1
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Margalha L, Elias A, Belda-Palazón B, Peixoto B, Confraria A, Baena-González E. HOS1 promotes plant tolerance to low-energy stress via the SnRK1 protein kinase. Plant J 2023. [PMID: 37077033 DOI: 10.1111/tpj.16250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Plants need to integrate internal and environmental signals to mount adequate stress responses. The NUCLEAR PORE COMPLEX (NPC) component HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) is emerging as such an integrator, affecting responses to cold, heat, light and salinity. Stress conditions often converge in a low-energy signal that activates SUCROSE NON-FERMENTING 1-RELATED KINASE 1 (SnRK1) to promote stress tolerance and survival. Here, we explored the role of HOS1 in the SnRK1-dependent response to low-energy stress in Arabidopsis thaliana, using darkness as a treatment and a combination of genetic, biochemical, and phenotypic assays. We show that the induction of starvation genes and plant tolerance to prolonged darkness are defective in the hos1 mutant. HOS1 interacts physically with the SnRK1α1 catalytic subunit in yeast-two-hybrid and in planta, and the nuclear accumulation of SnRK1α1 is reduced in the hos1 mutant. Likewise, another NPC mutant, nup160, exhibits lower activation of starvation genes and decreased tolerance to prolonged darkness. Importantly, defects in low-energy responses in the hos1 background are rescued by fusing SnRK1α1 to a potent nuclear localization signal, or by sugar supplementation during the dark treatment. Altogether, this work demonstrates the importance of HOS1 for the nuclear accumulation of SnRK1α1, which is key for plant tolerance to low-energy conditions.
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Affiliation(s)
- Leonor Margalha
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
| | - Alexandre Elias
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
| | - Borja Belda-Palazón
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
- Current address: IBMCP-CSIC-UPV, 46022, Valencia, Spain
| | - Bruno Peixoto
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
- Current address: Department of Biology, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB NOVA, 2780-157, Oeiras, Portugal
- Current address: Department of Biology, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
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Confraria A, Muñoz-Gasca A, Ferreira L, Baena-González E, Cubas P. Shoot Branching Phenotyping in Arabidopsis and Tomato. Methods Mol Biol 2022; 2494:47-59. [PMID: 35467200 DOI: 10.1007/978-1-0716-2297-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Shoot branching is an important trait that depends on the activity of axillary meristems and buds and their outgrowth into branches. It is remarkably plastic, being influenced by a number of external cues, such as light, temperature, soil nutrients, and mechanical manipulation. These are transduced into an internal hormone signaling network where auxin, cytokinins, and strigolactones play leading regulatory roles. Recently, sugars have also emerged as important signals promoting bud activation. These signals are in part integrated by the bud-specific growth repressor BRANCHED1 (BRC1).To understand how shoot branching is affected by particular growth conditions or in specific plant lines, it is necessary to count the number of branches and/or quantify other branch-related parameters. Here we describe how to perform such quantifications in Arabidopsis and in tomato.
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Affiliation(s)
- Ana Confraria
- Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal.
| | - Aitor Muñoz-Gasca
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Liliana Ferreira
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
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3
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Alves A, Confraria A, Lopes S, Costa B, Perdiguero P, Milhinhos A, Baena-González E, Correia S, Miguel CM. miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development. Front Plant Sci 2022; 13:857611. [PMID: 35371172 PMCID: PMC8965291 DOI: 10.3389/fpls.2022.857611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of several plant developmental processes including embryogenesis. Most miRNA families are conserved across major groups of plant species, but their regulatory roles have been studied mainly in model species like Arabidopsis and other angiosperms. In gymnosperms, miRNA-dependent regulation has been less studied since functional approaches in these species are often difficult to establish. Given the fundamental roles of auxin signaling in somatic embryogenesis (SE) induction and embryo development, we investigated a previously predicted interaction between miR160 and a putative target encoding AUXIN RESPONSE FACTOR 18 in Pinus pinaster (PpARF18) embryonic tissues. Phylogenetic analysis of AUXIN RESPONSE FACTOR 18 (ARF18) from Pinus pinaster and Picea abies, used here as a model system of conifer embryogenesis, showed their close relatedness to AUXIN RESPONSE FACTOR (ARF) genes known to be targeted by miR160 in other species, including Arabidopsis ARF10 and ARF16. By using a luciferase (LUC) reporter system for miRNA activity in Arabidopsis protoplasts, we have confirmed that P. pinaster miR160 (ppi-miR160) interacts in vivo with PpARF18 target site. When the primary miR160 from P. pinaster was overexpressed in protoplasts under non-limiting levels of ARGONAUTE1, a significant increase of miR160 target cleavage activity was observed. In contrast, co-expression of the primary miRNA and the target mimic MIM160 led to a decrease of miR160 activity. Our results further support that this interaction is functional during consecutive stages of SE in the conifer model P. abies. Expression analyses conducted in five stages of development, from proembryogenic masses (PEMs) to the mature embryo, show that conifer ARF18 is negatively regulated by miR160 toward the fully developed mature embryo when miR160 reached its highest expression level. This study reports the first in vivo validation of a predicted target site of a conifer miRNA supporting the conservation of miR160 interaction with ARF targets in gymnosperms. The approach used here should be useful for future characterization of miRNA functions in conifer embryogenesis.
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Affiliation(s)
- Ana Alves
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Susana Lopes
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Bruno Costa
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Perdiguero
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), Madrid, Spain
| | - Ana Milhinhos
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | - Sandra Correia
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Célia M. Miguel
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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4
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Belda-Palazón B, Adamo M, Valerio C, Ferreira LJ, Confraria A, Reis-Barata D, Rodrigues A, Meyer C, Rodriguez PL, Baena-González E. A dual function of SnRK2 kinases in the regulation of SnRK1 and plant growth. Nat Plants 2020; 6:1345-1353. [PMID: 33077877 DOI: 10.1038/s41477-020-00778-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/03/2020] [Indexed: 05/04/2023]
Abstract
Adverse environmental conditions trigger responses in plants that promote stress tolerance and survival at the expense of growth1. However, little is known of how stress signalling pathways interact with each other and with growth regulatory components to balance growth and stress responses. Here, we show that plant growth is largely regulated by the interplay between the evolutionarily conserved energy-sensing SNF1-related protein kinase 1 (SnRK1) protein kinase and the abscisic acid (ABA) phytohormone pathway. While SnRK2 kinases are main drivers of ABA-triggered stress responses, we uncover an unexpected growth-promoting function of these kinases in the absence of ABA as repressors of SnRK1. Sequestration of SnRK1 by SnRK2-containing complexes inhibits SnRK1 signalling, thereby allowing target of rapamycin (TOR) activity and growth under optimal conditions. On the other hand, these complexes are essential for releasing and activating SnRK1 in response to ABA, leading to the inhibition of TOR and growth under stress. This dual regulation of SnRK1 by SnRK2 kinases couples growth control with environmental factors typical for the terrestrial habitat and is likely to have been critical for the water-to-land transition of plants.
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Affiliation(s)
- Borja Belda-Palazón
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Mattia Adamo
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
- BPMP, University of Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Concetta Valerio
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
| | - Liliana J Ferreira
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
| | - Diana Reis-Barata
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal
| | - Américo Rodrigues
- MARE Marine and Environmental Sciences Centre, ESTM, Instituto Politécnico de Leiria, Peniche, Portugal
| | - Christian Meyer
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, GREEN-IT Bioresources for Sustainability, Oeiras, Portugal.
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Szakonyi D, Confraria A, Valerio C, Duque P, Staiger D. Editorial: Plant RNA Biology. Front Plant Sci 2019; 10:887. [PMID: 31338103 PMCID: PMC6629759 DOI: 10.3389/fpls.2019.00887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Affiliation(s)
| | | | | | - Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Margalha L, Confraria A, Baena-González E. SnRK1 and TOR: modulating growth-defense trade-offs in plant stress responses. J Exp Bot 2019; 70:2261-2274. [PMID: 30793201 DOI: 10.1093/jxb/erz066] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/07/2019] [Indexed: 05/11/2023]
Abstract
The evolutionarily conserved protein kinase complexes SnRK1 and TOR are central metabolic regulators essential for plant growth, development, and stress responses. They are activated by opposite signals, and the outcome of their activation is, in global terms, antagonistic. Similarly to their yeast and animal counterparts, SnRK1 is activated by the energy deficit often associated with stress to restore homeostasis, while TOR is activated in nutrient-rich conditions to promote growth. Recent evidence suggests that SnRK1 represses TOR in plants, revealing evolutionary conservation also in their crosstalk. Given their importance for integrating environmental information into growth and developmental programs, these signaling pathways hold great promise for reducing the growth penalties caused by stress. Here we review the literature connecting SnRK1 and TOR to plant stress responses. Although SnRK1 and TOR emerge mostly as positive regulators of defense and growth, respectively, the outcome of their activities in plant growth and performance is not always straightforward. Manipulation of both pathways under similar experimental setups, as well as further biochemical and genetic analyses of their molecular and functional interaction, is essential to fully understand the mechanisms through which these two metabolic pathways contribute to stress responses, growth, and development.
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Affiliation(s)
- Leonor Margalha
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,Oeiras, Portugal
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Abstract
Arabidopsis mesophyll protoplasts can be readily isolated and transfected in order to transiently express proteins of interest. As freshly isolated mesophyll protoplasts maintain essentially the same physiological characteristics of whole leaves, this cell-based transient expression system can be used to molecularly dissect the responses to various stress conditions. The response of stress-responsive promoters to specific stimuli can be accessed via reporter gene assays. Additionally, reporter systems can be easily engineered to address other levels of regulation, such as transcript and/or protein stability. Here we present a detailed protocol for using the Arabidopsis mesophyll protoplast system to study responses to environmental stress, including preparation of reporter and effector constructs, large scale DNA purification, protoplast isolation, transfection, treatment, and quantification of luciferase-based reporter gene activities.
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Affiliation(s)
- Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.
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Fàbregas N, Formosa-Jordan P, Confraria A, Siligato R, Alonso JM, Swarup R, Bennett MJ, Mähönen AP, Caño-Delgado AI, Ibañes M. Auxin influx carriers control vascular patterning and xylem differentiation in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005183. [PMID: 25922946 PMCID: PMC4414528 DOI: 10.1371/journal.pgen.1005183] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/29/2015] [Indexed: 12/23/2022] Open
Abstract
Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants.
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Affiliation(s)
- Norma Fàbregas
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Pau Formosa-Jordan
- Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Ana Confraria
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Riccardo Siligato
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jose M. Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ranjan Swarup
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham, United Kingdom
| | - Malcolm J. Bennett
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham, United Kingdom
| | - Ari Pekka Mähönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Marta Ibañes
- Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona, Spain
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Martinho C, Confraria A, Elias CA, Crozet P, Rubio-Somoza I, Weigel D, Baena-González E. Dissection of miRNA pathways using arabidopsis mesophyll protoplasts. Mol Plant 2015; 8:261-75. [PMID: 25680775 DOI: 10.1016/j.molp.2014.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/10/2014] [Accepted: 10/10/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this article, we describe a transient expression system in Arabidopsis mesophyll protoplasts, which is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, by either overexpression or the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up, and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.
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Affiliation(s)
- Cláudia Martinho
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Carlos Alexandre Elias
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Pierre Crozet
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal.
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Rubio-Somoza I, Zhou CM, Confraria A, Martinho C, von Born P, Baena-Gonzalez E, Wang JW, Weigel D. Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes. Curr Biol 2014; 24:2714-9. [DOI: 10.1016/j.cub.2014.09.058] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/15/2014] [Accepted: 09/22/2014] [Indexed: 11/28/2022]
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Martinho C, Confraria A, Elias CA, Crozet P, Rubio-Somoza I, Weigel D, Baena-González E. Dissection of miRNA pathways using Arabidopsis mesophyll protoplasts. Mol Plant 2014:ssu119. [PMID: 25343984 DOI: 10.1093/mp/ssu119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
microRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this paper, we describe a transient expression system in Arabidopsis mesophyll protoplasts that is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, either by overexpression or by the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.
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Affiliation(s)
- Cláudia Martinho
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal Present address: Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Carlos Alexandre Elias
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Pierre Crozet
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
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Crozet P, Margalha L, Confraria A, Rodrigues A, Martinho C, Adamo M, Elias CA, Baena-González E. Mechanisms of regulation of SNF1/AMPK/SnRK1 protein kinases. Front Plant Sci 2014; 5:190. [PMID: 24904600 PMCID: PMC4033248 DOI: 10.3389/fpls.2014.00190] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/22/2014] [Indexed: 05/17/2023]
Abstract
The SNF1 (sucrose non-fermenting 1)-related protein kinases 1 (SnRKs1) are the plant orthologs of the budding yeast SNF1 and mammalian AMPK (AMP-activated protein kinase). These evolutionarily conserved kinases are metabolic sensors that undergo activation in response to declining energy levels. Upon activation, SNF1/AMPK/SnRK1 kinases trigger a vast transcriptional and metabolic reprograming that restores energy homeostasis and promotes tolerance to adverse conditions, partly through an induction of catabolic processes and a general repression of anabolism. These kinases typically function as a heterotrimeric complex composed of two regulatory subunits, β and γ, and an α-catalytic subunit, which requires phosphorylation of a conserved activation loop residue for activity. Additionally, SNF1/AMPK/SnRK1 kinases are controlled by multiple mechanisms that have an impact on kinase activity, stability, and/or subcellular localization. Here we will review current knowledge on the regulation of SNF1/AMPK/SnRK1 by upstream components, post-translational modifications, various metabolites, hormones, and others, in an attempt to highlight both the commonalities of these essential eukaryotic kinases and the divergences that have evolved to cope with the particularities of each one of these systems.
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Affiliation(s)
| | | | | | - Américo Rodrigues
- Instituto Gulbenkian de CiênciaOeiras, Portugal
- Escola Superior de Turismo e Tecnologia do Mar de Peniche, Instituto Politécnico de LeiriaPeniche, Portugal
| | | | | | | | - Elena Baena-González
- Instituto Gulbenkian de CiênciaOeiras, Portugal
- *Correspondence: Elena Baena-González, Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal e-mail:
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Rodrigues A, Adamo M, Crozet P, Margalha L, Confraria A, Martinho C, Elias A, Rabissi A, Lumbreras V, González-Guzmán M, Antoni R, Rodriguez PL, Baena-González E. ABI1 and PP2CA phosphatases are negative regulators of Snf1-related protein kinase1 signaling in Arabidopsis. Plant Cell 2013; 25:3871-84. [PMID: 24179127 PMCID: PMC3877788 DOI: 10.1105/tpc.113.114066] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/27/2013] [Accepted: 09/15/2013] [Indexed: 05/17/2023]
Abstract
Plant survival under environmental stress requires the integration of multiple signaling pathways into a coordinated response, but the molecular mechanisms underlying this integration are poorly understood. Stress-derived energy deprivation activates the Snf1-related protein kinases1 (SnRK1s), triggering a vast transcriptional and metabolic reprogramming that restores homeostasis and promotes tolerance to adverse conditions. Here, we show that two clade A type 2C protein phosphatases (PP2Cs), established repressors of the abscisic acid (ABA) hormonal pathway, interact with the SnRK1 catalytic subunit causing its dephosphorylation and inactivation. Accordingly, SnRK1 repression is abrogated in double and quadruple pp2c knockout mutants, provoking, similarly to SnRK1 overexpression, sugar hypersensitivity during early seedling development. Reporter gene assays and SnRK1 target gene expression analyses further demonstrate that PP2C inhibition by ABA results in SnRK1 activation, promoting SnRK1 signaling during stress and once the energy deficit subsides. Consistent with this, SnRK1 and ABA induce largely overlapping transcriptional responses. Hence, the PP2C hub allows the coordinated activation of ABA and energy signaling, strengthening the stress response through the cooperation of two key and complementary pathways.
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Affiliation(s)
- Américo Rodrigues
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- Instituto Politécnico de Leiria, Escola Superior de Turismo e Tecnologia do Mar de Peniche, 2411-901 Peniche, Portugal
| | - Mattia Adamo
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Pierre Crozet
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | - Ana Confraria
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | | | - Agnese Rabissi
- Centre for Research in Agricultural Genomics, Bellaterra, Cerdanyola del Vallés, 08193 Barcelona, Spain
| | - Victoria Lumbreras
- Centre for Research in Agricultural Genomics, Bellaterra, Cerdanyola del Vallés, 08193 Barcelona, Spain
| | - Miguel González-Guzmán
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Regina Antoni
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, 46022 Valencia, Spain
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Confraria A, Martinho C, Elias A, Rubio-Somoza I, Baena-González E. miRNAs mediate SnRK1-dependent energy signaling in Arabidopsis. Front Plant Sci 2013; 4:197. [PMID: 23802004 PMCID: PMC3687772 DOI: 10.3389/fpls.2013.00197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/27/2013] [Indexed: 05/17/2023]
Abstract
The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24 nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to their role in plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1. By comparing the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis, we identified 831 starvation genes misregulated in the dcl1-9 mutant, out of which 155 are validated or predicted miRNA targets. Functional clustering analysis revealed that the main cellular processes potentially co-regulated by SnRK1 and miRNAs are translation and organelle function and uncover TCP transcription factors as one of the most highly enriched functional clusters. TCP repression during energy deprivation was impaired in miR319 knockdown (MIM319) plants, demonstrating the involvement of miR319 in the stress-dependent regulation of TCPs. Altogether, our data indicates that miRNAs are components of the SnRK1 signaling cascade contributing to the regulation of specific mRNA targets and possibly tuning down particular cellular processes during the stress response.
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Affiliation(s)
- Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Cláudia Martinho
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Alexandre Elias
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingen, Germany
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
- *Correspondence: Elena Baena-González, Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal e-mail:
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Wilson ID, Ribeiro DM, Bright J, Confraria A, Harrison J, Barros RS, Desikan R, Neill SJ, Hancock JT. Role of nitric oxide in regulating stomatal apertures. Plant Signal Behav 2009; 4:467-9. [PMID: 19816112 PMCID: PMC2676769 DOI: 10.4161/psb.4.5.8545] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 03/24/2009] [Indexed: 05/21/2023]
Abstract
During stomatal closure, nitric oxide (NO) operates as one of the key intermediates in the complex, abscisic acid (ABA)-mediated, guard cell signaling network that regulates this process. However, data concerning the role of NO in stomatal closure that occurs in turgid vs. dehydrated plants is limited. The data presented demonstrate that, while there is a requirement for NO during the ABA-induced stomatal closure of turgid leaves, such a requirement does not exist for ABA-enhanced stomatal closure observed to occur during conditions of rapid dehydration. The data also indicate that the ABA signaling pathway must be both functional and to some degree activated for guard cell NO signaling to occur. These observations are in line with the idea that the effects of NO in guard cells are mediated via a Ca(2+)-dependent rather than a Ca(2+)-independent ABA signaling pathway. It appears that there is a role for NO in the fine tuning of the stomatal apertures of turgid leaves that occurs in response to fluctuations in the prevailing environment.
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Affiliation(s)
- Ian D Wilson
- Centre for Research in Plant Science, Faculty of Health and Life Sciences, University of the West of England, Bristol, Bristol, UK.
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Ribeiro DM, Desikan R, Bright J, Confraria A, Harrison J, Hancock JT, Barros RS, Neill SJ, Wilson ID. Differential requirement for NO during ABA-induced stomatal closure in turgid and wilted leaves. Plant Cell Environ 2009; 32:46-57. [PMID: 19021879 DOI: 10.1111/j.1365-3040.2008.01906.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Abscisic acid (ABA)-induced stomatal closure is mediated by a complex, guard cell signalling network involving nitric oxide (NO) as a key intermediate. However, there is a lack of information concerning the role of NO in the ABA-enhanced stomatal closure seen in dehydrated plants. The data herein demonstrate that, while nitrate reductase (NR)1-mediated NO generation is required for the ABA-induced closure of stomata in turgid leaves, it is not required for ABA-enhanced stomatal closure under conditions leading to rapid dehydration. The results also show that NO signalling in the guard cells of turgid leaves requires the ABA-signalling pathway to be both capable of function and active. The alignment of this NO signalling with guard cell Ca(2+)-dependent/independent ABA signalling is discussed. The data also highlight a physiological role for NO signalling in turgid leaves and show that stomatal closure during the light-to-dark transition requires NR1-mediated NO generation and signalling.
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Affiliation(s)
- Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Minas Gerais, Brazil
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Santos I, Pires H, Almeida JM, Fidalgo F, Confraria A, Duarte M, Borlido J, Salema R. Phylogenetic relationship of potato CAT1 and CAT2 genes, their differential expression in non-photosynthetic organs and during leaf development, and their association with different cellular processes. Funct Plant Biol 2006; 33:639-651. [PMID: 32689273 DOI: 10.1071/fp06024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 03/30/2006] [Indexed: 06/11/2023]
Abstract
Plants contain multiple forms of catalase (CAT) and their specific functions remain uncertain. We cloned two potato cDNAs corresponding to CAT1 and CAT2 genes, analysed their phylogenetic relationship, and studied their expression and activity in different organs to gain clues to their functions. Phylogenetic trees and the alignment of CAT cDNA sequences provided evidence that CAT1 and CAT2 genes have high identity to catalases of other solanaceous species, but are not phylogenetically closely related to one another, which contradicts the phylogenetic closeness ascribed to these genes. Northern blot analyses revealed that expression of CAT genes is controlled by leaf developmental phase. CAT2 expression was higher in both very young and senescent leaves, whereas CAT1 mRNA accumulated mainly in mature leaf, where the lowest CAT2 expression occurred. CAT1 and CAT2 are also differentially expressed in root, sprout and petal. Expression and activity patterns are consistent with different physiological roles for CAT1 and CAT2 isoforms. CAT1 is considered to be associated with photorespiration whereas CAT2 would fulfill physiological roles unrelated to this process. CAT2 appears to be a multifunctional isoform, associated with glyoxysomal activity in leaf senescence, other processes in non-photosynthetic organs and defence, functions that in other solanaceous species are fulfilled by two different isoforms.
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Affiliation(s)
- Isabel Santos
- Botany Department, School of Sciences, University of Porto, Rua do Campo Alegre, 1191, 4150-180 Porto, Portugal
| | - Helena Pires
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - José M Almeida
- Botany Department, School of Sciences, University of Porto, Rua do Campo Alegre, 1191, 4150-180 Porto, Portugal
| | - Fernanda Fidalgo
- Botany Department, School of Sciences, University of Porto, Rua do Campo Alegre, 1191, 4150-180 Porto, Portugal
| | - Ana Confraria
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Márcia Duarte
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Júlio Borlido
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Roberto Salema
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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Almeida JM, Fidalgo F, Confraria A, Santos A, Pires H, Santos I. Effect of hydrogen peroxide on catalase gene expression, isoform activities and levels in leaves of potato sprayed with homobrassinolide and ultrastructural changes in mesophyll cells. Funct Plant Biol 2005; 32:707-720. [PMID: 32689169 DOI: 10.1071/fp04235] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2004] [Accepted: 05/06/2005] [Indexed: 06/11/2023]
Abstract
The effect of hydrogen peroxide (H2O2) on catalase (CAT) isoform activities and amounts and on mRNA levels was studied in leaves from potato plants untreated and treated with homobrassinolide (HBR). Northern blot analysis revealed that 100 mm H2O2 supplied through the leaf petiole for 4 h did not induce CAT expression. In contrast, CAT1 and CAT2 responded differently to longer treatment, as CAT2 transcript levels increased markedly whereas CAT1 transcript levels remained unchanged. Western blot analysis showed disparity between the level of CAT1 transcript and CAT1 amount, which actually decreased after 28 h. CAT2 amount correlated well with transcript accumulation and CAT2 activity as visualised by zymogram analysis. H2O2 modified the relative importance of CAT isoforms. After 4 h, CAT1 was prevalent in untreated and H2O2-treated leaves. After 28 h, CAT2 was prevalent in H2O2-treated leaves; therefore, the quantified increase in total CAT activity in these leaves was due to the rise in CAT2. HBR pre-treatment increased CAT2 basal level not changing the pattern of CAT responses to H2O2, only lowering its amplitude. Even so, ultrastructural studies showed that HBR significantly reduced H2O2 negative effects on cellular sub-structures, allowing better recovery of affected structures and reducing the macroscopic injury symptoms on leaves, thus data point to a HBR protective role.
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Affiliation(s)
- José M Almeida
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Fernanda Fidalgo
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Ana Confraria
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Arlete Santos
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Helena Pires
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Isabel Santos
- Institute for Molecular and Cellular Biology, University of Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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Abstract
Crossed aphasia is reported to be more frequent in traumatic series than in series of patients with other pathologies. A right-handed young man suffered a closed-head trauma and became aphasic and hemiparetic on the left. CT scan revealed a right frontal-lobe hematoma. Neuropsychological examination revealed a fluent aphasia and a Gerstmann syndrome. These signs were compatible with left supramarginal gyrus syndrome. However, the presence of a right frontal-lobe lesion suggested that this patient could be a crossed aphasic. Subsequent EEG study showed a left occipitotemporal focus and a right frontal one. Aphasic signs could thus be due to the left lesion, which was the result of a contrecoup mechanism. Fluent aphasias have been reported in closed-head trauma with right frontal impact. Attention is called for the possible bias of including cases like this in series of traumatic crossed aphasia.
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Castro-Caldas A, Guerreiro M, Confraria A. Transient and persistent right ear extinction in dichotic listening: subcortical lesions. Neurology 1984; 34:1418-22. [PMID: 6493489 DOI: 10.1212/wnl.34.11.1418] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nine patients with aphasia had right ear extinction in dichotic listening to words in the first month after an ischemic stroke; they were reassessed after 3 months. Four showed complete recovery from the right ear extinction; in five, the abnormality persisted. In those who recovered, CT revealed a subcortical lesion lateral to the frontal horn of the lateral ventricle without a lesion of Heschl's gyrus or geniculo-temporal pathways; a lesion in those structures was found in patients who did not recover. As reported for subcortical aphasia, a subcortical mechanism may explain contralateral ear extinction in dichotic listening.
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Abstract
Thirty-nine cases (37 from the literature and 2 personal) of crossed aphasia in dextrals due to stroke were reviewed concerning age, sex, and type of aphasia. Results showed that Broca's aphasics are younger than the remaining group, males predominate, and several types of aphasia have been described similarly to the aphasias due to left-hemisphere lesions in dextrals.
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