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Dutilleul C, Ribeiro I, Blanc N, Nezames CD, Deng XW, Zglobicki P, Palacio Barrera AM, Atehortùa L, Courtois M, Labas V, Giglioli-Guivarc'h N, Ducos E. ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis. Plant Cell Environ 2016; 39:185-98. [PMID: 26147561 DOI: 10.1111/pce.12605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 05/12/2023]
Abstract
The tagging-via-substrate approach designed for the capture of mammal prenylated proteins was adapted to Arabidopsis cell culture. In this way, proteins are in vivo tagged with an azide-modified farnesyl moiety and captured thanks to biotin alkyne Click-iT® chemistry with further streptavidin-affinity chromatography. Mass spectrometry analyses identified four small GTPases and ASG2 (ALTERED SEED GERMINATION 2), a protein previously associated to the seed germination gene network. ASG2 is a conserved protein in plants and displays a unique feature that associates WD40 domains and tetratricopeptide repeats. Additionally, we show that ASG2 has a C-terminal CaaX-box that is farnesylated in vitro. Protoplast transfections using CaaX prenyltransferase mutants show that farnesylation provokes ASG2 nucleus exclusion. Moreover, ASG2 interacts with DDB1 (DAMAGE DNA BINDING protein 1), and the subcellular localization of this complex depends on ASG2 farnesylation status. Finally, germination and root elongation experiments reveal that asg2 and the farnesyltransferase mutant era1 (ENHANCED RESPONSE TO ABSCISIC ACID (ABA) 1) behave in similar manners when exposed to ABA or salt stress. To our knowledge, ASG2 is the first farnesylated DWD (DDB1 binding WD40) protein related to ABA response in Arabidopsis that may be linked to era1 phenotypes.
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Affiliation(s)
- Christelle Dutilleul
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Iliana Ribeiro
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Nathalie Blanc
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Cynthia D Nezames
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Xing Wang Deng
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Piotr Zglobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Ana María Palacio Barrera
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Lucia Atehortùa
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Martine Courtois
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, UMR CNRS 7247, UFR, IFC, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, Nouzilly, F-37380, France
| | - Nathalie Giglioli-Guivarc'h
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Eric Ducos
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
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Seo KI, Lee JH, Nezames CD, Zhong S, Song E, Byun MO, Deng XW. ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling. Plant Cell 2014; 26:695-711. [PMID: 24563203 PMCID: PMC3967034 DOI: 10.1105/tpc.113.119974] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/26/2013] [Accepted: 02/05/2014] [Indexed: 05/17/2023]
Abstract
Members of the DDB1-CUL4-associated factors (DCAFs) family directly bind to DAMAGED DNA BINDING PROTEIN1 (DDB1) and function as the substrate receptors in CULLIN4-based E3 (CUL4) ubiquitin ligases, which regulate the selective ubiquitination of proteins. Here, we describe a DCAF protein, ABD1 (for ABA-hypersensitive DCAF1), that negatively regulates abscisic acid (ABA) signaling in Arabidopsis thaliana. ABD1 interacts with DDB1 in vitro and in vivo, indicating that it likely functions as a CUL4 E3 ligase substrate receptor. ABD1 expression is induced by ABA, and mutations in ABD1 result in ABA- and NaCl-hypersensitive phenotypes. Loss of ABD1 leads to hyperinduction of ABA-responsive genes and higher accumulation of the ABA-responsive transcription factor ABA INSENSITIVE5 (ABI5), hypersensitivity to ABA during seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, ultimately, increased drought tolerance. ABD1 directly interacts with ABI5 in yeast two-hybrid assays and associates with ABI5 in vivo by coimmunoprecipitation, and the interaction was found in the nucleus by bimolecular fluorescence complementation. Furthermore, loss of ABD1 results in a retardation of ABI5 degradation by the 26S proteasome. Taken together, these data suggest that the DCAF-CUL4 E3 ubiquitin ligase assembled with ABD1 is a negative regulator of ABA responses by directly binding to and affecting the stability of ABI5 in the nucleus.
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Affiliation(s)
- Kyoung-In Seo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Jae-Hoon Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Department of Biology Education, Pusan National University, Pusan 609-735, Korea
| | - Cynthia D. Nezames
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Shangwei Zhong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Eunyoung Song
- Department of Biology Education, Pusan National University, Pusan 609-735, Korea
| | - Myung-Ok Byun
- Department of Molecular Physiology and Biochemistry, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Address correspondence to
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Shi H, Zhong S, Mo X, Liu N, Nezames CD, Deng XW. HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis. Plant Cell 2013; 25:3770-84. [PMID: 24179122 PMCID: PMC3877798 DOI: 10.1105/tpc.113.117424] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/30/2013] [Accepted: 10/14/2013] [Indexed: 05/19/2023]
Abstract
Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that phytochrome-interacting factor1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, long hypocotyl in far-red1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1-PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1-PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1-PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.
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Affiliation(s)
- Hui Shi
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Shangwei Zhong
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Xiaorong Mo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Na Liu
- Yale Stem Cell Center and Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06519
| | - Cynthia D. Nezames
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Address correspondence to
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Dai M, Xue Q, Mccray T, Margavage K, Chen F, Lee JH, Nezames CD, Guo L, Terzaghi W, Wan J, Deng XW, Wang H. The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis. Plant Cell 2013; 25:517-34. [PMID: 23404889 PMCID: PMC3608775 DOI: 10.1105/tpc.112.105767] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/18/2012] [Accepted: 01/24/2013] [Indexed: 05/19/2023]
Abstract
The basic Leucine zipper transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) is a key regulator of abscisic acid (ABA)-mediated seed germination and postgermination seedling growth. While a family of SUCROSE NONFERMENTING1-related protein kinase2s (SnRK2s) is responsible for ABA-induced phosphorylation and stabilization of ABI5, the phosphatase(s) responsible for dephosphorylating ABI5 is still unknown. Here, we demonstrate that mutations in FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of Ser/Thr PROTEIN PHOSPHATASE6 (PP6), cause an ABA hypersensitive phenotype in Arabidopsis thaliana, including ABA-mediated inhibition of seed germination and seedling growth. Conversely, overexpression of FyPP causes reduced sensitivity to ABA. The ABA hypersensitive phenotype of FyPP loss-of-function mutants is ABI5 dependent, and the amount of phosphorylated and total ABI5 proteins inversely correlates with the levels of FyPP proteins. Moreover, FyPP proteins physically interact with ABI5 in vitro and in vivo, and the strength of the interaction depends on the ABI5 phosphorylation status. In vitro phosphorylation assays show that FyPP proteins directly dephosphorylate ABI5. Furthermore, genetic and biochemical assays show that FyPP proteins act antagonistically with SnRK2 kinases to regulate ABI5 phosphorylation and ABA responses. Thus, Arabidopsis PP6 phosphatase regulates ABA signaling through dephosphorylation and destabilization of ABI5.
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Affiliation(s)
- Mingqiu Dai
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Qin Xue
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Tyra Mccray
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Kathryn Margavage
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766
| | - Fang Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Jae-Hoon Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Department of Biology Education, Pusan National University, Busan 609-735, Korea
| | - Cynthia D. Nezames
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Liquan Guo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130062, China
| | - William Terzaghi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766
| | - Jianmin Wan
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing 100081, China
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing 100081, China
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
- College of Life Science, Capital Normal University, Beijing, 100048, China
- Address correspondence to
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Abstract
The ubiquitin-proteasome system is a key mechanism that plants use to generate adaptive responses in coping with various environmental stresses. Cullin-RING (CRL) complexes represent a predominant group of ubiquitin E3 ligases in this system. In this review, we focus on the CRL E3s that have been implicated in abiotic stress signaling pathways in Arabidopsis. By comparing and analyzing these cases, we hope to gain a better understanding on how CRL complexes work under various settings in an attempt to decipher the clues about the regulatory mechanism of CRL E3s.
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Affiliation(s)
- Liquan Guo
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven 06520, Connecticut, USA
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Nezames CD, Sjogren CA, Barajas JF, Larsen PB. The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum-dependent root growth inhibition. Plant Cell 2012; 24:608-21. [PMID: 22345493 PMCID: PMC3315236 DOI: 10.1105/tpc.112.095596] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 01/06/2012] [Accepted: 02/02/2012] [Indexed: 05/17/2023]
Abstract
Aluminum (Al) toxicity is a global issue that severely limits root growth in acidic soils. Isolation of suppressors of the Arabidopsis thaliana Al-hypersensitive mutant, als3-1, resulted in identification of a cell cycle checkpoint factor, ALUMINUM TOLERANT2 (ALT2), which monitors and responds to DNA damage. ALT2 is required for active stoppage of root growth after Al exposure, because alt2 loss-of-function mutants fail to halt root growth after Al exposure, do not accumulate CyclinB1;1 in the root tip, and fail to force differentiation of the quiescent center. Thus, alt2-1 mutants are highly tolerant of Al levels that are severely inhibitory to the wild type. The alt2-1 allele is a loss-of-function mutation in a protein containing a putative DDB1-binding WD40 motif, previously identified as TANMEI, which is required for assessment of DNA integrity, including monitoring of DNA crosslinks. alt2-1 and atr loss-of-function mutants, the latter of which affects the cell cycle checkpoint ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED, are severely sensitive to DNA crosslinking agents and have increased Al tolerance. These results suggest that Al likely acts as a DNA-damaging agent in vivo and that Al-dependent root growth inhibition, in part, arises from detection of and response to this damage by TANMEI/ALT2 and ATR, both of which actively halt cell cycle progression and force differentiation of the quiescent center.
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Affiliation(s)
| | | | | | - Paul B. Larsen
- Department of Biochemistry, University of California, Riverside, California 92521
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Nezames CD, Ochoa V, Larsen PB. Mutational loss of Arabidopsis SLOW WALKER2 results in reduced endogenous spermine concomitant with increased aluminum sensitivity. Funct Plant Biol 2012; 40:67-78. [PMID: 32481087 DOI: 10.1071/fp12234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 09/20/2012] [Indexed: 06/11/2023]
Abstract
A previously-identified Arabidopsis mutant with hypersensitivity to aluminum, als7-1 was studied further to determine the nature of the mutation and subsequently establish the biochemical basis of the increase in Al sensitivity. Physiological analysis revealed that the Al hypersensitivity phenotype is correlated with increased Al uptake and Al-dependent gene expression, indicating that als7-1 has a defect in an Al-exclusion mechanism. Cloning of the als7-1 mutation showed that it negatively affects the gene encoding the putative nucleolar localised ribosomal biogenesis factor SLOW WALKER2, which is required for normal gametogenesis and mitotic progression. Molecular analysis indicated that Al hypersensitivity in als7-1 is correlated with loss of expression of a factor required for S-adenosylmethionine recycling and reduced levels of endogenous polyamines in the mutant. Further analysis shows that Al-dependent root growth inhibition is reversed by addition of exogenous spermine, which is correlated with a significant reduction in Al uptake by spermine treated roots. Endogenous spermine likely functions to compete with Al3+ for binding to extra- and intracellular anionic sites, which suggests that increased spermine levels may be an effective means to improve root growth in Al toxic acid soil environments.
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Affiliation(s)
- Cynthia D Nezames
- Department of Biochemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Vanessa Ochoa
- Department of Biochemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Paul B Larsen
- Department of Biochemistry, University of California-Riverside, Riverside, CA 92521, USA
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