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Vittozzi Y, Krüger T, Majee A, Née G, Wenkel S. ABI5 binding proteins: key players in coordinating plant growth and development. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00065-7. [PMID: 38584080 DOI: 10.1016/j.tplants.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants' growth and development.
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Affiliation(s)
- Ylenia Vittozzi
- University of Copenhagen, Department of Plant & Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; NovoCrops Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Thorben Krüger
- University of Münster, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
| | - Adity Majee
- Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, 907 36 Umeå, Sweden
| | - Guillaume Née
- University of Münster, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany.
| | - Stephan Wenkel
- University of Copenhagen, Department of Plant & Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; NovoCrops Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, 907 36 Umeå, Sweden.
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2
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Xiao S, Jiang L, Wang C, Ow DW. Arabidopsis OXS3 family proteins repress ABA signaling through interactions with AFP1 in the regulation of ABI4 expression. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5721-5734. [PMID: 34037750 DOI: 10.1093/jxb/erab237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Abscisic acid (ABA) and the AP2/ERF (APETALA2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor called ABA INSENSITIVE 4 (ABI4) play pivotal roles in plant growth responses to environmental stress. An analysis of seedling development in Arabidopsis ABA hypersensitive mutants suggested that OXS3 (OXIDATIVE STRESS 3), OXS3b, O3L3 (OXS3 LIKE 3), O3L4, and O3L6 were negative regulators of ABI4 expression. We therefore characterized the roles of the OXS3 family members in ABA signaling. All the above five OXS3 proteins were found to interact with AFP1 (ABI FIVE BINDING PROTEIN 1) in yeast two hybrid assays. Seven OXS3 family members including two other members O3L1 and O3L5 were found to interact with histone H2A.X, although OXS3b, O3L3, and O3L5 showed weaker interactions. ChIP-qPCR analysis showed that the absence of some of these OXS3 family proteins was associated with increased occupancy of histone γ-H2A.X at the ABI4 promoter, which also corresponded with de-repression of ABI4 expression. Repression of ABI4 expression, however, required both AFP1 and OXS3, OXS3b or O3L6. We conclude that in the absence of stress, OXS3 family proteins regulate γ-H2A.X deposition at the ABI4 promoter and that together with AFP1, OXS3 family proteins function to prevent ABA-induced growth arrest by co-repressing ABI4 through decreased promoter occupancy of histone γ-H2A.X.
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Affiliation(s)
- Shimin Xiao
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Jiang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changhu Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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3
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Carianopol CS, Gazzarrini S. SnRK1α1 Antagonizes Cell Death Induced by Transient Overexpression of Arabidopsis thaliana ABI5 Binding Protein 2 (AFP2). FRONTIERS IN PLANT SCIENCE 2020; 11:582208. [PMID: 33133119 PMCID: PMC7550686 DOI: 10.3389/fpls.2020.582208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 06/01/2023]
Abstract
Plants are continuously exposed to environmental stressors. They have thus evolved complex signaling pathways to govern responses to a variety of stimuli. The hormone abscisic acid (ABA) has been implicated in modulating both abiotic and biotic stress responses in plants. ABI5 Binding Proteins (AFPs) are a family of negative regulators of bZIP transcription factors of the AREB/ABF family, which promote ABA responses. AFP2 interacts with Snf1-Related protein Kinase 1 (SnRK1), which belongs to a highly conserved heterotrimeric kinase complex that is activated to re-establish energy homeostasis following stress. However, the role of this interaction is currently unknown. Here, we show that transient overexpression of Arabidopsis thaliana AFP2 in Nicotiana benthamiana leaves induces cell death (CD). Using truncated AFP2 constructs, we demonstrate that CD induction by AFP2 is dependent on the EAR domain. Co-expression of the catalytic subunit SnRK1α1, but not SnRK1α2, rescues AFP2-induced CD. Overexpression of SnRK1α1 has little effect on AFP2 protein level and does not affect AFP2 subcellular localization. Our results show that a high level of AFP2 is detrimental for cell function and that SnRK1α1 antagonizes AFP2-induced CD most likely through a mechanism that does not involve AFP2 protein degradation or a change in subcellular localization.
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Affiliation(s)
- Carina Steliana Carianopol
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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4
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Hinckley WE, Keymanesh K, Cordova JA, Brusslan JA. The HAC1 histone acetyltransferase promotes leaf senescence and regulates the expression of ERF022. PLANT DIRECT 2019; 3:e00159. [PMID: 31468026 PMCID: PMC6710649 DOI: 10.1002/pld3.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 05/08/2023]
Abstract
Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our laboratory is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 43 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.
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Affiliation(s)
- Will E. Hinckley
- Department of Biological SciencesCalifornia State UniversityLong BeachCAUSA
| | | | | | - Judy A. Brusslan
- Department of Biological SciencesCalifornia State UniversityLong BeachCAUSA
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5
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Wang YG, Fu FL, Yu HQ, Hu T, Zhang YY, Tao Y, Zhu JK, Zhao Y, Li WC. Interaction network of core ABA signaling components in maize. PLANT MOLECULAR BIOLOGY 2018; 96:245-263. [PMID: 29344831 DOI: 10.1007/s11103-017-0692-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/06/2017] [Indexed: 05/08/2023]
Abstract
We defined a comprehensive core ABA signaling network in monocot maize, including the gene expression, subcellular localization and interaction network of ZmPYLs, ZmPP2Cs, ZmSnRK2s and the putative substrates. The phytohormone abscisic acid (ABA) plays an important role in plant developmental processes and abiotic stress responses. In Arabidopsis, ABA is sensed by the PYL ABA receptors, which leads to binding of the PP2C protein phosphatase and activation of the SnRK2 protein kinases. These components functioning diversely and redundantly in ABA signaling are little known in maize. Using Arabidopsis pyl112458 and snrk2.2/3/6 mutants, we identified several ABA-responsive ZmPYLs and ZmSnRK2s, and also ZmPP2Cs. We showed the gene expression, subcellular localization and interaction network of ZmPYLs, ZmPP2Cs, and ZmSnRK2s, and the isolation of putative ZmSnRK2 substrates by mass spectrometry in monocot maize. We found that the ABA dependency of PYL-PP2C interactions is contingent on the identity of the PP2Cs. Among 238 candidate substrates for ABA-activated protein kinases, 69 are putative ZmSnRK2 substrates. Besides homologs of previously reported putative AtSnRK2 substrates, 23 phosphoproteins have not been discovered in the dicot Arabidopsis. Thus, we have defined a comprehensive core ABA signaling network in monocot maize and shed new light on ABA signaling.
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Affiliation(s)
- Ying-Ge Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Hu
- Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuan-Yuan Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Tao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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6
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Lynch TJ, Erickson BJ, Miller DR, Finkelstein RR. ABI5-binding proteins (AFPs) alter transcription of ABA-induced genes via a variety of interactions with chromatin modifiers. PLANT MOLECULAR BIOLOGY 2017; 93:403-418. [PMID: 27942958 DOI: 10.1007/s11103-016-0569-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/28/2016] [Indexed: 05/29/2023]
Abstract
Overexpression of ABI5/ABF binding proteins (AFPs) results in extreme ABA resistance of seeds via multiple mechanisms repressing ABA response, including interactions with histone deacetylases and the co-repressor TOPLESS. Several ABI5/ABF binding proteins (AFPs) inhibit ABA response, resulting in extreme ABA resistance in transgenic Arabidopsis overexpression lines, but their mechanism of action has remained obscure. By analogy to the related Novel Interactor of JAZ (NINJA) protein, it was suggested that the AFPs interact with the co-repressor TOPLESS to inhibit ABA-regulated gene expression. This study shows that the AFPs that inhibit ABA response have intrinsic repressor activity in a heterologous system, which does not depend on the domain involved in the interaction with TOPLESS. This domain is also not essential for repressing ABA response in transgenic plants, but does contribute to stronger ABA resistance. Additional interactions between some AFPs and histone deacetylase subunits were observed in yeast two-hybrid and bimolecular fluorescence assays, consistent with a more direct mechanism of AFP-mediated repression of gene expression. Chemical inhibition of histone deacetylase activity by trichostatin A suppressed AFP effects on a small fraction of the ABI5-regulated genes tested. Collectively, these results suggest that the AFPs participate in multiple mechanisms modulating ABA response, including both TOPLESS-dependent and -independent chromatin modification.
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Affiliation(s)
- Tim J Lynch
- Molecular, Cellular, and Developmental Biology Department, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - B Joy Erickson
- Biomolecular Science and Engineering Program, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Dusty R Miller
- Biomolecular Science and Engineering Program, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
- Chemistry Department, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ruth R Finkelstein
- Molecular, Cellular, and Developmental Biology Department, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA.
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7
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Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife 2016; 5. [PMID: 27873573 PMCID: PMC5119886 DOI: 10.7554/elife.17214] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/25/2016] [Indexed: 12/27/2022] Open
Abstract
Leaf senescence is an essential part of the plant lifecycle during which nutrients are re-allocated to other tissues. The regulation of leaf senescence is a complex process. However, the underlying mechanism is poorly understood. Here, we uncovered a novel and the pivotal role of Arabidopsis HDA9 (a RPD3-like histone deacetylase) in promoting the onset of leaf senescence. We found that HDA9 acts in complex with a SANT domain-containing protein POWERDRESS (PWR) and transcription factor WRKY53. Our genome-wide profiling of HDA9 occupancy reveals that HDA9 directly binds to the promoters of key negative regulators of senescence and this association requires PWR. Furthermore, we found that PWR is important for HDA9 nuclear accumulation. This study reveals an uncharacterized epigenetic complex involved in leaf senescence and provides mechanistic insights into how a histone deacetylase along with a chromatin-binding protein contribute to a robust regulatory network to modulate the onset of plant aging.
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Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Aaron Lomax
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
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Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife 2016. [PMID: 27873573 DOI: 10.7554/elife.17214.001-10.7554/elife.17214.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Leaf senescence is an essential part of the plant lifecycle during which nutrients are re-allocated to other tissues. The regulation of leaf senescence is a complex process. However, the underlying mechanism is poorly understood. Here, we uncovered a novel and the pivotal role of Arabidopsis HDA9 (a RPD3-like histone deacetylase) in promoting the onset of leaf senescence. We found that HDA9 acts in complex with a SANT domain-containing protein POWERDRESS (PWR) and transcription factor WRKY53. Our genome-wide profiling of HDA9 occupancy reveals that HDA9 directly binds to the promoters of key negative regulators of senescence and this association requires PWR. Furthermore, we found that PWR is important for HDA9 nuclear accumulation. This study reveals an uncharacterized epigenetic complex involved in leaf senescence and provides mechanistic insights into how a histone deacetylase along with a chromatin-binding protein contribute to a robust regulatory network to modulate the onset of plant aging.
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Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Aaron Lomax
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
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Yang T, Zhang L, Hao H, Zhang P, Zhu H, Cheng W, Wang Y, Wang X, Wang C. Nuclear-localized AtHSPR links abscisic acid-dependent salt tolerance and antioxidant defense in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1274-94. [PMID: 26603028 DOI: 10.1111/tpj.13080] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 05/25/2023]
Abstract
Salt stress from soil or irrigation water limits plant growth. A T-DNA insertion mutant in C24, named athspr (Arabidopsis thaliana heat shock protein-related), showed several phenotypes, including reduced organ size and enhanced sensitivity to environmental cues. The athspr mutant is severely impaired under salinity levels at which wild-type (WT) plants grow normally. AtHSPR encodes a nuclear-localized protein with ATPase activity, and its expression was enhanced by high salinity and abscisic acid (ABA). Overexpression (OE) of AtHSPR significantly enhanced tolerance to salt stress by increasing the activities of the antioxidant system and by maintaining K(+) /Na(+) homeostasis. Quantitative RT-PCR analyses showed that OE of AtHSPR increased the expression of ABA/stress-responsive, salt overly sensitive (SOS)-related and antioxidant-related genes. In addition, ABA content was reduced in athspr plants with or without salt stress, and exogenous ABA restored WT-like salt tolerance to athspr plants. athspr exhibited increased leaf stomatal density and stomatal index, slower ABA-induced stomatal closure and reduced drought tolerance relative to the WT. AtHSPR OE enhanced drought tolerance by reducing leaf water loss and stomatal aperture. Transcript profiling in athspr showed a differential salt-stress response for genes involved in accumulation of reactive oxygen species (ROS), ABA signaling, cell death, stress response and photosynthesis. Taken together, our results suggested that AtHSPR is involved in salt tolerance in Arabidopsis through modulation of ROS levels, ABA-dependent stomatal closure, photosynthesis and K(+) /Na(+) homeostasis.
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Affiliation(s)
- Tao Yang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Liang Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Medical College, Shihezi University, Shihezi, 832002, China
| | - Hongyan Hao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Peng Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Haowei Zhu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Wei Cheng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Yongli Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Xinyu Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
| | - Chongying Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 73000, China
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Zhang Q, Zhao C, Li M, Sun W, Liu Y, Xia H, Sun M, Li A, Li C, Zhao S, Hou L, Picimbon JF, Wang X, Zhao Y. Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response. BMC PLANT BIOLOGY 2013; 13:180. [PMID: 24237587 PMCID: PMC4225614 DOI: 10.1186/1471-2229-13-180] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/04/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. The microRNAs from the halophyte species Thellungiella salsuginea (salt cress), which exhibits extreme salt stress tolerance, remain to be investigated. The sequenced genome of T. salsuginea and the availability of high-throughput sequencing technology enabled us to discover the conserved and novel miRNAs in this plant species. It is interesting to identify the microRNAs from T. salsuginea genome wide and study their roles in salt stress response. RESULTS In this study, two T. salsuginea small RNA libraries were constructed and sequenced using Solexa technology. We identified 109 miRNAs that had previously been reported in other plant species. A total of 137 novel miRNA candidates were identified, among which the miR* sequence of 26 miRNAs was detected. In addition, 143 and 425 target mRNAs were predicted for the previously identified and Thellungiella-specific miRNAs, respectively. A quarter of these putative targets encode transcription factors. Furthermore, numerous signaling factor encoding genes, defense-related genes, and transporter encoding genes were amongst the identified targets, some of which were shown to be important for salt tolerance. Cleavage sites of seven target genes were validated by 5' RACE, and some of the miRNAs were confirmed by qRT-PCR analysis. The expression levels of 26 known miRNAs in the roots and leaves of plants subjected to NaCl treatment were determined by Affymetrix microarray analysis. The expression of most tested miRNA families was up- or down-regulated upon NaCl treatment. Differential response patterns between the leaves and roots were observed for these miRNAs. CONCLUSIONS Our results indicated that diverse set of miRNAs of T. salsuginea were responsive to salt stress and could play an important role in the salt stress response.
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Affiliation(s)
- Quan Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Chuanzhi Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Ming Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Wei Sun
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Yan Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Han Xia
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Mingnan Sun
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Aiqin Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Changsheng Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Shuzhen Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Lei Hou
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Jean-François Picimbon
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Xingjun Wang
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China
| | - Yanxiu Zhao
- College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
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11
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Transcriptome analysis of Barbarea vulgaris infested with diamondback moth (Plutella xylostella) larvae. PLoS One 2013; 8:e64481. [PMID: 23696897 PMCID: PMC3655962 DOI: 10.1371/journal.pone.0064481] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 04/16/2013] [Indexed: 01/23/2023] Open
Abstract
Background The diamondback moth (DBM, Plutella xylostella) is a crucifer-specific pest that causes significant crop losses worldwide. Barbarea vulgaris (Brassicaceae) can resist DBM and other herbivorous insects by producing feeding-deterrent triterpenoid saponins. Plant breeders have long aimed to transfer this insect resistance to other crops. However, a lack of knowledge on the biosynthetic pathways and regulatory networks of these insecticidal saponins has hindered their practical application. A pyrosequencing-based transcriptome analysis of B. vulgaris during DBM larval feeding was performed to identify genes and gene networks responsible for saponin biosynthesis and its regulation at the genome level. Principal Findings Approximately 1.22, 1.19, 1.16, 1.23, 1.16, 1.20, and 2.39 giga base pairs of clean nucleotides were generated from B. vulgaris transcriptomes sampled 1, 4, 8, 12, 24, and 48 h after onset of P. xylostella feeding and from non-inoculated controls, respectively. De novo assembly using all data of the seven transcriptomes generated 39,531 unigenes. A total of 37,780 (95.57%) unigenes were annotated, 14,399 of which were assigned to one or more gene ontology terms and 19,620 of which were assigned to 126 known pathways. Expression profiles revealed 2,016–4,685 up-regulated and 557–5188 down-regulated transcripts. Secondary metabolic pathways, such as those of terpenoids, glucosinolates, and phenylpropanoids, and its related regulators were elevated. Candidate genes for the triterpene saponin pathway were found in the transcriptome. Orthological analysis of the transcriptome with four other crucifer transcriptomes identified 592 B. vulgaris-specific gene families with a P-value cutoff of 1e−5. Conclusion This study presents the first comprehensive transcriptome analysis of B. vulgaris subjected to a series of DBM feedings. The biosynthetic and regulatory pathways of triterpenoid saponins and other DBM deterrent metabolites in this plant were classified. The results of this study will provide useful data for future investigations on pest-resistance phytochemistry and plant breeding.
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Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ. Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. THE PLANT CELL 2012; 24:3530-57. [PMID: 23023172 PMCID: PMC3480286 DOI: 10.1105/tpc.112.102046] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/14/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.
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Affiliation(s)
- Oliver Windram
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Stuart McHattie
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Claire Hill
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard Hickman
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Emma Cooke
- Molecular Organization and Assembly of Cells Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dafyd J. Jenkins
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Laura Baxter
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Emily Breeze
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven J. Kiddle
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Johanna Rhodes
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Susanna Atwell
- Department of Plant Sciences, University of California, Davis, California 95616
| | | | - Youn-sung Kim
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Oliver Stegle
- Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tuebingen, Germany
| | - Karsten Borgwardt
- Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tuebingen, Germany
- Zentrum für Bioinformatik, Eberhard Karls Universität, 72076 Tuebingen, Germany
| | - Cunjin Zhang
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alex Tabrett
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Roxane Legaie
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan Moore
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bärbel Finkenstadt
- Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David L. Wild
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew Mead
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David Rand
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vicky Buchanan-Wollaston
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Katherine J. Denby
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- Address correspondence to
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Cui H, Hao Y, Kong D. SCARECROW has a SHORT-ROOT-independent role in modulating the sugar response. PLANT PHYSIOLOGY 2012; 158:1769-78. [PMID: 22312006 PMCID: PMC3320184 DOI: 10.1104/pp.111.191502] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/06/2012] [Indexed: 05/20/2023]
Abstract
Sugar is essential for all cellular activities, but at high levels it inhibits growth and development. How plants balance the tradeoffs between the need for sugars and their growth inhibitory effects is poorly understood. SHORT-ROOT (SHR) and SCARECROW (SCR) are key regulators of stem cell renewal and radial patterning in the root of Arabidopsis (Arabidopsis thaliana). Recently, we identified direct targets of SHR at the genome scale. Intriguingly, among the top-ranked list, we found a number of genes that are involved in stress responses. By chromatin immunoprecipitation-polymerase chain reaction (PCR), we showed that SHR and SCR regulate a similar but not identical set of stress response genes. Consistent with this, scr and shr were found to be hypersensitive to abscisic acid (ABA). We further showed that both mutants were hypersensitive to high levels of glucose (Glc) but responded normally to high salinity and osmoticum. The endogenous levels of sucrose, Glc, and fructose were also elevated in shr and scr. Intriguingly, although shr had sugar content and developmental defects similar to those of scr, it was much less sensitive to Glc. Chromatin immunoprecipitation-PCR and reverse transcription-PCR assays as well as transgenic studies with an ABA-INSENSITIVE2 (ABI4)-β-glucuronidase reporter construct revealed that in root, SCR, but not SHR, repressed ABI4 and ABI5 directly and specifically in the apical meristem. When combined with abi4, scr became much more tolerant of high Glc. Finally, transgenic plants expressing ABI4 under the control of the SCR promoter manifested a short-root phenotype. These results together suggest that SCR has a SHR-independent role in mitigating the sugar response and that this role of SCR is important for root growth.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA.
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Garcia ME, Lynch T, Peeters J, Snowden C, Finkelstein R. A small plant-specific protein family of ABI five binding proteins (AFPs) regulates stress response in germinating Arabidopsis seeds and seedlings. PLANT MOLECULAR BIOLOGY 2008; 67:643-58. [PMID: 18484180 DOI: 10.1007/s11103-008-9344-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2007] [Accepted: 05/05/2008] [Indexed: 05/23/2023]
Abstract
The transcription factor ABA-Insensitive5 (ABI5) is a key regulator of ABA signaling and stress response in Arabidopsis seeds and seedlings. Potential ABI5-interacting proteins were identified by a yeast two-hybrid screen; the most prevalent interactors were a family of four highly conserved plant-specific proteins with no domains of known function, but homology to a previously characterized ABI Five Binding Protein (AFP). This study compares expression and function of the family members. The AFPs are induced by ABA and/or dehydrating stresses in young seedlings, but the developmental timing of their induction differs. Mutations in AFP1 or AFP2 result in increased sensitivity to ABA and salt, whereas afp4 mutants are mildly ABA-resistant. AFP2, like AFP1, acts epistatically to ABI5. Reduced germination or seedling growth of the mutants under stress correlates with a higher level of ABI5 protein when compared to wild-type seedlings, but it is not clear whether this is a cause or effect of the reduced growth. Although both ABI5 and the AFPs are ABA-induced, the ABI5:AFP ratio increases at high ABA concentrations, maintaining growth inhibition under severe stress. An AFP2:GFP fusion, which complements the afp2 mutation, is nuclear-localized in seedlings exposed to stress, but becomes delocalized before being degraded following removal of stress. The AFPs may also interact to varying extents with many ABI5-related bZIP transcription factors. This study suggests that germination and seedling growth are regulated by antagonistic interactions among at least two functionally redundant families, the AFPs and the ABI5-related proteins, providing a mechanism to fine-tune seedling stress responses.
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Affiliation(s)
- Mary Emily Garcia
- Molecular, Cellular, and Developmental Biology Department, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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Jung C, Seo JS, Han SW, Koo YJ, Kim CH, Song SI, Nahm BH, Choi YD, Cheong JJ. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY 2008; 146:623-35. [PMID: 18162593 PMCID: PMC2245844 DOI: 10.1104/pp.107.110981] [Citation(s) in RCA: 424] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 12/16/2007] [Indexed: 05/05/2023]
Abstract
AtMYB44 belongs to the R2R3 MYB subgroup 22 transcription factor family in Arabidopsis (Arabidopsis thaliana). Treatment with abscisic acid (ABA) induced AtMYB44 transcript accumulation within 30 min. The gene was also activated under various abiotic stresses, such as dehydration, low temperature, and salinity. In transgenic Arabidopsis carrying an AtMYB44 promoter-driven beta-glucuronidase (GUS) construct, strong GUS activity was observed in the vasculature and leaf epidermal guard cells. Transgenic Arabidopsis overexpressing AtMYB44 is more sensitive to ABA and has a more rapid ABA-induced stomatal closure response than wild-type and atmyb44 knockout plants. Transgenic plants exhibited a reduced rate of water loss, as measured by the fresh-weight loss of detached shoots, and remarkably enhanced tolerance to drought and salt stress compared to wild-type plants. Microarray analysis and northern blots revealed that salt-induced activation of the genes that encode a group of serine/threonine protein phosphatases 2C (PP2Cs), such as ABI1, ABI2, AtPP2CA, HAB1, and HAB2, was diminished in transgenic plants overexpressing AtMYB44. By contrast, the atmyb44 knockout mutant line exhibited enhanced salt-induced expression of PP2C-encoding genes and reduced drought/salt stress tolerance compared to wild-type plants. Therefore, enhanced abiotic stress tolerance of transgenic Arabidopsis overexpressing AtMYB44 was conferred by reduced expression of genes encoding PP2Cs, which have been described as negative regulators of ABA signaling.
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Affiliation(s)
- Choonkyun Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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