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Argueso CT, Kieber JJ. Cytokinin: From autoclaved DNA to two-component signaling. THE PLANT CELL 2024; 36:1429-1450. [PMID: 38163638 PMCID: PMC11062471 DOI: 10.1093/plcell/koad327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 01/03/2024]
Abstract
Since its first identification in the 1950s as a regulator of cell division, cytokinin has been linked to many physiological processes in plants, spanning growth and development and various responses to the environment. Studies from the last two and one-half decades have revealed the pathways underlying the biosynthesis and metabolism of cytokinin and have elucidated the mechanisms of its perception and signaling, which reflects an ancient signaling system evolved from two-component elements in bacteria. Mutants in the genes encoding elements involved in these processes have helped refine our understanding of cytokinin functions in plants. Further, recent advances have provided insight into the mechanisms of intracellular and long-distance cytokinin transport and the identification of several proteins that operate downstream of cytokinin signaling. Here, we review these processes through a historical lens, providing an overview of cytokinin metabolism, transport, signaling, and functions in higher plants.
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Affiliation(s)
- Cristiana T Argueso
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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2
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Park SJ, Park JS, Yang JH, Moon KB, Shin SY, Jeon JH, Kim HS, Lee HJ. MicroRNA396 negatively regulates shoot regeneration in tomato. HORTICULTURE RESEARCH 2024; 11:uhad291. [PMID: 38371631 PMCID: PMC10873581 DOI: 10.1093/hr/uhad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.
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Affiliation(s)
- Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Jin Ho Yang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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3
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Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW. The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin. Proc Natl Acad Sci U S A 2024; 121:e2319335121. [PMID: 38198526 PMCID: PMC10801921 DOI: 10.1073/pnas.2319335121] [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: 11/04/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1RD-DBD) as well as the ARR1DBD-DNA complex from Arabidopsis. Analyses of the ARR1DBD-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1RD-DBD and ARR1DBD-DNA structures reveals that unphosphorylated ARR1RD-DBD exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.
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Affiliation(s)
- Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Jian-Xu Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai201602, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Miao-Lian Ma
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
- Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
- New Cornerstone Science Laboratory, Shanghai200032, China
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4
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Vysotskaya L, Akhiyarova G, Seldimirova O, Nuzhnaya T, Galin I, Ivanov R, Kudoyarova G. Effect of ipt Gene Induction in Transgenic Tobacco Plants on Hydraulic Conductance, Formation of Apoplastic Barriers and Aquaporin Activity under Heat Shock. Int J Mol Sci 2023; 24:9860. [PMID: 37373010 DOI: 10.3390/ijms24129860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Cytokinins are known to keep stomata open, which supports gas exchange and correlates with increased photosynthesis. However, keeping the stomata open can be detrimental if the increased transpiration is not compensated for by water supply to the shoots. In this study, we traced the effect of ipt (isopentenyl transferase) gene induction, which increases the concentration of cytokinins in transgenic tobacco plants, on transpiration and hydraulic conductivity. Since water flow depends on the conductivity of the apoplast, the deposition of lignin and suberin in the apoplast was studied by staining with berberine. The effect of an increased concentration of cytokinins on the flow of water through aquaporins (AQPs) was revealed by inhibition of AQPs with HgCl2. It was shown that an elevated concentration of cytokinins in ipt-transgenic plants increases hydraulic conductivity by enhancing the activity of aquaporins and reducing the formation of apoplastic barriers. The simultaneous effect of cytokinins on both stomatal and hydraulic conductivity makes it possible to coordinate the evaporation of water from leaves and its flow from roots to leaves, thereby maintaining the water balance and leaf hydration.
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Affiliation(s)
- Lidiya Vysotskaya
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Guzel Akhiyarova
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Oksana Seldimirova
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Tatiana Nuzhnaya
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Ilshat Galin
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Ruslan Ivanov
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
| | - Guzel Kudoyarova
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Pr. Octyabrya 69, 450054 Ufa, Russia
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5
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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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6
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Mahto RK, Ambika, Singh C, Chandana BS, Singh RK, Verma S, Gahlaut V, Manohar M, Yadav N, Kumar R. Chickpea Biofortification for Cytokinin Dehydrogenase via Genome Editing to Enhance Abiotic-Biotic Stress Tolerance and Food Security. Front Genet 2022; 13:900324. [PMID: 35669196 PMCID: PMC9164125 DOI: 10.3389/fgene.2022.900324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Globally more than two billion people suffer from micronutrient malnutrition (also known as "hidden hunger"). Further, the pregnant women and children in developing nations are mainly affected by micronutrient deficiencies. One of the most important factors is food insecurity which can be mitigated by improving the nutritional values through biofortification using selective breeding and genetic enhancement techniques. Chickpea is the second most important legume with numerous economic and nutraceutical properties. Therefore, chickpea production needs to be increased from the current level. However, various kind of biotic and abiotic stresses hamper global chickpea production. The emerging popular targets for biofortification in agronomic crops include targeting cytokinin dehydrogenase (CKX). The CKXs play essential roles in both physiological and developmental processes and directly impact several agronomic parameters i.e., growth, development, and yield. Manipulation of CKX genes using genome editing tools in several crop plants reveal that CKXs are involved in regulation yield, shoot and root growth, and minerals nutrition. Therefore, CKXs have become popular targets for yield improvement, their overexpression and mutants can be directly correlated with the increased yield and tolerance to various stresses. Here, we provide detailed information on the different roles of CKX genes in chickpea. In the end, we discuss the utilization of genome editing tool clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to engineer CKX genes that can facilitate trait improvement. Overall, recent advancements in CKX and their role in plant growth, stresses and nutrient accumulation are highlighted, which could be used for chickpea improvement.
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Affiliation(s)
| | - Ambika
- Department of Genetics and Plant Breeding, UAS, Bangalore, India
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Shruti Verma
- NCoE-SAM, Department of Pediatrics, KSCH, Lady Hardinge Medical College, New Delhi, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Palampur, India
| | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Neelam Yadav
- Centre of Food Technology, University of Allahabad, Prayagraj, India
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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7
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Zou J, Lü P, Jiang L, Liu K, Zhang T, Chen J, Yao Y, Cui Y, Gao J, Zhang C. Regulation of rose petal dehydration tolerance and senescence by RhNAP transcription factor via the modulation of cytokinin catabolism. MOLECULAR HORTICULTURE 2021; 1:13. [PMID: 37789474 PMCID: PMC10515265 DOI: 10.1186/s43897-021-00016-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 08/02/2021] [Indexed: 10/05/2023]
Abstract
Petals and leaves share common evolutionary origins but have different phenotypic characteristics, such as the absence of stomata in the petals of most angiosperm species. Plant NAC transcription factor, NAP, is involved in ABA responses and regulates senescence-associated genes, and especially those that affect stomatal movement. However, the regulatory mechanisms and significance of NAP action in senescing astomatous petals is unclear. A major limiting factor is failure of flower opening and accelerated senescence. Our goal is to understand the finely regulatory mechanism of dehydration tolerance and aging in rose flowers. We functionally characterized RhNAP, an AtNAP-like transcription factor gene that is induced by dehydration and aging in astomatous rose petals. Cytokinins (CKs) are known to delay petal senescence and we found that a cytokinin oxidase/dehydrogenase gene 6 (RhCKX6) shares similar expression patterns with RhNAP. Silencing of RhNAP or RhCKX6 expression in rose petals by virus induced gene silencing markedly reduced petal dehydration tolerance and delayed petal senescence. Endogenous CK levels in RhNAP- or RhCKX6-silenced petals were significantly higher than those of the control. Moreover, RhCKX6 expression was reduced in RhNAP-silenced petals. This suggests that the expression of RhCKX6 is regulated by RhNAP. Yeast one-hybrid experiments and electrophoresis mobility shift assays showed that RhNAP binds to the RhCKX6 promoter in heterologous in vivo system and in vitro, respectively. Furthermore, the expression of putative signal transduction and downstream genes of ABA-signaling pathways were also reduced due to the repression of PP2C homolog genes by RhNAP in rose petals. Taken together, our study indicates that the RhNAP/RhCKX6 interaction represents a regulatory step enhancing dehydration tolerance in young rose petals and accelerating senescence in mature petals in a stomata-independent manner.
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Affiliation(s)
- Jing Zou
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Peitao Lü
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwei Jiang
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kun Liu
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Tao Zhang
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jin Chen
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Yao
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yusen Cui
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Junping Gao
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Changqing Zhang
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China.
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8
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Polko JK, Potter KC, Burr CA, Schaller GE, Kieber JJ. Meta-analysis of transcriptomic studies of cytokinin-treated rice roots defines a core set of cytokinin response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1387-1402. [PMID: 34165836 DOI: 10.1111/tpj.15386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 05/25/2023]
Abstract
Cytokinins regulate diverse aspects of plant growth and development, primarily through modulation of gene expression. The cytokinin-responsive transcriptome has been thoroughly described in dicots, especially Arabidopsis, but much less so in monocots. Here, we present a meta-analysis of five different transcriptomic analyses of rice (Oryza sativa) roots treated with cytokinin, including three previously unpublished experiments. We developed a treatment method in which hormone is added to the media of rice seedlings grown in sterile hydroponic culture under a continuous airflow, which resulted in minimal perturbation of the seedlings, thus greatly reducing changes in gene expression in the absence of exogenous hormone. We defined a core set of 205 upregulated and 86 downregulated genes that were differentially expressed in at least three of the transcriptomic datasets. This core set includes genes encoding the type-A response regulators (RRs) and cytokinin oxidases/dehydrogenases, which have been shown to be primary cytokinin response genes. GO analysis revealed that the upregulated genes were enriched for terms related to cytokinin/hormone signaling and metabolism, while the downregulated genes were significantly enriched for genes encoding transporters. Variations of type-B RR binding motifs were significantly enriched in the promoters of the upregulated genes, as were binding sites for other potential partner transcription factors. The promoters of the downregulated genes were generally enriched for distinct cis-acting motifs and did not include the type-B RR binding motif. This analysis provides insight into the molecular mechanisms underlying cytokinin action in a monocot and provides a useful foundation for future studies of this hormone in rice and other cereals.
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Affiliation(s)
- Joanna K Polko
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin C Potter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian A Burr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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9
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DAP-Seq Identification of Transcription Factor-Binding Sites in Potato. Methods Mol Biol 2021. [PMID: 34448158 DOI: 10.1007/978-1-0716-1609-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Plant growth and adaptation to environmental fluctuations involve a tight control of cellular processes which, to a great extent, are mediated by changes at the transcriptional level. This regulation is exerted by transcription factors (TFs), a group of regulatory proteins that control gene expression by directly binding to the gene promoter regions via their cognate TF-binding sites (TFBS). The nature of TFBS defines the pattern of expression of the various plant loci, the precise combinatorial assembly of these elements being key in conferring plant's adaptation ability and in domestication. As such, TFs are main potential targets for biotechnological interventions, prompting in the last decade notable protein-DNA interaction efforts toward definition of their TFBS. Distinct methods based on in vivo or in vitro approaches defined the TFBS for many TFs, mainly in Arabidopsis, but comprehensive information on the transcriptional networks for many regulators is still lacking, especially in crops. In this chapter, detailed protocols for DAP-seq studies to unbiased identification of TFBS in potato are provided. This methodology relies on the affinity purification of genomic DNA-protein complexes in vitro, and high-throughput sequencing of the eluted DNA fragments. DAP-seq outperforms other in vitro DNA-motif definition strategies, such as protein-binding microarrays and SELEX-seq, since the protein of interest is directly bound to the genomic DNA extracted from plants yielding all the potential sites bound by the TF in the genome. Actually, data generated from DAP-seq experiments are highly similar to those out of ChIP-seq methods, but are generated much faster. We also provide a standard procedure to the analysis of the DAP-seq data, addressed to non-experienced users, that involves two consecutive steps: (1) processing of raw data (trimming, filtering, and read alignment) and (2) peak calling and identification of enriched motifs. This method allows identification of the binding profiles of dozens of TFs in crops, in a timely manner.
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10
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Yang X, Kang Y, Liu Y, Shi M, Zhang W, Fan Y, Yao Y, Li H, Qin S. Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112682. [PMID: 34419646 DOI: 10.1016/j.ecoenv.2021.112682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.
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Affiliation(s)
- Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanhong Yao
- Dingxi Academy of Agricultural Sciences, Dingxi 743000, China
| | - Hong Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
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11
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Leuendorf JE, Schmülling T. Meeting at the DNA: Specifying Cytokinin Responses through Transcription Factor Complex Formation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10071458. [PMID: 34371661 PMCID: PMC8309282 DOI: 10.3390/plants10071458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 05/10/2023]
Abstract
Cytokinin is a plant hormone regulating numerous biological processes. Its diverse functions are realized through the expression control of specific target genes. The transcription of the immediate early cytokinin target genes is regulated by type-B response regulator proteins (RRBs), which are transcription factors (TFs) of the Myb family. RRB activity is controlled by phosphorylation and protein degradation. Here, we focus on another step of regulation, the interaction of RRBs among each other or with other TFs to form active or repressive TF complexes. Several examples in Arabidopsis thaliana illustrate that RRBs form homodimers or complexes with other TFs to specify the cytokinin response. This increases the variability of the output response and provides opportunities of crosstalk between the cytokinin signaling pathway and other cellular signaling pathways. We propose that a targeted approach is required to uncover the full extent and impact of RRB interaction with other TFs.
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12
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Bhaskar A, Paul LK, Sharma E, Jha S, Jain M, Khurana JP. OsRR6, a type-A response regulator in rice, mediates cytokinin, light and stress responses when over-expressed in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:98-112. [PMID: 33581623 DOI: 10.1016/j.plaphy.2021.01.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/28/2021] [Indexed: 05/27/2023]
Abstract
Plants have evolved a complex network of components that sense and respond to diverse signals. In the present study, we have characterized OsRR6, a type-A response regulator, which is part of the two-component sensor-regulator machinery in rice. The expression of OsRR6 is induced by exogenous cytokinin and various abiotic stress treatments, including drought, cold and salinity stress. Organ-specific expression analysis revealed that its expression is high in anther and low in shoot apical meristem. The Arabidopsis plants constitutively expressing OsRR6 (OsRR6OX) exhibited reduced cytokinin sensitivity, adventitious root formation and enhanced anthocyanin accumulation in seeds. OsRR6OX plants were more tolerant to drought and salinity conditions when compared to wild-type. The hypocotyl growth in OsRR6OX seedlings was significantly inhibited under red, far-red and blue-light conditions and also a decline in transcript levels of OsRR6 was observed in rice under the above monochromatic as well as white light treatments. Transcriptome profiling revealed that the genes associated with defense responses and anthocyanin metabolism are up-regulated in OsRR6OX seedlings. Comparative transcriptome analysis showed that the genes associated with phenylpropanoid and triterpenoid biosynthesis are enriched among differentially expressed genes in OsRR6OX seedlings of Arabidopsis, which is in conformity with reanalysis of the transcriptome data performed in rice transgenics for OsRR6. Further, genes like DREB1A/CBF3, COR15A, KIN1, ERD10 and RD29A are significantly upregulated in OsRR6OX seedlings when subjected to ABA and abiotic stress treatments. Thus, a negative regulator of cytokinin signaling, OsRR6, plays a positive role in imparting abiotic stress tolerance.
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Affiliation(s)
- Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Laju K Paul
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Sampoornananda Jha
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Mukesh Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India; School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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13
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Vaughan-Hirsch J, Tallerday EJ, Burr CA, Hodgens C, Boeshore SL, Beaver K, Melling A, Sari K, Kerr ID, Šimura J, Ljung K, Xu D, Liang W, Bhosale R, Schaller GE, Bishopp A, Kieber JJ. Function of the pseudo phosphotransfer proteins has diverged between rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:159-173. [PMID: 33421204 DOI: 10.1111/tpj.15156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
The phytohormone cytokinin plays a significant role in nearly all aspects of plant growth and development. Cytokinin signaling has primarily been studied in the dicot model Arabidopsis, with relatively little work done in monocots, which include rice (Oryza sativa) and other cereals of agronomic importance. The cytokinin signaling pathway is a phosphorelay comprised of the histidine kinase receptors, the authentic histidine phosphotransfer proteins (AHPs) and type-B response regulators (RRs). Two negative regulators of cytokinin signaling have been identified: the type-A RRs, which are cytokinin primary response genes, and the pseudo histidine phosphotransfer proteins (PHPs), which lack the His residue required for phosphorelay. Here, we describe the role of the rice PHP genes. Phylogenic analysis indicates that the PHPs are generally first found in the genomes of gymnosperms and that they arose independently in monocots and dicots. Consistent with this, the three rice PHPs fail to complement an Arabidopsis php mutant (aphp1/ahp6). Disruption of the three rice PHPs results in a molecular phenotype consistent with these elements acting as negative regulators of cytokinin signaling, including the induction of a number of type-A RR and cytokinin oxidase genes. The triple php mutant affects multiple aspects of rice growth and development, including shoot morphology, panicle architecture, and seed fill. In contrast to Arabidopsis, disruption of the rice PHPs does not affect root vascular patterning, suggesting that while many aspects of key signaling networks are conserved between monocots and dicots, the roles of at least some cytokinin signaling elements are distinct.
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Affiliation(s)
| | - Emily J Tallerday
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian A Burr
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Charlie Hodgens
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Samantha L Boeshore
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kevin Beaver
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Allison Melling
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kartika Sari
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
- FKIP, Universitas Muhammadiyah Metro, Lampung, 34111, Indonesia
| | - Ian D Kerr
- University of Nottingham, Loughborough, NG7 2UH, UK
| | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Dawei Xu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanqi Liang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rahul Bhosale
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
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14
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Shao Y, Lehner KR, Zhou H, Taylor I, Zhu M, Mao C, Benfey PN. VAP-RELATED SUPPRESSORS OF TOO MANY MOUTHS (VST) family proteins are regulators of root system architecture. PLANT PHYSIOLOGY 2021; 185:457-468. [PMID: 33721897 PMCID: PMC8133634 DOI: 10.1093/plphys/kiaa036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
Root system architecture (RSA) is a key factor in the efficiency of nutrient capture and water uptake in plants. Understanding the genetic control of RSA will be useful in minimizing fertilizer and water usage in agricultural cropping systems. Using a hydroponic screen and a gel-based imaging system, we identified a rice (Oryza sativa) gene, VAP-RELATED SUPPRESSOR OF TOO MANY MOUTHS1 (OsVST1), which plays a key role in controlling RSA. This gene encodes a homolog of the VAP-RELATED SUPPRESSORS OF TOO MANY MOUTHS (VST) proteins in Arabidopsis (Arabidopsis thaliana), which promote signaling in stomata by mediating plasma membrane-endoplasmic reticulum contacts. OsVST1 mutants have shorter primary roots, decreased root meristem size, and a more compact RSA. We show that the Arabidopsis VST triple mutants have similar phenotypes, with reduced primary root growth and smaller root meristems. Expression of OsVST1 largely complements the short root length and reduced plant height in the Arabidopsis triple mutant, supporting conservation of function between rice and Arabidopsis VST proteins. In a field trial, mutations in OsVST1 did not adversely affect grain yield, suggesting that modulation of this gene could be used as a way to optimize RSA without an inherent yield penalty.
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Affiliation(s)
- Yanlin Shao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kevin R Lehner
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Hongzhu Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Isaiah Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
- HHMI, Duke University, Durham, NC 27708, USA
| | - Mingyuan Zhu
- Department of Biology, Duke University, Durham, NC 27708, USA
- HHMI, Duke University, Durham, NC 27708, USA
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA
- HHMI, Duke University, Durham, NC 27708, USA
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15
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Hnatuszko-Konka K, Gerszberg A, Weremczuk-Jeżyna I, Grzegorczyk-Karolak I. Cytokinin Signaling and De Novo Shoot Organogenesis. Genes (Basel) 2021; 12:265. [PMID: 33673064 PMCID: PMC7917986 DOI: 10.3390/genes12020265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/16/2022] Open
Abstract
The ability to restore or replace injured tissues can be undoubtedly named among the most spectacular achievements of plant organisms. One of such regeneration pathways is organogenesis, the formation of individual organs from nonmeristematic tissue sections. The process can be triggered in vitro by incubation on medium supplemented with phytohormones. Cytokinins are a class of phytohormones demonstrating pleiotropic effects and a powerful network of molecular interactions. The present study reviews existing knowledge on the possible sequence of molecular and genetic events behind de novo shoot organogenesis initiated by cytokinins. Overall, the review aims to collect reactions encompassed by cytokinin primary responses, starting from phytohormone perception by the dedicated receptors, to transcriptional reprogramming of cell fate by the last module of multistep-phosphorelays. It also includes a brief reminder of other control mechanisms, such as epigenetic reprogramming.
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Affiliation(s)
- Katarzyna Hnatuszko-Konka
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Aneta Gerszberg
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Izabela Weremczuk-Jeżyna
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
| | - Izabela Grzegorczyk-Karolak
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
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16
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Halawa M, Cortleven A, Schmülling T, Heyl A. Characterization of CHARK, an unusual cytokinin receptor of rice. Sci Rep 2021; 11:1722. [PMID: 33462253 PMCID: PMC7814049 DOI: 10.1038/s41598-020-80223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/21/2020] [Indexed: 11/14/2022] Open
Abstract
The signal transduction of the plant hormone cytokinin is mediated by a His-to-Asp phosphorelay. The canonical cytokinin receptor consists of an extra cytoplasmic hormone binding domain named cyclase/histidine kinase associated sensory extracellular (CHASE) and cytoplasmic histidine kinase and receiver domains. In addition to classical cytokinin receptors, a different type receptor—named CHASE domain receptor serine/threonine kinase (CHARK)—is also present in rice. It contains the same ligand binding domain as other cytokinin receptors but has a predicted Ser/Thr—instead of a His-kinase domain. Bioinformatic analysis indicates that CHARK is a retrogene and a product of trans-splicing. Here, we analyzed whether CHARK can function as a bona fide cytokinin receptor. A biochemical assay demonstrated its ability to bind cytokinin. Transient expression of CHARK in protoplasts increased their response to cytokinin. Expression of CHARK in an Arabidopsis receptor double mutant complemented its growth defects and restored the ability to activate cytokinin response genes, clearly demonstrating that CHARK functions as a cytokinin receptor. We propose that the CHARK gene presents an evolutionary novelty in the cytokinin signaling system.
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Affiliation(s)
- Mhyeddeen Halawa
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Alexander Heyl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany. .,Biology Department, Adelphi University, 1 South Avenue, Garden City, NY, 11530-0701, USA.
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17
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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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18
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Cattani AM, da Silveira Falavigna V, Silveira CP, Buffon V, Dos Santos Maraschin F, Pasquali G, Revers LF. Type-B cytokinin response regulators link hormonal stimuli and molecular responses during the transition from endo- to ecodormancy in apple buds. PLANT CELL REPORTS 2020; 39:1687-1703. [PMID: 32959122 DOI: 10.1007/s00299-020-02595-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Cytokinin together with MdoBRR1, MdoBRR8 and MdoBRR10 genes participate in the downregulation of MdoDAM1, contributing to the transition from endo- to ecodormancy in apple buds. The final step of cytokinin (CK) signaling pathway culminates in the activation of type-B response regulators (BRRs), important transcriptional factors in the modulation of CK-responsive genes. In this study, we performed a genome-wide analysis aiming to identify apple BRR family members and understand their involvement in bud dormancy control. The investigation identified ten MdoBRR protein-coding genes. A higher expression of three MdoBRR (MdoBRR1, MdoBRR9 and MdoBRR10) was observed in dormant buds in comparison to other developmental stages. Interestingly, in ecodormant buds these three MdoBRR genes were upregulated in a CK-dependent manner. Transcription profiles, determined during dormancy cycle under field and artificially controlled conditions, revealed that MdoBRR1 and MdoBRR8 played important roles in the transition from endo- to ecodormancy, probably mediated by endogenous CK stimuli. The expression of MdoBRR7, MdoBRR9, and MdoBRR10 was induced in ecodormant buds exposed to warm temperatures, indicating a putative role in growth resumption after chilling requirement fulfillment. Contrasting expression patternsin vivo between MdoBRRs and MdoDAM1, an essential dormancy establishment regulator, were observed during dormancy cycle and in CK-treated buds. Thereafter, in vivo transactivation assays showed that CK stimuli combined with transient overexpression of MdoBRR1, MdoBRR8, and MdoBRR10 resulted in downregulation of the reporter gene gusA driven by the MdoDAM1 promoter. These pieces of evidences point to the integration of CK-triggered responses through MdoBRRs that are able to downregulate MdoDAM1, contributing to dormancy release in apple.
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Affiliation(s)
- Amanda Malvessi Cattani
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Plant Molecular Genetics, Embrapa Uva e Vinho, Bento Gonçalves, RS, Brazil
| | | | | | - Vanessa Buffon
- Laboratory of Plant Molecular Genetics, Embrapa Uva e Vinho, Bento Gonçalves, RS, Brazil
| | | | - Giancarlo Pasquali
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luís Fernando Revers
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Laboratory of Plant Molecular Genetics, Embrapa Uva e Vinho, Bento Gonçalves, RS, Brazil.
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19
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Shi F, Wang M, An Y. Overexpression of a B-type cytokinin response regulator ( OsORR2) reduces plant height in rice. PLANT SIGNALING & BEHAVIOR 2020; 15:1780405. [PMID: 32552330 PMCID: PMC8570751 DOI: 10.1080/15592324.2020.1780405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 05/19/2023]
Abstract
Cytokinin plays crucial roles in regulating plant growth and development, with the signal transduction mediated by type-A and type-B response regulators (RRs).While much genetic knowledge about RRs on regulating plant height remains unclear. Here, we found that overexpressing an OsORR2 gene (a type-B RR) could reduce plant height in rice compared with the wild type (WT). Using quantitative real time (RT-qPCR) assay, OsORR2was expressed widely in most tissues such as root, culm, sheath, leaf, and panicle. Strong signals were detected in leaf mesophyll cells and anther by in situ hybridization assays (ISH). The subcellular localization of OsORR2 was in cell nucleus. In addition, we found that the transcriptional expression levels of type-A RR genes such as OsRR9, OsRR10, OsRR12, and OsRR13 were significantly up-regulated in the overexpression transgenic plants (OE) plants. Taken together, our data suggested that OsORR2was involved in the development of plant height in rice and provided a foundation for future deep molecular research of the type-B RRs.
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Affiliation(s)
- Fachao Shi
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Engineering Research Center for Pesticide & Fertilizer, Guangzhou, China
| | - Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuxing An
- Guangdong Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Engineering Research Center for Pesticide & Fertilizer, Guangzhou, China
- CONTACT Yuxing an Bioengineering Building No.1905, Shiliugang road 10#, Haizhu District, Gungzhou city, China
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20
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Yamburenko MV, Worthen JM, Zeenat A, Azhar BJ, Swain S, Couitt AR, Shakeel SN, Kieber JJ, Schaller GE. Functional Analysis of the Rice Type-B Response Regulator RR22. FRONTIERS IN PLANT SCIENCE 2020; 11:577676. [PMID: 33240296 PMCID: PMC7683409 DOI: 10.3389/fpls.2020.577676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/14/2020] [Indexed: 05/15/2023]
Abstract
The phytohormone cytokinin plays a critical role in regulating growth and development throughout the life cycle of the plant. The primary transcriptional response to cytokinin is mediated by the action of the type-B response regulators (RRs), with much of our understanding for their functional roles being derived from studies in the dicot Arabidopsis. To examine the roles played by type-B RRs in a monocot, we employed gain-of-function and loss-of-function mutations to characterize RR22 function in rice. Ectopic overexpression of RR22 in rice results in an enhanced cytokinin response based on molecular and physiological assays. Phenotypes associated with enhanced activity of RR22 include effects on leaf and root growth, inflorescence architecture, and trichome formation. Analysis of four Tos17 insertion alleles of RR22 revealed effects on inflorescence architecture, trichomes, and development of the stigma brush involved in pollen capture. Both loss- and gain-of-function RR22 alleles affected the number of leaf silica-cell files, which provide mechanical stability and improve resistance to pathogens. Taken together, these results indicate that a delicate balance of cytokinin transcriptional activity is necessary for optimal growth and development in rice.
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Affiliation(s)
- Maria V. Yamburenko
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Jennifer M. Worthen
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Asyia Zeenat
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Beenish J. Azhar
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Swadhin Swain
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Adam R. Couitt
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Samina N. Shakeel
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Joseph J. Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- *Correspondence: G. Eric Schaller,
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21
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Li Y, Liu F, Li P, Wang T, Zheng C, Hou B. An Arabidopsis Cytokinin-Modifying Glycosyltransferase UGT76C2 Improves Drought and Salt Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:560696. [PMID: 33224159 PMCID: PMC7674613 DOI: 10.3389/fpls.2020.560696] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/09/2020] [Indexed: 05/10/2023]
Abstract
Drought and salt stresses are common environmental threats that negatively affect rice development and yield. Here we report that the overexpression of AtUGT76C2, a cytokinin glycosyltransferase, in rice modulates cytokinin homeostasis and confers the plants an eminent property in drought and salt tolerance. The transgenic plants exhibit sensitivity to salt and drought stress as well as abscisic acid during the germination stage and the postgermination stage while showing enhanced tolerance to drought and salinity at the young seedling stage and the mature stage. The overexpression of UGT76C2 decreases the endogenous cytokinin level and enhances root growth, which greatly contributes to stress adaptation. In addition, the transgenic plants also show enhanced ROS scavenging activity, reduced ion leakage under salt stress, smaller stomatal opening, and more proline and soluble sugar accumulation, which demonstrate that UGT76C2 acts as an important player in abiotic stress response in rice. To explore the molecular mechanism of UGT76C2 in response to stress adaptation, the expressions of eight stress-responsive genes including OsSOS1, OsPIP2.1, OsDREB2A, OsCOIN, OsABF2, OsRAB16, OsP5CR, and OsP5CS1 were detected, which showed notable upregulation in UGT76C2 overexpression plants under salt and drought stresses. Our results reveal that the ectopic expression of AtUGT76C2 confers the transgenic rice many traits in improving drought and salt stress tolerance in both developmental and physiological levels. It is believed that AtUGT76C2 could be a promising candidate gene for cultivating saline- and drought-tolerant rice.
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Affiliation(s)
- Yanjie Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Fangfei Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Pan Li
- College of Pharmacy>, Liaocheng University, Liaocheng, China
| | - Ting Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Bingkai Hou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Bingkai Hou,
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22
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Gujjar RS, Supaibulwatana K. The Mode of Cytokinin Functions Assisting Plant Adaptations to Osmotic Stresses. PLANTS (BASEL, SWITZERLAND) 2019; 8:E542. [PMID: 31779090 PMCID: PMC6963579 DOI: 10.3390/plants8120542] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/15/2023]
Abstract
Plants respond to abiotic stresses by activating a specific genetic program that supports survival by developing robust adaptive mechanisms. This leads to accelerated senescence and reduced growth, resulting in negative agro-economic impacts on crop productivity. Cytokinins (CKs) customarily regulate various biological processes in plants, including growth and development. In recent years, cytokinins have been implicated in adaptations to osmotic stresses with improved plant growth and yield. Endogenous CK content under osmotic stresses can be enhanced either by transforming plants with a bacterial isopentenyl transferase (IPT) gene under the control of a stress inducible promoter or by exogenous application of synthetic CKs. CKs counteract osmotic stress-induced premature senescence by redistributing soluble sugars and inhibiting the expression of senescence-associated genes. Elevated CK contents under osmotic stress antagonize abscisic acid (ABA) signaling and ABA mediated responses, delay leaf senescence, reduce reactive oxygen species (ROS) damage and lipid peroxidation, improve plant growth, and ameliorate osmotic stress adaptability in plants.
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Affiliation(s)
- Ranjit Singh Gujjar
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- Division of Crop Improvement, Indian Institute of Sugarcane Research, Lucknow 226002, India
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23
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Zhao J, Yu N, Ju M, Fan B, Zhang Y, Zhu E, Zhang M, Zhang K. ABC transporter OsABCG18 controls the shootward transport of cytokinins and grain yield in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6277-6291. [PMID: 31504730 PMCID: PMC6859808 DOI: 10.1093/jxb/erz382] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/16/2019] [Indexed: 05/05/2023]
Abstract
Cytokinins are one of the most important phytohormones and play essential roles in multiple life processes in planta. Root-derived cytokinins are transported to the shoots via long-distance transport. The mechanisms of long-distance transport of root-derived cytokinins remain to be demonstrated. In this study, we report that OsABCG18, a half-size ATP-binding cassette transporter from rice (Oryza sativa L.), is essential for the long-distance transport of root-derived cytokinins. OsABCG18 encodes a plasma membrane protein and is primarily expressed in the vascular tissues of the root, stem, and leaf midribs. Cytokinin profiling, as well as [14C]trans-zeatin tracer, and xylem sap assays, demonstrated that the shootward transport of root-derived cytokinins was significantly suppressed in the osabcg18 mutants. Transport assays in tobacco (Nicotiana benthamiana) indicated that OsABCG18 exhibited efflux transport activities for various substrates of cytokinins. While the mutation reduced root-derived cytokinins in the shoot and grain yield, overexpression of OsABCG18 significantly increased cytokinins in the shoot and improved grain yield. The findings for OsABCG18 as a transporter for long-distance transport of cytokinin provide new insights into the cytokinin transport mechanism and a novel strategy to increase cytokinins in the shoot and promote grain yield.
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Affiliation(s)
- Jiangzhe Zhao
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Ningning Yu
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Min Ju
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Biao Fan
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yanjun Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Engao Zhu
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Mengyuan Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- Correspondence:
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24
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Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. PLANT & CELL PHYSIOLOGY 2019; 60:2343-2355. [PMID: 31318417 DOI: 10.1093/pcp/pcz132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/01/2019] [Indexed: 05/09/2023]
Abstract
Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control the architecture of adventitious root remain largely unknown. Here, we studied the modulations in global genes activity in developing rice adventitious root by genome-wide RNA sequencing in response to external auxin and cytokinin signaling cues. We further analyzed spatiotemporal regulations of key developmental regulators emerged from our global transcriptome analysis. Interestingly, some of the key cell fate determinants such as homeodomain transcription factor (TF), OsHOX12, no apical meristem protein, OsNAC39, APETALA2/ethylene response factor, OsAP2/ERF-40 and WUSCHEL-related homeobox, OsWOX6.1 and OsWOX6.2, specifically expressed in adventitious root primordia. Functional analysis of one of these regulators, an auxin-induced TF containing AP2/ERF domain, OsAP2/ERF-40, demonstrates its sufficiency to confer the adventitious root fate. The ability to trigger the root developmental program is largely attributed to OsAP2/ERF-40-mediated dose-dependent transcriptional activation of genes that can facilitate generating effective auxin response, and OsERF3-OsWOX11-OsRR2 pathway. Our studies reveal gene regulatory network operating in response to hormone signaling pathways and identify a novel TF regulating adventitious root developmental program, a key agronomically important quantitative trait, upstream of OsERF3-OsWOX11-OsRR2 pathway.
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Affiliation(s)
- Ananya Neogy
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Tushar Garg
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anil Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Zeenu Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
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25
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Worthen JM, Yamburenko MV, Lim J, Nimchuk ZL, Kieber JJ, Schaller GE. Type-B response regulators of rice play key roles in growth, development and cytokinin signaling. Development 2019; 146:dev.174870. [PMID: 31160418 DOI: 10.1242/dev.174870] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Cytokinins are plant hormones with crucial roles in growth and development. Although cytokinin signaling is well characterized in the model dicot Arabidopsis, we are only beginning to understand its role in monocots, such as rice (Oryza sativa) and other cereals of agronomic importance. Here, we used primarily a CRISPR/Cas9 gene-editing approach to characterize the roles of a key family of transcription factors, the type-B response regulators (RRs), in cytokinin signaling in rice. Results from the analysis of single rr mutants as well as higher-order rr21/22/23 mutant lines revealed functional overlap as well as subfunctionalization within members of the gene family. Mutant phenotypes associated with decreased activity of rice type-B RRs included effects on leaf and root growth, inflorescence architecture, flower development and fertilization, trichome formation and cytokinin sensitivity. Development of the stigma brush involved in pollen capture was compromised in the rr21/22/23 mutant, whereas anther development was compromised in the rr24 mutant. Novel as well as conserved roles for type-B RRs in the growth and development of a monocot compared with dicots were identified.
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Affiliation(s)
- Jennifer M Worthen
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Maria V Yamburenko
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jeewoo Lim
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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26
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Freese NH, Estrada AR, Blakley IC, Duan J, Loraine AE. Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing. PLANT DIRECT 2019; 3:e00136. [PMID: 31245776 PMCID: PMC6589529 DOI: 10.1002/pld3.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/12/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Alternatively spliced genes produce multiple spliced isoforms, called transcript variants. In differential alternative splicing, transcript variant abundance differs across sample types. Differential alternative splicing is common in animal systems and influences cellular development in many processes, but its extent and significance is not as well known in plants. To investigate differential alternative splicing in plants, we examined RNA-Seq data from rice seedlings. The data included three biological replicates per sample type, approximately 30 million sequence alignments per replicate, and four sample types: roots and shoots treated with exogenous cytokinin delivered hydroponically or a mock treatment. Cytokinin treatment triggered expression changes in thousands of genes but had negligible effect on splicing patterns. However, many genes were differentially spliced between mock-treated roots and shoots, indicating that our methods were sufficiently sensitive to detect differential splicing between data sets. Quantitative fragment analysis of reverse transcriptase-PCR products made from newly prepared rice samples confirmed 9 of 10 differential splicing events between rice roots and shoots. Differential alternative splicing typically changed the relative abundance of splice variants that co-occurred in a data set. Analysis of a similar (but less deeply sequenced) RNA-Seq data set from Arabidopsis showed the same pattern. In both the Arabidopsis and rice RNA-Seq data sets, most genes annotated as alternatively spliced had small minor variant frequencies. Of splicing choices with abundant support for minor forms, most alternative splicing events were located within the protein-coding sequence and maintained the annotated reading frame. A tool for visualizing protein annotations in the context of genomic sequence (ProtAnnot) together with a genome browser (Integrated Genome Browser) were used to visualize and assess effects of differential splicing on gene function. In general, differentially spliced regions coincided with conserved protein domains, indicating that differential alternative splicing is likely to affect protein function between root and shoot tissue in rice.
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Affiliation(s)
- Nowlan H. Freese
- Department of Bioinformatics and GenomicsUniversity of North Carolina at CharlotteCharlotteNorth Carolina
| | - April R. Estrada
- Department of Bioinformatics and GenomicsUniversity of North Carolina at CharlotteCharlotteNorth Carolina
| | - Ivory C. Blakley
- Department of Bioinformatics and GenomicsUniversity of North Carolina at CharlotteCharlotteNorth Carolina
| | - Jinjie Duan
- Department of BiomedicineAarhus UniversityAarhus CDenmark
| | - Ann E. Loraine
- Department of Bioinformatics and GenomicsUniversity of North Carolina at CharlotteCharlotteNorth Carolina
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27
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Cortleven A, Leuendorf JE, Frank M, Pezzetta D, Bolt S, Schmülling T. Cytokinin action in response to abiotic and biotic stresses in plants. PLANT, CELL & ENVIRONMENT 2019; 42:998-1018. [PMID: 30488464 DOI: 10.1111/pce.13494] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 05/20/2023]
Abstract
The phytohormone cytokinin was originally discovered as a regulator of cell division. Later, it was described to be involved in regulating numerous processes in plant growth and development including meristem activity, tissue patterning, and organ size. More recently, diverse functions for cytokinin in the response to abiotic and biotic stresses have been reported. Cytokinin is required for the defence against high light stress and to protect plants from a novel type of abiotic stress caused by an altered photoperiod. Additionally, cytokinin has a role in the response to temperature, drought, osmotic, salt, and nutrient stress. Similarly, the full response to certain plant pathogens and herbivores requires a functional cytokinin signalling pathway. Conversely, different types of stress impact cytokinin homeostasis. The diverse functions of cytokinin in responses to stress and crosstalk with other hormones are described. Its emerging roles as a priming agent and as a regulator of growth-defence trade-offs are discussed.
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Affiliation(s)
- Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Jan Erik Leuendorf
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Manuel Frank
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Daniela Pezzetta
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Sylvia Bolt
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195, Berlin, Germany
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28
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Wang L, Qiao H. New Insights in Transcriptional Regulation of the Ethylene Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:790. [PMID: 31275338 PMCID: PMC6591485 DOI: 10.3389/fpls.2019.00790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/31/2019] [Indexed: 05/19/2023]
Abstract
As any living organisms, plants must respond to a wide variety of environmental stimuli. Plant hormones regulate almost all aspects of plant growth and development. Among all the plant hormones, ethylene is the only gaseous plant hormone that plays pleiotropic roles in plant growth, plant development and stress responses. Transcription regulation is one main mechanism by which a cell orchestrates gene activity. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Here we review the progress of transcription regulation in the ethylene response.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- *Correspondence: Hong Qiao,
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29
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Ni J, Shah FA, Liu W, Wang Q, Wang D, Zhao W, Lu W, Huang S, Fu S, Wu L. Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum. BMC PLANT BIOLOGY 2018; 18:96. [PMID: 29848288 PMCID: PMC5975670 DOI: 10.1186/s12870-018-1314-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/18/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sapium sebiferum, whose seeds contain high level of fatty acids, has been considered as one of the most important oil plants. However, the high male to female flower ratio limited the seed yield improvement and its industrial potentials. Thus, the study of the sex determination in S. sebiferum is of significant importance in increasing the seed yield. RESULTS In this study, we demonstrated that in S. sebiferum, cytokinin (CK) had strong feminization effects on the floral development. Exogenous application with 6-benzylaminopurine (6-BA) or thidiazuron (TDZ) significantly induced the development of female flowers and increased the fruit number. Interestingly, the feminization effects of cytokinin were also detected on the androecious genotype of S. sebiferum which only produce male flowers. To further investigate the mechanism underlying the role of cytokinin in the flower development and sex differentiation, we performed the comparative transcriptome analysis of the floral buds of the androecious plants subjected to 6-BA. The results showed that there were separately 129, 352 and 642 genes differentially expressed at 6 h, 12 h and 24 h after 6-BA treatment. Functional analysis of the differentially expressed genes (DEGs) showed that many genes are related to the hormonal biosynthesis and signaling, nutrients translocation and cell cycle. Moreover, there were twenty one flowering-related genes identified to be differentially regulated by 6-BA treatment. Specifically, the gynoecium development-related genes SPATULA (SPT), KANADI 2 (KAN2), JAGGED (JAG) and Cytochrome P450 78A9 (CYP79A9) were significantly up-regulated, whereas the expression of PISTILLATA (PI), TATA Box Associated Factor II 59 (TAFII59) and MYB Domain Protein 108 (MYB108) that were important for male organ development was down-regulated in response to 6-BA treatment, demonstrating that cytokinin could directly target the floral organ identity genes to regulate the flower sex. CONCLUSIONS Our work demonstrated that cytokinin is a potential regulator in female flower development in S. sebiferum. The transcriptome analysis of the floral sex transition from androecious to monoecious in response to cytokinin treatment on the androecious S. sebiferum provided valuable information related to the mechanism of sex determination in the perennial woody plants.
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Affiliation(s)
- Jun Ni
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Faheem Afzal Shah
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, Anhui China
| | - Wenbo Liu
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Qiaojian Wang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, Anhui China
| | - Dongdong Wang
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, Anhui China
| | - Weiwei Zhao
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Weili Lu
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Shengwei Huang
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
| | - Songling Fu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, Anhui China
| | - Lifang Wu
- Key laboratory of high magnetic field and Ion beam physical biology,Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031 China
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30
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Abstract
The phytohormone cytokinin plays diverse roles in plant development, influencing many agriculturally important processes, including growth, nutrient responses and the response to biotic and abiotic stresses. Cytokinin levels in plants are regulated by biosynthesis and inactivation pathways. Cytokinins are perceived by membrane-localized histidine-kinase receptors and are transduced through a His-Asp phosphorelay to activate a family of transcription factors in the nucleus. Here, and in the accompanying poster, we summarize the current understanding of cytokinin metabolism, transport and signaling, and discuss how this phytohormone regulates changes in gene expression to mediate its pleiotropic effects.
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Affiliation(s)
- Joseph J Kieber
- University of North Carolina, Biology Department, Chapel Hill, NC 27599-3280, USA
| | - G Eric Schaller
- Dartmouth College, Department of Biological Sciences, Hanover, NH 03755, USA
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31
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Chinnapandi B, Bucki P, Braun Miyara S. SlWRKY45, nematode-responsive tomato WRKY gene, enhances susceptibility to the root knot nematode; M. javanica infection. PLANT SIGNALING & BEHAVIOR 2017; 12:e1356530. [PMID: 29271721 PMCID: PMC5792125 DOI: 10.1080/15592324.2017.1356530] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 05/21/2023]
Abstract
The fluctuation of tomato's WRKY defense regulators during infection by the root knot nematode Meloidogyne javanica was analyzed: and the spatial and temporal expression of SlWRKY45 was studied in depth with regard to its response to nematode infection, phytohormones, and wounding. Expression of WRKY45 increased substantially within 5 d upon infection and continued through feeding-site development and gall maturation. Histological analysis of nematode feeding sites indicated that WRKY45 was highly expressed within the feeding cells and associated vascular parenchyma cells. Responses of SlWRKY45 promoters to several phytohormones showed that WRKY45 was highly induced by specific phytohormones, including cytokinin, auxin, and the defense-signaling molecule salicylic acid (SA), but not by the jasmonates. Overexpressing tomato lines were generated, and infection tests showed that, significantly, roots over-expressing SlWRKY45 contained substantially increased number of females, indicating that WRKY45 overexpression supported faster nematode development. qRT-PCR tests have shown roots overexpressing WRKY45 suppressed the jasmonic acid and salicylic acid marker genes, proteinase inhibitor (PI), and pathogenesis related protein (PR1), respectively, and also the cytokinin response factors CRF1 and CRF6. Overall, this study indicated SlWRKY45 to be a potential transcription factor whose manipulation by the invading nematode might be critical for coordination of hormone signals supporting favorable condition for nematode development in root tissue.
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Affiliation(s)
- Bharathiraja Chinnapandi
- Department of Entomology and the Nematology and Chemistry Units, Agricultural Research Organization (ARO), the Volcani Center, Rishon Lezion, Israel
| | - Patricia Bucki
- Department of Entomology and the Nematology and Chemistry Units, Agricultural Research Organization (ARO), the Volcani Center, Rishon Lezion, Israel
| | - Sigal Braun Miyara
- Department of Entomology and the Nematology and Chemistry Units, Agricultural Research Organization (ARO), the Volcani Center, Rishon Lezion, Israel
- CONTACT Sigal Braun Miyara, PhD , Department of Entomology and the Nematology and Chemistry Units, ARO, Volcani Center, HaMaccabim Road, P.O. Box 15159, Rishon Lezion 7528809, Israel
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