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Kao YT, Fleming WA, Ventura MJ, Bartel B. Genetic Interactions between PEROXIN12 and Other Peroxisome-Associated Ubiquitination Components. PLANT PHYSIOLOGY 2016; 172:1643-1656. [PMID: 27650450 PMCID: PMC5100787 DOI: 10.1104/pp.16.01211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/15/2016] [Indexed: 05/28/2023]
Abstract
Most eukaryotic cells require peroxisomes, organelles housing fatty acid β-oxidation and other critical metabolic reactions. Peroxisomal matrix proteins carry peroxisome-targeting signals that are recognized by one of two receptors, PEX5 or PEX7, in the cytosol. After delivering the matrix proteins to the organelle, these receptors are removed from the peroxisomal membrane or matrix. Receptor retrotranslocation not only facilitates further rounds of matrix protein import but also prevents deleterious PEX5 retention in the membrane. Three peroxisome-associated ubiquitin-protein ligases in the Really Interesting New Gene (RING) family, PEX2, PEX10, and PEX12, facilitate PEX5 retrotranslocation. However, the detailed mechanism of receptor retrotranslocation remains unclear in plants. We identified an Arabidopsis (Arabidopsis thaliana) pex12 Glu-to-Lys missense allele that conferred severe peroxisomal defects, including impaired β-oxidation, inefficient matrix protein import, and decreased growth. We compared this pex12-1 mutant to other peroxisome-associated ubiquitination-related mutants and found that RING peroxin mutants displayed elevated PEX5 and PEX7 levels, supporting the involvement of RING peroxins in receptor ubiquitination in Arabidopsis. Also, we observed that disruption of any Arabidopsis RING peroxin led to decreased PEX10 levels, as seen in yeast and mammals. Peroxisomal defects were exacerbated in RING peroxin double mutants, suggesting distinct roles of individual RING peroxins. Finally, reducing function of the peroxisome-associated ubiquitin-conjugating enzyme PEX4 restored PEX10 levels and partially ameliorated the other molecular and physiological defects of the pex12-1 mutant. Future biochemical analyses will be needed to determine whether destabilization of the RING peroxin complex observed in pex12-1 stems from PEX4-dependent ubiquitination on the pex12-1 ectopic Lys residue.
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Affiliation(s)
- Yun-Ting Kao
- Biochemistry and Cell Biology Program, Department of BioSciences, Rice University, Houston, Texas 77005 (Y.-T.K., W.A.F., M.J.V., B.B.)
| | - Wendell A Fleming
- Biochemistry and Cell Biology Program, Department of BioSciences, Rice University, Houston, Texas 77005 (Y.-T.K., W.A.F., M.J.V., B.B.)
| | - Meredith J Ventura
- Biochemistry and Cell Biology Program, Department of BioSciences, Rice University, Houston, Texas 77005 (Y.-T.K., W.A.F., M.J.V., B.B.)
| | - Bonnie Bartel
- Biochemistry and Cell Biology Program, Department of BioSciences, Rice University, Houston, Texas 77005 (Y.-T.K., W.A.F., M.J.V., B.B.)
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Liu T, Longhurst AD, Talavera-Rauh F, Hokin SA, Barton MK. The Arabidopsis transcription factor ABIG1 relays ABA signaled growth inhibition and drought induced senescence. eLife 2016; 5:e13768. [PMID: 27697148 PMCID: PMC5050019 DOI: 10.7554/elife.13768] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 08/31/2016] [Indexed: 01/04/2023] Open
Abstract
Drought inhibits plant growth and can also induce premature senescence. Here we identify a transcription factor, ABA INSENSITIVE GROWTH 1 (ABIG1) required for abscisic acid (ABA) mediated growth inhibition, but not for stomatal closure. ABIG1 mRNA levels are increased both in response to drought and in response to ABA treatment. When treated with ABA, abig1 mutants remain greener and produce more leaves than comparable wild-type plants. When challenged with drought, abig1 mutants have fewer yellow, senesced leaves than wild-type. Induction of ABIG1 transcription mimics ABA treatment and regulates a set of genes implicated in stress responses. We propose a model in which drought acts through ABA to increase ABIG1 transcription which in turn restricts new shoot growth and promotes leaf senescence. The results have implications for plant breeding: the existence of a mutant that is both ABA resistant and drought resistant points to new strategies for isolating drought resistant genetic varieties.
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Affiliation(s)
- Tie Liu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Adam D Longhurst
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Samuel A Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - M Kathryn Barton
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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The Roles of β-Oxidation and Cofactor Homeostasis in Peroxisome Distribution and Function in Arabidopsis thaliana. Genetics 2016; 204:1089-1115. [PMID: 27605050 DOI: 10.1534/genetics.116.193169] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/06/2016] [Indexed: 11/18/2022] Open
Abstract
Key steps of essential metabolic pathways are housed in plant peroxisomes. We conducted a microscopy-based screen for anomalous distribution of peroxisomally targeted fluorescence in Arabidopsis thaliana This screen uncovered 34 novel alleles in 15 genes affecting oil body mobilization, fatty acid β-oxidation, the glyoxylate cycle, peroxisome fission, and pexophagy. Partial loss-of-function of lipid-mobilization enzymes conferred peroxisomes clustered around retained oil bodies without other notable defects, suggesting that this microscopy-based approach was sensitive to minor perturbations, and that fatty acid β-oxidation rates in wild type are higher than required for normal growth. We recovered three mutants defective in PECTIN METHYLESTERASE31, revealing an unanticipated role in lipid mobilization for this cytosolic enzyme. Whereas mutations reducing fatty acid import had peroxisomes of wild-type size, mutations impairing fatty acid β-oxidation displayed enlarged peroxisomes, possibly caused by excess fatty acid β-oxidation intermediates in the peroxisome. Several fatty acid β-oxidation mutants also displayed defects in peroxisomal matrix protein import. Impairing fatty acid import reduced the large size of peroxisomes in a mutant defective in the PEROXISOMAL NAD+ TRANSPORTER (PXN), supporting the hypothesis that fatty acid accumulation causes pxn peroxisome enlargement. The diverse mutants isolated in this screen will aid future investigations of the roles of β-oxidation and peroxisomal cofactor homeostasis in plant development.
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54
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Chaiwanon J, Wang W, Zhu JY, Oh E, Wang ZY. Information Integration and Communication in Plant Growth Regulation. Cell 2016; 164:1257-1268. [PMID: 26967291 DOI: 10.1016/j.cell.2016.01.044] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 12/20/2022]
Abstract
Plants are equipped with the capacity to respond to a large number of diverse signals, both internal ones and those emanating from the environment, that are critical to their survival and adaption as sessile organisms. These signals need to be integrated through highly structured intracellular networks to ensure coherent cellular responses, and in addition, spatiotemporal actions of hormones and peptides both orchestrate local cell differentiation and coordinate growth and physiology over long distances. Further, signal interactions and signaling outputs vary significantly with developmental context. This review discusses our current understanding of the integrated intracellular and intercellular signaling networks that control plant growth.
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Affiliation(s)
- Juthamas Chaiwanon
- Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wenfei Wang
- Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Jia-Ying Zhu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Eunkyoo Oh
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Zhi-Yong Wang
- Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
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55
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Rowe JH, Topping JF, Liu J, Lindsey K. Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. THE NEW PHYTOLOGIST 2016; 211:225-39. [PMID: 26889752 PMCID: PMC4982081 DOI: 10.1111/nph.13882] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/06/2016] [Indexed: 05/17/2023]
Abstract
Understanding the mechanisms regulating root development under drought conditions is an important question for plant biology and world agriculture. We examine the effect of osmotic stress on abscisic acid (ABA), cytokinin and ethylene responses and how they mediate auxin transport, distribution and root growth through effects on PIN proteins. We integrate experimental data to construct hormonal crosstalk networks to formulate a systems view of root growth regulation by multiple hormones. Experimental analysis shows: that ABA-dependent and ABA-independent stress responses increase under osmotic stress, but cytokinin responses are only slightly reduced; inhibition of root growth under osmotic stress does not require ethylene signalling, but auxin can rescue root growth and meristem size; osmotic stress modulates auxin transporter levels and localization, reducing root auxin concentrations; PIN1 levels are reduced under stress in an ABA-dependent manner, overriding ethylene effects; and the interplay among ABA, ethylene, cytokinin and auxin is tissue-specific, as evidenced by differential responses of PIN1 and PIN2 to osmotic stress. Combining experimental analysis with network construction reveals that ABA regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.
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Affiliation(s)
- James H. Rowe
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Jennifer F. Topping
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Junli Liu
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Keith Lindsey
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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Chai C, Wang Y, Valliyodan B, Nguyen HT. Comprehensive Analysis of the Soybean (Glycine max) GmLAX Auxin Transporter Gene Family. FRONTIERS IN PLANT SCIENCE 2016; 7:282. [PMID: 27014306 PMCID: PMC4783406 DOI: 10.3389/fpls.2016.00282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/22/2016] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin plays a critical role in regulation of plant growth and development as well as plant responses to abiotic stresses. This is mainly achieved through its uneven distribution in plant via a polar auxin transport process. Auxin transporters are major players in polar auxin transport. The AUXIN RESISTENT 1/LIKE AUX1 (AUX/LAX) auxin influx carriers belong to the amino acid permease family of proton-driven transporters and function in the uptake of indole-3-acetic acid (IAA). In this study, genome-wide comprehensive analysis of the soybean AUX/LAX (GmLAX) gene family, including phylogenic relationships, chromosome localization, and gene structure, was carried out. A total of 15 GmLAX genes, including seven duplicated gene pairs, were identified in the soybean genome. They were distributed on 10 chromosomes. Despite their higher percentage identities at the protein level, GmLAXs exhibited versatile tissue-specific expression patterns, indicating coordinated functioning during plant growth and development. Most GmLAXs were responsive to drought and dehydration stresses and auxin and abscisic acid (ABA) stimuli, in a tissue- and/or time point- sensitive mode. Several GmLAX members were involved in responding to salt stress. Sequence analysis revealed that promoters of GmLAXs contained different combinations of stress-related cis-regulatory elements. These studies suggest that the soybean GmLAXs were under control of a very complex regulatory network, responding to various internal and external signals. This study helps to identity candidate GmLAXs for further analysis of their roles in soybean development and adaption to adverse environments.
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Affiliation(s)
| | | | | | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of MissouriColumbia, MO, USA
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57
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Zhang GZ, Jin SH, Jiang XY, Dong RR, Li P, Li YJ, Hou BK. Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 90:77-93. [PMID: 26496910 DOI: 10.1007/s11103-015-0395-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/19/2015] [Indexed: 05/06/2023]
Abstract
The formation of auxin glucose conjugate is proposed to be one of the molecular modifications controlling auxin homeostasis. However, the involved mechanisms and relevant physiological significances are largely unknown or poorly understood. In this study, Arabidopsis UGT75D1 was at the first time identified to be an indole-3-butyric acid (IBA) preferring glycosyltransferase. Assessment of enzyme activity and IBA conjugates in transgenic plants ectopically expressing UGT75D1 indicated that the UGT75D1 catalytic specificity was maintained in planta. It was found that the expression pattern of UGT75D1 was specific in germinating seeds. Consistently, we found that transgenic seedlings with over-produced UGT75D1 exhibited smaller cotyledons and cotyledon epidermal cells than the wild type. In addition, UGT75D1 was found to be up-regulated under mannitol, salt and ABA treatments and the over-expression lines were tolerant to osmotic and salt stresses during germination, resulting in an increased germination rate. Quantitative RT-PCR analysis revealed that the mRNA levels of ABA INSENSITIVE 3 (ABI3) and ABI5 gene in ABA signaling were substantially down-regulated in the transgenic lines under stress treatments. Interestingly, AUXIN RESPONSE FACTOR 16 (ARF16) gene of transgenic lines was also dramatically down-regulated under the same stress conditions. Since ARF16 functions as an activator of ABI3 transcription, we supposed that UGT75D1 might play a role in stress tolerance during germination through modulating ARF16-ABI3 signaling. Taken together, our work indicated that, serving as the IBA preferring glycosyltransferase but distinct from other auxin glycosyltransferases identified so far, UGT75D1 might be a very important player mediating a crosstalk between cotyledon development and stress tolerance of germination at the early stage of plant growth.
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Affiliation(s)
- Gui-Zhi Zhang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Shang-Hui Jin
- School of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao-Yi Jiang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Rui-Rui Dong
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Pan Li
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Yan-Jie Li
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Bing-Kai Hou
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Chinese Ministry of Education; School of Life Sciences, Shandong University, Jinan, 250100, China.
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58
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Van de Poel B, Smet D, Van Der Straeten D. Ethylene and Hormonal Cross Talk in Vegetative Growth and Development. PLANT PHYSIOLOGY 2015; 169:61-72. [PMID: 26232489 PMCID: PMC4577414 DOI: 10.1104/pp.15.00724] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/29/2015] [Indexed: 05/20/2023]
Abstract
Ethylene is a gaseous plant hormone that most likely became a functional hormone during the evolution of charophyte green algae, prior to land colonization. From this ancient origin, ethylene evolved into an important growth regulator that is essential for myriad plant developmental processes. In vegetative growth, ethylene appears to have a dual role, stimulating and inhibiting growth, depending on the species, tissue, and cell type, developmental stage, hormonal status, and environmental conditions. Moreover, ethylene signaling and response are part of an intricate network in cross talk with internal and external cues. Besides being a crucial factor in the growth control of roots and shoots, ethylene can promote flowering, fruit ripening and abscission, as well as leaf and petal senescence and abscission and, hence, plays a role in virtually every phase of plant life. Last but not least, together with jasmonates, salicylate, and abscisic acid, ethylene is important in steering stress responses.
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Affiliation(s)
- Bram Van de Poel
- Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dajo Smet
- Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Physiology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
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59
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Abscisic Acid: Hidden Architect of Root System Structure. PLANTS 2015; 4:548-72. [PMID: 27135341 PMCID: PMC4844405 DOI: 10.3390/plants4030548] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/01/2015] [Accepted: 08/03/2015] [Indexed: 01/15/2023]
Abstract
Plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. The hormone Abscisic Acid (ABA) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. Curiously, ABA controls different aspects of root architecture in different plant species, perhaps providing some insight into the great diversity of root architecture in different plants, both from different taxa and from different environments. ABA is an ancient signaling pathway, acquired well before the diversification of land plants. Nonetheless, how this ancient signaling module is implemented or interacts within a larger signaling network appears to vary in different species. This review will examine the role of ABA in the control of root architecture, focusing on the regulation of lateral root formation in three plant species, Arabidopsis thaliana, Medicago truncatula and Oryza sativa. We will consider how the implementation of the ABA signaling module might be a target of natural selection, to help contribute to the diversity of root architecture in nature.
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60
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Li J, Xu HH, Liu WC, Zhang XW, Lu YT. Ethylene Inhibits Root Elongation during Alkaline Stress through AUXIN1 and Associated Changes in Auxin Accumulation. PLANT PHYSIOLOGY 2015; 168:1777-91. [PMID: 26109425 PMCID: PMC4528753 DOI: 10.1104/pp.15.00523] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/23/2015] [Indexed: 05/03/2023]
Abstract
Soil alkalinity causes major reductions in yield and quality of crops worldwide. The plant root is the first organ sensing soil alkalinity, which results in shorter primary roots. However, the mechanism underlying alkaline stress-mediated inhibition of root elongation remains to be further elucidated. Here, we report that alkaline conditions inhibit primary root elongation of Arabidopsis (Arabidopsis thaliana) seedlings by reducing cell division potential in the meristem zones and that ethylene signaling affects this process. The ethylene perception antagonist silver (Ag(+)) alleviated the inhibition of root elongation by alkaline stress. Moreover, the ethylene signaling mutants ethylene response1-3 (etr1-3), ethylene insensitive2 (ein2), and ein3-1 showed less reduction in root length under alkaline conditions, indicating a reduced sensitivity to alkalinity. Ethylene biosynthesis also was found to play a role in alkaline stress-mediated root inhibition; the ethylene overproducer1-1 mutant, which overproduces ethylene because of increased stability of 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE5, was hypersensitive to alkaline stress. In addition, the ethylene biosynthesis inhibitor cobalt (Co(2+)) suppressed alkaline stress-mediated inhibition of root elongation. We further found that alkaline stress caused an increase in auxin levels by promoting expression of auxin biosynthesis-related genes, but the increase in auxin levels was reduced in the roots of the etr1-3 and ein3-1 mutants and in Ag(+)/Co(2+)-treated wild-type plants. Additional genetic and physiological data showed that AUXIN1 (AUX1) was involved in alkaline stress-mediated inhibition of root elongation. Taken together, our results reveal that ethylene modulates alkaline stress-mediated inhibition of root growth by increasing auxin accumulation by stimulating the expression of AUX1 and auxin biosynthesis-related genes.
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Affiliation(s)
- Juan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China (J.L., W.-C.L., X.-W.Z., Y.-T.L.); andJiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China (H.-H.X.)
| | - Heng-Hao Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China (J.L., W.-C.L., X.-W.Z., Y.-T.L.); andJiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China (H.-H.X.)
| | - Wen-Cheng Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China (J.L., W.-C.L., X.-W.Z., Y.-T.L.); andJiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China (H.-H.X.)
| | - Xiao-Wei Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China (J.L., W.-C.L., X.-W.Z., Y.-T.L.); andJiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China (H.-H.X.)
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China (J.L., W.-C.L., X.-W.Z., Y.-T.L.); andJiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China (H.-H.X.)
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61
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Enders TA, Oh S, Yang Z, Montgomery BL, Strader LC. Genome Sequencing of Arabidopsis abp1-5 Reveals Second-Site Mutations That May Affect Phenotypes. THE PLANT CELL 2015; 27:1820-6. [PMID: 26106149 PMCID: PMC4531353 DOI: 10.1105/tpc.15.00214] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/18/2015] [Accepted: 06/04/2015] [Indexed: 05/19/2023]
Abstract
Auxin regulates numerous aspects of plant growth and development. For many years, investigating roles for AUXIN BINDING PROTEIN1 (ABP1) in auxin response was impeded by the reported embryo lethality of mutants defective in ABP1. However, identification of a viable Arabidopsis thaliana TILLING mutant defective in the ABP1 auxin binding pocket (abp1-5) allowed inroads into understanding ABP1 function. During our own studies with abp1-5, we observed growth phenotypes segregating independently of the ABP1 lesion, leading us to sequence the genome of the abp1-5 line described previously. We found that the abp1-5 line we sequenced contains over 8000 single nucleotide polymorphisms in addition to the ABP1 mutation and that at least some of these mutations may originate from the Arabidopsis Wassilewskija accession. Furthermore, a phyB null allele in the abp1-5 background is likely causative for the long hypocotyl phenotype previously attributed to disrupted ABP1 function. Our findings complicate the interpretation of abp1-5 phenotypes for which no complementation test was conducted. Our findings on abp1-5 also provide a cautionary tale illustrating the need to use multiple alleles or complementation lines when attributing roles to a gene product.
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Affiliation(s)
- Tara A Enders
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Sookyung Oh
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Zhenbiao Yang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Beronda L Montgomery
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, Missouri 63130
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62
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Michniewicz M, Frick EM, Strader LC. Gateway-compatible tissue-specific vectors for plant transformation. BMC Res Notes 2015; 8:63. [PMID: 25884475 PMCID: PMC4352289 DOI: 10.1186/s13104-015-1010-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 02/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding regulation of developmental events has increasingly required the use of tissue-specific expression of diverse genes affecting plant growth and environmental responses. FINDINGS To allow for cloning of presumptive promoters with tissue-specific activities, we created two plant expression vectors with multiple cloning sites upstream of a Gateway cassette for expression of either untagged or YFP-tagged genes of interest. For fast and easy tissue-specific expression of desired genes, we further developed an initial set of Gateway-compatible tissue-specific gene expression vectors that allow for the expression of YFP-tagged or untagged proteins driven by the ALCOHOL DEHYDROGENASE1, CHLOROPHYLL A/B BINDING PROTEIN 1, COBRA LIKE1, EXPANSIN7, LATERAL ORGAN BOUNDARIES-DOMAIN 16, SCARECROW, UBIQUITIN10, and WOODEN LEG upstream regulatory regions. CONCLUSIONS These vectors provide an invaluable resource to the plant community, allowing for rapid generation of a variety of tissue-specific expression constructs.
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Affiliation(s)
- Marta Michniewicz
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.
| | - Elizabeth M Frick
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.
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63
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Thole JM, Strader LC. Next-generation sequencing as a tool to quickly identify causative EMS-generated mutations. PLANT SIGNALING & BEHAVIOR 2015; 10:e1000167. [PMID: 26039464 PMCID: PMC4622007 DOI: 10.1080/15592324.2014.1000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The advent of next generation sequencing has influenced every aspect of biological research. Many labs are now using whole genome sequencing in Arabidopsis thaliana as a means to quickly identify EMS-generated mutations present in isolated mutants. Following identification of these mutations, examination of T-DNA insertional alleles defective in candidate genes or complementation of the mutant phenotype with a wild type copy of candidate genes can be used to verify which mutation is causative for the phenotype of interest. Here, we discuss the benefits and pitfalls of using this method to identify mutations underlying phenotypes.
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Affiliation(s)
- J. M. Thole
- Department of Biology; St. Louis University, St. Louis, MO, USA
| | - L. C. Strader
- Department of Biology; Washington University in St. Louis, St. Louis, MO, USA
- Correspondence to: Lucia Strader;
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