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Li S, Zhao Y, Wu P, Grierson D, Gao L. Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39016673 DOI: 10.1111/jipb.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high-quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis-related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening-related and defense-related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non-climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high-quality fruit and decrease food waste and related economic losses.
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Affiliation(s)
- Shan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yu Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Lei Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Yan Z, Hou J, Leng B, Yao G, Ma C, Sun Y, Zhang F, Mu C, Liu X. Genome-Wide Investigation of the CRF Gene Family in Maize and Functional Analysis of ZmCRF9 in Response to Multiple Abiotic Stresses. Int J Mol Sci 2024; 25:7650. [PMID: 39062894 PMCID: PMC11276700 DOI: 10.3390/ijms25147650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The cytokinin response factors (CRFs) are pivotal players in regulating plant growth, development, and responses to diverse stresses. Despite their significance, comprehensive information on CRF genes in the primary food crop, maize, remains scarce. In this study, a genome-wide analysis of CRF genes in maize was conducted, resulting in the identification of 12 members. Subsequently, we assessed the chromosomal locations, gene duplication events, evolutionary relationships, conserved motifs, and gene structures of all ZmCRF members. Analysis of ZmCRF promoter regions indicated the presence of cis-regulatory elements associated with plant growth regulation, hormone response, and various abiotic stress responses. The expression patterns of maize CRF genes, presented in heatmaps, exhibited distinctive patterns of tissue specificity and responsiveness to multiple abiotic stresses. qRT-PCR experiments were conducted on six selected genes and confirmed the involvement of ZmCRF genes in the plant's adaptive responses to diverse environmental challenges. In addition, ZmCRF9 was demonstrated to positively regulate cold and salt tolerance. Ultimately, we explored the putative interaction partners of ZmCRF proteins. In summary, this systematic overview and deep investigation of ZmCRF9 provides a solid foundation for further exploration into how these genes contribute to the complex interplay of plant growth, development, and responses to stress.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Jing Hou
- School of Agriculture, Ludong University, Yantai 264001, China;
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250300, China;
| | - Yue Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
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Gentile D, Serino G, Frugis G. CRF transcription factors in the trade-off between abiotic stress response and plant developmental processes. Front Genet 2024; 15:1377204. [PMID: 38694876 PMCID: PMC11062136 DOI: 10.3389/fgene.2024.1377204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/04/2024] [Indexed: 05/04/2024] Open
Abstract
Climate change-induced environmental stress significantly affects crop yield and quality. In response to environmental stressors, plants use defence mechanisms and growth suppression, creating a resource trade-off between the stress response and development. Although stress-responsive genes have been widely engineered to enhance crop stress tolerance, there is still limited understanding of the interplay between stress signalling and plant growth, a research topic that can provide promising targets for crop genetic improvement. This review focuses on Cytokinin Response Factors (CRFs) transcription factor's role in the balance between abiotic stress adaptation and sustained growth. CRFs, known for their involvement in cytokinin signalling and abiotic stress responses, emerge as potential targets for delaying senescence and mitigating yield penalties under abiotic stress conditions. Understanding the molecular mechanisms regulated by CRFs paves the way for decoupling stress responses from growth inhibition, thus allowing the development of crops that can adapt to abiotic stress without compromising development. This review highlights the importance of unravelling CRF-mediated pathways to address the growing need for resilient crops in the face of evolving climatic conditions.
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Affiliation(s)
- Davide Gentile
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Rome, Italy
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Rome, Italy
| | - Giovanna Serino
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Rome, Italy
| | - Giovanna Frugis
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Rome, Italy
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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Liao C, Shen H, Gao Z, Wang Y, Zhu Z, Xie Q, Wu T, Chen G, Hu Z. Overexpression of SlCRF6 in tomato inhibits leaf development and affects plant morphology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111921. [PMID: 37949361 DOI: 10.1016/j.plantsci.2023.111921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/10/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Cytokinin response factors (CRFs) are transcription factors (TFs) that are specific to plants and have diverse functions in plant growth and stress responses. However, the precise roles of CRFs in regulating tomato plant architecture and leaf development have not been comprehensively investigated. Here, we identified a novel CRF, SlCRF6, which is involved in the regulation of plant growth via the gibberellin (GA) signaling pathway. SlCRF6-overexpressing (SlCRF6-OE) plants displayed pleiotropic phenotypic changes, including reduced internode length and leaf size, which caused dwarfism in tomato plants. This dwarfism could be alleviated by application of exogenous GA3. Remarkably, quantitative real-time PCR (qRTPCR), a dual luciferase reporter assay and a yeast one-hybrid (Y1H) assay revealed that SlCRF6 promoted the expression of SlDELLA (a GA signal transduction inhibitor) in vivo. Furthermore, transgenic plants displayed variegated leaves and diminished chlorophyll content, resulting in decreased photosynthetic efficiency and less starch than in wild-type (WT) plants. The results of transient expression assays and Y1H assays indicated that SlCRF6 suppressed the expression of SlPHAN (leaf morphology-related gene). Collectively, these findings suggest that SlCRF6 plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.
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Affiliation(s)
- Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Hui Shen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Zihan Gao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Yunshu Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Zhiguo Zhu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China; College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang 332000, Jiangxi, PR China.
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Ting Wu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, PR China.
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Zhou Y, Zheng R, Peng Y, Chen J, Zhu X, Xie K, Su Q, Huang R, Zhan S, Peng D, Zhao K, Liu ZJ. Bioinformatic Assessment and Expression Profiles of the AP2/ERF Superfamily in the Melastoma dodecandrum Genome. Int J Mol Sci 2023; 24:16362. [PMID: 38003550 PMCID: PMC10671166 DOI: 10.3390/ijms242216362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
AP2/ERF transcription factors play crucial roles in various biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, limited research has been conducted on the AP2/ERF genes of Melastoma dodecandrum for breeding of this potential fruit crop. Leveraging the recently published whole genome sequence, we conducted a comprehensive assessment of this superfamily and explored the expression patterns of AP2/ERF genes at a genome-wide level. A significant number of genes, totaling 218, were discovered to possess the AP2 domain sequence and displayed notable structural variations among five subfamilies. An uneven distribution of these genes was observed on 12 pseudochromosomes as the result of gene expansion facilitated by segmental duplications. Analysis of cis-acting elements within promoter sites and 87.6% miRNA splicing genes predicted their involvement in multiple hormone responses and abiotic stresses through transcriptional and post-transcriptional regulations. Transcriptome analysis combined with qRT-PCR results indicated that certain candidate genes are involved in tissue formation and the response to developmental changes induced by IAA hormones. Overall, our study provides valuable insights into the evolution of ERF genes in angiosperms and lays a solid foundation for future breeding investigations aimed at improving fruit quality and enhancing adaptation to barren land environments.
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Affiliation(s)
- Yuzhen Zhou
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Ruiyue Zheng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Yukun Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Jiemin Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Xuanyi Zhu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Kai Xie
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Qiuli Su
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Ruiliu Huang
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Suying Zhan
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Donghui Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Zhong-Jian Liu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (R.Z.); (Y.P.); (J.C.); (X.Z.); (K.X.); (Q.S.); (R.H.); (S.Z.); (D.P.)
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Li L, Zheng Q, Jiang W, Xiao N, Zeng F, Chen G, Mak M, Chen ZH, Deng F. Molecular Regulation and Evolution of Cytokinin Signaling in Plant Abiotic Stresses. PLANT & CELL PHYSIOLOGY 2023; 63:1787-1805. [PMID: 35639886 DOI: 10.1093/pcp/pcac071] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/04/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of crops faces increasing challenges from global climate change and human activities, which leads to increasing instances of many abiotic stressors to plants. Among the abiotic stressors, drought, salinity and excessive levels of toxic metals cause reductions in global agricultural productivity and serious health risks for humans. Cytokinins (CKs) are key phytohormones functioning in both normal development and stress responses in plants. Here, we summarize the molecular mechanisms on the biosynthesis, metabolism, transport and signaling transduction pathways of CKs. CKs act as negative regulators of both root system architecture plasticity and root sodium exclusion in response to salt stress. The functions of CKs in mineral-toxicity tolerance and their detoxification in plants are reviewed. Comparative genomic analyses were performed to trace the origin, evolution and diversification of the critical regulatory networks linking CK signaling and abiotic stress. We found that the production of CKs and their derivatives, pathways of signal transduction and drought-response root growth regulation are evolutionarily conserved in land plants. In addition, the mechanisms of CK-mediated sodium exclusion under salt stress are suggested for further investigations. In summary, we propose that the manipulation of CK levels and their signaling pathways is important for plant abiotic stress and is, therefore, a potential strategy for meeting the increasing demand for global food production under changing climatic conditions.
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Affiliation(s)
- Lijun Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Qingfeng Zheng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Nayun Xiao
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Michelle Mak
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
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Král D, Šenkyřík JB, Ondřej V. Expression of Genes Involved in ABA and Auxin Metabolism and LEA Gene during Embryogenesis in Hemp. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212995. [PMID: 36365448 PMCID: PMC9657790 DOI: 10.3390/plants11212995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 05/14/2023]
Abstract
The level of phytohormones such as abscisic acid (ABA) and auxins (Aux) changes dynamically during embryogenesis. Knowledge of the transcriptional activity of the genes of their metabolic pathways is essential for a deeper understanding of embryogenesis itself; however, it could also help breeding programs of important plants, such as Cannabis sativa, attractive for the pharmaceutical, textile, cosmetic, and food industries. This work aimed to find out how genes of metabolic pathways of Aux (IAA-1, IAA-2, X15-1, X15-2) and ABA (PP2C-1) alongside one member of the LEA gene family (CanLea34) are expressed in embryos depending on the developmental stage and the embryo cultivation in vitro. Walking stick (WS) and mature (M) cultivated and uncultivated embryos of C. sativa cultivars 'KC Dora' and 'USO 31' were analyzed. The RT-qPCR results indicated that for the development of immature (VH) embryos, the genes (IAA-1, IAA-2) are likely to be fundamental. Only an increased expression of the CanLea34 gene was characteristic of the fully maturated (M) embryos. In addition, this feature was significantly increased by cultivation. In conclusion, the cultivation led to the upsurge of expression of all studied genes.
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Li S, Wu P, Yu X, Cao J, Chen X, Gao L, Chen K, Grierson D. Contrasting Roles of Ethylene Response Factors in Pathogen Response and Ripening in Fleshy Fruit. Cells 2022; 11:cells11162484. [PMID: 36010560 PMCID: PMC9406635 DOI: 10.3390/cells11162484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Fleshy fruits are generally hard and unpalatable when unripe; however, as they mature, their quality is transformed by the complex and dynamic genetic and biochemical process of ripening, which affects all cell compartments. Ripening fruits are enriched with nutrients such as acids, sugars, vitamins, attractive volatiles and pigments and develop a pleasant taste and texture and become attractive to eat. Ripening also increases sensitivity to pathogens, and this presents a crucial problem for fruit postharvest transport and storage: how to enhance pathogen resistance while maintaining ripening quality. Fruit development and ripening involve many changes in gene expression regulated by transcription factors (TFs), some of which respond to hormones such as auxin, abscisic acid (ABA) and ethylene. Ethylene response factor (ERF) TFs regulate both fruit ripening and resistance to pathogen stresses. Different ERFs regulate fruit ripening and/or pathogen responses in both fleshy climacteric and non-climacteric fruits and function cooperatively or independently of other TFs. In this review, we summarize the current status of studies on ERFs that regulate fruit ripening and responses to infection by several fungal pathogens, including a systematic ERF transcriptome analysis of fungal grey mould infection of tomato caused by Botrytis cinerea. This deepening understanding of the function of ERFs in fruit ripening and pathogen responses may identify novel approaches for engineering transcriptional regulation to improve fruit quality and pathogen resistance.
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Affiliation(s)
- Shan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: (S.L.); (D.G.)
| | - Pan Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofen Yu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jinping Cao
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
| | - Xia Chen
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Zijinggang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Correspondence: (S.L.); (D.G.)
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10
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Mandal S, Ghorai M, Anand U, Samanta D, Kant N, Mishra T, Rahman MH, Jha NK, Jha SK, Lal MK, Tiwari RK, Kumar M, Radha, Prasanth DA, Mane AB, Gopalakrishnan AV, Biswas P, Proćków J, Dey A. Cytokinin and abiotic stress tolerance -What has been accomplished and the way forward? Front Genet 2022; 13:943025. [PMID: 36017502 PMCID: PMC9395584 DOI: 10.3389/fgene.2022.943025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/27/2022] Open
Abstract
More than a half-century has passed since it was discovered that phytohormone cytokinin (CK) is essential to drive cytokinesis and proliferation in plant tissue culture. Thereafter, cytokinin has emerged as the primary regulator of the plant cell cycle and numerous developmental processes. Lately, a growing body of evidence suggests that cytokinin has a role in mitigating both abiotic and biotic stress. Cytokinin is essential to defend plants against excessive light exposure and a unique kind of abiotic stress generated by an altered photoperiod. Secondly, cytokinin also exhibits multi-stress resilience under changing environments. Furthermore, cytokinin homeostasis is also affected by several forms of stress. Therefore, the diverse roles of cytokinin in reaction to stress, as well as its interactions with other hormones, are discussed in detail. When it comes to agriculture, understanding the functioning processes of cytokinins under changing environmental conditions can assist in utilizing the phytohormone, to increase productivity. Through this review, we briefly describe the biological role of cytokinin in enhancing the performance of plants growth under abiotic challenges as well as the probable mechanisms underpinning cytokinin-induced stress tolerance. In addition, the article lays forth a strategy for using biotechnological tools to modify genes in the cytokinin pathway to engineer abiotic stress tolerance in plants. The information presented here will assist in better understanding the function of cytokinin in plants and their effective investigation in the cropping system.
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Affiliation(s)
- Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Uttpal Anand
- CytoGene Research & Development LLP, Barabanki, Uttar Pradesh, India
| | - Dipu Samanta
- Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, West Bengal, India
| | - Nishi Kant
- School of Health and Allied Science, ARKA Jain University, Jamshedpur, Jharkhand, India
| | - Tulika Mishra
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, South Korea
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Milan Kumar Lal
- Division of Crop Physiology, Biochemistry and Post Harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rahul Kumar Tiwari
- Division of Crop Physiology, Biochemistry and Post Harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | | | - Abhijit Bhagwan Mane
- Department of Zoology, Dr. Patangrao Kadam Mahavidhyalaya (affiliated to Shivaji University Kolhapur), Ramanandnagar (Burli), Sangli, Maharashtra, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Protha Biswas
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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11
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Insight into Membrane Stability and Physiological Responses of Selected Salt-Tolerant and Salt-Sensitive Cell Lines of Troyer Citrange (Citrus sinensis [L.] x Citrus trifoliata [L.] Raf.) under Salt Stress. SUSTAINABILITY 2022. [DOI: 10.3390/su14159583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of this study was to evaluate the membrane integrity and some physiological responses of rootstock citrus calli under exposure to different concentrations of NaCl. Selected salt-tolerant cell lines were compared with salt-sensitive calli of Troyer’s citrange (Citrus sinensis [L.] x Citrus trifoliata [L.] Raf.) (TC) with respect to growth, water content, Na+, K+ and Cl− ion content as well as cell membrane stability under exposure to different NaCl concentrations. The results show that the stressed sensitive lines have a consistently high ion efflux. The values recorded for these sensitive calli are 3 to 6 times higher than those of the tolerant calli. Thus, only selected halotolerant calli were able to maintain the integrity of their membranes under salt stress conditions. In the sensitive calli, NaCl always induces a slowing down of growth even from 4 g L−1, and the reduction in the relative growth rate is higher than 50% and reaches more than 90% for the three culture durations at 8 g L−1 NaCl. For the salt-tolerant selected lines, the relative growth rate seems to be slightly slowed down until the second month of culture but becomes equal to that of the control at the third month, whether at 4 or 8 g L−1 NaCl. At the end of the third month, the relative growth rate of the selected calli is 100% at 8 g L−1 NaCl. The water content is twice as high in the selected tolerant calli as in the sensitive ones after three months of salt treatment at 8 g L−1 NaCl. After long-term culture, the halotolerant calli absorbed similar or even higher amounts of Na+ and Cl− than the salt-sensitive lines. However, by the 3rd month, the recorded accumulation rate dropped in the unselected but continued to increase in the tolerant calli (4-fold higher at 12 g L−1 NaCl than the control). Furthermore, exposure of both types of calli (salt-sensitive and salt-tolerant) to equal concentrations of NaCl resulted in greater loss of K+ by the NaCl-sensitive lines. However, for tolerant lines, K+ uptake is not affected at 4 g L−1 NaCl and the decrease in tissue content is less than 25% at 8 g L−1 NaCl. From this observation, it can be concluded that growth and the ability to retain high levels of internal K+ are correlated.
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12
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Keshishian EA, Cliver BR, McLaughlin WF, Hallmark HT, Plačková L, Goertzen LR, Novák O, Cobine PA, Leisner CP, Rashotte AM. CYTOKININ RESPONSE FACTOR 2 is involved in modulating the salt stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1097-1110. [PMID: 35262971 DOI: 10.1111/tpj.15726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Cytokinin has strong connections to development and a growing role in the abiotic stress response. Here we show that CYTOKININ RESPONSE FACTOR 2 (CRF2) is additionally involved in the salt (NaCl) stress response. CRF2 promoter-GUS expression indicates CRF2 involvement in the response to salt stress as well as the previously known cytokinin response. Interestingly, CRF2 mutant seedlings are quite similar to the wild type (WT) under non-stressed conditions yet have many distinct changes in response to salt stress. Cytokinin levels measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) that increased in the WT after salt stress are decreased in crf2, potentially from CRF2 regulation of cytokinin biosynthesis genes. Ion content measured by inductively coupled plasma optical emission spectrometry (ICP-OES) was increased in the WT for Na, K, Mn, Ca and Mg after salt stress, whereas the corresponding Ca and Mg increases are lacking in crf2. Many genes examined by RNA-seq analysis were altered transcriptionally by salt stress in both the WT and crf2, yet interestingly approximately one-third of salt-modified crf2 transcripts (2655) showed unique regulation. Different transcript profiles for salt stress in crf2 compared with the WT background was further supported through an examination of co-expressed genes by weighted gene correlation network analysis (WGCMA) and principal component analysis (PCA). Additionally, Gene Ontology (GO) enrichment terms found from salt-treated transcripts revealed most photosynthesis-related terms as only being affected in crf2, leading to an examination of chlorophyll levels and the efficiency of photosystem II (via the ratio of variable fluorescence to maximum fluorescence, Fv /Fm ) as well as physiology after salt treatment. Salt stress-treated crf2 plants had both reduced chlorophyll levels and lower Fv /Fm values compared with the WT, suggesting that CRF2 plays a role in the modulation of salt stress responses linked to photosynthesis.
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Affiliation(s)
- Erika A Keshishian
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Brannan R Cliver
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - H Tucker Hallmark
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lenka Plačková
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, CZ-783 71, Olomouc, Czech Republic
| | - Leslie R Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, CZ-783 71, Olomouc, Czech Republic
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Aaron M Rashotte
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
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13
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Skalak J, Nicolas KL, Vankova R, Hejatko J. Signal Integration in Plant Abiotic Stress Responses via Multistep Phosphorelay Signaling. FRONTIERS IN PLANT SCIENCE 2021; 12:644823. [PMID: 33679861 PMCID: PMC7925916 DOI: 10.3389/fpls.2021.644823] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/26/2021] [Indexed: 05/02/2023]
Abstract
Plants growing in any particular geographical location are exposed to variable and diverse environmental conditions throughout their lifespan. The multifactorial environmental pressure resulted into evolution of plant adaptation and survival strategies requiring ability to integrate multiple signals that combine to yield specific responses. These adaptive responses enable plants to maintain their growth and development while acquiring tolerance to a variety of environmental conditions. An essential signaling cascade that incorporates a wide range of exogenous as well as endogenous stimuli is multistep phosphorelay (MSP). MSP mediates the signaling of essential plant hormones that balance growth, development, and environmental adaptation. Nevertheless, the mechanisms by which specific signals are recognized by a commonly-occurring pathway are not yet clearly understood. Here we summarize our knowledge on the latest model of multistep phosphorelay signaling in plants and the molecular mechanisms underlying the integration of multiple inputs including both hormonal (cytokinins, ethylene and abscisic acid) and environmental (light and temperature) signals into a common pathway. We provide an overview of abiotic stress responses mediated via MSP signaling that are both hormone-dependent and independent. We highlight the mutual interactions of key players such as sensor kinases of various substrate specificities including their downstream targets. These constitute a tightly interconnected signaling network, enabling timely adaptation by the plant to an ever-changing environment. Finally, we propose possible future directions in stress-oriented research on MSP signaling and highlight its potential importance for targeted crop breeding.
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Affiliation(s)
- Jan Skalak
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Katrina Leslie Nicolas
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
- *Correspondence: Jan Hejatko,
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14
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Li P, Chai Z, Lin P, Huang C, Huang G, Xu L, Deng Z, Zhang M, Zhang Y, Zhao X. Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.). BMC Genomics 2020; 21:685. [PMID: 33008299 PMCID: PMC7531145 DOI: 10.1186/s12864-020-07076-x] [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: 03/26/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide. RESULTS A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum. CONCLUSIONS In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.
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Affiliation(s)
- Peiting Li
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhe Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Pingping Lin
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaohua Huang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guoqiang Huang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangnian Xu
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinwang Zhao
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530005, China. .,Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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15
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Research Progress on the Roles of Cytokinin in Plant Response to Stress. Int J Mol Sci 2020; 21:ijms21186574. [PMID: 32911801 PMCID: PMC7555750 DOI: 10.3390/ijms21186574] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/05/2023] Open
Abstract
Cytokinins promote plant growth and development under normal plant growth conditions and also play an important role in plant resistance to stress. Understanding the working mechanisms of cytokinins under adverse conditions will help to make full use of cytokinins in agriculture to increase production and efficiency of land use. In this article, we review the progress that has been made in cytokinin research in plant response to stress and propose its future application prospects.
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16
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Aremu AO, Fawole OA, Makunga NP, Masondo NA, Moyo M, Buthelezi NMD, Amoo SO, Spíchal L, Doležal K. Applications of Cytokinins in Horticultural Fruit Crops: Trends and Future Prospects. Biomolecules 2020; 10:biom10091222. [PMID: 32842660 PMCID: PMC7563339 DOI: 10.3390/biom10091222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Cytokinins (CKs) are a chemically diverse class of plant growth regulators, exhibiting wide-ranging actions on plant growth and development, hence their exploitation in agriculture for crop improvement and management. Their coordinated regulatory effects and cross-talk interactions with other phytohormones and signaling networks are highly sophisticated, eliciting and controlling varied biological processes at the cellular to organismal levels. In this review, we briefly introduce the mode of action and general molecular biological effects of naturally occurring CKs before highlighting the great variability in the response of fruit crops to CK-based innovations. We present a comprehensive compilation of research linked to the application of CKs in non-model crop species in different phases of fruit production and management. By doing so, it is clear that the effects of CKs on fruit set, development, maturation, and ripening are not necessarily generic, even for cultivars within the same species, illustrating the magnitude of yet unknown intricate biochemical and genetic mechanisms regulating these processes in different fruit crops. Current approaches using genomic-to-metabolomic analysis are providing new insights into the in planta mechanisms of CKs, pinpointing the underlying CK-derived actions that may serve as potential targets for improving crop-specific traits and the development of new solutions for the preharvest and postharvest management of fruit crops. Where information is available, CK molecular biology is discussed in the context of its present and future implications in the applications of CKs to fruits of horticultural significance.
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Affiliation(s)
- Adeyemi O. Aremu
- Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Olaniyi A. Fawole
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Nokwanda P. Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Nqobile A. Masondo
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Mack Moyo
- Department of Horticulture, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa;
| | - Nana M. D. Buthelezi
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
| | - Stephen O. Amoo
- Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa;
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
- Agricultural Research Council, Roodeplaat Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (L.S.); (K.D.)
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (L.S.); (K.D.)
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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17
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Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. 3 Biotech 2020; 10:139. [PMID: 32158635 DOI: 10.1007/s13205-020-2120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
APETALA2/Ethylene-Responsive transcription factors (AP2/ERF), with their multifunctional roles in plant development, hormone signaling and stress tolerance, are important candidates for engineering crop plants. Here, we report identification and analysis of gene structure, phylogenetic distribution, expression, chromosomal localization and cis-acting promoter analysis of AP2/ERF genes in the C4 crop plant sorghum. We identified 158 ERF genes in sorghum with 52 of them encoding dehydration-responsive binding elements (DREB) while 106 code for ERF subfamily proteins. Phylogenetic analysis organized sorghum ERF proteins into 11 distinct groups exhibiting clade-specific expansion. About 68% ERF genes have paralogs indicating gene duplications as major cause of expansion of ERF family in sorghum. Analysis of spatiotemporal expression patterns using publicly available data revealed their tissue/genotype-preferential accumulation. In addition, 40 ERF genes exhibited differential accumulation in response to heat and/or drought stress. About 25% of the segmental gene pairs and eleven tandem duplicated genes exhibited high correlation (> 0.7) in their expression patterns indicating genetic redundancy. Comparative phylogenomic analysis of sorghum ERFs with 74 genetically characterized ERF genes from other plant species provided significant clues to sorghum ERF functions. Overall data generated here provides an overview of evolutionary relationship among ERF gene family members in sorghum and with respect to previously characterized ERF genes from other plant species. This information will be instrumental in initiating functional genomic studies of ERF candidates in sorghum.
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18
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Hallmark HT, Rashotte AM. Review - Cytokinin Response Factors: Responding to more than cytokinin. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110251. [PMID: 31623789 DOI: 10.1016/j.plantsci.2019.110251] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 05/12/2023]
Abstract
Cytokinin Response Factors (CRFs) are a family of transcription factors which make up a side branch of the classical cytokinin two-component signaling pathway. CRFs were originally identified and have been primarily studied in Arabidopsis thaliana, although orthologs have be found throughout all land plants. Research into the evolution of CRFs as sub-group members of the larger APETALA2/Ethylene Response Factor (AP2/ERF) family has yielded interesting and useful insights related to the functional roles of CRFs in plants. Recent studies of CRFs suggest that these transcription factors are a lot more than just a group of cytokinin related genes and play important roles in both plant development and environmental stress response. This review focuses on recent advances in understanding the roles of CRFs beyond cytokinin, in reproductive development and abiotic stress response, as well as to other environmental cues.
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Affiliation(s)
- H Tucker Hallmark
- 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University, USA
| | - Aaron M Rashotte
- 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University, USA.
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19
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Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors. Sci Rep 2019; 9:13387. [PMID: 31527685 PMCID: PMC6746799 DOI: 10.1038/s41598-019-49741-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/31/2019] [Indexed: 01/17/2023] Open
Abstract
Expression patterns of genes are controlled by short regions of DNA in promoter regions known as cis-regulatory elements. How expression patterns change due to alterations in cis-regulatory elements in the context of gene duplication are not well studied in plants. Over 300 promoter sequences from a small, well-conserved family of plant transcription factors known as Cytokinin Response Factors (CRFs) were examined for conserved motifs across several known clades present in Angiosperms. General CRF and lineage specific motifs were identified. Once identified, significantly enriched motifs were then compared to known transcription factor binding sites to elucidate potential functional roles. Additionally, presence of similar motifs shows that levels of conservation exist between different CRFs across land plants, likely occurring through processes of neo- or sub-functionalization. Furthermore, significant patterns of motif conservation are seen within and between CRF clades suggesting cis-regulatory regions have been conserved throughout CRF evolution.
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Jin X, Yin X, Ndayambaza B, Zhang Z, Min X, Lin X, Wang Y, Liu W. Genome-Wide Identification and Expression Profiling of the ERF Gene Family in Medicago sativa L. Under Various Abiotic Stresses. DNA Cell Biol 2019; 38:1056-1068. [PMID: 31403329 DOI: 10.1089/dna.2019.4881] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factor represents one of the largest plant-specific transcriptional regulators in plants. ERF plays important roles in the regulation of various developmental processes and acts as a mediator in plant external stress responses. However, the research of the ERF gene family is still limited in alfalfa (Medicago sativa L.), one of the most important forage legume species in the world. In the present study, a total of 159 ERF genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, signal peptide prediction, and expression patterns under salt, drought, and low-temperature stresses of these ERF genes were comprehensively analyzed. The ERF genes family in alfalfa could be classified into 10 groups and predicted to be strongly homologous. Based on the structure and functions relationships, the III and IV subfamilies were more likely to play functions in abiotic stresses and 18 MsERF genes were selected for further quantitative real-time PCR validation in different stresses treatment. The results showed that all these MsERF genes were upregulated under three stresses except MsERF008. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole-genome level, which would provide primary understanding for exploring ERF-mediated tolerance in alfalfa.
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Affiliation(s)
- Xiaoyu Jin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xiaofan Yin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Boniface Ndayambaza
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xueyang Min
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xiaoshan Lin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
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Wang L, Ma H, Lin J. Angiosperm-Wide and Family-Level Analyses of AP2/ ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2019; 10:196. [PMID: 30863419 PMCID: PMC6399210 DOI: 10.3389/fpls.2019.00196] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.
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Affiliation(s)
- Linbo Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Juan Lin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
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22
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Kong L, Zhao K, Gao Y, Miao L, Chen C, Deng H, Liu Z, Yu X. Comparative analysis of cytokinin response factors in Brassica diploids and amphidiploids and insights into the evolution of Brassica species. BMC Genomics 2018; 19:728. [PMID: 30285607 PMCID: PMC6171139 DOI: 10.1186/s12864-018-5114-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/25/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including cytokinin response factors (CRFs). Although CRFs take vital part in the growth of Arabidopsis thaliana and Solanum lycopersicum, little information of the CRFs in the Brassica U-triangle species has been known yet. Results We identified and compared 141 CRFs in the diploids and amphidiploids of Brassica species, including B. rapa, B. oleracea, B. nigra, B. napus, and B. juncea. For all the 141 CRFs, the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the Ka/Ks ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the CRFs. The expression profiles of CRFs in different tissues and under various stresses were analyzed in B. oleracea, B. nigra, and B. napus. The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition, AtCRF11 and its ortholog BrCRF11a were identified to be related to primary root growth in Arabidopsis. Conclusion This study performed a genome-wide comparative analysis of the CRFs in the diploids and amphidiploids of the Brassica U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the CRF homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the CRF homologous genes in the Brassica A and C genomes and the distinctiveness of those in the B genome, and the CRF homologous genes in B subgenome were considerably influenced by the A subgenome of B. juncea. In addition, we identified a new function of the Clade V CRFs related to root growth, which also clarified the functional conservation between Arabidopsis and B. rapa. These results not only offer useful information on the functional analysis of CRFs but also provide new insights into the evolution of Brassica species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5114-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Kun Zhao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Yingying Gao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Liming Miao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Chaoquan Chen
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Hang Deng
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Zhenning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, Shandong, China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China.
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit. Genes (Basel) 2018; 9:genes9050266. [PMID: 29883429 PMCID: PMC5977206 DOI: 10.3390/genes9050266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71.60–72.80%) and CHH was found least frequently (10.70–12.50%). The level of DNA methylation was different among different tomato genomic regions. The differentially methylated regions (DMRs) and the differentially expressed genes (DEGs) were conjointly analyzed and 3030 different expressed genes were found, of which several are involved in ethylene synthesis and signaling transduction (such as ACS, ACO, MADS-Box, ERFs, and F-box). Furthermore, the relationships between DNA methylation and microRNAs (miRNAs) were also deciphered, providing basic information for the further study of DNA methylation and small RNAs involved in the ethylene pathway.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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Qin L, Wang L, Guo Y, Li Y, Ümüt H, Wang Y. An ERF transcription factor from Tamarix hispida, ThCRF1, can adjust osmotic potential and reactive oxygen species scavenging capability to improve salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:154-166. [PMID: 29223337 DOI: 10.1016/j.plantsci.2017.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 05/22/2023]
Abstract
Ethylene-Responsive Factors (ERFs) are plant-specific transcription factors (TFs) involved in multiple biological processes, especially in abiotic stress tolerance. However, the ERFs from woody halophytes that are involved in salt stress have been little studied. In the present investigation, we characterized a subfamily member of ERF TFs from Tamarix hispida, ThCRF1, which responds to salt stress. ThCRF1 is a nuclear protein that binds to the motifs including TTG, DRE and GCC-box. Transient transformation was performed to generate T. hispida overexpressing ThCRF1 and RNA interference (RNAi)-silenced ThCRF1 to analyze its function using gain- and loss-of-function methods. Overexpression of ThCRF1 in T. hispida significantly improved tolerance to salt-shock-induced stress; by contrast, RNAi-silence of ThCRF1 significantly decreased tolerance to salt-shock-induced stress. Further experiments showed that ThCRF1 induces the expression of genes including those encoding pyrroline-5-carboxylate synthetase (P5CS), trehalose-6-phosphate synthase (TPS), trehalose-6-phosphate phosphatase (TPP), superoxide dismutase (SOD) and peroxidase (POD), which lead to enhanced proline and trehalose levels and increased SOD and POD activities. These results were further confirmed by studying transgenic Arabidopsis plants overexpressing ThCRF1. Therefore, the results suggested that ThCRF1 improves tolerance to salt-shock-induced stress by enhancing trehalose and proline biosynthesis to adjust the osmotic potential, and by improving SOD and POD activities to increase reactive oxygen species scavenging capability.
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Affiliation(s)
- Liping Qin
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Key Laboratory of Oasis Ecology, College of Resources & Environmental Sciences, Xinjiang University, Urumqi, 830046, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yong Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yan Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Halik Ümüt
- Key Laboratory of Oasis Ecology, College of Resources & Environmental Sciences, Xinjiang University, Urumqi, 830046, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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Bielach A, Hrtyan M, Tognetti VB. Plants under Stress: Involvement of Auxin and Cytokinin. Int J Mol Sci 2017; 18:E1427. [PMID: 28677656 PMCID: PMC5535918 DOI: 10.3390/ijms18071427] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Plant growth and development are critically influenced by unpredictable abiotic factors. To survive fluctuating changes in their environments, plants have had to develop robust adaptive mechanisms. The dynamic and complementary actions of the auxin and cytokinin pathways regulate a plethora of developmental processes, and their ability to crosstalk makes them ideal candidates for mediating stress-adaptation responses. Other crucial signaling molecules responsible for the tremendous plasticity observed in plant morphology and in response to abiotic stress are reactive oxygen species (ROS). Proper temporal and spatial distribution of ROS and hormone gradients is crucial for plant survival in response to unfavorable environments. In this regard, the convergence of ROS with phytohormone pathways acts as an integrator of external and developmental signals into systemic responses organized to adapt plants to their environments. Auxin and cytokinin signaling pathways have been studied extensively. Nevertheless, we do not yet understand the impact on plant stress tolerance of the sophisticated crosstalk between the two hormones. Here, we review current knowledge on the function of auxin and cytokinin in redirecting growth induced by abiotic stress in order to deduce their potential points of crosstalk.
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Affiliation(s)
- Agnieszka Bielach
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
| | - Monika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
| | - Vanesa B Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Czech 62500, Brno, Czech Republic.
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26
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Li P, Shu YN, Fu S, Liu YQ, Zhou XP, Liu SS, Wang XW. Vector and nonvector insect feeding reduces subsequent plant susceptibility to virus transmission. THE NEW PHYTOLOGIST 2017; 215:699-710. [PMID: 28382644 DOI: 10.1111/nph.14550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 02/26/2017] [Indexed: 06/07/2023]
Abstract
The interactions of vector-virus-plant have important ecological and evolutionary implications. While the tripartite interactions have received some attention, little is known about whether vector infestation affects subsequent viral transmission and infection. Working with the whitefly Bemisia tabaci, begomovirus and tobacco/tomato, we demonstrate that pre-infestation of plants by the whitefly vector reduced subsequent plant susceptibility to viral transmission. Pre-infestation by the cotton bollworm, a nonvector of the virus, likewise repressed subsequent viral transmission. The two types of insects, with piercing and chewing mouthparts, respectively, activated different plant signaling pathways in the interactions. Whitefly pre-infestation activated the salicylic acid (SA) signaling pathway, leading to deposition of callose that inhibited begomovirus replication/movement. Although cotton bollworm infestation elicited the jasmonic acid (JA) defense pathway and was beneficial to virus replication, the pre-infested plants repelled whiteflies from feeding and so decreased virus transmission. Experiments using a pharmaceutical approach with plant hormones or a genetic approach using hormone transgenic or mutant plants further showed that SA played a negative but JA played a positive role in begomovirus infection. These novel findings indicate that both vector and nonvector insect feeding of a plant may have substantial negative consequences for ensuing viral transmission and infection.
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Affiliation(s)
- Ping Li
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan-Ni Shu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shuai Fu
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yin-Quan Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xue-Ping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
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Albrecht T, Argueso CT. Should I fight or should I grow now? The role of cytokinins in plant growth and immunity and in the growth-defence trade-off. ANNALS OF BOTANY 2017; 119:725-735. [PMID: 27864225 PMCID: PMC5379597 DOI: 10.1093/aob/mcw211] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/28/2016] [Accepted: 08/31/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Perception and activation of plant immunity require a remarkable level of signalling plasticity and control. In Arabidopsis and other plant species, constitutive defence activation leads to resistance to a broad spectrum of biotrophic pathogens, but also frequently to stunted growth and reduced seed set. Plant hormones are important integrators of the physiological responses that influence the outcome of plant-pathogen interactions. SCOPE We review the mechanisms by which the plant hormone cytokinin regulates both plant growth and response to pathogens, and how cytokinins may connect these two processes, ultimately affecting the growth trade-offs observed in plant immunity.
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Affiliation(s)
| | - Cristiana T. Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
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28
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Phukan UJ, Jeena GS, Tripathi V, Shukla RK. Regulation of Apetala2/Ethylene Response Factors in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:150. [PMID: 28270817 PMCID: PMC5318435 DOI: 10.3389/fpls.2017.00150] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/25/2017] [Indexed: 05/18/2023]
Abstract
Multiple environmental stresses affect growth and development of plants. Plants try to adapt under these unfavorable condition through various evolutionary mechanisms like physiological and biochemical alterations connecting various network of regulatory processes. Transcription factors (TFs) like APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERFs) are an integral component of these signaling cascades because they regulate expression of a wide variety of down stream target genes related to stress response and development through different mechanism. This downstream regulation of transcript does not always positively or beneficially affect the plant but also they display some developmental defects like senescence and reduced growth under normal condition or sensitivity to stress condition. Therefore, tight auto/cross regulation of these TFs at transcriptional, translational and domain level is crucial to understand. The present manuscript discuss the multiple regulation and advantage of plasticity and specificity of these family of TFs to a wide or single downstream target(s) respectively. We have also discussed the concern which comes with the unwanted associated traits, which could only be averted by further study and exploration of these AP2/ERFs.
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Affiliation(s)
- Ujjal J. Phukan
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
| | - Gajendra S. Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
| | - Vineeta Tripathi
- Botany Division, CSIR-Central Drug Research InstituteLucknow, India
| | - Rakesh K. Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
- *Correspondence: Rakesh K. Shukla
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Zwack PJ, Compton MA, Adams CI, Rashotte AM. Cytokinin response factor 4 (CRF4) is induced by cold and involved in freezing tolerance. PLANT CELL REPORTS 2016; 35:573-84. [PMID: 26650835 DOI: 10.1007/s00299-015-1904-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/11/2015] [Accepted: 11/17/2015] [Indexed: 05/19/2023]
Abstract
Cytokinin response factor 4 (CRF4) shows a short-term induction by cold (4 °C) that appears to play a role in non-acclimated freezing tolerance as seen in mutant and overexpression lines. Responses to abiotic stresses, such as cold stress, are critical to plant growth and optimal production. Examination of Arabidopsis cytokinin response factors (CRFs) showed transcriptional induction after exposure to cold (4 °C). In particular, CRF4 was strongly induced in both root and shoot tissues. As CRF4 is one of several CRFs not transcriptionally regulated by cytokinin, we further investigated its response to cold. Peak CRF4 induction occurred 6 h post cold exposure, after which expression was maintained at moderately elevated levels during extended cold and subsequent treatment recovery. Examination of CRF4 mutant and overexpression lines under standard (non-cold) conditions revealed little difference from WT. One exception was a small, but significant increase in primary root growth of overexpression plants (CRF4OX). Under cold conditions, the only phenotype observed was a reduction in the rate of germination of CRF4OX seeds. The pattern of CRF4 expression along with the lack of strong phenotype at 4 °C led us to hypothesize that cold induction of CRF4 could play a role in short-term cold acclimation leading to increased freeze tolerance. Examination of CRF4OX and crf4 plants exposed to freezing temperatures revealed mutants lacking expression of CRF4 were more sensitive to freezing, while CRF4OXs with increased levels CRF4 levels were more tolerant. Altered transcript expression of CBF and COR15a cold signaling pathway genes in crf4 mutant and overexpression lines suggest that CRF4 may be potentially connected to this pathway. Overall this indicates that CRF4 plays an important role in both cold response and freezing stress.
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Affiliation(s)
- Paul J Zwack
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Margaret A Compton
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Cami I Adams
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA
| | - Aaron M Rashotte
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, USA.
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Zwack PJ, Rashotte AM. Interactions between cytokinin signalling and abiotic stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4863-71. [PMID: 25911740 DOI: 10.1093/jxb/erv172] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants have evolved elaborate mechanisms for sensing and responding to sub-optimal environmental conditions. Abiotic stresses caused by these conditions trigger a wide range of local and long-distance signals which must be co-ordinated and integrated into whole-plant processes, such as development, in order for the plant to respond properly and survive. Several hormones function as key regulators of stress tolerance, connecting local stimuli to systemic responses. Cytokinin is a hormone well known for its role in numerous aspects of growth and development, although abundant evidence also indicates that cytokinin functions in stress responses as well. At present, a full understanding of the effects of cytokinin on plant resistance to stress is lacking, possibly as a result of the complex interactions between cytokinin and stress signalling. Current knowledge of the physiological relationship between cytokinin and abiotic stress, based on measurements of cytokinin levels under stress conditions and the effects of cytokinin treatment on stress tolerance, has been examined here. A pattern of transcriptional regulation of stress-related genes by cytokinin in different plant species has also been identified. In addition, research regarding the role of specific cytokinin signalling components in a variety of stress responses is presented. We discuss what this body of research collectively implies with regard to cross-talk between cytokinin and abiotic stress tolerance.
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Affiliation(s)
- Paul J Zwack
- 101 Rouse Life Sciences Building, Department of Biological Sciences, Auburn University, Auburn, AL 36849-5407, USA
| | - Aaron M Rashotte
- 101 Rouse Life Sciences Building, Department of Biological Sciences, Auburn University, Auburn, AL 36849-5407, USA
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Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress. Mol Genet Genomics 2015; 290:2049-61. [PMID: 25971861 DOI: 10.1007/s00438-015-1061-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022]
Abstract
AP2/ERF is a large transcription factor family that regulates plant physiological processes, such as plant development and stress response. Carrot (Daucus carota L.) is an important economical crop with a genome size of 480 Mb; the draft genome sequencing of this crop has been completed by our group. However, little is known about the AP2/ERF factors in carrot. In this study, a total of 267 putative AP2/ERF factors were identified from the whole-genome sequence of carrot. These AP2/ERF proteins were phylogenetically clustered into five subfamilies based on their similarity to the amino acid sequences from Arabidopsis. The distribution and comparative genome analysis of the AP2/ERF factors among plants showed the AP2/ERF factors had expansion during the evolutionary process, and the AP2 domain was highly conserved during evolution. The number of AP2/ERF factors in land plants expanded during their evolution. A total of 60 orthologous and 145 coorthologous AP2/ERF gene pairs between carrot and Arabidopsis were identified, and the interaction network of orthologous genes was constructed. The expression patterns of eight AP2/ERF family genes from each subfamily (DREB, ERF, AP2, and RAV) were related to abiotic stresses. Yeast one-hybrid and β-galactosidase activity assays confirmed the DRE and GCC box-binding activities of DREB subfamily genes. This study is the first to identify and characterize the AP2/ERF transcription factors in carrot using whole-genome analysis, and the findings may serve as references for future functional research on the transcription factors in carrot.
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Rao G, Sui J, Zeng Y, He C, Zhang J. Genome-wide analysis of the AP2/ERF gene family in Salix arbutifolia. FEBS Open Bio 2015; 5:132-7. [PMID: 25830086 PMCID: PMC4354408 DOI: 10.1016/j.fob.2015.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/15/2015] [Accepted: 02/18/2015] [Indexed: 01/08/2023] Open
Abstract
We identified 173 AP2/ERF superfamily genes in Salix arbutifolia. A comparative analysis of AP2/ERF superfamily genes was performed. The phylogenic trees of AP2/ERF superfamily have been constructed.
AP2/ERF genes encode transcriptional regulators with a variety of functions in plant growth and development and in response to biotic and abiotic stresses. To date, there are no detailed classification and expression profiles for AP2/ERF genes in Salix. In this study, a comprehensive computational analysis identified 173 AP2/ERF superfamily genes in willow (Salix arbutifolia), by using in silico cloning methods with the use of the AP2/ERF conserved domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the results of phylogenetic analyses and the number of AP2/ERF domains, the AP2/ERF genes were classified into four groups: AP2, RAV, ERF and Soloist. The expression profile was analyzed using transcriptome data from different tissues. A comparative analysis of AP2/ERF superfamily genes among Salix, Populus and Arabidopsis was performed. The Salix DREB, AP2 and RAV groups had a similar number to those in Arabidopsis, and the size of the ERF subfamily in Salix was about 1.4-fold that of Arabidopsis. The Salix DREB subfamily was smaller compared to Populus, while the other families were similar in size to those in Populus. These results will be useful for future functional analyses of the ERF family genes.
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Affiliation(s)
- Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jinkai Sui
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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