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Mallik R, Prasad P, Kundu A, Sachdev S, Biswas R, Dutta A, Roy A, Mukhopadhyay J, Bag SK, Chaudhuri S. Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194644. [PMID: 33068782 DOI: 10.1016/j.bbagrm.2020.194644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/12/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022]
Abstract
AtHMGB15 belongs to a group of ARID-HMG proteins which are plant specific. The presence of two known DNA binding domains: AT rich interacting domain (ARID) and High Mobility Group (HMG)-box, in one polypeptide, makes this protein intriguing. Although proteins containing individual HMG and ARID domains have been characterized, not much is known about the role of ARID-HMG proteins. Promoter analysis of AtHMGB15 showed the presence of various stress responsive cis regulatory elements along with MADS-box containing transcription factors. Our result shows that the expression of AtHMGB15 increased significantly upon application of cold stress. Using ChIP-chip approach, we have identified 6128 and 4689 significantly enriched loci having AtHMGB15 occupancy under control and cold stressed condition respectively. GO analysis shows genes belonging to abiotic stress response, cold response and root development were AtHMGB15 targets during cold stress. DNA binding and footprinting assays further identified A(A/C)--ATA---(A/T)(A/T) as AtHMGB15 binding motif. The enriched probe distribution in both control and cold condition shows a bias of AtHMGB15 binding towards the transcribed (gene body) region. Further, the expression of cold stress responsive genes decreased in athmgb15 knockout plants compared to wild-type. Taken together, binding enrichment of AtHMGB15 to the promoter and upstream to stress loci suggest an unexplored role of the protein in stress induced transcription regulation.
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Affiliation(s)
- Rwitie Mallik
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Priti Prasad
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Anindya Kundu
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Sonal Sachdev
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Ruby Biswas
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Jayanta Mukhopadhyay
- Department of Chemistry, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India.
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102
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Datir SS. Invertase inhibitors in potato: towards a biochemical and molecular understanding of cold-induced sweetening. Crit Rev Food Sci Nutr 2020; 61:3804-3818. [PMID: 32838549 DOI: 10.1080/10408398.2020.1808876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Invertase inhibitors classified as cell wall/apoplastic and vacuolar belonging to the pectin methylesterase family, play a major role in cold-induced sweetening (CIS) process of potato tubers. The CIS process is controlled at the post-translational level via an interaction between invertase (cell wall/apoplastic and vacuolar) by their compartment-specific inhibitors (cell wall/apoplastic and vacuolar). Invertase inhibitors have been cloned, sequenced and functionally characterized from potato cultivars differing in their CIS ability. The secondary structure of the invertase inhibitors consisted of seven alpha-helices and four conserved cysteine residues. The well-conserved three amino acids i.e. Pro-Lys-Phe are known to interact with invertase. Location of the genes encoding cell wall/apoplastic and vacuolar invertase inhibitors on potato chromosome number twelve in a tandem orientation without any intervening genes suggest their divergence into the cell wall and vacuole forms following the event of gene duplication. Under cold storage conditions, the vacuolar invertase inhibitor gene showed developmentally regulated alternative splicing and produce hybrid mRNAs which were the result of mRNA splicing of an upstream region of vacuolar invertase inhibitor gene to a downstream region of the apoplastic invertase inhibitor gene. Transgenic potato tubers overexpressing invertase inhibitors resulted in decreased invertase activity, low reducing sugars and improved processing quality making invertase inhibitors highly potential candidate genes for overcoming CIS. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene-editing technology offers transgene-free breeding for developing CIS resistant potato cultivars. Moreover, the post-transcriptional regulation of invertase inhibitors during cold storage can be warranted. This review summarizes progress and current knowledge on biochemical and molecular approaches used for the understanding of invertase inhibitors with special reference to key findings in potato.
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Affiliation(s)
- Sagar S Datir
- Biology Department, Biosciences Complex, Queen's University, Kingston, Ontario, Canada
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103
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Tiwari B, Habermann K, Arif MA, Weil HL, Garcia-Molina A, Kleine T, Mühlhaus T, Frank W. Identification of small RNAs during cold acclimation in Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:298. [PMID: 32600430 PMCID: PMC7325139 DOI: 10.1186/s12870-020-02511-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/22/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes. RESULT We subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation. CONCLUSION In A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.
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Affiliation(s)
- Bhavika Tiwari
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Kristin Habermann
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - M. Asif Arif
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Antoni Garcia-Molina
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Department of Biology I, Plant Molecular Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Technische Universität Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Wolfgang Frank
- Department of Biology I, Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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Bittner A, van Buer J, Baier M. Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana. BMC PLANT BIOLOGY 2020; 20:281. [PMID: 32552683 PMCID: PMC7301481 DOI: 10.1186/s12870-020-02487-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/10/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression. RESULTS Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in non-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 μmol quanta m- 2 s- 1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment. CONCLUSION A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.
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Affiliation(s)
- Andras Bittner
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Jörn van Buer
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
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105
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Zheng X, Shi M, Wang J, Yang N, Wang K, Xi J, Wu C, Xi T, Zheng J, Zhang J. Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat ( Triticum aestivum L.). Front Genet 2020; 11:462. [PMID: 32595694 PMCID: PMC7300213 DOI: 10.3389/fgene.2020.00462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to -6°C for 4 h at the four-leave stage. Leaves of the control group and freezing-treated group were used to perform cDNA library construction. PacBio SMRT sequencing yielded 51,570 high-quality isoforms from leaves of control sample of Zhoumai 18, encoded by 20,366 gene loci. In total, 73,695 transcript isoforms, corresponding to 23,039 genes, were identified from the freezing-treated leaves. Compared with transcripts from the International Wheat Genome Sequencing Consortium RefSeq v1.1, 57,667 novel isoforms were discovered, which were annotated 21,672 known gene loci, as well as 3,399 novel gene loci. Transcriptome characterization including alterative spliced events, alternative polydenylation sites, transcription factors, and fusion transcripts were also analyzed. Freezing-responsive genes and signals were uncovered and proved that the ICE-ERF-COR pathway and ABA signal transduction play a vital role in the freezing response of wheat. In this study, PacBio sequencing and Illumina sequencing were applied to investigate the freezing tolerance in common wheat, and the transcriptome results provide insights into the molecular regulation mechanisms under freezing treatment.
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Affiliation(s)
- Xingwei Zheng
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Mengmeng Shi
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jian Wang
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Na Yang
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Ke Wang
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Jilong Xi
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Caixia Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Tianyuan Xi
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiancheng Zhang
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
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Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol 2020; 40:750-776. [PMID: 32522044 DOI: 10.1080/07388551.2020.1768509] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.
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Affiliation(s)
- Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guo-Ming Xing
- Collaborative Innovation Center for Improving Quality and Increased Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Novikova DD, Cherenkov PA, Sizentsova YG, Mironova VV. metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. Genes (Basel) 2020; 11:genes11060634. [PMID: 32526881 PMCID: PMC7348973 DOI: 10.3390/genes11060634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.
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Affiliation(s)
- Daria D. Novikova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Pavel A. Cherenkov
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
| | - Yana G. Sizentsova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
- Correspondence:
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108
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Illgen S, Zintl S, Zuther E, Hincha DK, Schmülling T. Characterisation of the ERF102 to ERF105 genes of Arabidopsis thaliana and their role in the response to cold stress. PLANT MOLECULAR BIOLOGY 2020; 103:303-320. [PMID: 32185689 PMCID: PMC7220888 DOI: 10.1007/s11103-020-00993-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/04/2020] [Indexed: 05/19/2023]
Abstract
The four phylogenetically closely related ERF102 to ERF105 transcription factors of Arabidopsis thaliana are regulated by different stresses and are involved in the response to cold stress. The ETHYLENE RESPONSE FACTOR (ERF) genes of Arabidopsis thaliana form a large family encoding plant-specific transcription factors. Here, we characterise the four phylogenetically closely related ERF102/ERF5, ERF103/ERF6, ERF104 and ERF105 genes. Expression analyses revealed that these four genes are similarly regulated by different hormones and abiotic stresses. Analyses of tissue-specific expression using promoter:GUS reporter lines revealed their predominant expression in root tissues including the root meristem (ERF103), the quiescent center (ERF104) and the root vasculature (all). All GFP-ERF fusion proteins were nuclear-localised. The analysis of insertional mutants, amiRNA lines and 35S:ERF overexpressing transgenic lines indicated that ERF102 to ERF105 have only a limited impact on regulating shoot and root growth. Previous work had shown a role for ERF105 in the cold stress response. Here, measurement of electrolyte leakage to determine leaf freezing tolerance and expression analyses of cold-responsive genes revealed that the combined activity of ERF102 and ERF103 is also required for a full cold acclimation response likely involving the CBF regulon. These results suggest a common function of these ERF genes in the response to cold stress.
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Affiliation(s)
- Sylvia Illgen
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Stefanie Zintl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany.
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109
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Zhou H, He Y, Zhu Y, Li M, Song S, Bo W, Li Y, Pang X. Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars. BMC PLANT BIOLOGY 2020; 20:240. [PMID: 32460709 PMCID: PMC7254757 DOI: 10.1186/s12870-020-02450-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/19/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between 'Dongzao' (low freezing tolerance cultivar) and 'Jinsixiaozao' (high freezing tolerance cultivar) using RNA-Seq. RESULTS More than 20,000 genes were detected at chilling (4 °C) and freezing (- 10 °C, - 20 °C, - 30 °C and - 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress. CONCLUSIONS Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.
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Affiliation(s)
- Heying Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ying He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yongsheng Zhu
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan, 430074, China
| | - Meiyu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shuang Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yingyue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoming Pang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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Li J, Zhang M, Sun J, Mao X, Wang J, Liu H, Zheng H, Li X, Zhao H, Zou D. Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. Front Genet 2020; 11:477. [PMID: 32457808 PMCID: PMC7225358 DOI: 10.3389/fgene.2020.00477] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/17/2020] [Indexed: 11/26/2022] Open
Abstract
Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.
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Affiliation(s)
- Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xinrui Mao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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Zhou L, He YJ, Li J, Li LZ, Liu Y, Chen HY. An eggplant SmICE1a gene encoding MYC-type ICE1-like transcription factor enhances freezing tolerance in transgenic Arabidopsis thaliana. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:450-458. [PMID: 32009285 DOI: 10.1111/plb.13095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/21/2020] [Indexed: 05/21/2023]
Abstract
Low temperature is a crucial environmental factor affecting the quality and production of eggplant. Therefore, it is necessary to explore the molecular mechanisms of low temperature response. We isolated an ICE (inducer of CBF expression) gene from Solanum melongena, named SmICE1a. We then analysed structure, transcriptional activity and expression patterns of SmICE1a. Moreover, we also expressed SmICE1a in Arabidopsis thaliana. Bioinformatics and expression analysis showed that SmICE1a has a typical S-rich motif, ZIP region, bHLH and ACT-like domain. The gene SmICE1a had transcriptional activity in yeast and was localized to the nucleus following transient expression in tobacco leaves, which suggests that SmICE1a is a transcription factor. A dual-LUC assay revealed that SmICE1a can enhance expression of SmCBF. Overexpression of SmICE1a in Arabidopsis increased freezing tolerance and caused multiple biochemical changes: transgenic lines have higher proline content and lower electrolyte leakage and malondialdehyde than the wild type in cold conditions. The expression of AtCBF and their target genes, AtCOR15A, AtCOR47, AtKIN1 and AtRD29A, were up-regulated in SmICE1a-overexpressing plants under low temperatures. Based on these results, we suggest that SmICE1a plays an important role in cold response, which may help to understand the cold response mechanism in eggplant and could be used to enhance cold tolerance of eggplant in future.
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Affiliation(s)
- L Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Y J He
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - J Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - L Z Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Y Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - H Y Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Liu Y, Wu C, Hu X, Gao H, Wang Y, Luo H, Cai S, Li G, Zheng Y, Lin C, Zhu Q. Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis). TREE PHYSIOLOGY 2020; 40:538-556. [PMID: 31860727 DOI: 10.1093/treephys/tpz133] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 05/20/2023]
Abstract
Most bamboo species including Moso bamboo (Phyllostachys edulis) are tropical or subtropical plants that greatly contribute to human well-being. Low temperature is one of the main environmental factors restricting bamboo growth and geographic distribution. Our knowledge of the molecular changes during bamboo adaption to cold stress remains limited. Here, we provided a general overview of the cold-responsive transcriptional profiles in Moso bamboo by systematically analyzing its transcriptomic response under cold stress. Our results showed that low temperature induced strong morphological and biochemical alternations in Moso bamboo. To examine the global gene expression changes in response to cold, 12 libraries (non-treated, cold-treated 0.5, 1 and 24 h at -2 °C) were sequenced using an Illumina sequencing platform. Only a few differentially expressed genes (DEGs) were identified at early stage, while a large number of DEGs were identified at late stage in this study, suggesting that the majority of cold response genes in bamboo are late-responsive genes. A total of 222 transcription factors from 24 different families were differentially expressed during 24-h cold treatment, and the expressions of several well-known C-repeat/dehydration responsive element-binding factor negative regulators were significantly upregulated in response to cold, indicating the existence of special cold response networks. Our data also revealed that the expression of genes related to cell wall and the biosynthesis of fatty acids were altered in response to cold stress, indicating their potential roles in the acquisition of bamboo cold tolerance. In summary, our studies showed that both plant kingdom-conserved and species-specific cold response pathways exist in Moso bamboo, which lays the foundation for studying the regulatory mechanisms underlying bamboo cold stress response and provides useful gene resources for the construction of cold-tolerant bamboo through genetic engineering in the future.
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Affiliation(s)
- Yuanyuan Liu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chu Wu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Hu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongye Gao
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yue Wang
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Luo
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Cai
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guowei Li
- College of Life Science, Shandong Normal University, Jinan 250000, China
| | - Yushan Zheng
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Qiang Zhu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Kidokoro S, Kim JS, Ishikawa T, Suzuki T, Shinozaki K, Yamaguchi-Shinozaki K. DREB1A/CBF3 Is Repressed by Transgene-Induced DNA Methylation in the Arabidopsis ice1 -1 Mutant. THE PLANT CELL 2020; 32:1035-1048. [PMID: 32034036 PMCID: PMC7145508 DOI: 10.1105/tpc.19.00532] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/17/2019] [Accepted: 02/03/2020] [Indexed: 05/22/2023]
Abstract
DREB1/CBFs are key transcription factors involved in plant cold stress adaptation. The expression of DREB1/CBFs triggers a cold-responsive transcriptional cascade, after which many stress tolerance genes are expressed. Thus, elucidating the mechanisms of cold stress-inducible DREB1/CBF expression is important to understand the molecular mechanisms of plant cold stress responses and tolerance. We analyzed the roles of a transcription factor, INDUCER OF CBF EXPRESSION1 (ICE1), that is well known as an important transcriptional activator in the cold-inducible expression of DREB1A/CBF3 in Arabidopsis (Arabidopsis thaliana). ice1-1 is a widely accepted mutant allele known to abolish cold-inducible DREB1A expression, and this evidence has strongly supported ICE1-DREB1A regulation for many years. However, in ice1-1 outcross descendants, we unexpectedly discovered that ice1-1 DREB1A repression was genetically independent of the ice1-1 allele ICE1(R236H). Moreover, neither ICE1 overexpression nor double loss-of-function mutation of ICE1 and its homolog SCRM2 altered DREB1A expression. Instead, a transgene locus harboring a reporter gene in the ice1-1 genome was responsible for altering DREB1A expression. The DREB1A promoter was hypermethylated due to the transgene. We showed that DREB1A repression in ice1-1 results from transgene-induced silencing and not genetic regulation by ICE1. The ICE1(R236H) mutation has also been reported as scrm-D, which confers constitutive stomatal differentiation. The scrm-D phenotype and the expression of a stomatal differentiation marker gene were confirmed to be linked to the ICE1(R236H) mutation. We propose that the current ICE1-DREB1 regulatory model should be revalidated without the previous assumptions.
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Affiliation(s)
- Satoshi Kidokoro
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - June-Sik Kim
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomona Ishikawa
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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114
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Jian H, Xie L, Wang Y, Cao Y, Wan M, Lv D, Li J, Lu K, Xu X, Liu L. Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses. PeerJ 2020; 8:e8704. [PMID: 32266113 PMCID: PMC7120054 DOI: 10.7717/peerj.8704] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/06/2020] [Indexed: 01/04/2023] Open
Abstract
The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ling Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yanhua Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yanru Cao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Mengyuan Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dianqiu Lv
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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115
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Tang K, Zhao L, Ren Y, Yang S, Zhu JK, Zhao C. The transcription factor ICE1 functions in cold stress response by binding to the promoters of CBF and COR genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:258-263. [PMID: 32068336 DOI: 10.1111/jipb.12918] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 05/25/2023]
Abstract
A recent paper by Kidokoro et al. (2020) in The Plant Cell reported a transgene-dependent transcriptional silencing phenomenon in the dominant ice1-1 Arabidopsis mutant containing the CBF3-LUC reporter, and questioned whether ICE1 may regulate CBF genes and may be involved in plant cold response. Here, we evaluate available evidence supporting the involvement of ICE1 in plant cold response, and provide ChIP-seq data showing ICE1 binding to the promoters of CBF genes and other regulatory genes known to be critical for cold response as well as to the promoters of some COR genes.
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Affiliation(s)
- Kai Tang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Lun Zhao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Yuying Ren
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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116
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Kim Y, Park SU, Shin DM, Pham G, Jeong YS, Kim SH. ATBS1-INTERACTING FACTOR 2 negatively regulates dark- and brassinosteroid-induced leaf senescence through interactions with INDUCER OF CBF EXPRESSION 1. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1475-1490. [PMID: 31783407 PMCID: PMC7031079 DOI: 10.1093/jxb/erz533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/28/2019] [Indexed: 05/25/2023]
Abstract
ATBS1-INTERACTING FACTOR 2 (AIF2) is a non-DNA-binding basic helix-loop-helix (bHLH) transcription factor. We demonstrated that AIF2 retards dark-triggered and brassinosteroid (BR)-induced leaf senescence in Arabidopsis thaliana. Dark-triggered BR synthesis and the subsequent activation of BRASSINAZOLE RESISTANT 1 (BZR1), a BR signaling positive regulator, result in BZR1 binding to the AIF2 promoter in a dark-dependent manner, reducing AIF2 transcript levels and accelerating senescence. BR-induced down-regulation of AIF2 protein stability partly contributes to the progression of dark-induced leaf senescence. Furthermore, AIF2 interacts with INDUCER OF CBF EXPRESSION 1 (ICE1) via their C-termini. Formation of the AIF2-ICE1 complex and subsequent up-regulation of C-REPEAT BINDING FACTORs (CBFs) negatively regulates dark-triggered, BR-induced leaf senescence. This involves antagonistic down-regulation of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), modulated through AIF2-dependent inhibition of ICE1's binding to the promoter. PIF4-dependent activities respond to dark-induced early senescence and may promote BR synthesis and BZR1 activation to suppress AIF2 and accelerate dark-induced senescence. Taken together, these findings suggest a coordination of AIF2 and ICE1 functions in maintaining stay-green traits.
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Affiliation(s)
- Yoon Kim
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
| | - Seon-U Park
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
| | - Dong-Min Shin
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
| | - Giang Pham
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
| | - You Seung Jeong
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
| | - Soo-Hwan Kim
- Division of Biological Science and Technology, Yonsei University, Wonju-Si, Republic of Korea
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Ke L, Lei W, Yang W, Wang J, Gao J, Cheng J, Sun Y, Fan Z, Yu D. Genome-wide identification of cold responsive transcription factors in Brassica napus L. BMC PLANT BIOLOGY 2020; 20:62. [PMID: 32028890 PMCID: PMC7006134 DOI: 10.1186/s12870-020-2253-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cold stress is one of the primary environmental factors that affect plant growth and productivity, especially for crops like Brassica napus that live through cold seasons. Till recently, although a number of genes and pathways involved in B. napus cold response have been revealed by independent studies, a genome-wide identification of the key regulators and the regulatory networks is still lack. In this study, we investigated the transcriptomes of cold stressed semi-winter and winter type rapeseeds in short day condition, mainly with the purpose to systematically identify the functional conserved transcription factors (TFs) in cold response of B. napus. RESULTS Global modulation of gene expression was observed in both the semi-winter type line (158A) and the winter type line (SGDH284) rapeseeds, in response to a seven-day chilling stress in short-day condition. Function analysis of differentially expressed genes (DEGs) revealed enhanced stresses response mechanisms and inhibited photosynthesis in both lines, as well as a more extensive inhibition of some primary biological processes in the semi-winter type line. Over 400 TFs were differentially expressed in response to cold stress, including 56 of them showed high similarity to the known cold response TFs and were consistently regulated in 158A and SGDH284, as well as 25 TFs which targets were over-represented in the total DEGs. A further investigation based on their interactions indicated the critical roles of several TFs in cold response of B. napus. CONCLUSION In summary, our results revealed the alteration of gene expression in cold stressed semi-winter and winter ecotype B. napus lines and provided a valuable collection of candidate key regulators involved in B. napus response to cold stress, which could expand our understanding of plant stress response and benefit the future improvement of the breed of rapeseeds.
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Affiliation(s)
- Liping Ke
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Weixia Lei
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Weiguang Yang
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jinyu Wang
- Wenzhou - Kean University, Wenzhou, 325060, China
| | - Janfang Gao
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jinhua Cheng
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhixiong Fan
- Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Wang S, Guo T, Wang Z, Kang J, Yang Q, Shen Y, Long R. Expression of Three Related to ABI3/VP1 Genes in Medicago truncatula Caused Increased Stress Resistance and Branch Increase in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:611. [PMID: 32523590 PMCID: PMC7261895 DOI: 10.3389/fpls.2020.00611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/21/2020] [Indexed: 05/18/2023]
Abstract
Related to ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1(VP1)(RAV) transcription factors, which encode a B3 domain and an APETALA2(AP2) domain, belong to the APETALA2/ethylene-responsive element binding factor(AP2/ERF) or B3 superfamily and play an important role in regulating plant growth and development and responding to abiotic stress. Although there have been many functional studies on RAV, the functional differences between RAVs are not clear. Therefore, in this study, the functional differences of RAVs of Medicago truncatula were analyzed. Based on sequence data from the plant transcription factor database and the M. truncatula genome database, we cloned three RAV genes from M. truncatula, named MtRAV1, MtRAV2, and MtRAV3. The cis-acting elements of these genes promoters were predicted, and the expression patterns of MtRAVs under exogenous conditions (4°C, NaCl, Polyethylene Glycol, Abscisic acid) were analyzed. MtRAVs transgenic Arabidopsis thaliana were obtained and subjected to adversity treatment. Subcellular localization results indicated that MtRAVs were located in the nucleus. A much lower expression level was observed for MtRAV3 than the levels of MtRAV1 and MtRAV2 in M. truncatula for growth in normal conditions, but under 4°C or PEG and NaCl treatment, the expression level of MtRAV3 was significantly increased. Only the MtRAV3 overexpression transgenic plants showed strong cold resistance, but the overexpressed MtRAV1 and MtRAV2 transgenic plants showed no difference from wild type plants. MtRAV transgenic plants exhibited similar response to exogenous mannitol, NaCl, and ABA, and the expression of some adverse-related marker genes were up-regulated, such as COLD REGULATED 414 THYLAKOID MEMBRANE 1 (COR414-TM1), Arabidopsis thaliana drought-induced 21 (AtDI21), and Arabidopsis thaliana phosphatidylinositol-specific phospholipase C (ATPLC). MtRAVs transgenic Arabidopsis thaliana exhibited increasing of branch number. These results indicated that there was some function redundancy during MtRAVs proteins of M. truncatula, and MtRAV3 has increased function compared to the other two genes. The results of this study should provide the foundation for future application of MtRAVs in legumes.
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Affiliation(s)
- Shumin Wang
- College of Agro-Grassland Sciences, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Guo
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yixin Shen
- College of Agro-Grassland Sciences, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Yixin Shen,
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ruicai Long,
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119
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Lim CW, Lee SC. ABA-Dependent and ABA-Independent Functions of RCAR5/PYL11 in Response to Cold Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:587620. [PMID: 33101352 PMCID: PMC7545830 DOI: 10.3389/fpls.2020.587620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/09/2020] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana has 14 abscisic acid (ABA) receptors-PYR1/PYLs/RCARs-which have diverse and redundant functions in ABA signaling; however, the precise role of these ABA receptors remains to be elucidated. Here, we report the functional characterization of RCAR5/PYL11 in response to cold stress. Expression of RCAR5 gene in dry seeds and leaves was ABA-dependent and ABA-independent, respectively. Under cold stress conditions, seed germination was negatively affected by the level of RCAR5 expression, which was dependent on ABA and was regulated by HAB1, OST1, and ABI5-downstream components of RCAR5 in ABA signaling. Leaves of RCAR5-overexpressing plants showed enhanced stomatal closure-independent of ABA-and high expression levels of cold, dehydration, and/or ABA-responsive genes compared to those of wild-type; these traits conferred enhanced freezing tolerance. Our data suggest that RCAR5 functions in response to cold stress by delaying seed germination and inducing rapid stomatal closure via ABA-dependent and ABA-independent pathways, respectively.
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Long X, Li H, Yang J, Xin L, Fang Y, He B, Huang D, Tang C. Characterization of a vacuolar sucrose transporter, HbSUT5, from Hevea brasiliensis: involvement in latex production through regulation of intracellular sucrose transport in the bark and laticifers. BMC PLANT BIOLOGY 2019; 19:591. [PMID: 31881921 PMCID: PMC6935173 DOI: 10.1186/s12870-019-2209-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Sucrose (Suc), as the precursor molecule for rubber biosynthesis in Hevea brasiliensis, is transported via phloem-mediated long-distance transport from leaves to laticifers in trunk bark, where latex (cytoplasm of laticifers) is tapped for rubber. In our previous report, six Suc transporter (SUT) genes have been cloned in Hevea tree, among which HbSUT3 is verified to play an active role in Suc loading to the laticifers. In this study, another latex-abundant SUT isoform, HbSUT5, with expressions only inferior to HbSUT3 was characterized especially for its roles in latex production. RESULTS Both phylogenetic analysis and subcellular localization identify HbSUT5 as a tonoplast-localized SUT protein under the SUT4-clade (=type III). Suc uptake assay in baker's yeast reveals HbSUT5 to be a typical Suc-H+ symporter, but its high affinity for Suc (Km = 2.03 mM at pH 5.5) and the similar efficiency in transporting both Suc and maltose making it a peculiar SUT under the SUT4-clade. At the transcript level, HbSUT5 is abundantly and preferentially expressed in Hevea barks. The transcripts of HbSUT5 are conspicuously decreased both in Hevea latex and bark by two yield-stimulating treatments of tapping and ethephon, the patterns of which are contrary to HbSUT3. Under the ethephon treatment, the Suc level in latex cytosol decreases significantly, but that in latex lutoids (polydispersed vacuoles) changes little, suggesting a role of the decreased HbSUT5 expression in Suc compartmentalization in the lutoids and thus enhancing the Suc sink strength in laticifers. CONCLUSIONS Our findings provide insights into the roles of a vacuolar sucrose transporter, HbSUT5, in Suc exchange between lutoids and cytosol in rubber-producing laticifers.
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Affiliation(s)
- Xiangyu Long
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Heping Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China
- Subtropical Agriculture Research Institute, Fujian Academy of Agricultural Sciences, Zhangzhou, 363005, Fujian, China
| | - Jianghua Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Lusheng Xin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China
| | - Yongjun Fang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Bin He
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China
| | - Debao Huang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China
| | - Chaorong Tang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China.
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Guo J, Ren Y, Tang Z, Shi W, Zhou M. Characterization and expression profiling of the ICE-CBF-COR genes in wheat. PeerJ 2019; 7:e8190. [PMID: 31803544 PMCID: PMC6886486 DOI: 10.7717/peerj.8190] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/11/2019] [Indexed: 11/30/2022] Open
Abstract
Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Yongkang Ren
- Research Center of Biotechnology, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Zhaohui Tang
- College of Agronomy, Shanxi Agricultural University, Taigu, China.,Research Center of Biotechnology, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Meixue Zhou
- College of Agronomy, Shanxi Agricultural University, Taigu, China.,School of Land and Food, University of Tasmania, Hobart, Australia
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Gao B, Bian XC, Yang F, Chen MX, Das D, Zhu XR, Jiang Y, Zhang J, Cao YY, Wu CF. Comprehensive transcriptome analysis of faba bean in response to vernalization. PLANTA 2019; 251:22. [PMID: 31781953 DOI: 10.1007/s00425-019-03308-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/02/2019] [Indexed: 05/20/2023]
Abstract
This study unravels the transcriptional response of a highly productive faba bean cultivar under vernalization treatment. Faba bean (Vicia faba L.) is a member of the Leguminosae family and an important food crop worldwide providing valuable nutrients for humans. However, genome-wide studies and comprehensive sequencing resources of faba bean remain limited. Vernalization is crucial for enhanced yields in a number of winter-sown crops. However, the effects of vernalization on faba bean remain unknown. In this study, we generated a high-quality transcriptome assembly and functional annotation source for vernalized faba bean (Vicia faba L.) cv. Tongxian-2, a domesticated cultivar from southern China. A total of 369.9 million clean Illumina paired-end RNA-Seq reads were generated, and the transcriptome was assembled into 68,683 unigene sequences, with an average length of 1018 bp and an N50 of 1652 bp. Comprehensive functional annotation provided putative functional descriptions for more than 70% of the faba bean transcripts. We annotated a total of 1560 faba bean transcripts encoding transcription factors (TFs) belonging to 55 distinct TF families. The bHLH (168 transcripts), ERF (123 transcripts) and WRKY (105 transcripts) contained the largest number of TFs in response to vernalization. Genome-wide transcript changes comparing vernalized and unvernalized seedlings were investigated using bioinformatics approaches, which revealed a strong repression of photosynthesis and carbon metabolism, while genes participating in 'response to stress' were significantly induced. We also specifically identified vernalization-induced twenty-two 'pollen-pistil interaction' genes. A detailed functional annotation and expression profile analyses unveiled a number of protein kinases, which were specifically induced in vernalized seedlings. We also identified a total of 6852 simple sequence repeats (SSRs) in 6552 transcripts, representing a valuable genomic molecular marker resource for faba bean. In summary, this study provides new insights into the vernalization process in this economically valuable crop. The transcriptome data obtained provides us with a valuable candidate gene resource for future functional and molecular breeding studies. These data will contribute to the genome annotation for ensuing genome projects.
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Affiliation(s)
- Bei Gao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
- College of Life Sciences, Nantong University, Nantong, China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao-Chun Bian
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Feng Yang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mo-Xian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Debatosh Das
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiu-Ru Zhu
- College of Life Sciences, Nantong University, Nantong, China
| | - Yong Jiang
- National Oceanographic Center, Qingdao, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yun-Ying Cao
- College of Life Sciences, Nantong University, Nantong, China.
| | - Chun-Fang Wu
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.
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Caballo C, Castro P, Gil J, Millan T, Rubio J, Die JV. Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5. PLoS One 2019; 14:e0224212. [PMID: 31644597 PMCID: PMC6808423 DOI: 10.1371/journal.pone.0224212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/08/2019] [Indexed: 01/23/2023] Open
Abstract
Chickpea production may be seriously threatened by Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. ciceris. F. oxysporum race 5 is the most important race in the Mediterranean basin. Recently, the region responsible for resistance race 5 has been delimited within a region on chromosome 2 that spans 820 kb. To gain a better understanding of this genomic region, we used a transcriptomic approach based on quantitative real-time PCR to analyze the expression profiles of 22 selected candidate genes. We used a pair of near-isogenic lines (NILs) differing in their sensitivity to Fusarium race 5 (resistant vs susceptible) to monitor the transcriptional changes over a time-course experiment (24, 48, and 72 hours post inoculation, hpi). Qualitative differences occurred during the timing of regulation. A cluster of 12 genes were induced by the resistant NIL at 24 hpi, whereas a second cluster contained 9 genes induced by the susceptible NIL at 48 hpi. Their possible functions in the molecular defence of chickpea is discussed. Our study provides new insight into the molecular defence against Fusarium race 5 and demonstrates that development of NILs is a rich resource to facilitate the detection of candidate genes. The new genes regulated here may be useful against other Fusarium races.
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Affiliation(s)
- Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Patricia Castro
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Juan Gil
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Teresa Millan
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Josefa Rubio
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Jose V. Die
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
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Wang P, Yang Y, Shi H, Wang Y, Ren F. Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine. BMC Genomics 2019; 20:740. [PMID: 31615400 PMCID: PMC6794902 DOI: 10.1186/s12864-019-6111-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022] Open
Abstract
Background Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). Result Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses. Conclusion Our study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.
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Affiliation(s)
- Pengfei Wang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.
| | - Yang Yang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China
| | - Hongmei Shi
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.
| | - Yongmei Wang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.,Shandong engineering research center for cultivation and deep-processing of grape, Jinan, People's Republic of China.,Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, People's Republic of China
| | - Fengshan Ren
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China. .,Shandong engineering research center for cultivation and deep-processing of grape, Jinan, People's Republic of China. .,Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, People's Republic of China.
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Guo H, Wu T, Li S, He Q, Yang Z, Zhang W, Gan Y, Sun P, Xiang G, Zhang H, Deng H. The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice. Int J Mol Sci 2019; 20:ijms20205089. [PMID: 31615063 PMCID: PMC6829347 DOI: 10.3390/ijms20205089] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/09/2019] [Accepted: 10/12/2019] [Indexed: 01/22/2023] Open
Abstract
Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.
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Affiliation(s)
- Hui Guo
- State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410013, China.
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Tingkai Wu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| | - Shuxing Li
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Qiang He
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Zhanlie Yang
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Wuhan Zhang
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Yu Gan
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Pingyong Sun
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Guanlun Xiang
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Hongyu Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| | - Huafeng Deng
- State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410013, China.
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Li MY, Liu JX, Hao JN, Feng K, Duan AQ, Yang QQ, Xu ZS, Xiong AS. Genomic identification of AP2/ERF transcription factors and functional characterization of two cold resistance-related AP2/ERF genes in celery (Apium graveolens L.). PLANTA 2019; 250:1265-1280. [PMID: 31236696 DOI: 10.1007/s00425-019-03222-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/20/2019] [Indexed: 05/09/2023]
Abstract
This study analyzed the AP2/ERF transcription factors in celery and showed that two dehydration-responsive-element-binding (DREB) transcription factors, AgDREB1 and AgDREB2, contribute to the enhanced resistance to abiotic stress in transgenic Arabidopsis. The AP2/ERF family is a large family of transcription factors (TFs) in higher plants that plays a central role in plant growth, development, and response to environmental stress. Here, 209 AP2/ERF family members were identified in celery based on genomic and transcriptomic data. The TFs were classified into four subfamilies (i.e., DREB, ERF, RAV, and AP2) and Soloist. Evolution analysis indicated that the AP2/ERF TFs are ancient molecules and have expanded in the long-term evolution process of plants and whole-genome duplication events. AgAP2/ERF proteins may be associated with multiple biological processes as predicted by the interaction network. The expression profiles and sequence alignment analysis of the TFs in the DREB-A1 group showed that eight genes could be divided into four branches. Two genes, AgDREB1 and AgDREB2, from the DREB-A1 group were selected for further analysis. Subcellular localization assay suggested that the two proteins are nuclear proteins. Yeast one hybrid assay demonstrated that the two proteins could bind to the dehydration-responsive element (DRE). The overexpression of AgDREB1 and AgDREB2 in Arabidopsis induced the increased tolerance to cold treatment and the up-regulation of the COR genes expression. AgDREB1 and AgDREB2 might function as transcriptional activators in regulating the downstream genes by binding to corresponding DRE to enhance stress tolerance in celery.
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Affiliation(s)
- Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Jian-Nan Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Qing-Qing Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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Liu C, Yang X, Yan Z, Fan Y, Feng G, Liu D. Analysis of differential gene expression in cold-tolerant vs. cold-sensitive varieties of snap bean (Phaseolus vulgaris L.) in response to low temperature stress. Genes Genomics 2019; 41:1445-1455. [PMID: 31535316 DOI: 10.1007/s13258-019-00870-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/04/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Snap bean, Phaseolus vulgaris L., as a warm-season vegetable, low temperature stress seriously affect the yield and quality. At present, little is known about the genes and molecular regulation mechanism in cold response in snap bean exposed to low temperature. OBJECTIVES Our objectives were to identify the low temperature response genes in snap bean and to examine differences in the gene response between cold-tolerant and cold-sensitive genotypes. METHODS We used two highly inbred snap bean lines in this study, the cold-tolerant line '120', and the cold-sensitive line '093'. The plants were grown to the three leaf and one heart stage and exposed to 4 °C low temperature. We used RNA sequencing (RNA-seq) to analyze the differences of gene expression. RESULTS 988 and 874 cold-responsive genes were identified in 'T120 vs CK120' and 'T093 vs CK093' ('T' stands for low temperature treatment, and 'CK' stands for control at room temperature), respectively. Of these, 555 and 442 genes were unique to cold-stressed lines '120' and '093', respectively compared to the control. Our analysis of these differentially expressed genes indicates that Ca2+, ROS, and hormones act as signaling molecules that play important roles in low temperature response in P. vulgaris. Altering the expression of genes in these signaling pathways activates expression of downstream response genes which can interact with other signaling regulatory networks. This may maintained the balance of ROS and hormones, making line '120' more cold-tolerant than line '093'. CONCLUSION Our results provide a preliminarily understanding of the molecular basis of low temperature response in snap bean, and also establish a foundation for the future genetic improvement of cold sensitivity in snap bean by incorporating genes for cold tolerance.
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Affiliation(s)
- Chang Liu
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Work Station of Science and Technique for Post-doctoral in Sugar Beet Institute Affiliated to Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Post-doctoral Research Station Affiliated To Northeast Agricultural University, 59 Mucai Road, Harbin, 150000, Heilongjiang, China
| | - Xiaoxu Yang
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Work Station of Science and Technique for Post-doctoral in Sugar Beet Institute Affiliated to Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Post-doctoral Research Station Affiliated To Northeast Agricultural University, 59 Mucai Road, Harbin, 150000, Heilongjiang, China
| | - Zhishan Yan
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Youjun Fan
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Guojun Feng
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.
| | - Dajun Liu
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.
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128
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Halder T, Upadhyaya G, Roy S, Biswas R, Das A, Bagchi A, Agarwal T, Ray S. Glycine rich proline rich protein from Sorghum bicolor serves as an antimicrobial protein implicated in plant defense response. PLANT MOLECULAR BIOLOGY 2019; 101:95-112. [PMID: 31236845 DOI: 10.1007/s11103-019-00894-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Sorghum glycine rich proline rich protein (SbGPRP1) exhibit antimicrobial properties and play a crucial role during biotic stress condition. Several proteins in plants build up the innate immune response system in plants which get triggered during the occurrence of biotic stress. Here we report the functional characterization of a glycine-rich proline-rich protein (SbGPRP1) from Sorghum which was previously demonstrated to be involved in abiotic stresses. Expression studies carried out with SbGPRP1 showed induced expression upon application of phytohormones like salicylic acid which might be the key in fine-tuning the expression level. Upon challenging the Sorghum plants with a compatible pathogen the SbGprp1 transcript was found to be upregulated. SbGPRP1 encodes a 197 amino acid polypeptide which was bacterially-expressed and purified for in vitro assays. Gram-positive bacteria like Bacillus and phytopathogen Rhodococcus fascians showed inhibited growth in the presence of the protein. The NPN assay, electrolytic leakage and SEM analysis showed membrane damage in bacterial cells. Ectopic expression of SbGPRP1 in tobacco plants led to enhanced tolerance towards infection caused by R. fascians. Though the N-terminal part of the protein showed disorderness the C-terminal end was quite capable of forming several α-helices which was correlated with CD spectroscopic analysis. Here, we have tried to determine the structural model for the protein and predicted the association of antimicrobial activity with the C-terminal region of the protein.
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Affiliation(s)
- Tanmoy Halder
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Gouranga Upadhyaya
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Shuddhanjali Roy
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Ria Biswas
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, West Bengal, 741235, India
| | - Arup Das
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, West Bengal, 741235, India
| | - Tanushree Agarwal
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Sudipta Ray
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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129
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Yang X, Wang R, Hu Q, Li S, Mao X, Jing H, Zhao J, Hu G, Fu J, Liu C. DlICE1, a stress-responsive gene from Dimocarpus longan, enhances cold tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:490-499. [PMID: 31442880 DOI: 10.1016/j.plaphy.2019.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/31/2019] [Accepted: 08/09/2019] [Indexed: 05/02/2023]
Abstract
ICE1 (inducer of CBF expression 1) encodes a typical MYC-like basic helix-loop- helix (bHLH) transcription factor that acts as a pivotal component in the cold signalling pathway. In this study, DlICE1, a novel ICE1-like gene, was isolated from the southern subtropical fruit tree longan (Dimocarpus longan Lour.). DlICE1 encodes a nuclear protein with a highly conserved bHLH domain. DlICE1 expression was slightly upregulated under cold stress. Overexpression of DlICE1 in Arabidopsis conferred enhanced cold tolerance via increased proline content, decreased ion leakage, and reduced malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. Expression of the ICE1-CBF cold signalling pathway genes, including AtCBF1/2/3 and cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47 and AtKIN1), was also significantly higher in DlICE1-overexpressing lines than in wild-type (WT) plants under cold stress. In conclusion, these findings indicate that DlICE1 is a member of the bHLH gene family and positively regulates cold tolerance in D. longan.
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Affiliation(s)
- Xiaoyan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Rui Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qinglei Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Silin Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaodan Mao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Haohao Jing
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jietang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiaxin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| | - Chengming Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
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Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses. PLANTS 2019; 8:plants8080288. [PMID: 31443248 PMCID: PMC6724123 DOI: 10.3390/plants8080288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
Abstract
Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.
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131
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Comparative Transcriptome Analyses Revealed Conserved and Novel Responses to Cold and Freezing Stress in Brassica napus L. G3-GENES GENOMES GENETICS 2019; 9:2723-2737. [PMID: 31167831 PMCID: PMC6686917 DOI: 10.1534/g3.119.400229] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°) and freezing (−4°) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.
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132
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Zheng J, Liu F, Zhu C, Li X, Dai X, Yang B, Zou X, Ma Y. Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses. PLoS One 2019; 14:e0219775. [PMID: 31329624 PMCID: PMC6645504 DOI: 10.1371/journal.pone.0219775] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/01/2019] [Indexed: 11/18/2022] Open
Abstract
WRKY proteins are a large group of plant transcription factors that are involved in various biological processes, including biotic and abiotic stress responses, hormone response, plant development, and metabolism. WRKY proteins have been identified in several plants, but only a few have been identified in Capsicum annuum. Here, we identified a total of 62 WRKY genes in the latest pepper genome. These genes were classified into three groups (Groups 1–3) based on the structural features of their proteins. The structures of the encoded proteins, evolution, and expression under normal growth conditions were analyzed and 35 putative miRNA target sites were predicted in 20 CaWRKY genes. Moreover, the response to cold or CMV treatments of selected WRKY genes were examined to validate the roles under stresses. And alternative splicing (AS) events of some CaWRKYs were also identified under CMV infection. Promoter analysis confirmed that CaWRKY genes are involved in growth, development, and biotic or abiotic stress responses in hot pepper. The comprehensive analysis provides fundamental information for better understanding of the signaling pathways involved in the WRKY-mediated regulation of developmental processes, as well as biotic and abiotic stress responses.
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Affiliation(s)
- Jingyuan Zheng
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Feng Liu
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chunhui Zhu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xuefeng Li
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiongze Dai
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Bozhi Yang
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xuexiao Zou
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yanqing Ma
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha, China
- * E-mail:
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Deng S, Ma J, Zhang L, Chen F, Sang Z, Jia Z, Ma L. De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress. BMC PLANT BIOLOGY 2019; 19:321. [PMID: 31319815 PMCID: PMC6637634 DOI: 10.1186/s12870-019-1933-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Magnolia wufengensis is a new species of Magnolia L. and has considerable ornamental and economic value due to its unique characteristics. However, because of its characteristic of poor low temperature resistance, M. wufengensis is hardly popularization and application in the north of China. Furthermore, the mechanisms of gene regulation and signaling pathways involved in the cold-stress response remained unclear in this species. In order to solve the above-mentioned problems, we performed de novo transcriptome assembly and compared the gene expression under the natural (25 °C) and cold (4 °C) conditions for M. wufengensis seedlings. RESULTS More than 46 million high-quality clean reads were produced from six samples (RNA was extracted from the leaves) and were used for performing de novo transcriptome assembly. A total of 59,764 non-redundant unigenes with an average length of 899 bp (N50 = 1,110) were generated. Among these unigenes, 31,038 unigenes exhibited significant sequence similarity to known genes, as determined by BLASTx searches (E-value ≤1.0E-05) against the Nr, SwissProt, String, GO, KEGG, and Cluster of COG databases. Based on a comparative transcriptome analysis, 3,910 unigenes were significantly differentially expressed (false discovery rate [FDR] < 0.05 and |log2FC (CT/CK)| ≥ 1) in the cold-treated samples, and 2,616 and 1,294 unigenes were up- and down-regulated by cold stress, respectively. Analysis of the expression patterns of 16 differentially expressed genes (DEGs) by quantitative real-time RT-PCR (qRT-PCR) confirmed the accuracy of the RNA-Seq results. Gene Ontology and KEGG pathway functional enrichment analyses allowed us to better understand these differentially expressed unigenes. The most significant transcriptomic changes observed under cold stress were related to plant hormone and signal transduction pathways, primary and secondary metabolism, and photosynthesis. In addition, 113 transcription factors, including members of the AP2-EREBP, bHLH, WRKY, MYB, NAC, HSF, and bZIP families, were identified as cold responsive. CONCLUSION We generated a genome-wide transcript profile of M. wufengensis and a de novo-assembled transcriptome that can be used to analyze genes involved in biological processes. In this study, we provide the first report of transcriptome sequencing of cold-stressed M. wufengensis. Our findings provide important clues not only for understanding the molecular mechanisms of cold stress in plants but also for introducing cold hardiness into M. wufengensis.
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Affiliation(s)
- Shixin Deng
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Lili Zhang
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Faju Chen
- Biotechnology Research Center, China Three Gorges University, Yichang, Hubei Province 443002 People’s Republic of China
| | - Ziyang Sang
- Forestry Bureau of Wufeng County, Wufeng, Hubei Province 443400 People’s Republic of China
| | - Zhongkui Jia
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Luyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, 100083 People’s Republic of China
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134
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Jasmonates: Mechanisms and functions in abiotic stress tolerance of plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101210] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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135
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Wang M, Dai W, Du J, Ming R, Dahro B, Liu J. ERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) contributes to cold tolerance by directly regulating expression of Prx1 involved in antioxidative process. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1316-1332. [PMID: 30575255 PMCID: PMC6576027 DOI: 10.1111/pbi.13056] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/13/2018] [Accepted: 12/02/2018] [Indexed: 05/09/2023]
Abstract
Ethylene-responsive factors (ERFs) have been revealed to play essential roles in a variety of physiological and biological processes in higher plants. However, functions and regulatory pathways of most ERFs in cold stress remain largely unclear. Here, we identified PtrERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) and deciphered its role in cold tolerance. PtrERF109 was drastically up-regulated by cold, ethylene and dehydration, but repressed by salt. PtrERF109 was localized in the nucleus and displayed transcriptional activity, and the C terminus is required for the activation. Overexpression of PtrERF109 conferred enhanced cold tolerance in transgenic tobacco and lemon plants, whereas VIGS (virus-induced gene silencing)-mediated suppression of PtrERF109 in trifoliate orange led to increased cold susceptibility. PtrERF109 overexpression caused extensive transcriptional reprogramming of several suites of stress-responsive genes. Prx1 encoding class III peroxidase (POD) was one of the antioxidant genes exhibiting the greatest induction. PtrERF109 was shown to directly bind to the promoter of PtrPrx1 (trifoliate orange Prx1 homologue) and positively activated its expression. In addition, the PtrERF109-overexpressing plants exhibited significantly higher POD activity and accumulated dramatically less H2 O2 and were more tolerant to oxidative stress, whereas the VIGS plants exhibited opposite trends, in comparison with wild type. Taken together, these results indicate that PtrERF109 as a positive regulator contributes to imparting cold tolerance by, at least partly, directly regulating the POD-encoding gene to maintain a robust antioxidant capacity for effectively scavenging the reactive oxygen species. Our findings gain insight into better understanding of transcriptional regulation of antioxidant genes in response to cold stress.
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Affiliation(s)
- Min Wang
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Wenshan Dai
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Juan Du
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ruhong Ming
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Bachar Dahro
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ji‐Hong Liu
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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Costa-Broseta Á, Perea-Resa C, Castillo MC, Ruíz MF, Salinas J, León J. Nitric oxide deficiency decreases C-repeat binding factor-dependent and -independent induction of cold acclimation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3283-3296. [PMID: 30869795 PMCID: PMC6598078 DOI: 10.1093/jxb/erz115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 05/28/2023]
Abstract
Plant tolerance to freezing temperatures is governed by endogenous components and environmental factors. Exposure to low non-freezing temperatures is a key factor in the induction of freezing tolerance in the process called cold acclimation. The role of nitric oxide (NO) in cold acclimation was explored in Arabidopsis using triple nia1nia2noa1-2 mutants that are impaired in the nitrate-dependent and nitrate-independent pathways of NO production, and are thus NO deficient. Here, we demonstrate that cold-induced NO accumulation is required to promote the full cold acclimation response through C-repeat Binding Factor (CBF)-dependent gene expression, as well as the CBF-independent expression of other cold-responsive genes such as Oxidation-Related Zinc Finger 2 (ZF/OZF2). NO deficiency also altered abscisic acid perception and signaling and the cold-induced production of anthocyanins, which are additional factors involved in cold acclimation.
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Affiliation(s)
- Álvaro Costa-Broseta
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia, Spain
| | - Carlos Perea-Resa
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Mari-Cruz Castillo
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia, Spain
| | - M Fernanda Ruíz
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Julio Salinas
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José León
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia, Spain
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Wang Y, Zhang J, Hu Z, Guo X, Tian S, Chen G. Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum. Int J Mol Sci 2019; 20:ijms20122961. [PMID: 31216621 PMCID: PMC6627509 DOI: 10.3390/ijms20122961] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 11/16/2022] Open
Abstract
MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.
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Affiliation(s)
- Yunshu Wang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Jianling Zhang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Zongli Hu
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Xuhu Guo
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Shibing Tian
- The Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China.
| | - Guoping Chen
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
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Pu Y, Liu L, Wu J, Zhao Y, Bai J, Ma L, Yue J, Jin J, Niu Z, Fang Y, Sun W. Transcriptome Profile Analysis of Winter Rapeseed ( Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress. Int J Mol Sci 2019; 20:ijms20112771. [PMID: 31195741 PMCID: PMC6600501 DOI: 10.3390/ijms20112771] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022] Open
Abstract
Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line "2016TS(G)10" (freezing-tolerance line) that was exposed to -2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.
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Affiliation(s)
- Yuanyuan Pu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Lijun Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Junyan Wu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yuhong Zhao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jing Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Li Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jinli Yue
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jiaojiao Jin
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Zaoxia Niu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Yan Fang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
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139
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Zhou B, Kang Y, Leng J, Xu Q. Genome-Wide Analysis of the miRNA-mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra. Genes (Basel) 2019; 10:genes10060430. [PMID: 31195761 PMCID: PMC6627750 DOI: 10.3390/genes10060430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/02/2022] Open
Abstract
Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance.
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Affiliation(s)
- Bo Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Yutong Kang
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Jingtong Leng
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Qijiang Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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140
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Song Q, Cheng S, Chen Z, Nie G, Xu F, Zhang J, Zhou M, Zhang W, Liao Y, Ye J. Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis. BMC PLANT BIOLOGY 2019; 19:199. [PMID: 31092208 PMCID: PMC6521437 DOI: 10.1186/s12870-019-1801-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/25/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA3) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA3 on F. hupehensis seed germination. RESULTS We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA3 (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA3 treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA3 contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA3 (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA3 signal transduction were also observed in the G group. GA3-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA3-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes. CONCLUSION Exogenous GA3 increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA3 on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.
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Affiliation(s)
- Qiling Song
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023 China
| | - Zexiong Chen
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160 China
| | - Gongping Nie
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
- Engineering Research Center of Ecology and Agricultural Use of Wetland (Ministry of Education), Yangtze University, Jingzhou, 434025 Hubei China
| | - Jian Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Mingqin Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 Hubei China
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141
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Kashyap P, Deswal R. Two ICE isoforms showing differential transcriptional regulation by cold and hormones participate in Brassica juncea cold stress signaling. Gene 2019; 695:32-41. [PMID: 30738965 DOI: 10.1016/j.gene.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/25/2018] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
C-repeat binding factor (CBF) dependent cold stress signaling cascade is well studied in the model plant arabidopsis but is relatively lesser studied in the crop plants. In the present study, two novel isoforms of an upstream regulator of CBF, Inducer of CBF expression (ICE), BjICE46 (1314 bp, accession number HQ446510) and BjICE53 (1494 bp, accession number HQ857208) were isolated from Brassica juncea seedlings. Genomic clones of both the isoforms (accession numbers HQ433510 and JX571043) showed three introns, out of which one intron was spanning the bHLH (basic helix-loop-helix) domain. Interestingly, the constitutive expression of BjICE53 was 21 fold higher than BjICE46. Real time quantitative expression (RT-qPCR) showed BjICE53 to be cold induced but non-responsive to phytohormones. Interestingly, BjICE46 was salinity stress induced and showed upregulation with methyl jasmonate (MeJa) and abscisic acid (ABA). This was supported by the presence of ABA, MeJa and defense related cis- acting regulatory elements in the promoter region of BjICE46. The downstream transcription factor BjCBF (645 bp) was also isolated. The promoter region of BjCBF showed three E-boxes, the binding site for ICE. BjCBF was expressed and purified from E. coli and binding of purified BjCBF with the DRE/CRT elements (present in the promoter of cold responsive genes) was EMSA confirmed. Overall, this study shows that ICE-CBF pathway is conserved in Brassica juncea along with the differential regulation of the ICE isoforms indicating cross-talk between cold and defense signaling.
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Affiliation(s)
- Prakriti Kashyap
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India.
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142
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Schubert M, Grønvold L, Sandve SR, Hvidsten TR, Fjellheim S. Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae. PLANT PHYSIOLOGY 2019; 180:404-419. [PMID: 30850470 PMCID: PMC6501083 DOI: 10.1104/pp.18.01448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/25/2019] [Indexed: 05/24/2023]
Abstract
The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.
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Affiliation(s)
- Marian Schubert
- Department of Plant Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Lars Grønvold
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Simen R Sandve
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, NO-1432 As, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umea, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
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143
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Abstract
Abnormal environmental temperature affects plant growth and threatens crop production. Understanding temperature signal sensing and the balance between defense and development in plants lays the foundation for improvement of temperature resilience. Here, we summarize the current understanding of cold signal perception/transduction as well as heat stress response. Dissection of plant responses to different levels of cold stresses (chilling and freezing) illustrates their common and distinct signaling pathways. Axillary bud differentiation in response to chilling is presented as an example of the trade-off between defense and development. Vernalization is a cold-dependent development adjustment mediated by O-GlcNAcylation and phosphorylation to sense long-term cold. Recent progress on major quantitative trait loci genes for heat tolerance has been summarized. Molecular mechanisms in utilizing temperature-sensitive sterility in super hybrid breeding in China are revealed. The way to improve crop temperature resilience using integrative knowledge of omics as well as systemic and synthetic biology, especially the molecular module program, is summarized.
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Affiliation(s)
- Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100093, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100093, China
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144
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MacGregor DR, Zhang N, Iwasaki M, Chen M, Dave A, Lopez‐Molina L, Penfield S. ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:277-290. [PMID: 30570804 PMCID: PMC6900779 DOI: 10.1111/tpj.14211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 12/12/2018] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a widespread and key adaptive trait that is essential for the establishment of soil seed banks and prevention of pre-harvest sprouting. Herein we demonstrate that the endosperm-expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1) play a role in determining the depth of primary dormancy in Arabidopsis. We show that ice1 or zou increases seed dormancy and the double mutant has an additive phenotype. This increased dormancy is associated with increased ABA levels, and can be separated genetically from any role in endosperm maturation because loss of ABA biosynthesis or DELAY OF GERMINATION 1 reverses the dormancy phenotype without affecting the aberrant seed morphology. Consistent with these results, ice1 endosperms had an increased capacity for preventing embryo greening, a phenotype previously associated with an increase in endospermic ABA levels. Although ice1 changes the expression of many genes, including some in ABA biosynthesis, catabolism and/or signalling, only ABA INSENSITIVE 3 is significantly misregulated in ice1 mutants. We also demonstrate that ICE1 binds to and inhibits expression of ABA INSENSITIVE 3. Our data demonstrate that Arabidopsis ICE1 and ZOU determine the depth of primary dormancy during maturation independently of their effect on endosperm development.
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Affiliation(s)
- Dana R. MacGregor
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address:
Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Naichao Zhang
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Mayumi Iwasaki
- Department of Plant Biology and Institute for Genetics and Genomics in Geneva (iGE3)University of Geneva30, Quai Ernest‐Ansermet CH‐1211Geneva4Switzerland
| | - Min Chen
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address:
College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Anuja Dave
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Luis Lopez‐Molina
- Department of Plant Biology and Institute for Genetics and Genomics in Geneva (iGE3)University of Geneva30, Quai Ernest‐Ansermet CH‐1211Geneva4Switzerland
| | - Steven Penfield
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
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Carther KFI, Ketehouli T, Ye N, Yang YH, Wang N, Dong YY, Yao N, Liu XM, Liu WC, Li XW, Wang FW, Li HY. Comprehensive Genomic Analysis and Expression Profiling of Diacylglycerol Kinase ( DGK) Gene Family in Soybean ( Glycine max) under Abiotic Stresses. Int J Mol Sci 2019; 20:E1361. [PMID: 30889878 PMCID: PMC6470530 DOI: 10.3390/ijms20061361] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
Diacylglycerol kinase (DGK) is an enzyme that plays a pivotal role in abiotic and biotic stress responses in plants by transforming the diacylglycerol into phosphatidic acid. However, there is no report on the characterization of soybean DGK genes in spite of the availability of the soybean genome sequence. In this study, we performed genome-wide analysis and expression profiling of the DGK gene family in the soybean genome. We identified 12 DGK genes (namely GmDGK1-12) which all contained conserved catalytic domains with protein lengths and molecular weights ranging from 436 to 727 amino acids (aa) and 48.62 to 80.93 kDa, respectively. Phylogenetic analyses grouped GmDGK genes into three clusters-cluster I, cluster II, and cluster III-which had three, four, and five genes, respectively. The qRT-PCR analysis revealed significant GmDGK gene expression levels in both leaves and roots coping with polyethylene glycol (PEG), salt, alkali, and salt/alkali treatments. This work provides the first characterization of the DGK gene family in soybean and suggests their importance in soybean response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of this gene family.
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Affiliation(s)
- Kue Foka Idrice Carther
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Toi Ketehouli
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Nan Ye
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Yan-Hai Yang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Nan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Yuan-Yuan Dong
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Na Yao
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Xiu-Ming Liu
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Wei-Can Liu
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Xiao-Wei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Fa-Wei Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Hai-Yan Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
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146
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Bokros N, Popescu SC, Popescu GV. Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions. BMC Bioinformatics 2019; 20:99. [PMID: 30871456 PMCID: PMC6419318 DOI: 10.1186/s12859-019-2624-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses of entire gene families are widely employed in the fields of evolutionary and functional genomics of both well established and newly sequenced plant genomes. Currently, plant gene families are typically identified using one of two major ways: 1) HMM-profile based searches using models built on Arabidopsis thaliana genes or 2) coding sequence homology searches using curated databases. Integrated databases containing functionally annotated genes and gene families have been developed for model organisms and several important crops; however, a comprehensive methodology for gene family annotation is currently lacking, preventing automated annotation of newly sequenced genomes. Results This paper proposes a combined measure of homology identification, motif conservation, phylogenomic and integrated gene expression analyses to define gene family structures in multiple plant species. The MAP3K gene families in seven plant species, including two currently unexamined species Gossypium hirsutum, and Zostera marina, were characterized to reveal new insights into their collective function and evolution and demonstrate the effectiveness of our novel methodology. Conclusion Compared with recent reports, this methodology performs significantly better for the identification and analysis of gene family members in several monocots/dicots, diploid as well as polyploid plant species. Electronic supplementary material The online version of this article (10.1186/s12859-019-2624-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Norbert Bokros
- Department of Biochemistry, Molecular Biology, Plant Pathology and Entomology, Mississippi State University, Mississippi State, MS, 39762, USA.,Institute for Genomics, Biocomputing and Bioengineering, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Plant Pathology and Entomology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing and Bioengineering, Mississippi State University, Mississippi State, MS, 39762, USA. .,The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
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147
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Choudhary S, Thakur S, Jaitak V, Bhardwaj P. Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum. Gene 2019; 690:1-10. [DOI: 10.1016/j.gene.2018.12.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/13/2018] [Indexed: 12/23/2022]
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148
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Chen R, Ma J, Luo D, Hou X, Ma F, Zhang Y, Meng Y, Zhang H, Guo W. CaMADS, a MADS-box transcription factor from pepper, plays an important role in the response to cold, salt, and osmotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:164-174. [PMID: 30823994 DOI: 10.1016/j.plantsci.2018.11.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/05/2018] [Accepted: 11/28/2018] [Indexed: 05/22/2023]
Abstract
MADS-box family transcription factors play essential roles in the growth and development of plants, and some MADS-box genes have also been found to participate in the stress-response. At present, little information regarding stress-related MADS-box genes is available in pepper. We isolated a MADS-box transcription factor gene from Capsicum annuum, which we named CaMADS. CaMADS expression is induced by low and high temperature, salt, and osmotic stress, and also by abscisic acid (ABA), salicylic acid (SA), methyl-jasmonic acid (MeJA), and CaCl2. To understand the function of CaMADS in the abiotic stress response, we generated pepper plants in which CaMADS expression was down-regulated using VIGS (Virus-induced Gene Silencing), and also transgenic Arabidopsis plants overexpressing CaMADS. We found that CaMADS-down-regulated seedlings were more seriously injured than WT after cold, NaCl, and mannitol treatment, and showed increased electrolyte leakage, malondialdehyde (MDA) levels, and lower chlorophyll content. CaMADS-overexpressing Arabidopsis plants were more tolerant to these stresses than WT, and showed significantly high survival rates and lower H2O2 and super oxide radical contents after cold treatment. CaMADS-overexpressing plants had higher germination rates and percentages of green cotyledons following NaCl and mannitol treatment. Root lengths and fresh weight in CaMADS-overexpressing plants were also significantly longer and higher, respectively, than in WT plants. Taken together, our results suggest that CaMADS functions as a positive stress-responsive transcription factor in the cold, salt, and osmotic stress signaling pathways.
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Affiliation(s)
- Rugang Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, China.
| | - Jihui Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dan Luo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaomeng Hou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fang Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yumeng Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuancheng Meng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huafeng Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weili Guo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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149
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Baier M, Bittner A, Prescher A, van Buer J. Preparing plants for improved cold tolerance by priming. PLANT, CELL & ENVIRONMENT 2019; 42:782-800. [PMID: 29974962 DOI: 10.1111/pce.13394] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 05/26/2023]
Abstract
Cold is a major stressor, which limits plant growth and development in many parts of the world, especially in the temperate climate zones. A large number of experimental studies has demonstrated that not only acclimation and entrainment but also the experience of single short stress events of various abiotic or biotic kinds (priming stress) can improve the tolerance of plants to chilling temperatures. This process, called priming, depends on a stress "memory". It does not change cold sensitivity per se but beneficially modifies the response to cold and can last for days, months, or even longer. Elicitor factors and antagonists accumulate due to increased biosynthesis or decreased degradation either during or after the priming stimulus. Comparison of priming studies investigating improved tolerance to chilling temperatures highlighted key regulatory functions of ROS/RNS and antioxidant enzymes, plant hormones, especially jasmonates, salicylates, and abscisic acid, and signalling metabolites, such as β- and γ-aminobutyric acid (BABA and GABA) and melatonin. We conclude that these elicitors and antagonists modify local and systemic cold tolerance by integration into cold-induced signalling cascades.
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Affiliation(s)
- Margarete Baier
- Plant Physiology, Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Andras Bittner
- Plant Physiology, Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Andreas Prescher
- Plant Physiology, Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Jörn van Buer
- Plant Physiology, Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
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van Buer J, Prescher A, Baier M. Cold-priming of chloroplast ROS signalling is developmentally regulated and is locally controlled at the thylakoid membrane. Sci Rep 2019; 9:3022. [PMID: 30816299 PMCID: PMC6395587 DOI: 10.1038/s41598-019-39838-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/29/2019] [Indexed: 12/31/2022] Open
Abstract
24 h exposure to 4 °C primes Arabidopsis thaliana in the pre-bolting rosette stage for several days against full cold activation of the ROS responsive genes ZAT10 and BAP1 and causes stronger cold-induction of pleiotropically stress-regulated genes. Transient over-expression of thylakoid ascorbate peroxidase (tAPX) at 20 °C mimicked and tAPX transcript silencing antagonized cold-priming of ZAT10 expression. The tAPX effect could not be replaced by over-expression of stromal ascorbate peroxidase (sAPX) demonstrating that priming is specific to regulation of tAPX availability and, consequently, regulated locally at the thylakoid membrane. Arabidopsis acquired cold primability in the early rosette stage between 2 and 4 weeks. During further rosette development, primability was widely maintained in the oldest leaves. Later formed and later maturing leaves were not primable demonstrating that priming is stronger regulated with plant age than with leaf age. In 4-week-old plants, which were strongest primable, the memory was fully erasable and lost seven days after priming. In summary, we conclude that cold-priming of chloroplast-to-nucleus ROS signalling by transient post-stress induction of tAPX transcription is a strategy to modify cell signalling for some time without affecting the alertness for activation of cold acclimation responses.
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Affiliation(s)
- Jörn van Buer
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Andreas Prescher
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Margarete Baier
- Plant Physiology, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.
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