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Pagano A, Gomes C, Timmerman E, Sulima P, Przyborowski JA, Kruszka D, Impens F, Paiva JAP. Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea. Front Plant Sci 2024; 14:1304327. [PMID: 38298602 PMCID: PMC10827895 DOI: 10.3389/fpls.2023.1304327] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Introduction DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. Methods The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects. Results and discussion After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.
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Affiliation(s)
- Andrea Pagano
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Paweł Sulima
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jerzy Andrzej Przyborowski
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dariusz Kruszka
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Jorge Almiro Pinto Paiva
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Macovei A, Rubio-Somoza I, Paiva JAP, Araújo S, Donà M. Editorial: MicroRNA Signatures in Plant Genome Stability and Genotoxic Stress. Front Plant Sci 2021; 12:683302. [PMID: 33968124 PMCID: PMC8100575 DOI: 10.3389/fpls.2021.683302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 03/25/2021] [Indexed: 05/21/2023]
Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
- *Correspondence: Anca Macovei
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution Laboratory (MoRE), Centre for Research in Agricultural Genomics (CRAG), Barcelona, Spain
| | - Jorge Almiro Pinto Paiva
- Institute of Plant Genetics of the Polish Academy of Sciences, Poznan, Poland
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Susana Araújo
- Association BLC3, Technology and Innovation Campus, Centre BIO–R&D Unit, Lagares da Beira, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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Boher P, Soler M, Sánchez A, Hoede C, Noirot C, Paiva JAP, Serra O, Figueras M. A comparative transcriptomic approach to understanding the formation of cork. Plant Mol Biol 2018; 96:103-118. [PMID: 29143299 DOI: 10.1007/s11103-017-0682-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 08/24/2017] [Accepted: 11/08/2017] [Indexed: 05/09/2023]
Abstract
The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.
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Affiliation(s)
- Pau Boher
- Laboratori del Suro, Faculty of Science, Biology Department, Universitat de Girona, C/ Maria Aurèlia Campmany 40, 17003, Girona, Spain
| | - Marçal Soler
- Laboratori del Suro, Faculty of Science, Biology Department, Universitat de Girona, C/ Maria Aurèlia Campmany 40, 17003, Girona, Spain
| | - Anna Sánchez
- Laboratori del Suro, Faculty of Science, Biology Department, Universitat de Girona, C/ Maria Aurèlia Campmany 40, 17003, Girona, Spain
| | - Claire Hoede
- PF Bioinfo GenoToul, MIAT, Université de Toulouse, INRA, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Céline Noirot
- PF Bioinfo GenoToul, MIAT, Université de Toulouse, INRA, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Jorge Almiro Pinto Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
- Institute of Plant Genetics, Department of Integrative Plant Biology, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznan, Poland
| | - Olga Serra
- Laboratori del Suro, Faculty of Science, Biology Department, Universitat de Girona, C/ Maria Aurèlia Campmany 40, 17003, Girona, Spain
| | - Mercè Figueras
- Laboratori del Suro, Faculty of Science, Biology Department, Universitat de Girona, C/ Maria Aurèlia Campmany 40, 17003, Girona, Spain.
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Paiva JAP, Garnier-Géré PH, Rodrigues JC, Alves A, Santos S, Graça J, Le Provost G, Chaumeil P, Da Silva-Perez D, Bosc A, Fevereiro P, Plomion C. Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season. New Phytol 2008; 179:1180-1194. [PMID: 18631295 DOI: 10.1111/j.1469-8137.2008.02536.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The seasonal effect is the most significant external source of variation affecting vascular cambial activity and the development of newly divided cells, and hence wood properties. Here, the effect of edapho-climatic conditions on the phenotypic and molecular plasticity of differentiating secondary xylem during a growing season was investigated. Wood-forming tissues of maritime pine (Pinus pinaster) were collected from the beginning to the end of the growing season in 2003. Data from examination of fibre morphology, Fourier-transform infrared spectroscopy (FTIR), analytical pyrolysis, and gas chromatography/mass spectrometry (GC/MS) were combined to characterize the samples. Strong variation was observed in response to changes in edapho-climatic conditions. A genomic approach was used to identify genes differentially expressed during this growing season. Out of 3512 studied genes, 19% showed a significant seasonal effect. These genes were clustered into five distinct groups, the largest two representing genes over-expressed in the early- or late-wood-forming tissues, respectively. The other three clusters were characterized by responses to specific edapho-climatic conditions. This work provides new insights into the plasticity of the molecular machinery involved in wood formation, and reveals candidate genes potentially responsible for the phenotypic differences found between early- and late-wood.
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Affiliation(s)
- J A P Paiva
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157 Oeiras, Portugal
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - P H Garnier-Géré
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - J C Rodrigues
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - A Alves
- Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Centre, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - S Santos
- Departamento de Engenharia Florestal, Instituto Superior de Agronomia, TULisbon, ISA-DEF, Tapada Ajuda, 1349-017 Lisboa, Portugal
| | - J Graça
- Departamento de Engenharia Florestal, Instituto Superior de Agronomia, TULisbon, ISA-DEF, Tapada Ajuda, 1349-017 Lisboa, Portugal
| | - G Le Provost
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - P Chaumeil
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
| | - D Da Silva-Perez
- Laboratoire Bois Process, FCBA InTechFibres, Domaine Universitaire, BP 251, 38044 Grenoble Cedex, France
| | - A Bosc
- INRA, UR Ecologie fonctionnelle et physique de l'Environnement, EPHYSE, 71 avenue Edouard Bourleaux, 33883 Villenave d'Ornon Cedex, France
| | - P Fevereiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República-EAN, 2780-157 Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1700 Lisboa, Portugal
| | - C Plomion
- INRA, UMR1202, BIOGECO, Domaine de l'Hermitage, 69 route d'Arcachon, F-33612 Cestas Cedex, France
- Université de Bordeaux, UMR1202, BIOGECO, Bât B8 RdC, Av des Facultés, F-33405 Talence, France
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