Wenqiang Tang
- From the ‡Hebei Collaboration Innovation Center for Cell Signaling; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; Hebei Key Laboratory of Molecular and Cellular Biology; College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China;
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242
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Han Z, Yu H, Zhao Z, Hunter D, Luo X, Duan J, Tian L. AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:310. [PMID: 27066015 PMCID: PMC4815178 DOI: 10.3389/fpls.2016.00310] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/29/2016] [Indexed: 05/20/2023]
Abstract
The histone deacetylases play important roles in the regulation of gene expression and the subsequent control of a number of important biological processes, including those involved in the response to environmental stress. A specific group of histone deacetylase genes, HD2, is present in plants. In Arabidopsis, HD2s include HD2A, HD2B, HD2C, and HD2D. Previous research showed that HD2A, HD2B, and HD2C are more related in terms of expression and function, but not HD2D. In this report, we studied different aspects of AtHD2D in Arabidopsis with respect to plant response to drought and other abiotic stresses. Bioinformatics analysis indicates that HD2D is distantly related to other HD2 genes. Transient expression in Nicotiana benthamiana and stable expression in Arabidopsis of AtHD2D fused with gfp showed that AtHD2D was expressed in the nucleus. Overexpression of AtHD2D resulted in developmental changes including fewer main roots, more lateral roots, and a higher root:shoot ratio. Seed germination and plant flowering time were delayed in transgenic plants expressing AtHD2D, but these plants exhibited higher degrees of tolerance to abiotic stresses, including drought, salt, and cold stresses. Physiological studies indicated that the malondialdehyde (MDA) content was high in wild-type plants but in plants overexpressing HD2D the MDA level increased slowly in response to stress conditions of drought, cold, and salt stress. Furthermore, electrolyte leakage in leaf cells of wild type plants increased but remained stable in transgenic plants. Our results indicate that AtHD2D is unique among HD2 genes and it plays a role in plant growth and development regulation and these changes can modulate plant stress responses.
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Affiliation(s)
- Zhaofen Han
- College of Life Science, Northwest A & F UniversityYangling, China
| | - Huimin Yu
- Department of E-A Information Engineering, Liaoning Institute of Science and TechnologyBenxi, China
| | - Zhong Zhao
- College of Forestry, Northwest A & F UniversityYangling, China
- *Correspondence: Zhong Zhao
| | - David Hunter
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-food CanadaLondon, ON, Canada
| | - Xinjuan Luo
- College of Life Science, Northwest A & F UniversityYangling, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-food CanadaLondon, ON, Canada
- Lining Tian
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243
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Zhang Y, Nan J, Yu B. OMICS Technologies and Applications in Sugar Beet. FRONTIERS IN PLANT SCIENCE 2016; 7:900. [PMID: 27446130 PMCID: PMC4916227 DOI: 10.3389/fpls.2016.00900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/07/2016] [Indexed: 05/08/2023]
Abstract
Sugar beet is a species of the Chenopodiaceae family. It is an important sugar crop that supplies approximately 35% of the sugar in the world. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss. And exhibits tolerance to salt stress. In this review, we have summarized OMICS technologies and applications in sugar beet including M14 for identification of novel genes, proteins related to biotic and abiotic stresses, apomixes and metabolites related to energy and food. An OMICS overview for the discovery of novel genes, proteins and metabolites in sugar beet has helped us understand the complex mechanisms underlying many processes such as apomixes, tolerance to biotic and abiotic stresses. The knowledge gained is valuable for improving the tolerance of sugar beet and other crops to biotic and abiotic stresses as well as for enhancing the yield of sugar beet for energy and food production.
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Affiliation(s)
- Yongxue Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Jingdong Nan
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Bing Yu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
- *Correspondence: Bing Yu
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Bustamante CA, Monti LL, Gabilondo J, Scossa F, Valentini G, Budde CO, Lara MV, Fernie AR, Drincovich MF. Differential Metabolic Rearrangements after Cold Storage Are Correlated with Chilling Injury Resistance of Peach Fruits. FRONTIERS IN PLANT SCIENCE 2016; 7:1478. [PMID: 27746802 PMCID: PMC5044465 DOI: 10.3389/fpls.2016.01478] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/16/2016] [Indexed: 05/18/2023]
Abstract
Reconfiguration of the metabolome is a key component involved in the acclimation to cold in plants; however, few studies have been devoted to the analysis of the overall metabolite changes after cold storage of fruits prior to consumption. Here, metabolite profiling of six peach varieties with differential susceptibility to develop mealiness, a chilling-injury (CI) symptom, was performed. According to metabolic content at harvest; after cold treatment; and after ripening, either following cold treatment or not; peach fruits clustered in distinct groups, depending on harvest-time, cold treatment, and ripening state. Both common and distinct metabolic responses among the six varieties were found; common changes including dramatic galactinol and raffinose rise; GABA, Asp, and Phe increase; and 2-oxo-glutarate and succinate decrease. Raffinose content after long cold treatment quantitatively correlated to the degree of mealiness resistance of the different peach varieties; and thus, raffinose emerges as a candidate biomarker of this CI disorder. Xylose increase after cold treatment was found only in the susceptible genotypes, indicating a particular cell wall reconfiguration of these varieties while being cold-stored. Overall, results indicate that peach fruit differential metabolic rearrangements due to cold treatment, rather than differential metabolic priming before cold, are better related with CI resistance. The plasticity of peach fruit metabolism renders it possible to induce a diverse metabolite array after cold, which is successful, in some genotypes, to avoid CI.
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Affiliation(s)
- Claudia A. Bustamante
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Laura L. Monti
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Julieta Gabilondo
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - Federico Scossa
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la FrutticolturaRome, Italy
| | - Gabriel Valentini
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - Claudio O. Budde
- Estación Experimental San Pedro, Instituto Nacional de Tecnología AgropecuariaSan Pedro, Argentina
| | - María V. Lara
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - María F. Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosario, Argentina
- *Correspondence: María F. Drincovich
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245
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Li Z, Hu G, Liu X, Zhou Y, Li Y, Zhang X, Yuan X, Zhang Q, Yang D, Wang T, Zhang Z. Transcriptome Sequencing Identified Genes and Gene Ontologies Associated with Early Freezing Tolerance in Maize. FRONTIERS IN PLANT SCIENCE 2016; 7:1477. [PMID: 27774095 PMCID: PMC5054024 DOI: 10.3389/fpls.2016.01477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/16/2016] [Indexed: 05/04/2023]
Abstract
Originating in a tropical climate, maize has faced great challenges as cultivation has expanded to the majority of the world's temperate zones. In these zones, frost and cold temperatures are major factors that prevent maize from reaching its full yield potential. Among 30 elite maize inbred lines adapted to northern China, we identified two lines of extreme, but opposite, freezing tolerance levels-highly tolerant and highly sensitive. During the seedling stage of these two lines, we used RNA-seq to measure changes in maize whole genome transcriptome before and after freezing treatment. In total, 19,794 genes were expressed, of which 4550 exhibited differential expression due to either treatment (before or after freezing) or line type (tolerant or sensitive). Of the 4550 differently expressed genes, 948 exhibited differential expression due to treatment within line or lines under freezing condition. Analysis of gene ontology found that these 948 genes were significantly enriched for binding functions (DNA binding, ATP binding, and metal ion binding), protein kinase activity, and peptidase activity. Based on their enrichment, literature support, and significant levels of differential expression, 30 of these 948 genes were selected for quantitative real-time PCR (qRT-PCR) validation. The validation confirmed our RNA-Seq-based findings, with squared correlation coefficients of 80% and 50% in the tolerance and sensitive lines, respectively. This study provided valuable resources for further studies to enhance understanding of the molecular mechanisms underlying maize early freezing response and enable targeted breeding strategies for developing varieties with superior frost resistance to achieve yield potential.
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Affiliation(s)
- Zhao Li
- Agronomy College of Northeast Agricultural UniversityHarbin, China
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
| | - Guanghui Hu
- Agronomy College of Northeast Agricultural UniversityHarbin, China
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
- Institute of Maize Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Xiangfeng Liu
- Agronomy College of Northeast Agricultural UniversityHarbin, China
| | - Yao Zhou
- Agronomy College of Northeast Agricultural UniversityHarbin, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xu Zhang
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
| | - Xiaohui Yuan
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
- Department of Computer Science, Wuhan University of TechnologyWuhan, China
| | - Qian Zhang
- Agronomy College of Northeast Agricultural UniversityHarbin, China
| | - Deguang Yang
- Agronomy College of Northeast Agricultural UniversityHarbin, China
- *Correspondence: Deguang Yang
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- Tianyu Wang
| | - Zhiwu Zhang
- Agronomy College of Northeast Agricultural UniversityHarbin, China
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
- Zhiwu Zhang
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246
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TAO X, YONG B, SHAO HH, MA XR. Cloning and abiotic stress resistance analyses of a new proline-glycine-alaninehistidine-rich protein gene from Ipomoea batatas (L.) Lam. Turk J Biol 2016. [DOI: 10.3906/biy-1509-76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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247
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Wang CL, Zhang SC, Qi SD, Zheng CC, Wu CA. Delayed germination of Arabidopsis seeds under chilling stress by overexpressing an abiotic stress inducible GhTPS11. Gene 2016; 575:206-12. [DOI: 10.1016/j.gene.2015.08.056] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 11/25/2022]
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248
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Hsiao YC, Liu LYD. A Stepwise Approach of Finding Dependent Variables via Coefficient of Intrinsic Dependence. J Comput Biol 2015; 23:42-55. [PMID: 26645623 DOI: 10.1089/cmb.2015.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The coefficient of intrinsic dependence (CID) is capable of determining associations among variables without making distributional or functional assumptions regarding random variables. In this study, we developed the partial coefficient of intrinsic dependence (pCID) to facilitate the step-by-step selection of variables that are relevant to a target variable. The strategy of selecting relevant variables using the CID along with the pCID can eliminate interference from other relevant variables. From simulation results, we observed that the proposed method is more sensitive to curvilinearity and more specific to linearity than the combination of Pearsons correlation coefficient and the partial correlation coefficient (PCC/pPCC). This property may provide the opportunity to index different levels of curvilinearity according to CID/pCID outcomes. In practice trials conducted using publicly available microarray data, the CID/pCID procedure successfully identified cold-responsive genes related to three C-repeat binding factors, and was especially effective at identifying some sample-specific gene-gene interactions. Therefore, the proposed strategy may be beneficial in meta-analysis to distinguish general forms of relationships from the noise.
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Affiliation(s)
- Ya-Chun Hsiao
- Department of Agronomy, National Taiwan University , Taipei, Taiwan
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University , Taipei, Taiwan
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249
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ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1. Sci Rep 2015; 5:17620. [PMID: 26626798 PMCID: PMC4667267 DOI: 10.1038/srep17620] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/30/2015] [Indexed: 01/31/2023] Open
Abstract
ICE1 transcription factor plays an important role in plant cold stress via regulating the expression of stress-responsive genes. In this study, a PuICE1 gene isolated from Pyrus ussuriensis was characterized for its function in cold tolerance. The expression levels of the PuICE1 were induced by cold, dehydration and salt, with the greatest induction under cold conditions. PuICE1 was localized in the nucleus and could bind specifically to the MYC element in the PuDREBa promoter. The PuICE1 fused to the GAL4 DNA-binding domain to have transcriptional activation activity. Ectopic expression of the PuICE1 in tomato conferred enhanced tolerance to cold stress at cold temperatures, less electrolyte leakage, less MDA content, higher chlorophyll content, higher survival rate, higher proline content, higher activities of enzymes. In additon, steady-state mRNA levels of six stress-responsive genes coding for either functional or regulatory genes were induced to higher levels in the transgenic lines by cold stress. Yeast two-hybrid, transient assay, split luciferase complementation and BiFC assays all revealed that PuHHP1 protein can physically interact with PuICE1. Taken together, these results demonstrated that PuICE1 plays a positive role in cold tolerance, which may be due to enhancement of PuDREBa transcriptional levels through interacting with the PuHHP1.
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250
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Huang X, Li K, Jin C, Zhang S. ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1. Sci Rep 2015; 5:17620. [PMID: 26626798 DOI: 10.1038/srep1762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/30/2015] [Indexed: 05/21/2023] Open
Abstract
ICE1 transcription factor plays an important role in plant cold stress via regulating the expression of stress-responsive genes. In this study, a PuICE1 gene isolated from Pyrus ussuriensis was characterized for its function in cold tolerance. The expression levels of the PuICE1 were induced by cold, dehydration and salt, with the greatest induction under cold conditions. PuICE1 was localized in the nucleus and could bind specifically to the MYC element in the PuDREBa promoter. The PuICE1 fused to the GAL4 DNA-binding domain to have transcriptional activation activity. Ectopic expression of the PuICE1 in tomato conferred enhanced tolerance to cold stress at cold temperatures, less electrolyte leakage, less MDA content, higher chlorophyll content, higher survival rate, higher proline content, higher activities of enzymes. In additon, steady-state mRNA levels of six stress-responsive genes coding for either functional or regulatory genes were induced to higher levels in the transgenic lines by cold stress. Yeast two-hybrid, transient assay, split luciferase complementation and BiFC assays all revealed that PuHHP1 protein can physically interact with PuICE1. Taken together, these results demonstrated that PuICE1 plays a positive role in cold tolerance, which may be due to enhancement of PuDREBa transcriptional levels through interacting with the PuHHP1.
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Affiliation(s)
- Xiaosan Huang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China, 210095
| | - Kongqing Li
- College of Rural Development, Nanjing Agricultural University, Nanjing, China, 210095
| | - Cong Jin
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China, 210095
| | - Shaoling Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China, 210095
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