1
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Tian H, Lyu R, Yi P. Crosstalk between Rho of Plants GTPase signalling and plant hormones. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3778-3796. [PMID: 38616410 DOI: 10.1093/jxb/erae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Rho of Plants (ROPs) constitute a plant-specific subset of small guanine nucleotide-binding proteins within the Cdc42/Rho/Rac family. These versatile proteins regulate diverse cellular processes, including cell growth, cell division, cell morphogenesis, organ development, and stress responses. In recent years, the dynamic cellular and subcellular behaviours orchestrated by ROPs have unveiled a notable connection to hormone-mediated organ development and physiological responses, thereby expanding our knowledge of the functions and regulatory mechanisms of this signalling pathway. This review delineates advancements in understanding the interplay between plant hormones and the ROP signalling cascade, focusing primarily on the connections with auxin and abscisic acid pathways, alongside preliminary discoveries in cytokinin, brassinosteroid, and salicylic acid responses. It endeavours to shed light on the intricate, coordinated mechanisms bridging cell- and tissue-level signals that underlie plant cell behaviour, organ development, and physiological processes, and highlights future research prospects and challenges in this rapidly developing field.
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Affiliation(s)
- Haoyu Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Ruohan Lyu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Peishan Yi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
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2
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Jin S, Wei M, Wei Y, Jiang Z. Insights into Plant Sensory Mechanisms under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:1907. [PMID: 39065434 PMCID: PMC11280238 DOI: 10.3390/plants13141907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
As sessile organisms, plants cannot survive in harmful environments, such as those characterized by drought, flood, heat, cold, nutrient deficiency, and salt or toxic metal stress. These stressors impair plant growth and development, leading to decreased crop productivity. To induce an appropriate response to abiotic stresses, plants must sense the pertinent stressor at an early stage to initiate precise signal transduction. Here, we provide an overview of recent progress in our understanding of the molecular mechanisms underlying plant abiotic stress sensing. Numerous biomolecules have been found to participate in the process of abiotic stress sensing and function as abiotic stress sensors in plants. Based on their molecular structure, these biomolecules can be divided into four groups: Ca2+-permeable channels, receptor-like kinases (RLKs), sphingolipids, and other proteins. This improved knowledge can be used to identify key molecular targets for engineering stress-resilient crops in the field.
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Affiliation(s)
- Songsong Jin
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.J.); (M.W.); (Y.W.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mengting Wei
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.J.); (M.W.); (Y.W.)
| | - Yunmin Wei
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.J.); (M.W.); (Y.W.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhonghao Jiang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.J.); (M.W.); (Y.W.)
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3
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Caumon H, Vernoux T. A matter of time: auxin signaling dynamics and the regulation of auxin responses during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad132. [PMID: 37042516 DOI: 10.1093/jxb/erad132] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/19/2023]
Abstract
As auxin is a major regulator of plant development, studying the signaling mechanisms by which auxin influences cellular activities is of primary importance. In this review, we describe the current knowledge on the different modalities of signaling, from the well-characterized canonical nuclear auxin pathway, to the more recently discovered or re-discovered non-canonical modes of auxin signaling. In particular, we discuss how both the modularity of the nuclear auxin pathway and the dynamic regulation of its core components allow to trigger specific transcriptomic responses. We highlight the fact that the diversity of modes of auxin signaling allows for a wide range of timescales of auxin responses, from second-scale cytoplasmic responses to minute/hour-scale modifications of gene expression. Finally, we question the extent to which the temporality of auxin signaling and responses contributes to development in both the shoot and the root meristems. We conclude by stressing the fact that future investigations should allow to build an integrative view not only of the spatial control, but also of the temporality of auxin-mediated regulation of plant development, from the cell to the whole organism.
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Affiliation(s)
- Hugo Caumon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France
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4
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Science is a rollercoaster. NATURE PLANTS 2022; 8:1129-1130. [PMID: 36241738 DOI: 10.1038/s41477-022-01267-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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5
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ABP1-TMK auxin perception for global phosphorylation and auxin canalization. Nature 2022; 609:575-581. [PMID: 36071161 DOI: 10.1038/s41586-022-05187-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/03/2022] [Indexed: 12/22/2022]
Abstract
The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1-3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.
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6
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Abstract
Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.
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Affiliation(s)
- Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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7
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The Role of SBI2/ALG12/EBS4 in the Regulation of Endoplasmic Reticulum-Associated Degradation (ERAD) Studied by a Null Allele. Int J Mol Sci 2022; 23:ijms23105811. [PMID: 35628619 PMCID: PMC9147235 DOI: 10.3390/ijms23105811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022] Open
Abstract
Redundancy and lethality is a long-standing problem in genetics but generating minimal and lethal phenotypes in the knockouts of the same gene by different approaches drives this problem to a new high. In Asn (N)-linked glycosylation, a complex and ubiquitous cotranslational and post-translational protein modification required for the transfer of correctly folded proteins and endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins, ALG12 (EBS4) is an α 1, 6-mannosyltransferase catalyzing a mannose into Glc3Man9GlcNAc2. In Arabidopsis, T-DNA knockout alg12-T is lethal while likely ebs4 null mutants isolated by forward genetics are most healthy as weak alleles, perplexing researchers and demanding further investigations. Here, we isolated a true null allele, sbi2, with the W258Stop mutation in ALG12/EBS4. sbi2 restored the sensitivity of brassinosteroid receptor mutants bri1-5, bri1-9, and bri1-235 with ER-trapped BRI1 to brassinosteroids. Furthermore, sbi2 maturated earlier than the wild-type. Moreover, concomitant with impaired and misfolded proteins accumulated in the ER, sbi2 had higher sensitivity to tunicamycin and salt than the wild-type. Our findings thus clarify the role of SBI2/ALG12/EBS4 in the regulation of the ERAD of misfolded glycoproteins, and plant growth and stress response. Further, our study advocates the necessity and importance of using multiple approaches to validate genetics study.
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Smokvarska M, Jaillais Y, Martinière A. Function of membrane domains in rho-of-plant signaling. PLANT PHYSIOLOGY 2021; 185:663-681. [PMID: 33793925 PMCID: PMC8133555 DOI: 10.1093/plphys/kiaa082] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/25/2020] [Indexed: 05/18/2023]
Abstract
In a crowded environment, establishing interactions between different molecular partners can take a long time. Biological membranes have solved this issue, as they simultaneously are fluid and possess compartmentalized domains. This nanoscale organization of the membrane is often based on weak, local, and multivalent interactions between lipids and proteins. However, from local interactions at the nanoscale, different functional properties emerge at the higher scale, and these are critical to regulate and integrate cellular signaling. Rho of Plant (ROP) proteins are small guanosine triphosphate hydrolase enzymes (GTPases) involved in hormonal, biotic, and abiotic signaling, as well as fundamental cell biological properties such as polarity, vesicular trafficking, and cytoskeleton dynamics. Association with the membrane is essential for ROP function, as well as their precise targeting within micrometer-sized polar domains (i.e. microdomains) and nanometer-sized clusters (i.e. nanodomains). Here, we review our current knowledge about the formation and the maintenance of the ROP domains in membranes. Furthermore, we propose a model for ROP membrane targeting and discuss how the nanoscale organization of ROPs in membranes could determine signaling parameters like signal specificity, amplification, and integration.
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Affiliation(s)
- Marija Smokvarska
- BPMP, CNRS, INRAE, Univ Montpellier, Montpellier SupAgro, 34060 Montpellier, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, CNRS, INRAE, Université de Lyon, ENS de Lyon, UCB Lyon 1, F-69342 Lyon, France
| | - Alexandre Martinière
- BPMP, CNRS, INRAE, Univ Montpellier, Montpellier SupAgro, 34060 Montpellier, France
- Author for communication:
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9
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Schwechheimer C, Yalovsky S, Žárský V. Auxin does not inhibit endocytosis of PIN1 and PIN2 auxin efflux carriers. PLANT PHYSIOLOGY 2021; 186:kiab132. [PMID: 33742679 PMCID: PMC8195515 DOI: 10.1093/plphys/kiab132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany
| | - Shaul Yalovsky
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
- Laboratory of Cell Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague, Czech Republic
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10
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Gelová Z, Gallei M, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovičová Z, Verstraeten I, Han H, Hajný J, Hauschild R, Čovanová M, Zwiewka M, Hoermayer L, Fendrych M, Xu T, Vernoux T, Friml J. Developmental roles of Auxin Binding Protein 1 in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110750. [PMID: 33487339 DOI: 10.1016/j.plantsci.2020.110750] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear. Here we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation. The gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.
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Affiliation(s)
- Zuzana Gelová
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Michelle Gallei
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Markéta Pernisová
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France; Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Géraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Xixi Zhang
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Matouš Glanc
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12844 Prague, Czech Republic
| | - Lanxin Li
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jaroslav Michalko
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Zlata Pavlovičová
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Inge Verstraeten
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Huibin Han
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jakub Hajný
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Robert Hauschild
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Milada Čovanová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Praha 6, Czech Republic
| | - Marta Zwiewka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lukas Hoermayer
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Matyáš Fendrych
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Tongda Xu
- FAFU-Joint Centre, Horticulture and Metabolic Biology Centre, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, People's Republic of China
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Jiří Friml
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria.
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11
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Arieti RS, Staiger CJ. Auxin-induced actin cytoskeleton rearrangements require AUX1. THE NEW PHYTOLOGIST 2020; 226:441-459. [PMID: 31859367 PMCID: PMC7154765 DOI: 10.1111/nph.16382] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/10/2019] [Indexed: 05/06/2023]
Abstract
The actin cytoskeleton is required for cell expansion and implicated in cellular responses to the phytohormone auxin. However, the mechanisms that coordinate auxin signaling, cytoskeletal remodeling and cell expansion are poorly understood. Previous studies examined long-term actin cytoskeleton responses to auxin, but plants respond to auxin within minutes. Before this work, an extracellular auxin receptor - rather than the auxin transporter AUXIN RESISTANT 1 (AUX1) - was considered to precede auxin-induced cytoskeleton reorganization. In order to correlate actin array organization and dynamics with degree of cell expansion, quantitative imaging tools established baseline actin organization and illuminated individual filament behaviors in root epidermal cells under control conditions and after indole-3-acetic acid (IAA) application. We evaluated aux1 mutant actin organization responses to IAA and the membrane-permeable auxin 1-naphthylacetic acid (NAA). Cell length predicted actin organization and dynamics in control roots; short-term IAA treatments stimulated denser and more parallel, longitudinal arrays by inducing filament unbundling within minutes. Although AUX1 is necessary for full actin rearrangements in response to auxin, cytoplasmic auxin (i.e. NAA) stimulated a lesser response. Actin filaments became more 'organized' after IAA stopped elongation, refuting the hypothesis that 'more organized' actin arrays universally correlate with rapid growth. Short-term actin cytoskeleton response to auxin requires AUX1 and/or cytoplasmic auxin.
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Affiliation(s)
- Ruthie S. Arieti
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907‐2064USA
- Purdue University Interdisciplinary Life Sciences Graduate Program (PULSe)Purdue UniversityWest LafayetteIN47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Christopher J. Staiger
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907‐2064USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIN47907USA
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12
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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13
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Engineered Artificial MicroRNA Precursors Facilitate Cloning and Gene Silencing in Arabidopsis and Rice. Int J Mol Sci 2019; 20:ijms20225620. [PMID: 31717686 PMCID: PMC6888491 DOI: 10.3390/ijms20225620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/02/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Plant genome sequences are presently deciphered at a staggering speed, due to the rapid advancement of high-throughput sequencing technologies. However, functional genomics significantly lag behind due to technical obstacles related to functional redundancy and mutant lethality. Artificial microRNA (amiRNA) technology is a specific, reversible, and multiplex gene silencing tool that has been frequently used in generating constitutive or conditional mutants for gene functional interrogation. The routine approach to construct amiRNA precursors involves multiple polymerase chain reactions (PCRs) that can increase both time and labor expenses, as well as the chance to introduce sequence errors. Here, we report a simplified method to clone and express amiRNAs in Arabidopsis and rice based on the engineered Arabidopsis miR319a or rice miR528 precursor, which harbor restriction sites to facilitate one-step cloning of a single PCR product. Stem-loop reverse-transcriptase quantitative PCR (RT-qPCR) and functional assays validated that amiRNAs can be accurately processed from these modified precursors and work efficiently in plant protoplasts. In addition, Arabidopsis transgenic plants overexpressing the modified miR319a precursor or its derived amiRNA could exhibit strong gene silencing phenotypes, as expected. The simplified amiRNA cloning strategy will be broadly useful for functional genomic studies in Arabidopsis and rice, and maybe other dicotyledon and monocotyledon species as well.
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14
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Kubeš M, Napier R. Non-canonical auxin signalling: fast and curious. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2609-2614. [PMID: 30854547 PMCID: PMC6506764 DOI: 10.1093/jxb/erz111] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 02/25/2019] [Indexed: 05/20/2023]
Affiliation(s)
- Martin Kubeš
- School of Live Sciences, University of Warwick, Coventry, UK
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Slechtitelu, Olomouc, Czech Republic
- University Hradec Kralove, Faculty of Science, Department of Biology, Rokitanskeho, CZ-50003 Hradec Kralove, Czech Republic
| | - Richard Napier
- School of Live Sciences, University of Warwick, Coventry, UK
- Correspondence: or
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15
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Matthes MS, Best NB, Robil JM, Malcomber S, Gallavotti A, McSteen P. Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling. MOLECULAR PLANT 2019; 12:298-320. [PMID: 30590136 DOI: 10.1016/j.molp.2018.12.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/02/2018] [Accepted: 12/16/2018] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin has been shown to be of pivotal importance in growth and development of land plants. The underlying molecular players involved in auxin biosynthesis, transport, and signaling are quite well understood in Arabidopsis. However, functional characterizations of auxin-related genes in economically important crops, specifically maize and rice, are still limited. In this article, we comprehensively review recent functional studies on auxin-related genes in both maize and rice, compared with what is known in Arabidopsis, and highlight conservation and diversification of their functions. Our analysis is illustrated by phylogenetic analysis and publicly available gene expression data for each gene family, which will aid in the identification of auxin-related genes for future research. Current challenges and future directions for auxin research in maize and rice are discussed. Developments in gene editing techniques provide powerful tools for overcoming the issue of redundancy in these gene families and will undoubtedly advance auxin research in crops.
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Affiliation(s)
- Michaela Sylvia Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Norman Bradley Best
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Janlo M Robil
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA.
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16
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Shevtsov S, Nevo-Dinur K, Faigon L, Sultan LD, Zmudjak M, Markovits M, Ostersetzer-Biran O. Control of organelle gene expression by the mitochondrial transcription termination factor mTERF22 in Arabidopsis thaliana plants. PLoS One 2018; 13:e0201631. [PMID: 30059532 PMCID: PMC6066234 DOI: 10.1371/journal.pone.0201631] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/18/2018] [Indexed: 11/28/2022] Open
Abstract
Mitochondria are key sites for cellular energy metabolism and are essential to cell survival. As descendants of eubacterial symbionts (specifically α-proteobacteria), mitochondria contain their own genomes (mtDNAs), RNAs and ribosomes. Plants need to coordinate their energy demands during particular growth and developmental stages. The regulation of mtDNA expression is critical for controlling the oxidative phosphorylation capacity in response to physiological or environmental signals. The mitochondrial transcription termination factor (mTERF) family has recently emerged as a central player in mitochondrial gene expression in various eukaryotes. Interestingly, the number of mTERFs has been greatly expanded in the nuclear genomes of plants, with more than 30 members in different angiosperms. The majority of the annotated mTERFs in plants are predicted to be plastid- or mitochondria-localized. These are therefore expected to play important roles in organellar gene expression in angiosperms. Yet, functions have been assigned to only a small fraction of these factors in plants. Here, we report the characterization of mTERF22 (At5g64950) which functions in the regulation of mtDNA transcription in Arabidopsis thaliana. GFP localization assays indicate that mTERF22 resides within the mitochondria. Disruption of mTERF22 function results in reduced mtRNA accumulation and altered organelle biogenesis. Transcriptomic and run-on experiments suggest that the phenotypes of mterf22 mutants are attributable, at least in part, to altered mitochondria transcription, and indicate that mTERF22 affects the expression of numerous mitochondrial genes in Arabidopsis plants.
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Affiliation(s)
- Sofia Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Keren Nevo-Dinur
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Lior Faigon
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Laure D. Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Michal Zmudjak
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Mark Markovits
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, Israel
- * E-mail:
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17
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Nikonorova N, Yue K, Beeckman T, De Smet I. Arabidopsis research requires a critical re-evaluation of genetic tools. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3541-3544. [PMID: 29701839 DOI: 10.1093/jxb/ery161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re)investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.
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Affiliation(s)
- Natalia Nikonorova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Kun Yue
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
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18
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Zhang Q, Xing HL, Wang ZP, Zhang HY, Yang F, Wang XC, Chen QJ. Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention. PLANT MOLECULAR BIOLOGY 2018; 96:445-456. [PMID: 29476306 PMCID: PMC5978904 DOI: 10.1007/s11103-018-0709-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/06/2018] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE We present novel observations of high-specificity SpCas9 variants, sgRNA expression strategies based on mutant sgRNA scaffold and tRNA processing system, and CRISPR/Cas9-mediated T-DNA integrations. Specificity of CRISPR/Cas9 tools has been a major concern along with the reports of their successful applications. We report unexpected observations of high frequency off-target mutagenesis induced by CRISPR/Cas9 in T1 Arabidopsis mutants although the sgRNA was predicted to have a high specificity score. We also present evidence that the off-target effects were further exacerbated in the T2 progeny. To prevent the off-target effects, we tested and optimized two strategies in Arabidopsis, including introduction of a mCherry cassette for a simple and reliable isolation of Cas9-free mutants and the use of highly specific mutant SpCas9 variants. Optimization of the mCherry vectors and subsequent validation found that fusion of tRNA with the mutant rather than the original sgRNA scaffold significantly improves editing efficiency. We then examined the editing efficiency of eight high-specificity SpCas9 variants in combination with the improved tRNA-sgRNA fusion strategy. Our results suggest that highly specific SpCas9 variants require a higher level of expression than their wild-type counterpart to maintain high editing efficiency. Additionally, we demonstrate that T-DNA can be inserted into the cleavage sites of CRISPR/Cas9 targets with high frequency. Altogether, our results suggest that in plants, continuous attention should be paid to off-target effects induced by CRISPR/Cas9 in current and subsequent generations, and that the tools optimized in this report will be useful in improving genome editing efficiency and specificity in plants and other organisms.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hui-Li Xing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhi-Ping Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hai-Yan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fang Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xue-Chen Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qi-Jun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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19
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Paponov IA, Dindas J, Król E, Friz T, Budnyk V, Teale W, Paponov M, Hedrich R, Palme K. Auxin-Induced Plasma Membrane Depolarization Is Regulated by Auxin Transport and Not by AUXIN BINDING PROTEIN1. FRONTIERS IN PLANT SCIENCE 2018; 9:1953. [PMID: 30705682 PMCID: PMC6344447 DOI: 10.3389/fpls.2018.01953] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/14/2018] [Indexed: 05/20/2023]
Abstract
Auxin is a molecule, which controls many aspects of plant development through both transcriptional and non-transcriptional signaling responses. AUXIN BINDING PROTEIN1 (ABP1) is a putative receptor for rapid non-transcriptional auxin-induced changes in plasma membrane depolarization and endocytosis rates. However, the mechanism of ABP1-mediated signaling is poorly understood. Here we show that membrane depolarization and endocytosis inhibition are ABP1-independent responses and that auxin-induced plasma membrane depolarization is instead dependent on the auxin influx carrier AUX1. AUX1 was itself not involved in the regulation of endocytosis. Auxin-dependent depolarization of the plasma membrane was also modulated by the auxin efflux carrier PIN2. These data establish a new connection between auxin transport and non-transcriptional auxin signaling.
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Affiliation(s)
- Ivan A. Paponov
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Norwegian Institute of Bioeconomy Research, Klepp, Norway
- *Correspondence: Ivan A. Paponov,
| | - Julian Dindas
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Elżbieta Król
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Tatyana Friz
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Vadym Budnyk
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Centre of Biological Systems Analysis and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - William Teale
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Martina Paponov
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Klaus Palme
- Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Renal Division, Department of Medicine, University Freiburg Medical Center, Freiburg, Germany
- Klaus Palme,
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20
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Dahlke RI, Fraas S, Ullrich KK, Heinemann K, Romeiks M, Rickmeyer T, Klebe G, Palme K, Lüthen H, Steffens B. Protoplast Swelling and Hypocotyl Growth Depend on Different Auxin Signaling Pathways. PLANT PHYSIOLOGY 2017; 175:982-994. [PMID: 28860155 PMCID: PMC5619902 DOI: 10.1104/pp.17.00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/29/2017] [Indexed: 05/10/2023]
Abstract
Members of the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN (TIR1/AFB) family are known auxin receptors. To analyze the possible receptor function of AUXIN BINDING PROTEIN1 (ABP1), an auxin receptor currently under debate, we performed different approaches. We performed a pharmacological approach using α-(2,4-dimethylphenylethyl-2-oxo)-indole-3-acetic acid (auxinole), α-(phenylethyl-2-oxo)-indole-3-acetic acid (PEO-IAA), and 5-fluoroindole-3-acetic acid (5-F-IAA) to discriminate between ABP1- and TIR1/AFB-mediated processes in Arabidopsis (Arabidopsis thaliana). We used a peptide of the carboxyl-terminal region of AtABP1 as a tool. We performed mutant analysis with the null alleles of ABP1, abp1-c1 and abp1-TD1, and the TILLING mutant abp1-5 We employed Coimbra, an accession that exhibits an amino acid exchange in the auxin-binding domain of ABP1. We measured either volume changes of single hypocotyl protoplasts or hypocotyl growth, both at high temporal resolution. 5-F-IAA selectively activated the TIR1/AFB pathway but did not induce protoplast swelling; instead, it showed auxin activity in the hypocotyl growth test. In contrast, PEO-IAA induced an auxin-like swelling response but no hypocotyl growth. The carboxyl-terminal peptide of AtABP1 induced an auxin-like swelling response. In the ABP1-related mutants and Coimbra, no auxin-induced protoplast swelling occurred. ABP1 seems to be involved in mediating rapid auxin-induced protoplast swelling, but it is not involved in the control of rapid auxin-induced growth.
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Affiliation(s)
- Renate I Dahlke
- Plant Physiology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Simon Fraas
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Philipps University, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Kirka Heinemann
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Maren Romeiks
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Thomas Rickmeyer
- Pharmaceutical Chemistry, University of Marburg, 35032 Marburg, Germany
| | - Gerhard Klebe
- Pharmaceutical Chemistry, University of Marburg, 35032 Marburg, Germany
| | - Klaus Palme
- Institute of Biology II, BIOSS Centre for Biological Signaling Studies, Institute for Advanced Sciences and Centre for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Hartwig Lüthen
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Bianka Steffens
- Plant Physiology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
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21
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Abstract
The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the 'Auxin 2016' meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants.
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Affiliation(s)
- Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon F-69342, France
| | - Stéphanie Robert
- Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Umeå 90183, Sweden
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22
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Hu Y, Vandenbussche F, Van Der Straeten D. Regulation of seedling growth by ethylene and the ethylene-auxin crosstalk. PLANTA 2017; 245:467-489. [PMID: 28188422 DOI: 10.1007/s00425-017-2651-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/08/2017] [Indexed: 05/06/2023]
Abstract
This review highlights that the auxin gradient, established by local auxin biosynthesis and transport, can be controlled by ethylene, and steers seedling growth. A better understanding of the mechanisms in Arabidopsis will increase potential applications in crop species. In dark-grown Arabidopsis seedlings, exogenous ethylene treatment triggers an exaggeration of the apical hook, the inhibition of both hypocotyl and root elongation, and radial swelling of the hypocotyl. These features are predominantly based on the differential cell elongation in different cells/tissues mediated by an auxin gradient. Interestingly, the physiological responses regulated by ethylene and auxin crosstalk can be either additive or synergistic, as in primary root and root hair elongation, or antagonistic, as in hypocotyl elongation. This review focuses on the crosstalk of these two hormones at the seedling stage. Before illustrating the crosstalk, ethylene and auxin biosynthesis, metabolism, transport and signaling are briefly discussed.
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Affiliation(s)
- Yuming Hu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Filip Vandenbussche
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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23
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Higaki T, Takigawa-Imamura H, Akita K, Kutsuna N, Kobayashi R, Hasezawa S, Miura T. Exogenous Cellulase Switches Cell Interdigitation to Cell Elongation in an RIC1-dependent Manner in Arabidopsis thaliana Cotyledon Pavement Cells. PLANT & CELL PHYSIOLOGY 2017; 58:106-119. [PMID: 28011873 DOI: 10.1093/pcp/pcw183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/19/2016] [Indexed: 05/08/2023]
Abstract
Pavement cells in cotyledons and true leaves exhibit a jigsaw puzzle-like morphology in most dicotyledonous plants. Among the molecular mechanisms mediating cell morphogenesis, two antagonistic Rho-like GTPases regulate local cell outgrowth via cytoskeletal rearrangements. Analyses of several cell wall-related mutants suggest the importance of cell wall mechanics in the formation of interdigitated patterns. However, how these factors are integrated is unknown. In this study, we observed that the application of exogenous cellulase to hydroponically grown Arabidopsis thaliana cotyledons switched the interdigitation of pavement cells to the production of smoothly elongated cells. The cellulase-induced inhibition of cell interdigitation was not observed in a RIC1 knockout mutant. This gene encodes a Rho-like GTPase-interacting protein important for localized cell growth suppression via microtubule bundling on concave cell interfaces. Additionally, to characterize pavement cell morphologies, we developed a mathematical model that considers the balance between cell and cell wall growth, restricted global cell growth orientation, and regulation of local cell outgrowth mediated by a Rho-like GTPase-cytoskeleton system. Our computational simulations fully support our experimental observations, and suggest that interdigitated patterns form because of mechanical buckling in the absence of Rho-like GTPase-dependent regulation of local cell outgrowth. Our model clarifies the cell wall mechanics influencing pavement cell morphogenesis.
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Affiliation(s)
- Takumi Higaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Hisako Takigawa-Imamura
- Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kae Akita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
- Research and Development Division, LPixel Inc., Bunkyo-ku, Tokyo, Japan
| | - Ryo Kobayashi
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Takashi Miura
- Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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24
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Jásik J, Bokor B, Stuchlík S, Mičieta K, Turňa J, Schmelzer E. Effects of Auxins on PIN-FORMED2 (PIN2) Dynamics Are Not Mediated by Inhibiting PIN2 Endocytosis. PLANT PHYSIOLOGY 2016; 172:1019-1031. [PMID: 27506239 PMCID: PMC5047079 DOI: 10.1104/pp.16.00563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/04/2016] [Indexed: 05/20/2023]
Abstract
By using the photoconvertible fluorescence protein Dendra2 as a tag we demonstrated that neither the naturally occurring auxins indole-3-acetic acid and indole-3-butyric acid, nor the synthetic auxin analogs 1-naphthaleneacetic acid and 2,4-dichlorophenoxyacetic acid nor compounds inhibiting polar auxin transport such as 2,3,5-triiodobenzoic acid and 1-N-naphthylphthalamic acid, were able to inhibit endocytosis of the putative auxin transporter PIN-FORMED2 (PIN2) in Arabidopsis (Arabidopsis thaliana) root epidermis cells. All compounds, except Indole-3-butyric acid, repressed the recovery of the PIN2-Dendra2 plasma membrane pool after photoconversion when they were used in high concentrations. The synthetic auxin analogs 1-naphthaleneacetic acid and 2,4-dichlorophenoxyacetic acid showed the strongest inhibition. Auxins and auxin transport inhibitors suppressed also the accumulation of both newly synthesized and endocytotic PIN2 pools in Brefeldin A compartments (BFACs). Furthermore, we demonstrated that all compounds are also interfering with BFAC formation. The synthetic auxin analogs caused the highest reduction in the number and size of BFACs. We concluded that auxins and inhibitors of auxin transport do affect PIN2 turnover in the cells, but it is through the synthetic rather than the endocytotic pathway. The study also confirmed inappropriateness of the BFA-based approach to study PIN2 endocytosis because the majority of PIN2 accumulating in BFACs is newly synthesized and not derived from the plasma membrane.
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Affiliation(s)
- Ján Jásik
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
| | - Boris Bokor
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
| | - Stanislav Stuchlík
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
| | - Karol Mičieta
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
| | - Ján Turňa
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
| | - Elmon Schmelzer
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia (J.J., B.B., S.S., K.M., J.T.); Institute of Botany, Slovak Academy of Sciences, 845 23 Bratislava (J.J.); Department of Molecular Biology, Comenius University, Faculty of Natural Sciences, Mlynská dolina, 842 15 Bratislava, Slovakia (S.S., J.T.); Department of Botany, Faculty of Natural Sciences, Comenius University, 811 02 Bratislava, Slovakia (K.M.); and Central Microscopy, Max Planck Institute for Plant Breeding Research, 508 29 Cologne, Germany (E.S.)
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25
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Strader LC, Zhao Y. Auxin perception and downstream events. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:8-14. [PMID: 27131035 PMCID: PMC5050066 DOI: 10.1016/j.pbi.2016.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/12/2016] [Accepted: 04/15/2016] [Indexed: 05/18/2023]
Abstract
Auxin responses have been arbitrarily divided into two categories: genomic and non-genomic effects. Genomic effects are largely mediated by SCFTIR1/AFB-Aux/IAA auxin receptor complexes whereas it has been postulated that AUXIN BINDING PROTEIN 1 (ABP1) controls the non-genomic effects. However, the roles of ABP1 in auxin signaling and plant development were recently called into question. In this paper, we present recent progress in understanding the SCFTIR1/AFB-Aux/IAA pathway. In more detail, we discuss the current understanding of ABP1 research and provide an updated view of ABP1-related genetic materials. Further, we propose a model in which auxin efflux carriers may play a role in auxin perception and we briefly describe recent insight on processes downstream of auxin perception.
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Affiliation(s)
- Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093-0116, USA.
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26
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Labusch C, Effendi Y, Fulda M, Scherer GFE. Transcription of TIR1-Controlled Genes Can be Regulated within 10 Min by an Auxin-Induced Process. Can TIR1 be the Receptor? FRONTIERS IN PLANT SCIENCE 2016; 7:995. [PMID: 27462327 PMCID: PMC4939301 DOI: 10.3389/fpls.2016.00995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/22/2016] [Indexed: 05/30/2023]
Abstract
ABP1 and TIR1/AFBs are known as auxin receptors. ABP1 is linked to auxin responses several of which are faster than 10 min. TIR1 regulates auxin-induced transcription of early auxin genes also within minutes. We use transcription of such TIR1-dependent genes as indicator of TIR1 activity to show the rapid regulation of TIR1 by exogenous auxin. To this end, we used quantification of transcription of a set of fifteen early auxin-induced reporter genes at t = 10 and t = 30 min to measure this as a TIR1-dependent auxin response. We conducted this study in 22 mutants of auxin transporters (pin5, abcb1, abcb19, and aux1/lax3), protein kinases and phosphatases (ibr5, npr1, cpk3, CPK3-OX, d6pk1, d6pkl1-1, d6pkl3-2, d6pkl1-1/d6pkl2-2, and d6pkl1-1/d6pkl3-2), of fatty acid metabolism (fad2-1, fad6-1, ssi2, lacs4, lacs9, and lacs4/lacs9) and receptors (tir1, tir1/afb2, and tir1/afb3) and compared them to the wild type. After 10 min auxin application, in 18 out of 22 mutants mis-regulated expression of at least one reporter was found, and in 15 mutants transcription of two-to-three out of five selected auxin reporter genes was mis-regulated. After 30 min of auxin application to mutant plants, mis-regulation of reporter genes ranged from one to 13 out of 15 tested reporter genes. Those genes chosen as mutants were themselves not regulated in their expression by auxin for at least 1 h, excluding an influence of TIR1/AFBs on their transcription. The expression of TIR1/AFB genes was also not modulated by auxin for up to 3 h. Together, this excludes a feedback or feedforward of these mutant genes/proteins on TIR1/AFBs output of transcription in this auxin-induced response. However, an auxin-induced response needed an as yet unknown auxin receptor. We suggest that the auxin receptor necessary for the fast auxin-induced transcription modulation could be, instead, ABP1. The alternative hypothesis would be that auxin-induced expression of a protein, initiated by TIR1/AFBs receptors, could initiate these responses and that this unknown protein regulated TIR1/AFB activities within 10 min.
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Affiliation(s)
- Corinna Labusch
- Abteilung Molekulare Ertragsphysiologie, Institut für Gartenbauliche Produktionssysteme, Leibniz Universität HannoverHannover, Germany
| | - Yunus Effendi
- Abteilung Molekulare Ertragsphysiologie, Institut für Gartenbauliche Produktionssysteme, Leibniz Universität HannoverHannover, Germany
- Department of Biology, University of Al Azhar IndonesiaJakarta, Indonesia
| | - Martin Fulda
- Abteilung Biochemie der Pflanzen, Albrecht-von-Haller-Institut der Pflanzenwissenschaften, Universität GöttingenGöttingen, Germany
| | - Günther F. E. Scherer
- Abteilung Molekulare Ertragsphysiologie, Institut für Gartenbauliche Produktionssysteme, Leibniz Universität HannoverHannover, Germany
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Gao X, Chen J, Dai X, Zhang D, Zhao Y. An Effective Strategy for Reliably Isolating Heritable and Cas9-Free Arabidopsis Mutants Generated by CRISPR/Cas9-Mediated Genome Editing. PLANT PHYSIOLOGY 2016; 171:1794-800. [PMID: 27208253 PMCID: PMC4936589 DOI: 10.1104/pp.16.00663] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/13/2016] [Indexed: 05/18/2023]
Abstract
Mutations generated by CRISPR/Cas9 in Arabidopsis (Arabidopsis thaliana) are often somatic and are rarely heritable. Isolation of mutations in Cas9-free Arabidopsis plants can ensure the stable transmission of the identified mutations to next generations, but the process is laborious and inefficient. Here, we present a simple visual screen for Cas9-free T2 seeds, allowing us to quickly obtain Cas9-free Arabidopsis mutants in the T2 generation. To demonstrate this in principle, we targeted two sites in the AUXIN-BINDING PROTEIN1 (ABP1) gene, whose function as a membrane-associated auxin receptor has been challenged recently. We obtained many T1 plants with detectable mutations near the target sites, but only a small fraction of T1 plants yielded Cas9-free abp1 mutations in the T2 generation. Moreover, the mutations did not segregate in Mendelian fashion in the T2 generation. However, mutations identified in the Cas9-free T2 plants were stably transmitted to the T3 generation following Mendelian genetics. To further simplify the screening procedure, we simultaneously targeted two sites in ABP1 to generate large deletions, which can be easily identified by PCR. We successfully generated two abp1 alleles that contained 1,141- and 711-bp deletions in the ABP1 gene. All of the Cas9-free abp1 alleles we generated were stable and heritable. The method described here allows for effectively isolating Cas9-free heritable CRISPR mutants in Arabidopsis.
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Affiliation(s)
- Xiuhua Gao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116 (X.G., J.C., X.D., D.Z., Y.Z.);Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (X.G.);College of Life Sciences, Xiamen University, Xiamen 361005, China (J.C.); andCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China (D.Z.)
| | - Jilin Chen
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116 (X.G., J.C., X.D., D.Z., Y.Z.);Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (X.G.);College of Life Sciences, Xiamen University, Xiamen 361005, China (J.C.); andCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China (D.Z.)
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116 (X.G., J.C., X.D., D.Z., Y.Z.);Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (X.G.);College of Life Sciences, Xiamen University, Xiamen 361005, China (J.C.); andCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China (D.Z.)
| | - Da Zhang
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116 (X.G., J.C., X.D., D.Z., Y.Z.);Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (X.G.);College of Life Sciences, Xiamen University, Xiamen 361005, China (J.C.); andCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China (D.Z.)
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116 (X.G., J.C., X.D., D.Z., Y.Z.);Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (X.G.);College of Life Sciences, Xiamen University, Xiamen 361005, China (J.C.); andCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China (D.Z.)
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Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D. A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. THE PLANT CELL 2016; 28:606-9. [PMID: 26956491 PMCID: PMC4826003 DOI: 10.1105/tpc.15.00502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 03/08/2016] [Indexed: 05/08/2023]
Affiliation(s)
| | | | - Joseph R Ecker
- HHMI-The Salk Institute for Biological StudiesLa Jolla, California 92037
| | | | - Detlef Weigel
- Max Planck Institute for Developmental Biology72076 Tübingen, Germany
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Abstract
As a prominent regulator of plant growth and development, the hormone auxin plays an essential role in controlling cell division and expansion. Auxin-responsive gene transcription is mediated through the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX (TIR1/AFB) pathway. Roles for TIR1/AFB pathway components in auxin response are understood best, but additional factors implicated in auxin responses require more study. The function of these factors, including S-Phase Kinase-Associated Protein 2A (SKP2A), SMALL AUXIN UP RNAs (SAURs), INDOLE 3-BUTYRIC ACID RESPONSE5 (IBR5), and AUXIN BINDING PROTEIN1 (ABP1), has remained largely obscure. Recent advances have begun to clarify roles for these factors in auxin response while also raising additional questions to be answered.
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Affiliation(s)
- Samantha K Powers
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130-4899, USA
| | - Lucia C Strader
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130-4899, USA
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Michalko J, Glanc M, Perrot-Rechenmann C, Friml J. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000Res 2016; 5:86. [PMID: 26925228 PMCID: PMC4748827 DOI: 10.12688/f1000research.7654.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2016] [Indexed: 01/07/2023] Open
Abstract
The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.
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Affiliation(s)
- Jaroslav Michalko
- Institute of Science and Technology Austria, Klosterneuberg, Austria
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Matouš Glanc
- Institute of Science and Technology Austria, Klosterneuberg, Austria
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic
| | | | - Jiří Friml
- Institute of Science and Technology Austria, Klosterneuberg, Austria
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