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Borghi M, Pacifico D, Crucitti D, Squartini A, Berger MMJ, Gamboni M, Carimi F, Lehad A, Costa A, Gallusci P, Fernie AR, Zottini M. Smart selection of soil microbes for resilient and sustainable viticulture. Plant J 2024. [PMID: 38329213 DOI: 10.1111/tpj.16674] [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] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
The grapevine industry is of high economic importance in several countries worldwide. Its growing market demand led to an acceleration of the entire production processes, implying increasing use of water resources at the expense of environmental water balance and the hydrological cycle. Furthermore, in recent decades climate change and the consequent expansion of drought have further compromised water availability, making current agricultural systems even more fragile from ecological and economical perspectives. Consequently, farmers' income and welfare are increasingly unpredictable and unstable. Therefore, it is urgent to improve the resilience of vineyards, and of agro-ecosystems in general, by developing sustainable and environmentally friendly farming practices by more rational biological and natural resources use. The PRIMA project PROSIT addresses these challenges by characterizing and harnessing grapevine-associated microbiota to propose innovative and sustainable agronomic practices. PROSIT aims to determine the efficacy of natural microbiomes transferred from grapevines adapted to arid climate to commonly cultivated grapevine cultivars. In doing so it will test those natural microbiome effects on drought tolerance. This multidisciplinary project will utilize in vitro culture techniques, bioimaging, microbiological tests, metabolomics, metabarcoding and epigenetic analyses. These will be combined to shed light on molecular mechanisms triggered in plants by microbial associations upon water stress. To this end it is hoped that the project will serve as a blueprint not only for studies uncovering the microbiome role in drought stress in a wide range of species, but also for analyzing its effect on a wide range of stresses commonly encountered in modern agricultural systems.
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Affiliation(s)
- Monica Borghi
- Department of Biology, Utah State University, Logan, Utah, 84321-5305, USA
| | - Davide Pacifico
- IBBR CNR - Institute of Biosciences and Bioresources, via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Dalila Crucitti
- IBBR CNR - Institute of Biosciences and Bioresources, via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Andrea Squartini
- Department of Agronomy, Animals, Food, Natural Resources, and Environment, Università degli Studi di Padova, Viale dell'Università 16, 35020, Legnaro, Padua, Italy
| | - Margot M J Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, University of Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leyssottes, 33882, Villenave d'Ornon, France
| | - Mauro Gamboni
- IBBR CNR - Institute of Biosciences and Bioresources, via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Francesco Carimi
- IBBR CNR - Institute of Biosciences and Bioresources, via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Arezki Lehad
- ENSA, Rue Hassan Badi, Belfort, El Harrach, 16000, Algeria
| | - Alex Costa
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milano, Italy
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, University of Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leyssottes, 33882, Villenave d'Ornon, France
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Michela Zottini
- Department of Biology, Università degli Studi di Padova, via U. Bassi 58b, 35131, Padova, Italy
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2
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Noronha H, Silva A, Garcia V, Billet K, Dias ACP, Lanoue A, Gallusci P, Gerós H. Grapevine woody tissues accumulate stilbenoids following bud burst. Planta 2023; 258:118. [PMID: 37962720 PMCID: PMC10645632 DOI: 10.1007/s00425-023-04270-5] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
MAIN CONCLUSION After bud burst, a transcriptional reprogramming of the shikimate and phenylpropanoid pathways occurs in grapevine canes resulting in the accumulation of stilbenoids like resveratrol and viniferin. Stilbenoids are phenylpropanoid compounds with important biological properties and biotechnological applications that are synthesized in grapevine in response to different stresses. Although they are found in woody tissues, such as canes and buds, their biosynthesis and accumulation have been essentially described in berries. We have previously shown that transcripts encoding secondary metabolism enzymes accumulate in grapevine canes following the transition from dormancy (E-L 1) to bud burst (E-L 4) suggesting that secondary metabolites may accumulate in grapevine canes during this transition. In the present study, using UPLC-MS we demonstrate the accumulation of important metabolites such as ferulic acid and the stilbenoids E-resveratrol, E-piceatannol and E-ε-viniferin. Stilbenoids accumulation correlated with the increased expression of several stilbene synthase genes and of VviMYB14, encoding a transcription factor that regulates stilbene biosynthesis. In addition, a general stimulation of the plastidial shikimate pathway was observed. Taken together, results show that important secondary metabolites accumulate in the woody canes during bud burst. These findings may aid biotechnological approaches aimed at extracting biologically active phenolic compounds, including stilbenoids, from grapevine woody tissues.
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Affiliation(s)
- Henrique Noronha
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.
| | - Angélica Silva
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Virginie Garcia
- UMR EGFV, Bordeaux Sciences Agro, INRAE, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882, Villenave d'Ornon, France
| | - Kévin Billet
- EA 2106 Biomolécules et Biotechnologies Végétales, UFR des Sciences Pharmaceutiques, Université de Tours, 31 Av. Monge, 37200, Tours, France
| | - Alberto C P Dias
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Arnaud Lanoue
- EA 2106 Biomolécules et Biotechnologies Végétales, UFR des Sciences Pharmaceutiques, Université de Tours, 31 Av. Monge, 37200, Tours, France
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRAE, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882, Villenave d'Ornon, France
| | - Hernâni Gerós
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
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3
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Gallusci P, Agius DR, Moschou PN, Dobránszki J, Kaiserli E, Martinelli F. Deep inside the epigenetic memories of stressed plants. Trends Plant Sci 2023; 28:142-153. [PMID: 36404175 DOI: 10.1016/j.tplants.2022.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Recent evidence sheds light on the peculiar type of plant intelligence. Plants have developed complex molecular networks that allow them to remember, choose, and make decisions depending on the stress stimulus, although they lack a nervous system. Being sessile, plants can exploit these networks to optimize their resources cost-effectively and maximize their fitness in response to multiple environmental stresses. Even more interesting is the capability to transmit this experience to the next generation(s) through epigenetic modifications that add to the classical genetic inheritance. In this opinion article, we present concepts and perspectives regarding the capabilities of plants to sense, perceive, remember, re-elaborate, respond, and to some extent transmit to their progeny information to adapt more efficiently to climate change.
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Affiliation(s)
- Philippe Gallusci
- Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d'Ornon, France
| | - Dolores R Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta; Ġ.F. Abela Junior College, Ġuzè Debono Square, Msida, Malta
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden; Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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4
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Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel) 2022; 13:genes13071256. [PMID: 35886036 PMCID: PMC9316115 DOI: 10.3390/genes13071256] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.
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Affiliation(s)
- Junhua Kong
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Virginie Garcia
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Enric Zehraoui
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Linda Stammitti
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Ghislaine Hilbert
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Christel Renaud
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Stéphane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Alain Delaunay
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Stéphanie Cluzet
- Unité de Recherche Oenologie, Faculté des Sciences Pharmaceutiques, University Bordeaux, EA4577, USC 1366 INRA, Equipe Molécules d’Intérêt Biologique (GESVAB), ISVV, CEDEX, 33882 Villenave d’Ornon, France;
| | - Fatma Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - David Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Emeline Teyssier
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
- Correspondence: ; Tel.: +33-5-5757-5928
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
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5
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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6
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Rubio B, Stammitti L, Cookson SJ, Teyssier E, Gallusci P. Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine. Hortic Res 2022; 9:uhab067. [PMID: 35048109 PMCID: PMC8935936 DOI: 10.1093/hr/uhab067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/24/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Grafting is an ancient method that has been intensively used for the clonal propagation of vegetables and woody trees. Despite its importance in agriculture the physiological and molecular mechanisms underlying phenotypic changes of plants following grafting are still poorly understood. In the present study, we analyse the populations of small RNAs in homo and heterografts and take advantage of the sequence differences in the genomes of heterograft partners to analyse the possible exchange of small RNAs. We demonstrate that the type of grafting per se dramatically influences the small RNA populations independently of genotypes but also show genotype specific effects. In addition, we demonstrate that bilateral exchanges of small RNAs, mainly short interfering RNAs, may occur in heterograft with the preferential transfer of small RNAs from the scion to the rootstock. Altogether, the results suggest that small RNAs may have an important role in the phenotype modifications observed in heterografts.
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Affiliation(s)
- Bernadette Rubio
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Linda Stammitti
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Sarah Jane Cookson
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Emeline Teyssier
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Philippe Gallusci
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
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7
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Noronha H, Garcia V, Silva A, Delrot S, Gallusci P, Gerós H. Molecular reprogramming in grapevine woody tissues at bud burst. Plant Sci 2021; 311:110984. [PMID: 34482904 DOI: 10.1016/j.plantsci.2021.110984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/15/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Perennial woody plants undergo a period of dormancy from the beginning of autumn until the end of spring. Whereas the molecular and physiological events that characterize dormancy release of buds have been described in detail, those occurring in woody tissues underneath the buds are mostly unknown. To bridge this gap, the mRNA populations of cane segments located underneath the bud were analyzed at bud dormancy (E-L 1) and at bud burst (E-L 4). They revealed an important reprogramming of gene expression suggesting that cell division, cell wall metabolism and the mobilization of sugars are the main metabolic and cellular events occurring in cane woody tissues at bud burst. Also, the upregulation of several genes of sugar metabolism, encoding starch- and sucrose-degrading enzymes and sugar transporters, correlates with the decrease in starch and soluble sugars in woody tissues concomitant with increased sucrose synthase and α-amylolytic biochemical activities. The latter is likely due to the VviAMY2 gene that encodes a functional α-amylase as observed after its heterologous expression in yeast. Taken together, these results are consistent with starch and sugar mobilization in canes being primarily involved in grapevine secondary growth initiation and supporting the growth of the emerging bud.
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Affiliation(s)
- Henrique Noronha
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Virginie Garcia
- UMR EGFV, Bordeaux Sciences Agro, INRAE, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, Villenave d'Ornon, 33882, France
| | - Angélica Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Serge Delrot
- UMR EGFV, Bordeaux Sciences Agro, INRAE, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, Villenave d'Ornon, 33882, France
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRAE, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, Villenave d'Ornon, 33882, France.
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal; Centre of Biological Engineering (CEB), Department of Engineering, University of Minho, Braga, Portugal
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8
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Mladenov V, Fotopoulos V, Kaiserli E, Karalija E, Maury S, Baranek M, Segal N, Testillano PS, Vassileva V, Pinto G, Nagel M, Hoenicka H, Miladinović D, Gallusci P, Vergata C, Kapazoglou A, Abraham E, Tani E, Gerakari M, Sarri E, Avramidou E, Gašparović M, Martinelli F. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. Int J Mol Sci 2021; 22:7118. [PMID: 34281171 PMCID: PMC8268041 DOI: 10.3390/ijms22137118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022] Open
Abstract
Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
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Affiliation(s)
- Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus;
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Erna Karalija
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Stephane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France;
| | - Miroslav Baranek
- Mendeleum—Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Naama Segal
- Israel Oceanographic and Limnological Research, The National Center for Mariculture (NCM), P.O.B. 1212, Eilat 88112, Israel;
| | - Pilar S. Testillano
- Center of Biological Research Margarita Salas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Glória Pinto
- Centre for Environmental and Marine Studies (CESAM), Biology Department, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany;
| | - Dragana Miladinović
- Laboratory for Biotechnology, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—CS5000833882 Villenave d’Ornon, 33076 Bordeaux, France;
| | - Chiara Vergata
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (HAO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Evaggelia Avramidou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, 10000 Zagreb, Croatia;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
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9
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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. New Phytol 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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10
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Abstract
Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post-translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening.
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Affiliation(s)
- Dengguo Tang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRAE, Bordeaux Science Agro, Villenave d'Ormon, 33140, France
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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11
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Yao M, Chen W, Kong J, Zhang X, Shi N, Zhong S, Ma P, Gallusci P, Jackson S, Liu Y, Hong Y. METHYLTRANSFERASE1 and Ripening Modulate Vivipary during Tomato Fruit Development. Plant Physiol 2020; 183:1883-1897. [PMID: 32503901 PMCID: PMC7401104 DOI: 10.1104/pp.20.00499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 05/04/2023]
Abstract
Vivipary, wherein seeds germinate prior to dispersal while still associated with the maternal plant, is an adaptation to extreme environments. It is normally inhibited by the establishment of dormancy. The genetic framework of vivipary has been well studied; however, the role of epigenetics in vivipary remains unknown. Here, we report that silencing of METHYLTRANSFERASE1 (SlMET1) promoted precocious seed germination and seedling growth within the tomato (Solanum lycopersicum) epimutant Colorless non-ripening (Cnr) fruits. This was associated with decreases in abscisic acid concentration and levels of mRNA encoding 9-cis-epoxycarotenoid-dioxygenase (SlNCED), which is involved in abscisic acid biosynthesis. Differentially methylated regions were identified in promoters of differentially expressed genes, including SlNCED SlNCED knockdown also induced viviparous seedling growth in Cnr fruits. Strikingly, Cnr ripening reversion suppressed vivipary. Moreover, neither SlMET1/SlNCED-virus-induced gene silencing nor transgenic SlMET1-RNA interference produced vivipary in wild-type tomatoes; the latter affected leaf architecture, arrested flowering, and repressed seed development. Thus, a dual pathway in ripening and SlMET1-mediated epigenetics coordinates the blockage of seed vivipary.
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Affiliation(s)
- Mengqin Yao
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Junhua Kong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, University of California, San Diego, California 92093
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom
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12
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Lai T, Wang X, Ye B, Jin M, Chen W, Wang Y, Zhou Y, Blanks AM, Gu M, Zhang P, Zhang X, Li C, Wang H, Liu Y, Gallusci P, Tör M, Hong Y. Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death. J Exp Bot 2020; 71:2995-3011. [PMID: 32016417 PMCID: PMC7260717 DOI: 10.1093/jxb/eraa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/01/2020] [Indexed: 05/19/2023]
Abstract
SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ' 30KRKR33' at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR's ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR's induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
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Affiliation(s)
- Tongfei Lai
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bishun Ye
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yingying Zhou
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Andrew M Blanks
- Cell and Developmental Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mei Gu
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Chunyang Li
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux Science Agro, Villenave d’Ornon, France
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Correspondence: , or
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13
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Belouah I, Bénard C, Denton A, Blein-Nicolas M, Balliau T, Teyssier E, Gallusci P, Bouchez O, Usadel B, Zivy M, Gibon Y, Colombié S. Transcriptomic and proteomic data in developing tomato fruit. Data Brief 2020; 28:105015. [PMID: 31909114 PMCID: PMC6938935 DOI: 10.1016/j.dib.2019.105015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 01/06/2023] Open
Abstract
Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure. From 34,725 possible transcripts identified in the tomato, 22,877 were quantified in at least one of the nine developmental stages. For the proteome analysis, label-free liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used. Peptide ions, and subsequently the proteins from which they were derived, were quantified by integrating the signal intensities obtained from extracted ion currents (XIC) with the MassChroQ software. Absolute concentrations of individual proteins were estimated for 2375 proteins by using a mixed effects model from log10-transformed intensities and normalized to the total protein content. Transcriptomics data are available via GEO repository with accession number GSE128739. The raw MS output files and identification data were deposited on-line using the PROTICdb database (http://moulon.inra.fr/protic/tomato_fruit_development) and MS proteomics data have also been deposited to the ProteomeXchange with the dataset identifier PXD012877. The main added value of these quantitative datasets is their use in a mathematical model to estimate protein turnover in developing tomato fruit.
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Affiliation(s)
- Isma Belouah
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Camille Bénard
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Alisandra Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Mélisande Blein-Nicolas
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Thierry Balliau
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Emeline Teyssier
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, CS 50008, 33882 Villenave-d’Ornon, France
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, CS 50008, 33882 Villenave-d’Ornon, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Michel Zivy
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Yves Gibon
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
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14
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Noronha H, Silva A, Dai Z, Gallusci P, Rombolà AD, Delrot S, Gerós H. A molecular perspective on starch metabolism in woody tissues. Planta 2018; 248:559-568. [PMID: 30022278 PMCID: PMC6096779 DOI: 10.1007/s00425-018-2954-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/11/2018] [Indexed: 05/20/2023]
Abstract
MAIN CONCLUSION The elucidation of the molecular mechanisms of starch synthesis and mobilization in perennial woody tissues is of the utmost scientific and agricultural importance. Starch is the main carbohydrate reserve in plants and is fundamental in human nutrition and several industrial processes. In leaves, starch accumulated during the day is degraded throughout the night and the resulting sugars, glucose and maltose, are exported to the cytosol by the specialized transmembrane translocators pGT and MEX, respectively. Nevertheless, the degradation of the starch granule is a complex process not completely elucidated. While the mechanisms of starch mobilization during germination in the dead endosperm of cereal seeds are well described, the molecular and biochemical mechanisms involved in starch storage in the heterotrophic tissues of woody plants and its utilization in spring and winter are still puzzling. It is known that some biochemical steps of starch synthesis are conserved in heterotrophic tissues and in the leaves, but some aspects are particular to sink organs. From an agronomic standpoint, the knowledge on starch storage and mobilization in woody tissues is pivotal to understand (and to optimize) some common practices in the field that modify source-sink relationships, such as pruning and defoliation. Soluble sugars resulting from starch are also pivotal to cold adaptation, and in several fruits, such as banana and kiwifruit, starch may provide soluble sugars during ripening. In this review, we explore the recent advances on the molecular mechanisms and regulations involved in starch synthesis and mobilization, with a focus on perennial woody tissues.
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Affiliation(s)
- Henrique Noronha
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Angélica Silva
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Zhanwu Dai
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Adamo D Rombolà
- Department of Agricultural Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Serge Delrot
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Vila Real, Portugal.
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal.
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15
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Noronha H, Silva A, Dai Z, Gallusci P, Rombolà AD, Delrot S, Gerós H. Correction to: A molecular perspective on starch metabolism in woody tissues. Planta 2018; 248:569. [PMID: 30073511 PMCID: PMC6096776 DOI: 10.1007/s00425-018-2963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The original article was corrected.
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Affiliation(s)
- Henrique Noronha
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Angélica Silva
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | - Zhanwu Dai
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Adamo D Rombolà
- Department of Agricultural Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Serge Delrot
- UMR EGFV, Bordeaux Science Agro, INRA, Université de Bordeaux, Villenave D'Ornon, France
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Vila Real, Portugal.
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal.
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16
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Chen W, Zhang X, Fan Y, Li B, Ryabov E, Shi N, Zhao M, Yu Z, Qin C, Zheng Q, Zhang P, Wang H, Jackson S, Cheng Q, Liu Y, Gallusci P, Hong Y. A Genetic Network for Systemic RNA Silencing in Plants. Plant Physiol 2018; 176:2700-2719. [PMID: 29439213 PMCID: PMC5884585 DOI: 10.1104/pp.17.01828] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/25/2018] [Indexed: 05/20/2023]
Abstract
Non-cell autonomous RNA silencing can spread from cell to cell and over long distances in animals and plants. However, the genetic requirements and signals involved in plant mobile gene silencing are poorly understood. Here, we identified a DICER-LIKE2 (DCL2)-dependent mechanism for systemic spread of posttranscriptional RNA silencing, also known as posttranscriptional gene silencing (PTGS), in Nicotiana benthamiana Using a suite of transgenic DCL RNAi lines coupled with a GFP reporter, we demonstrated that N. benthamiana DCL1, DCL2, DCL3, and DCL4 are required to produce microRNAs and 22, 24, and 21nt small interfering RNAs (siRNAs), respectively. All investigated siRNAs produced in local incipient cells were present at low levels in distal tissues. Inhibition of DCL2 expression reduced the spread of gene silencing, while suppression of DCL3 or DCL4 expression enhanced systemic PTGS. In contrast to DCL4 RNAi lines, DCL2-DCL4 double-RNAi lines developed systemic PTGS similar to that observed in DCL2 RNAi. We further showed that the 21 or 24 nt local siRNAs produced by DCL4 or DCL3 were not involved in long-distance gene silencing. Grafting experiments demonstrated that DCL2 was required in the scion to respond to the signal, but not in the rootstock to produce/send the signal. These results suggest a coordinated DCL genetic pathway in which DCL2 plays an essential role in systemic PTGS in N. benthamiana, while both DCL4 and DCL3 attenuate systemic PTGS. We discuss the potential role of 21, 22, and 24 nt siRNAs in systemic PTGS.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yaya Fan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Bin Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Eugene Ryabov
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mei Zhao
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Qianqian Zheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, United Kingdom
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17
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Gallusci P, Dai Z, Génard M, Gauffretau A, Leblanc-Fournier N, Richard-Molard C, Vile D, Brunel-Muguet S. Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues. Trends Plant Sci 2017; 22:610-623. [PMID: 28587758 DOI: 10.1016/j.tplants.2017.04.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [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: 12/07/2016] [Revised: 04/12/2017] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | | | - Arnaud Gauffretau
- UMR Agronomie, AgroParisTech, INRA, 78850, Thiverval-Grignon, France
| | | | - Céline Richard-Molard
- UMR ECOSYS, INRA AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Denis Vile
- LEPSE, INRA-SupAgro, 34060, Montpellier, France
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18
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Qin C, Li B, Fan Y, Zhang X, Yu Z, Ryabov E, Zhao M, Wang H, Shi N, Zhang P, Jackson S, Tör M, Cheng Q, Liu Y, Gallusci P, Hong Y. Roles of Dicer-Like Proteins 2 and 4 in Intra- and Intercellular Antiviral Silencing. Plant Physiol 2017; 174:1067-1081. [PMID: 28455401 PMCID: PMC5462052 DOI: 10.1104/pp.17.00475] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/26/2017] [Indexed: 05/23/2023]
Abstract
RNA silencing is an innate antiviral mechanism conserved in organisms across kingdoms. Such a cellular defense involves DICER or DICER-LIKEs (DCLs) that process plant virus RNAs into viral small interfering RNAs (vsiRNAs). Plants encode four DCLs that play diverse roles in cell-autonomous intracellular virus-induced RNA silencing (known as VIGS) against viral invasion. VIGS can spread between cells. However, the genetic basis and involvement of vsiRNAs in non-cell-autonomous intercellular VIGS remains poorly understood. Using GFP as a reporter gene together with a suite of DCL RNAi transgenic lines, here we show that despite the well-established activities of DCLs in intracellular VIGS and vsiRNA biogenesis, DCL4 acts to inhibit intercellular VIGS whereas DCL2 is required (likely along with DCL2-processed/dependent vsiRNAs and their precursor RNAs) for efficient intercellular VIGS trafficking from epidermal to adjacent cells. DCL4 imposed an epistatic effect on DCL2 to impede cell-to-cell spread of VIGS. Our results reveal previously unknown functions for DCL2 and DCL4 that may form a dual defensive frontline for intra- and intercellular silencing to double-protect cells from virus infection in Nicotiana benthamiana.
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Affiliation(s)
- Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Bin Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Yaya Fan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Eugene Ryabov
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Mei Zhao
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Hui Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Stephen Jackson
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Mahmut Tör
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Qi Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Yule Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Philippe Gallusci
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.)
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.)
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., B.L., Y.F., X.Z., Z.Y., E.R., M.Z., H.W., N.S., P.C., Y.H.);
- Warwick-Hangzhou RNA Signalling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom (E.R., S.J., Y.H.);
- Institute of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom (M.T.);
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.);
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France (P.G.)
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19
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Fortes AM, Gallusci P. Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. Front Plant Sci 2017; 8:82. [PMID: 28220131 PMCID: PMC5292615 DOI: 10.3389/fpls.2017.00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants. In this perspective, we discuss the contribution of epigenetic mechanisms to our understanding of plant responses to biotic and abiotic stresses. This regulation of gene expression in response to environment raises important biological questions for perennial species such as grapevine which is asexually propagated and grown worldwide in contrasting terroirs and environmental conditions. However, most species used for epigenomic studies are annual herbaceous plants, and epigenome dynamics has been poorly investigated in perennial woody plants, including grapevine. In this context, we propose grape as an essential model for epigenetic and epigenomic studies in perennial woody plants of agricultural importance.
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Affiliation(s)
- Ana M. Fortes
- Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas, Universidade de LisboaLisboa, Portugal
- *Correspondence: Ana M. Fortes, Philippe Gallusci,
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du VinVillenave-d’Ornon, France
- *Correspondence: Ana M. Fortes, Philippe Gallusci,
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Berthelot K, Estevez Y, Quiliano M, Baldera-Aguayo PA, Zimic M, Pribat A, Bakleh ME, Teyssier E, Gallusci P, Gardrat C, Lecomte S, Peruch F. HbIDI, SlIDI and EcIDI: A comparative study of isopentenyl diphosphate isomerase activity and structure. Biochimie 2016; 127:133-43. [PMID: 27163845 DOI: 10.1016/j.biochi.2016.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
In this study, we cloned, expressed and purified the isopentenyl diphosphate isomerases (IDIs) from two plants, Hevea brasiliensis and Solanum lycopersicum, and compared them to the already well characterized Escherichia coli IDI. Phylogenetic analysis showed high homology between the three enzymes. Their catalytic activity was investigated in vitro with recombinant purified enzymes and in vivo by complementation colorimetric tests. The three enzymes displayed consistent activities both in vitro and in vivo. In term of structure, studied by ATR-FTIR and molecular modeling, it is clear that both plant enzymes are more related to their human homologue than to E. coli IDI. But it is assumed that EcIDI represent the minimalistic part of the catalytic core, as both plant enzymes present a supplementary sequence forming an extra α-helice surrounding the catalytic site that could facilitate the biocatalysis. New potential biotechnological applications may be envisaged.
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Affiliation(s)
- Karine Berthelot
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France; CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
| | - Yannick Estevez
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Miguel Quiliano
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia y Nutrición, Universidad de Navarra, C/. Irunlarrea 1, 31008, Pamplona, Navarra, Spain
| | - Pedro A Baldera-Aguayo
- Department of Systems Biology and Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University in the City of New York, NY, 10032, USA; Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Anne Pribat
- INRA Bordeaux-Aquitaine, UMR 1332 Biologie du Fruit et Pathologie, F-33882, Villenave d'Ornon, France
| | - Marc-Elias Bakleh
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Emeline Teyssier
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Philippe Gallusci
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Christian Gardrat
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Sophie Lecomte
- CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Frédéric Peruch
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
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21
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Boureau L, How-Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J, Stammitti L, Pribat A, Bowler C, Hong Y, Gallusci P. A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. Plant Mol Biol 2016; 90:485-501. [PMID: 26846417 DOI: 10.1007/s11103-016-0436-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 05/21/2015] [Accepted: 01/08/2016] [Indexed: 05/21/2023]
Abstract
The Enhancer of Zeste Polycomb group proteins, which are encoded by a small gene family in Arabidopsis thaliana, participate to the control of plant development. In the tomato (Solanum lycopersicum), these proteins are encoded by three genes (SlEZ1, SlEZ2 and SlEZ3) that display specific expression profiles. Using a gene specific RNAi strategy, we demonstrate that repression of SlEZ2 correlates with a general reduction of H3K27me3 levels, indicating that SlEZ2 is part of an active PRC2 complex. Reduction of SlEZ2 gene expression impacts the vegetative development of tomato plants, consistent with SlEZ2 having retained at least some of the functions of the Arabidopsis CURLY LEAF (CLF) protein. Notwithstanding, we observed significant differences between transgenic SlEZ2 RNAi tomato plants and Arabidopsis clf mutants. First, we found that reduced SlEZ2 expression has dramatic effects on tomato fruit development and ripening, functions not described in Arabidopsis for the CLF protein. In addition, repression of SlEZ2 has no significant effect on the flowering time or the control of flower organ identity, in contrast to the Arabidopsis clf mutation. Taken together, our results are consistent with a diversification of the function of CLF orthologues in plants, and indicate that although partly conserved amongst plants, the function of EZ proteins need to be newly investigated for non-model plants because they might have been recruited to specific developmental processes.
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Affiliation(s)
- L Boureau
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Laboratory of Hematology, Centre Hospitalier Universitaire de Bordeaux - Hopital Haut Leveque, 5 Avenue Magellan, 33600, Pessac, France
| | - A How-Kit
- Laboratory for Functional Genomics, Foundation Jean Dausset - CEPH, 75010, Paris, France
| | - E Teyssier
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - S Drevensek
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université, Paris-Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, 91405, Orsay, France
| | - M Rainieri
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - J Joubès
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Laboratoire de Biogenèse Membranaire, UMR5200, CNRS, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - L Stammitti
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - A Pribat
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
| | - C Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - Y Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
| | - P Gallusci
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France.
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France.
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22
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Gallusci P, Hodgman C, Teyssier E, Seymour GB. DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening. Front Plant Sci 2016; 7:807. [PMID: 27379113 PMCID: PMC4905957 DOI: 10.3389/fpls.2016.00807] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/23/2016] [Indexed: 05/19/2023]
Abstract
Fruit ripening is a developmental process that results in the leaf-like carpel organ of the flower becoming a mature ovary primed for dispersal of the seeds. Ripening in fleshy fruits involves a profound metabolic phase change that is under strict hormonal and genetic control. This work reviews recent developments in our understanding of the epigenetic regulation of fruit ripening. We start by describing the current state of the art about processes involved in histone post-translational modifications and the remodeling of chromatin structure and their impact on fruit development and ripening. However, the focus of the review is the consequences of changes in DNA methylation levels on the expression of ripening-related genes. This includes those changes that result in heritable phenotypic variation in the absence of DNA sequence alterations, and the mechanisms for their initiation and maintenance. The majority of the studies described in the literature involve work on tomato, but evidence is emerging that ripening in other fruit species may also be under epigenetic control. We discuss how epigenetic differences may provide new targets for breeding and crop improvement.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d’Ornon, France
- *Correspondence: Philippe Gallusci,
| | - Charlie Hodgman
- School of Biosciences, University of Nottingham Sutton Bonington, UK
| | - Emeline Teyssier
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d’Ornon, France
| | - Graham B. Seymour
- School of Biosciences, University of Nottingham Sutton Bonington, UK
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23
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How-Kit A, Daunay A, Mazaleyrat N, Busato F, Daviaud C, Teyssier E, Deleuze JF, Gallusci P, Tost J. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants. Plant Mol Biol 2015; 88:471-485. [PMID: 26072424 DOI: 10.1007/s11103-015-0336-8] [Citation(s) in RCA: 11] [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] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 06/04/2023]
Abstract
Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.
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Affiliation(s)
- Alexandre How-Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 75010, Paris, France,
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24
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Zhou T, Zhang H, Lai T, Qin C, Shi N, Wang H, Jin M, Zhong S, Fan Z, Liu Y, Wu Z, Jackson S, Giovannoni JJ, Rolin D, Gallusci P, Hong Y. Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening. Sci Rep 2012; 2:836. [PMID: 23150786 PMCID: PMC3495281 DOI: 10.1038/srep00836] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/12/2012] [Indexed: 11/10/2022] Open
Abstract
Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of virus technology to express genes to induce phenotypes or to complement mutants in order to understand the function of plant genes is not well documented. Here we exploit Potato virus X as a tool for virus-induced gene complementation (VIGC). Using VIGC in tomato, we demonstrated that ectopic viral expression of LeMADS-RIN, which encodes a MADS-box transcription factor (TF), resulted in functional complementation of the non-ripening rin mutant phenotype and caused fruits to ripen. Comparative gene expression analysis indicated that LeMADS-RIN up-regulated expression of the SBP-box (SQUAMOSA promoter binding protein-like) gene LeSPL-CNR, but down-regulated the expression of LeHB-1, an HD-Zip homeobox TF gene. Our data support the hypothesis that a transcriptional network may exist among key TFs in the modulation of fruit ripening in tomato.
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Affiliation(s)
- Tao Zhou
- Warwick HRI and School of Life Science, University of Warwick, Warwick, UK
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25
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Boulila-Zoghlami L, Gallusci P, Holzer FM, Basset GJ, Djebali W, Chaïbi W, Walling LL, Brouquisse R. Up-regulation of leucine aminopeptidase-A in cadmium-treated tomato roots. Planta 2011; 234:857-863. [PMID: 21744092 DOI: 10.1007/s00425-011-1468-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/21/2011] [Indexed: 05/31/2023]
Abstract
The effects of cadmium (Cd) on aminopeptidase (AP) activities and Leucine-AP (LAP) expression were investigated in the roots of tomato (Solanum lycopersicum L., var Ibiza) plants. Three-week-old plants were grown for 10 days in the presence of 0.3-300 μM Cd and compared to control plants grown in the absence of Cd. AP activities were measured using six different p-nitroanilide (p-NA) substrates. Leu, Met, Arg, Pro and Lys hydrolyzing activities increased in roots of Cd-treated plants, while Phe-pNA cleavage was not enhanced after Cd treatments. The use of peptidase inhibitors showed that most of the Leu-pNA hydrolyzing activity was related to one or several metallo-APs. Changes in Lap transcripts, protein and activities were measured in the roots of 0 and 30-μM Cd-treated plants. LapA transcript levels increased in Cd-treated roots, whereas LapN RNAs levels were not modified. To assess amount of Leu-pNA hydrolyzing activity associated with the hexameric LAPs, LAP activity was measured following immunoprecipitation with a LAP polyclonal antiserum. LAP activity increased in Cd-treated roots. There was a corresponding increase in LAP-A protein levels detected in 2D-immunoblots. The role of LAP-A in the proteolytic response to Cd stress is discussed.
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Affiliation(s)
- Latifa Boulila-Zoghlami
- Département de Biologie, Faculté des Sciences de Tunis El Manar, Unité de Recherche de Biologie et Physiologie Cellulaires Végétales, 1060 Tunis, Tunisia
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26
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Hédiji H, Djebali W, Cabasson C, Maucourt M, Baldet P, Bertrand A, Boulila Zoghlami L, Deborde C, Moing A, Brouquisse R, Chaïbi W, Gallusci P. Effects of long-term cadmium exposure on growth and metabolomic profile of tomato plants. Ecotoxicol Environ Saf 2010; 73:1965-74. [PMID: 20846723 DOI: 10.1016/j.ecoenv.2010.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/06/2010] [Accepted: 08/12/2010] [Indexed: 05/21/2023]
Abstract
The response of tomato plants to long-term cadmium exposure was evaluated after a 90-days long culture in hydroponic conditions (0, 20, and 100 μM CdCl(2)). Cadmium preferentially accumulated in roots, and to a lower extent in upper parts of plants. Absolute quantification of 28 metabolites was obtained through (1)H NMR, HPLC-PDA, and colorimetric methods. The principal component analysis showed a clear separation between control and Cd treated samples. Proline and total ascorbate amounts were reduced in Cd-treated leaves, whereas α-tocopherol, asparagine, and tyrosine accumulation increased, principally in 100 μM Cd treated leaves. Carotenoid and chlorophyll contents decreased only in 100 μM Cd-mature-leaves, which correlate with a reduced expression of genes essential for isoprenoid and carotenoid accumulations. Our results show that tomato plants acclimatize during long-term exposure to 20 μM Cd. On the contrary, 100μM Cd treatment results in drastic physiological and metabolic perturbations leading to plant growth limitation and fruit set abortion.
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Affiliation(s)
- Hédia Hédiji
- UR Biologie et Physiologie Cellulaires Végétales, Département de Biologie, Faculté des Sciences de Tunis, El Manar, 1060 Tunis, Tunisia
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27
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How Kit A, Boureau L, Stammitti-Bert L, Rolin D, Teyssier E, Gallusci P. Functional analysis of SlEZ1 a tomato enhancer of zeste (E(z)) gene demonstrates a role in flower development. Plant Mol Biol 2010; 74:201-13. [PMID: 20582715 DOI: 10.1007/s11103-010-9657-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 06/10/2010] [Indexed: 05/10/2023]
Abstract
The Enhancer of Zeste (E(z)) Polycomb group (PcG) proteins, which are encoded by a small gene family in Arabidopsis thaliana, have been shown to participate to the control of flowering and seed development. For the time being, little is known about the function of these proteins in other plants. In tomato E(z) proteins are encoded by at least two genes namely SlEZ1 and SlEZ2 while a third gene, SlEZ3, is likely to encode a truncated non-functional protein. The analysis of the corresponding mRNA demonstrates that these two genes are differentially regulated during plant and fruit development. We also show that SlEZ1 and SlEZ2 are targeted to the nuclei. These results together with protein sequence analysis makes it likely that both proteins are functional E(z) proteins. The characterisation of SlEZ1 RNAi lines suggests that although there might be some functional redundancy between SlEZ1 and SlEZ2 in most plant organs, the former protein is likely to play specific function in flower development.
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Affiliation(s)
- A How Kit
- UMR Biologie du Fruit, INRA, Universités Bordeaux 1 et Bordeaux 2, CR INRA de Bordeaux, 71 Avenue Edouard Bourleaux, BP 81, 33883 Villenave d'Ornon Cedex, France
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28
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Mortain-Bertrand A, Stammitti L, Telef N, Colardelle P, Brouquisse R, Rolin D, Gallusci P. Effects of exogenous glucose on carotenoid accumulation in tomato leaves. Physiol Plant 2008; 134:246-256. [PMID: 18494861 DOI: 10.1111/j.1399-3054.2008.01130.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [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
To investigate the effect of carbohydrate on carotenoid accumulation in leaves, excised plants of tomato (Lycopersicum esculentum var. cerasiformae, wva 106) were supplied with glucose through the transpiration stream for 48 h. We report here that sugar accumulation in leaves led to a decrease of carotenoid content, which was related to the reduction of Chl. The decrease in carotenoid amount correlated with a sugar-induced repression of genes encoding enzymes of the carotenoid and of the Rohmer pathways. The lower 1-deoxy-D-xylulose-5-phosphate synthase transcript level probably leads to a decreased metabolic flux through the methylerythritol pathway and subsequently to a lower amount of substrate available for plastidic isoprenoid synthesis. Differences between responses of young (sink) and mature (source) leaves to carbohydrate accumulation are discussed.
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29
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Horchani F, Gallusci P, Baldet P, Cabasson C, Maucourt M, Rolin D, Aschi-Smiti S, Raymond P. Prolonged root hypoxia induces ammonium accumulation and decreases the nutritional quality of tomato fruits. J Plant Physiol 2008; 165:1352-1359. [PMID: 18180072 DOI: 10.1016/j.jplph.2007.10.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2007] [Revised: 10/24/2007] [Accepted: 10/24/2007] [Indexed: 05/25/2023]
Abstract
Here we examined the effects of root hypoxia (1-2% oxygen) on the physiology of the plant and on the biochemical composition of fruits in tomato (Solanum lycopersicum cv. Micro-Tom) plants submitted to gradual root hypoxia at first flower anthesis. Root hypoxia enhanced nitrate absorption with a concomitant release of nitrite and ammonium into the medium, a reduction of leaf photosynthetic activity and chlorophyll content, and an acceleration of fruit maturation, but did not affect final fruit size. Quantitative metabolic profiling of mature pericarp extracts by (1)H NMR showed that levels of major metabolites including sugars, organic acids and amino acids were not modified. However, ammonium concentration increased dramatically in fruit flesh, and ascorbate and lycopene concentrations decreased. Our data indicate that the unfavorable effects of root hypoxia on fruit quality cannot be explained by two of the well-known effects of root hypoxia on the plant, namely a decrease in photosynthesis or an excess in ethylene production, but may instead result from disturbances in the supply of either growth regulators or ammonium, by the roots.
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Affiliation(s)
- Faouzi Horchani
- Département des Sciences Biologiques, Faculté des Sciences de Tunis, UR d'Ecologie Végétale,Campus Universitaire, Tunis, Tunisia
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30
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Teyssier E, Bernacchia G, Maury S, How Kit A, Stammitti-Bert L, Rolin D, Gallusci P. Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta 2008; 228:391-9. [PMID: 18488247 DOI: 10.1007/s00425-008-0743-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 04/17/2008] [Indexed: 05/18/2023]
Abstract
Tomato fruit cells are characterized by a strong increase in nuclear ploidy during fruit development. Average ploidy levels increased to similar levels (above 50C) in two distinct fruit tissues, pericarp and locular tissue. However, ploidy profiles differed significantly between these two tissues suggesting a tissue-specific control of endoreduplication in tomato fruit. To determine possible relationships between endoreduplication and epigenetic mechanisms, the methylation status of genomic DNA from pericarp and locular tissue of tomato fruit was analysed. Pericarp genomic DNA was characterized by an increase of CG and/or CNG methylation at the 5S and 18S rDNA loci and at gyspsy-like retrotransposon sequences during fruit growth. A sharp decrease of the global DNA methylation level together with a reduction of methylation at the rDNA loci was also observed in pericarp during fruit ripening. Inversely, no major variation of DNA methylation either global or locus-specific, was observed in locular tissue. Thus, tissue-specific variations of DNA methylation are unlikely to be triggered by the induction of endoreduplication in fruit tissues, but may reflect tissue-specific ploidy profiles. Expression analysis of eight putative tomato DNA methyltransferases encoding genes showed that one chromomethylase (CMT) and two rearranged methyltransferases (DRMs) are preferentially expressed in the pericarp during fruit growth and could be involved in the locus-specific increase of methylation observed at this developmental phase in the pericarp.
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Affiliation(s)
- E Teyssier
- INRA, UMR 619, BP 81, 33883, Villenave d'Ornon, France
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31
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Djebali W, Gallusci P, Polge C, Boulila L, Galtier N, Raymond P, Chaibi W, Brouquisse R. Modifications in endopeptidase and 20S proteasome expression and activities in cadmium treated tomato (Solanum lycopersicum L.) plants. Planta 2008; 227:625-39. [PMID: 17952456 DOI: 10.1007/s00425-007-0644-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 09/28/2007] [Indexed: 05/13/2023]
Abstract
The effects of cadmium (Cd) on cellular proteolytic responses were investigated in the roots and leaves of tomato (Solanum lycopersicum L., var Ibiza) plants. Three-week-old plants were grown for 3 and 10 days in the presence of 0.3-300 microM Cd and compared to control plants grown in the absence of Cd. Roots of Cd treated plants accumulated four to fivefold Cd as much as mature leaves. Although 10 days of culture at high Cd concentrations inhibited plant growth, tomato plants recovered and were still able to grow again after Cd removal. Tomato roots and leaves are not modified in their proteolytic response with low Cd concentrations (< or =3 microM) in the incubation medium. At higher Cd concentration, protein oxidation state and protease activities are modified in roots and leaves although in different ways. The soluble protein content of leaves decreased and protein carbonylation level increased indicative of an oxidative stress. Conversely, protein content of roots increased from 30 to 50%, but the amount of oxidized proteins decreased by two to threefold. Proteolysis responded earlier in leaves than in root to Cd stress. Additionally, whereas cysteine- and metallo-endopeptidase activities, as well as proteasome chymotrypsin activity and subunit expression level, increased in roots and leaves, serine-endopeptidase activities increased only in leaves. This contrasted response between roots and leaves may reflect differences in Cd compartmentation and/or complexation, antioxidant responses and metabolic sensitivity to Cd between plant tissues. The up-regulation of the 20S proteasome gene expression and proteolytic activity argues in favor of the involvement of the 20S proteasome in the degradation of oxidized proteins in plants.
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Affiliation(s)
- Wahbi Djebali
- Département de Biologie, Faculté des Sciences de Tunis El Manar, Unité de Recherche de Biologie et Physiologie Cellulaires Végétales, 1060 Tunis, Tunisia
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32
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Télef N, Stammitti-Bert L, Mortain-Bertrand A, Maucourt M, Carde JP, Rolin D, Gallusci P. Sucrose deficiency delays lycopene accumulation in tomato fruit pericarp discs. Plant Mol Biol 2006; 62:453-69. [PMID: 16915514 DOI: 10.1007/s11103-006-9033-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 06/13/2006] [Indexed: 05/11/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening is characterized by a massive accumulation of carotenoids (mainly lycopene) as chloroplasts change to chromoplasts. To address the question of the role of sugars in controlling carotenoid accumulation, fruit pericarp discs (mature green fruits) were cultured in vitro in the presence of various sucrose concentrations. A significant difference in soluble sugar content was achieved depending on external sucrose availability. Sucrose limitation delayed and reduced lycopene and phytoene accumulation, with no significant effect on other carotenoids. Chlorophyll degradation and starch catabolism were not affected by variations of sucrose availability. The reduction of lycopene synthesis observed in sucrose-limited conditions was mediated through metabolic changes illustrated by reduced hexose accumulation levels. In addition, variations of sucrose availability modulated PSY1 gene expression. Taken together our results suggest that the modulation of carotenoid accumulation by sucrose availability occurs at the metabolic level and involves the differential regulation of genes involved in carotenoid biosynthesis.
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Affiliation(s)
- Nadège Télef
- UMR Physiologie et Biotechnologie Végétales, INRA, Université Bordeaux 1, Université Victor Segalen Bordeaux 2, CR INRA de Bordeaux, 71 Avenue Edouard Bourleaux, BP 81, 33883, Villenave d'Ornon Cedex, France
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33
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Gaffe J, Bru JP, Causse M, Vidal A, Stamitti-Bert L, Carde JP, Gallusci P. LEFPS1, a tomato farnesyl pyrophosphate gene highly expressed during early fruit development. Plant Physiol 2000; 123:1351-1362. [PMID: 10938353 PMCID: PMC59093 DOI: 10.1104/pp.123.4.1351] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Accepted: 04/20/2000] [Indexed: 05/23/2023]
Abstract
Farnesyl pyrophosphate synthase (FPS) catalyzes the synthesis of farnesyl pyrophosphate, a key intermediate in sterol and sesquiterpene biosynthesis. Using a polymerase chain reaction-based approach, we have characterized LeFPS1, a tomato (Lycoperscion esculentum cv Wva 106) fruit cDNA, which encodes a functional FPS. We demonstrate that tomato FPSs are encoded by a small multigenic family with genes located on chromosomes 10 and 12. Consistent with farnesyl pyrophosphate requirement in sterol biosynthesis, FPS genes are ubiquitously expressed in tomato plants. Using an LeFPS1 specific probe, we show that the corresponding gene can account for most of FPS mRNA in most plant organs, but not during young seedling development, indicating a differential regulation of FPS genes in tomato. FPS gene expression is also under strict developmental control: FPS mRNA was mainly abundant in young organs and decreased as organs matured with the exception of fruits that presented a biphasic accumulation pattern. In this latter case in situ hybridization studies have shown that FPS mRNA is similarly abundant in all tissues of young fruit. Taken together our results suggest that several FPS isoforms are involved in tomato farnesyl pyrophosphate metabolism and that FPS genes are mostly expressed in relation to cell division and enlargement.
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Affiliation(s)
- J Gaffe
- Laboratoire de Biologie Cellulaire et Moléculaire du Dévelopement des Plantes, Université de Bordeaux 1, Avenue des Facultés, 33405 Talence, France
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Gallusci P, Varotto S, Matsuoko M, Maddaloni M, Thompson RD. Regulation of cytosolic pyruvate, orthophosphate dikinase expression in developing maize endosperm. Plant Mol Biol 1996; 31:45-55. [PMID: 8704158 DOI: 10.1007/bf00020605] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pyruvate orthophosphate dikinase (PPDK, E.C. 2.7.9.1) is an abundant enzyme in the leaves of C4 plants associated with the dicarboxylic acid pathways of CO2 fixation in the dark. PPDK activity has also been detected in the seeds of maize and other, non-C4 cereals, where its role has yet to be established. Using an anti-PPDK serum, two cross-reacting species of M(r) close to 90 000 were detected in developing maize endosperm of wild-type plants. In two independent opaque-2 mutant lines, one of the polypeptides was absent and the other was reduced in level. Similarly, endosperm PPDK mRNA levels were greatly reduced in the opaque-2 maize lines compared to wild type, suggesting that endosperm PPDK gene expression is under Opaque-2 control. However, a low level of PPDK mRNA could still be detected in these mutants, indicating that PPDK gene expression is not absolutely dependent on Opaque-2 but rather can be modulated by it. This interpretation was reinforced by the demonstration that the distribution of PPDK transcripts is not affected in o2 mutants, although the level is reduced, and that PPDK mRNA is detectable prior to 02 mRNA during the maturation of wild-type maize endosperm. Using oligonucleotides specific for the different maize PPDK genes, the o2 mutations were shown to affect only cyPPDKZml gene expression in maize line A69Y.
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Affiliation(s)
- P Gallusci
- Max-Planck-Institut für Züchtungsforschung, Köln, Germany
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Maddaloni M, Donini G, Balconi C, Rizzi E, Gallusci P, Forlani F, Lohmer S, Thompson R, Salamini F, Motto M. The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms. Mol Gen Genet 1996; 250:647-54. [PMID: 8676867 DOI: 10.1007/bf02174452] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The maize Opaque-2 (O2) protein is a transcription factor of the basic/leucine-zipper class, involved in the regulation of endosperm proteins including the 22kDa alpha-zein storage proteins and b32 protein. In this study we have focussed our attention on the relationship between O2 and the cyPPDK1 gene, which encodes a cytoplasmic pyruvate orthophosphate dikinase (PPDK) isoform. The results of this study showed that PPDK activity is detectable in wild-type maize endosperms, while in o2 mutant endosperms, the levels of PPDK protein, mRNA and enzymatic activity are reduced, indicating that O2 is involved in the regulation of cyPPDK1 in this tissue. By employing transient expression experiments in tobacco mesophyll protoplasts, we have demonstrated that the O2 protein can activate expression of a chloramphenicol acetyl transferase reporter gene placed under the control of the cyPPDK1 promoter. An in vitro binding assay and DNaseI footprint analysis demonstrated that a specific sequence in the cyPPDK1 promoter can be recognized and protected by maize O2 protein. The regulation by the O2 locus of cyPPDK1 reported here, and control of alpha-zein synthesis by O2 suggest that the O2 protein may play a more general role in maize endosperm development than previously thought.
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Affiliation(s)
- M Maddaloni
- Istituto Sperimentale per la Cerealicoltura, Bergamo, Italy
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Gallusci P, Salamini F, Thompson RD. Differences in cell type-specific expression of the gene Opaque 2 in maize and transgenic tobacco. Mol Gen Genet 1994; 244:391-400. [PMID: 8078465 DOI: 10.1007/bf00286691] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Opaque 2 (O2) gene encodes a transcriptional activator of the basic region/leucine zipper family, which controls the synthesis of a major storage protein class in maize endosperm, the 22 kDa alpha-zeins, and of several other non-zein polypeptides including b32. We demonstrate, by analysing O2 mRNAs in different organs of maize plants, that the O2 gene is only active in the endosperm. Its transcription is precisely controlled during seed development: O2 mRNAs are first detected 10 days after pollination and accumulate in the endosperm over a period of 20 days. When introduced into tobacco plants, the O2 promoter directs the expression of the beta-glucuronidase (GUS) reporter gene in endosperm, but also in the embryo, cotyledons and pollen. The first 185 bp of the O2 promoter is sufficient for developmentally regulated expression in tobacco seeds. A distinct cis-acting element, located between positions -185 and -520, directs expression in the cotyledons of tobacco seedlings. The possible origins of this breakdown in promoter specificity in the heterologous host are discussed.
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Affiliation(s)
- P Gallusci
- Max-Planck-Institut für Züchtungsforschung, Köln, Germany
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Barker DG, Bianchi S, Blondon F, Dattée Y, Duc G, Essad S, Flament P, Gallusci P, Génier G, Guy P, Muel X, Tourneur J, Dénarié J, Huguet T. Medicago truncatula, a model plant for studying the molecular genetics of theRhizobium-legume symbiosis. Plant Mol Biol Rep 1990. [PMID: 0 DOI: 10.1007/bf02668879] [Citation(s) in RCA: 163] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Barker DG, Gallusci P, Lullien V, Khan H, Ghérardi M, Huguet T. Identification of two groups of leghemoglobin genes in alfalfa (Medicago sativa) and a study of their expression during root nodule development. Plant Mol Biol 1988; 11:761-772. [PMID: 24272626 DOI: 10.1007/bf00019516] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/1988] [Accepted: 09/12/1988] [Indexed: 06/02/2023]
Abstract
Differential screening of an alfalfa root nodule cDNA library with either root or nodule mRNA resulted in the isolation of two groups of leghemoglobin cDNA which differ significantly in sequence. Analysis of one member of each group revealed a divergence within the coding region of 15% at the nucleotide level and 14% at the amino acid level. The 3' non-coding sequences are 25% divergent but are highly conserved over a stretch of 54 nucleotides which contains two sequence motifs common to leghemoglobin genes from other plant species. Southern blotting analysis with exon-specific probes has shown that there are approximately twice as many leghemoglobin gene copies in the alfalfa genome corresponding to one type of cDNA as compared with the other. Using the same criterium of DNA sequence relatedness these two distinct groups of leghemoglobin genes have also been identified in the genomes of the diploid annual Medicago truncatula and the closely related genus, Melilotus. Transcripts corresponding to both groups of leghemoglobin genes are first detected in alfalfa nodules 9-10 days after Rhizobium inoculation. Thereafter, mRNA levels increase rapidly and synchronously, reaching a maximum approximately 2 days later. There is a 2-3 fold difference in the steady-state levels of the two mRNA populations and this is maintained throughout the subsequent two weeks of nodule growth. The absence of any detectable transcription during the early stages of nodule development and the apparent co-ordinate expression of leghemoglobin genes in alfalfa contrasts with the situation in soybean and suggests that important differences in leghemoglobin gene regulation exist between these two distantly related legume species.
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Affiliation(s)
- D G Barker
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, BP 27, 31326, Castanet-Tolosan Cedex, France
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