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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. Plant Cell 2024:koae095. [PMID: 38635902 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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Vladejić J, Kovacik M, Zwyrtková J, Szurman-Zubrzycka M, Doležel J, Pecinka A. Zeocin-induced DNA damage response in barley and its dependence on ATR. Sci Rep 2024; 14:3119. [PMID: 38326519 PMCID: PMC10850495 DOI: 10.1038/s41598-024-53264-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
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Affiliation(s)
- Jovanka Vladejić
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia.
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3
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Kaduchová K, Čmiel V, Koláčková V, Pecinka A. EasyClick: an improved system for confocal microscopy of live roots with a user-optimized sample holder. Planta 2023; 259:22. [PMID: 38095727 PMCID: PMC10721658 DOI: 10.1007/s00425-023-04293-y] [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: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
MAIN CONCLUSION We describe a user-optimized sample holder EasyClick for medium-sized plants that reduces root side movements and thus greatly extends the duration of live cell confocal microscopy. Preparation and mounting of the samples are key factors for successful live cell microscopy. To acquire biologically relevant data, it is necessary to minimize stress and avoid physical damage to plant tissues during the installation of the sample into the microscope. This is challenging, particularly when the whole plant is mounted as the living sample needs to be properly anchored in the microscopic system to obtain high-quality and high-resolution data. Here, we present a user-optimized sample holder EasyClick for live cell inverted confocal microscopic analysis of plant roots with diameters from 0.3 to 0.7 mm. The EasyClick holder was tested on an inverted confocal microscope using germinating plants of several cereals. Nevertheless, it can be directly used on other types of inverted microscopes from various producers and on different plant species. The EasyClick holder effectively restricts root lateral and vertical movements. This greatly improves the conditions for time-lapse microscopy of the samples of interest.
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Affiliation(s)
- Kateřina Kaduchová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 779 00, Olomouc, Czech Republic
| | - Vratislav Čmiel
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3082/12, 61600, Brno, Czech Republic.
| | - Veronika Koláčková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic.
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Lelkes E, Jemelková J, Holá M, Štefanovie B, Kolesár P, Vágnerová R, Dvořák Tomaštíková E, Pecinka A, Angelis KJ, Paleček JJ. Characterization of the conserved features of the NSE6 subunit of the Physcomitrium patens SMC5/6 complex. Plant J 2023; 115:1084-1099. [PMID: 37191775 DOI: 10.1111/tpj.16282] [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] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes are molecular machines ensuring chromatin organization at higher levels. They play direct roles in cohesion, condensation, replication, transcription, and DNA repair. Their cores are composed of long-armed SMC, kleisin, and kleisin-associated subunits. Additional factors, like NSE6 within SMC5/6, bind to SMC core complexes and regulate their activities. In the human HsNSE6/SLF2, we recently identified a new CANIN domain. Here we tracked down its sequence homology to lower plants, selected the bryophyte Physcomitrium patens, and analyzed PpNSE6 protein-protein interactions to explore its conservation in detail. We identified a previously unrecognized core sequence motif conserved from yeasts to humans within the NSE6 CANIN domain. This motif mediates the interaction between NSE6 and its NSE5 partner in yeasts and plants. In addition, the CANIN domain and its preceding PpNSE6 sequences bind both PpSMC5 and PpSMC6 arms. Interestingly, we mapped the PpNSE6-binding site at the PpSMC5 arm right next to the PpNSE2-binding surface. The position of NSE6 at SMC arms suggests its role in the regulation of SMC5/6 dynamics. Consistent with the regulatory role of NSE6 subunits, Ppnse6 mutant lines were viable and sensitive to the DNA-damaging drug bleomycin and lost a large portion of rDNA copies. These moss mutants also exhibited reduced growth and developmental aberrations. Altogether, our data showed the conserved function of the NSE6 subunit and architecture of the SMC5/6 complex across species.
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Affiliation(s)
- Edit Lelkes
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jitka Jemelková
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Marcela Holá
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Barbora Štefanovie
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Peter Kolesár
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Radka Vágnerová
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Karel J Angelis
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Jan J Paleček
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
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5
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Kaduchová K, Marchetti C, Ovečka M, Galuszka P, Bergougnoux V, Šamaj J, Pecinka A. Spatial organization and dynamics of chromosomes and microtubules during barley mitosis. Plant J 2023. [PMID: 37326283 DOI: 10.1111/tpj.16355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/28/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
Mitosis and cytokinesis are fundamental processes through which somatic cells increase their numbers and allow plant growth and development. Here, we analyzed the organization and dynamics of mitotic chromosomes, nucleoli, and microtubules in living cells of barley root primary meristems using a series of newly developed stable fluorescent protein translational-fusion lines and time-lapse confocal microscopy. The median duration of mitosis from prophase until the end of telophase was 65.2 and 78.2 minutes until the end of cytokinesis. We showed that barley chromosomes frequently start condensation before mitotic preprophase as defined by the organization of microtubules, and maintain it even after entering into the new interphase. Furthermore, we found that the process of chromosome condensation does not finish at metaphase, but gradually continues until the end of mitosis. In summary, our study features resources for in vivo analysis of barley nuclei and chromosomes, and their dynamics during mitotic cell cycle.
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Affiliation(s)
- Kateřina Kaduchová
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Cintia Marchetti
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute (CATRIN), Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Petr Galuszka
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Véronique Bergougnoux
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute (CATRIN), Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
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6
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. Front Plant Sci 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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7
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Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. Plant Cell 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
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Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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8
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Nowicka A, Ferková Ľ, Said M, Kovacik M, Zwyrtková J, Baroux C, Pecinka A. Non-Rabl chromosome organization in endoreduplicated nuclei of barley embryo and endosperm tissues. J Exp Bot 2023; 74:2527-2541. [PMID: 36705553 DOI: 10.1093/jxb/erad036] [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] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 06/06/2023]
Abstract
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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Affiliation(s)
- Anna Nowicka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ľuboslava Ferková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
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9
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Dvořák Tomaštíková E, Yang F, Mlynárová K, Hafidh S, Schořová Š, Kusová A, Pernisová M, Přerovská T, Klodová B, Honys D, Fajkus J, Pecinka A, Schrumpfová PP. RUVBL proteins are involved in plant gametophyte development. Plant J 2023; 114:325-337. [PMID: 36752686 DOI: 10.1111/tpj.16136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
The proper development of male and female gametophytes is critical for successful sexual reproduction and requires a carefully regulated series of events orchestrated by a suite of various proteins. RUVBL1 and RUVBL2, plant orthologues of human Pontin and Reptin, respectively, belong to the evolutionarily highly conserved AAA+ family linked to a wide range of cellular processes. Previously, we found that RUVBL1 and RUVBL2A mutations are homozygous lethal in Arabidopsis. Here, we report that RUVBL1 and RUVBL2A play roles in reproductive development. We show that mutant plants produce embryo sacs with an abnormal structure or with various numbers of nuclei. Although pollen grains of heterozygous mutant plants exhibit reduced viability and reduced pollen tube growth in vitro, some of the ruvbl pollen tubes are capable of targeting ovules in vivo. Similarly, some ruvbl ovules retain the ability to attract wild-type pollen tubes but fail to develop further. The activity of the RUVBL1 and RUVBL2A promoters was observed in the embryo sac, pollen grains, and tapetum cells and, for RUVBL2A, also in developing ovules. In summary, we show that the RUVBL proteins are essential for the proper development of both male and particularly female gametophytes in Arabidopsis.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Fen Yang
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Kristína Mlynárová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Markéta Pernisová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Božena Klodová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 00, Praha 2, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, CZ-165 02, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 00, Praha 2, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
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10
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Vladejić J, Yang F, Dvořák Tomaštíková E, Doležel J, Palecek JJ, Pecinka A. Analysis of BRCT5 domain-containing proteins reveals a new component of DNA damage repair in Arabidopsis. Front Plant Sci 2022; 13:1023358. [PMID: 36578335 PMCID: PMC9791218 DOI: 10.3389/fpls.2022.1023358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The integrity of plant genetic information is constantly challenged by various internal and external factors. Therefore, plants use a sophisticated molecular network to identify, signal and repair damaged DNA. Here, we report on the identification and analysis of four uncharacterized Arabidopsis BRCT5 DOMAIN CONTAINING PROTEINs (BCPs). Proteins with the BRCT5 domain are frequently involved in the maintenance of genome stability across eukaryotes. The screening for sensitivity to induced DNA damage identified BCP1 as the most interesting candidate. We show that BCP1 loss of function mutants are hypersensitive to various types of DNA damage and accumulate an increased number of dead cells in root apical meristems upon DNA damage. Analysis of publicly available sog1 transcriptomic and SOG1 genome-wide DNA binding data revealed that BCP1 is inducible by gamma radiation and is a direct target of this key DNA damage signaling transcription factor. Importantly, bcp1 plants showed a reduced frequency of somatic homologous recombination in response to both endogenous and induced DNA damage. Altogether, we identified a novel plant-specific DNA repair factor that acts downstream of SOG1 in homology-based repair.
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Affiliation(s)
- Jovanka Vladejić
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Fen Yang
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Jan J. Palecek
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
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11
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Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus 2022; 13:277-299. [PMID: 36447428 PMCID: PMC9754023 DOI: 10.1080/19491034.2022.2144013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
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Affiliation(s)
- Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Anna Nowicka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Kateřina Kaduchová
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Michaela Kubová
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Mohammad A. Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Christophe Tatout
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Isabelle Colas
- The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, Scotland UK
| | | | - Sophie Desset
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Sarah Mermet
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Aurélia Boulaflous-Stevens
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | | | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Devin Routh
- Service and Support for Science IT (S3IT), Universität Zürich, Zürich, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland,CONTACT Célia Baroux Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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12
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Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. Theor Appl Genet 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
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13
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Zuo S, Yadala R, Yang F, Talbert P, Fuchs J, Schubert V, Ahmadli U, Rutten T, Pecinka A, Lysak MA, Lermontova I. Recurrent Plant-Specific Duplications of KNL2 and Its Conserved Function as a Kinetochore Assembly Factor. Mol Biol Evol 2022; 39:msac123. [PMID: 35671323 PMCID: PMC9210943 DOI: 10.1093/molbev/msac123] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 02/21/2022] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
KINETOCHORE NULL2 (KNL2) plays key role in the recognition of centromeres and new CENH3 deposition. To gain insight into the origin and diversification of the KNL2 gene, we reconstructed its evolutionary history in the plant kingdom. Our results indicate that the KNL2 gene in plants underwent three independent ancient duplications in ferns, grasses and eudicots. Additionally, we demonstrated that previously unclassified KNL2 genes could be divided into two clades αKNL2 and βKNL2 in eudicots and γKNL2 and δKNL2 in grasses, respectively. KNL2s of all clades encode the conserved SANTA domain, but only the αKNL2 and γKNL2 groups additionally encode the CENPC-k motif. In the more numerous eudicot sequences, signatures of positive selection were found in both αKNL2 and βKNL2 clades, suggesting recent or ongoing adaptation. The confirmed centromeric localization of βKNL2 and mutant analysis suggests that it participates in loading of new CENH3, similarly to αKNL2. A high rate of seed abortion was found in heterozygous βKNL2 plants and the germinated homozygous mutants did not develop beyond the seedling stage. Taken together, our study provides a new understanding of the evolutionary diversification of the plant kinetochore assembly gene KNL2, and suggests that the plant-specific duplicated KNL2 genes are involved in centromere and/or kinetochore assembly for preserving genome stability.
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Affiliation(s)
- Sheng Zuo
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Ramakrishna Yadala
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Fen Yang
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Paul Talbert
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Ulkar Ahmadli
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Inna Lermontova
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany
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14
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Yang F, Pecinka A. Multiple Roles of SMC5/6 Complex during Plant Sexual Reproduction. Int J Mol Sci 2022; 23:ijms23094503. [PMID: 35562893 PMCID: PMC9099584 DOI: 10.3390/ijms23094503] [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: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Chromatin-based processes are essential for cellular functions. Structural maintenance of chromosomes (SMCs) are evolutionarily conserved molecular machines that organize chromosomes throughout the cell cycle, mediate chromosome compaction, promote DNA repair, or control sister chromatid attachment. The SMC5/6 complex is known for its pivotal role during the maintenance of genome stability. However, a dozen recent plant studies expanded the repertoire of SMC5/6 complex functions to the entire plant sexual reproductive phase. The SMC5/6 complex is essential in meiosis, where its activity must be precisely regulated to allow for normal meiocyte development. Initially, it is attenuated by the recombinase RAD51 to allow for efficient strand invasion by the meiosis-specific recombinase DMC1. At later stages, it is essential for the normal ratio of interfering and non-interfering crossovers, detoxifying aberrant joint molecules, preventing chromosome fragmentation, and ensuring normal chromosome/sister chromatid segregation. The latter meiotic defects lead to the production of diploid male gametes in Arabidopsis SMC5/6 complex mutants, increased seed abortion, and production of triploid offspring. The SMC5/6 complex is directly involved in controlling normal embryo and endosperm cell divisions, and pioneer studies show that the SMC5/6 complex is also important for seed development and normal plant growth in cereals.
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Affiliation(s)
- Fen Yang
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
- Correspondence:
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15
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Prochazkova K, Finke A, Tomaštíková ED, Filo J, Bente H, Dvořák P, Ovečka M, Šamaj J, Pecinka A. Zebularine induces enzymatic DNA-protein crosslinks in 45S rDNA heterochromatin of Arabidopsis nuclei. Nucleic Acids Res 2021; 50:244-258. [PMID: 34904670 PMCID: PMC8754632 DOI: 10.1093/nar/gkab1218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Loss of genome stability leads to reduced fitness, fertility and a high mutation rate. Therefore, the genome is guarded by the pathways monitoring its integrity and neutralizing DNA lesions. To analyze the mechanism of DNA damage induction by cytidine analog zebularine, we performed a forward-directed suppressor genetic screen in the background of Arabidopsis thaliana zebularine-hypersensitive structural maintenance of chromosomes 6b (smc6b) mutant. We show that smc6b hypersensitivity was suppressed by the mutations in EQUILIBRATIVE NUCLEOSIDE TRANSPORTER 3 (ENT3), DNA METHYLTRANSFERASE 1 (MET1) and DECREASE IN DNA METHYLATION 1 (DDM1). Superior resistance of ent3 plants to zebularine indicated that ENT3 is likely necessary for the import of the drug to the cells. Identification of MET1 and DDM1 suggested that zebularine induces DNA damage by interference with the maintenance of CG DNA methylation. The same holds for structurally similar compounds 5-azacytidine and 2-deoxy-5-azacytidine. Based on our genetic and biochemical data, we propose that zebularine induces enzymatic DNA–protein crosslinks (DPCs) of MET1 and zebularine-containing DNA in Arabidopsis, which was confirmed by native chromatin immunoprecipitation experiments. Moreover, zebularine-induced DPCs accumulate preferentially in 45S rDNA chromocenters in a DDM1-dependent manner. These findings open a new avenue for studying genome stability and DPC repair in plants.
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Affiliation(s)
| | | | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Jaroslav Filo
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Heinrich Bente
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Ales Pecinka
- To whom correspondence should be addressed. Tel: +420 585 238 709;
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16
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Yang F, Fernández-Jiménez N, Tučková M, Vrána J, Cápal P, Díaz M, Pradillo M, Pecinka A. Defects in meiotic chromosome segregation lead to unreduced male gametes in Arabidopsis SMC5/6 complex mutants. Plant Cell 2021; 33:3104-3119. [PMID: 34240187 PMCID: PMC8462810 DOI: 10.1093/plcell/koab178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Structural maintenance of chromosome 5/6 (SMC5/6) complex is a crucial factor for preserving genome stability. Here, we show that mutants for several Arabidopsis (Arabidopsis thaliana) SMC5/6 complex subunits produce triploid offspring. This phenotype is caused by a meiotic defect leading to the production of unreduced male gametes. The SMC5/6 complex mutants show an absence of chromosome segregation during the first and/or the second meiotic division, as well as a partially disorganized microtubule network. Importantly, although the SMC5/6 complex is partly required for the repair of SPO11-induced DNA double-strand breaks, the nonreduction described here is SPO11-independent. The measured high rate of ovule abortion suggests that, if produced, such defects are maternally lethal. Upon fertilization with an unreduced pollen, the unbalanced maternal and paternal genome dosage in the endosperm most likely causes seed abortion observed in several SMC5/6 complex mutants. In conclusion, we describe the function of the SMC5/6 complex in the maintenance of gametophytic ploidy in Arabidopsis.
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Affiliation(s)
- Fen Yang
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nadia Fernández-Jiménez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Martina Tučková
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Mariana Díaz
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Author for correspondence:
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17
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Perutka Z, Kaduchová K, Chamrád I, Beinhauer J, Lenobel R, Petrovská B, Bergougnoux V, Vrána J, Pecinka A, Doležel J, Šebela M. Proteome Analysis of Condensed Barley Mitotic Chromosomes. Front Plant Sci 2021; 12:723674. [PMID: 34497629 PMCID: PMC8419432 DOI: 10.3389/fpls.2021.723674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.
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Affiliation(s)
- Zdeněk Perutka
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Kateřina Kaduchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Beáta Petrovská
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Véronique Bergougnoux
- Department of Molecular Biology, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
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18
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Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, Gy I, Camilleri C, Effgen S, Koornneef M, Pecinka A, Loudet O, Schneeberger K. The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Mol Biol Evol 2021; 38:1225-1240. [PMID: 33247726 PMCID: PMC8042742 DOI: 10.1093/molbev/msaa306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.
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Affiliation(s)
- Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vipul Patel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Klasen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Petra Pecinkova
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sigi Effgen
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czech Republic
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
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19
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Samakovli D, Tichá T, Vavrdová T, Závorková N, Pecinka A, Ovečka M, Šamaj J. HEAT SHOCK PROTEIN 90 proteins and YODA regulate main body axis formation during early embryogenesis. Plant Physiol 2021; 186:1526-1544. [PMID: 33856486 PMCID: PMC8260137 DOI: 10.1093/plphys/kiab171] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/01/2021] [Indexed: 05/23/2023]
Abstract
The YODA (YDA) kinase pathway is intimately associated with the control of Arabidopsis (Arabidopsis thaliana) embryo development, but little is known regarding its regulators. Using genetic analysis, HEAT SHOCK PROTEIN 90 (HSP90) proteins emerge as potent regulators of YDA in the process of embryo development and patterning. This study is focused on the characterization and quantification of early embryonal traits of single and double hsp90 and yda mutants. HSP90s genetic interactions with YDA affected the downstream signaling pathway to control the development of both basal and apical cell lineage of embryo. Our results demonstrate that the spatiotemporal expression of WUSCHEL-RELATED HOMEOBOX 8 (WOX8) and WOX2 is changed when function of HSP90s or YDA is impaired, suggesting their essential role in the cell fate determination and possible link to auxin signaling during early embryo development. Hence, HSP90s together with YDA signaling cascade affect transcriptional networks shaping the early embryo development.
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Affiliation(s)
- Despina Samakovli
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Tereza Tichá
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Tereza Vavrdová
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Natálie Závorková
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc 779 00, Czech Republic
| | - Miroslav Ovečka
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Jozef Šamaj
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
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20
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Markus C, Pecinka A, Merotto A. Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana. Int J Mol Sci 2021; 22:3314. [PMID: 33804990 PMCID: PMC8037345 DOI: 10.3390/ijms22073314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 11/24/2022] Open
Abstract
Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.
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Affiliation(s)
- Catarine Markus
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil;
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Experimental Botany, Czech Academy Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil;
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21
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Nowicka A, Kovacik M, Tokarz B, Vrána J, Zhang Y, Weigt D, Doležel J, Pecinka A. Dynamics of endoreduplication in developing barley seeds. J Exp Bot 2021; 72:268-282. [PMID: 33005935 DOI: 10.1093/jxb/eraa453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/25/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Seeds are complex biological systems comprising three genetically distinct tissues: embryo, endosperm, and maternal tissues (including seed coats and pericarp) nested inside one another. Cereal grains represent a special type of seeds, with the largest part formed by the endosperm, a specialized triploid tissue ensuring embryo protection and nourishment. We investigated dynamic changes in DNA content in three of the major seed tissues from the time of pollination up to the dry seed. We show that the cell cycle is under strict developmental control in different seed compartments. After an initial wave of active cell division, cells switch to endocycle and most endoreduplication events are observed in the endosperm and seed maternal tissues. Using different barley cultivars, we show that there is natural variation in the kinetics of this process. During the terminal stages of seed development, specific and selective loss of endoreduplicated nuclei occurs in the endosperm. This is accompanied by reduced stability of the nuclear genome, progressive loss of cell viability, and finally programmed cell death. In summary, our study shows that endopolyploidization and cell death are linked phenomena that frame barley grain development.
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Affiliation(s)
- Anna Nowicka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Krakow, Poland
| | - Martin Kovacik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Barbara Tokarz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Yueqi Zhang
- Research School Biology (RSB), University of Western Australia (UWA), Crawley, Perth, Australia
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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22
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Makowski W, Królicka A, Nowicka A, Zwyrtková J, Tokarz B, Pecinka A, Banasiuk R, Tokarz KM. Transformed tissue of Dionaea muscipula J. Ellis as a source of biologically active phenolic compounds with bactericidal properties. Appl Microbiol Biotechnol 2021; 105:1215-1226. [PMID: 33447868 PMCID: PMC7843487 DOI: 10.1007/s00253-021-11101-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/02/2020] [Accepted: 01/05/2021] [Indexed: 01/27/2023]
Abstract
Abstract The Venus flytrap (Dionaea muscipula J. Ellis) is a carnivorous plant able to synthesize large amounts of phenolic compounds, such as phenylpropanoids, flavonoids, phenolic acids, and 1,4-naphtoquinones. In this study, the first genetic transformation of D. muscipula tissues is presented. Two wild-type Rhizobium rhizogenes strains (LBA 9402 and ATCC 15834) were suitable vector organisms in the transformation process. Transformation led to the formation of teratoma (transformed shoot) cultures with the bacterial rolB gene incorporated into the plant genome in a single copy. Using high-pressure liquid chromatography, we demonstrated that transgenic plants were characterized by an increased quantity of phenolic compounds, including 1,4-naphtoquinone derivative, plumbagin (up to 106.63 mg × g−1 DW), and phenolic acids (including salicylic, caffeic, and ellagic acid), in comparison to non-transformed plants. Moreover, Rhizobium-mediated transformation highly increased the bactericidal properties of teratoma-derived extracts. The antibacterial properties of transformed plants were increased up to 33% against Staphylococcus aureus, Enterococcus faecalis, and Escherichia coli and up to 7% against Pseudomonas aeruginosa. For the first time, we prove the possibility of D. muscipula transformation. Moreover, we propose that transformation may be a valuable tool for enhancing secondary metabolite production in D. muscipula tissue and to increase bactericidal properties against human antibiotic-resistant bacteria. Key points • Rhizobium-mediated transformation created Dionaea muscipula teratomas. • Transformed plants had highly increased synthesis of phenolic compounds. • The MBC value was connected with plumbagin and phenolic acid concentrations.
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Affiliation(s)
- Wojciech Makowski
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland.
| | - Aleksandra Królicka
- Intercollegiate Faculty of Biotechnology UG and MUG, Laboratory of Biologically Active Compounds, University of Gdansk, Gdansk, Poland.
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.,The Franciszek Górski Institute of Plant Physiology, The Polish Academy of Sciences, Krakow, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Barbara Tokarz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Rafał Banasiuk
- Institute of Biotechnology and Molecular Medicine, Gdansk, Poland
| | - Krzysztof Michał Tokarz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
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23
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Yang F, Fernández Jiménez N, Majka J, Pradillo M, Pecinka A. Structural Maintenance of Chromosomes 5/6 Complex Is Necessary for Tetraploid Genome Stability in Arabidopsis thaliana. Front Plant Sci 2021; 12:748252. [PMID: 34675953 PMCID: PMC8525318 DOI: 10.3389/fpls.2021.748252] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/06/2021] [Indexed: 05/04/2023]
Abstract
Polyploidization is a common phenomenon in the evolution of flowering plants. However, only a few genes controlling polyploid genome stability, fitness, and reproductive success are known. Here, we studied the effects of loss-of-function mutations in NSE2 and NSE4A subunits of the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex in autotetraploid Arabidopsis thaliana plants. The diploid nse2 and nse4a plants show partially reduced fertility and produce about 10% triploid offspring with two paternal and one maternal genome copies. In contrast, the autotetraploid nse2 and nse4a plants were almost sterile and produced hexaploid and aneuploid progeny with the extra genome copies or chromosomes coming from both parents. In addition, tetraploid mutants had more severe meiotic defects, possibly due to the presence of four homologous chromosomes instead of two. Overall, our study suggests that the SMC5/6 complex is an important player in the maintenance of tetraploid genome stability and that autotetraploid Arabidopsis plants have a generally higher frequency of but also higher tolerance for aneuploidy compared to diploids.
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Affiliation(s)
- Fen Yang
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Natural Sciences, Palacký University, Olomouc, Czechia
| | - Nadia Fernández Jiménez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Joanna Majka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- *Correspondence: Ales Pecinka,
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24
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Abstract
Understanding the mechanisms regulating the development of cereal seeds is essential for plant breeding and increasing yield. However, the analysis of cereal seeds is challenging owing to the minute size, the liquid character of some tissues, and the tight inter-tissue connections. Here, we demonstrate a detailed protocol for dissection of the embryo, endosperm, and seed maternal tissues at early, middle, and late stages of barley seed development. The protocol is based on a manual tissue dissection using fine-pointed tools and a binocular microscope, followed by ploidy analysis-based purity control. Seed maternal tissues and embryos are diploid, while the endosperm is triploid tissue. This allows the monitoring of sample purity using flow cytometry. Additional measurements revealed the high quality of RNA isolated from such samples and their usability for high-sensitivity analysis. In conclusion, this protocol describes how to practically dissect pure tissues from developing grains of cultivated barley and potentially also other cereals.
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Affiliation(s)
- Martin Kovacik
- Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany
| | - Anna Nowicka
- Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany; The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology
| | - Ales Pecinka
- Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany;
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25
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Strejčková B, Čegan R, Pecinka A, Milec Z, Šafář J. Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat. BMC Plant Biol 2020; 20:175. [PMID: 33050875 PMCID: PMC7557041 DOI: 10.1186/s12870-020-02384-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. RESULTS Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals. CONCLUSIONS The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Radim Čegan
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200, Brno, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic.
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Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. J Exp Bot 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
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Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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Nowicka A, Tokarz B, Zwyrtková J, Dvořák Tomaštíková E, Procházková K, Ercan U, Finke A, Rozhon W, Poppenberger B, Otmar M, Niezgodzki I, Krečmerová M, Schubert I, Pecinka A. Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. Plant J 2020; 102:68-84. [PMID: 31733119 DOI: 10.1111/tpj.14612] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/02/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Repetitive DNA sequences and some genes are epigenetically repressed by transcriptional gene silencing (TGS). When genetic mutants are not available or problematic to use, TGS can be suppressed by chemical inhibitors. However, informed use of epigenetic inhibitors is partially hampered by the absence of any systematic comparison. In addition, there is emerging evidence that epigenetic inhibitors cause genomic instability, but the nature of this damage and its repair remain unclear. To bridge these gaps, we compared the effects of 5-azacytidine (AC), 2'-deoxy-5-azacytidine (DAC), zebularine and 3-deazaneplanocin A (DZNep) on TGS and DNA damage repair. The most effective inhibitor of TGS was DAC, followed by DZNep, zebularine and AC. We confirmed that all inhibitors induce DNA damage and suggest that this damage is repaired by multiple pathways with a critical role of homologous recombination and of the SMC5/6 complex. A strong positive link between the degree of cytidine analog-induced DNA demethylation and the amount of DNA damage suggests that DNA damage is an integral part of cytidine analog-induced DNA demethylation. This helps us to understand the function of DNA methylation in plants and opens the possibility of using epigenetic inhibitors in biotechnology.
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Affiliation(s)
- Anna Nowicka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, PL-30 239, Krakow, Poland
| | - Barbara Tokarz
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Unit of Botany and Plant Physiology, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. 29 Listopada 54, PL-31 425, Krakow, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Klára Procházková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Ugur Ercan
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Andreas Finke
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Miroslav Otmar
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Igor Niezgodzki
- Biogeosystem Modelling Group, ING PAN - Institute of Geological Sciences Polish Academy of Sciences, Research Center in Krakow, Senacka 1, PL-31 002, Krakow, Poland
| | - Marcela Krečmerová
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland, DE-06466, Gatersleben, OT, Germany
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
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Boudichevskaia A, Houben A, Fiebig A, Prochazkova K, Pecinka A, Lermontova I. Depletion of KNL2 Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in Arabidopsis. Int J Mol Sci 2019; 20:ijms20225726. [PMID: 31731608 PMCID: PMC6888302 DOI: 10.3390/ijms20225726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 11/17/2022] Open
Abstract
Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) of Arabidopsis thaliana that is involved in the licensing of centromeres for the cenH3 recruitment. We also demonstrated that a knockout mutant for KNL2 shows mitotic and meiotic defects, slower development, reduced growth rate, and fertility. To analyze an effect of KNL2 mutation on global gene transcription of Arabidopsis, we performed RNA-sequencing experiments using seedling and flower bud tissues of knl2 and wild-type plants. The transcriptome data analysis revealed a high number of differentially expressed genes (DEGs) in knl2 plants. The set was enriched in genes involved in the regulation of the cell cycle, transcription, development, and DNA damage repair. In addition to comprehensive information regarding the effects of KNL2 mutation on the global gene expression, physiological changes in plants are also presented, which provides an integrated understanding of the critical role played by KNL2 in plant growth and development.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
- Correspondence: (A.B.); (I.L.); Tel.: +49/39482 5477 (A.B.); +49/39482 5570 (I.L.)
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
| | - Klara Prochazkova
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (A.P.)
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (A.P.)
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
- Correspondence: (A.B.); (I.L.); Tel.: +49/39482 5477 (A.B.); +49/39482 5570 (I.L.)
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29
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Finke A, Mandáková T, Nawaz K, Vu GTH, Novák P, Macas J, Lysak MA, Pecinka A. Genome invasion by a hypomethylated satellite repeat in Australian crucifer Ballantinia antipoda. Plant J 2019; 99:1066-1079. [PMID: 31074166 DOI: 10.1111/tpj.14380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 07/07/2017] [Revised: 04/02/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
Repetitive sequences are ubiquitous components of all eukaryotic genomes. They contribute to genome evolution and the regulation of gene transcription. However, the uncontrolled activity of repetitive sequences can negatively affect genome functions and stability. Therefore, repetitive DNAs are embedded in a highly repressive heterochromatic environment in plant cell nuclei. Here, we analyzed the sequence, composition and the epigenetic makeup of peculiar non-pericentromeric heterochromatic segments in the genome of the Australian crucifer Ballantinia antipoda. By the combination of high throughput sequencing, graph-based clustering and cytogenetics, we found that the heterochromatic segments consist of a mixture of unique sequences and an A-T-rich 174 bp satellite repeat (BaSAT1). BaSAT1 occupies about 10% of the B. antipoda nuclear genome in >250 000 copies. Unlike many other highly repetitive sequences, BaSAT1 repeats are hypomethylated; this contrasts with the normal patterns of DNA methylation in the B. antipoda genome. Detailed analysis of several copies revealed that these non-methylated BaSAT1 repeats were also devoid of heterochromatic histone H3K9me2 methylation. However, the factors decisive for the methylation status of BaSAT1 repeats remain currently unknown. In summary, we show that even highly repetitive sequences can exist as hypomethylated in the plant nuclear genome.
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Affiliation(s)
- Andreas Finke
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
| | - Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC - Central-European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Kashif Nawaz
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Agricultural and Biotechnological Research (CRH), Olomouc, 77900, Czech Republic
| | - Giang T H Vu
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
| | - Petr Novák
- Biology Centre, The Czech Academy of Sciences, České Budejovice, 37005, Czech Republic
| | - Jiri Macas
- Biology Centre, The Czech Academy of Sciences, České Budejovice, 37005, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC - Central-European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, 50829, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Agricultural and Biotechnological Research (CRH), Olomouc, 77900, Czech Republic
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Díaz M, Pečinková P, Nowicka A, Baroux C, Sakamoto T, Gandha PY, Jeřábková H, Matsunaga S, Grossniklaus U, Pecinka A. The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. Plant Cell 2019; 31:1579-1597. [PMID: 31036599 PMCID: PMC6635853 DOI: 10.1105/tpc.18.00043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2019] [Accepted: 04/26/2019] [Indexed: 05/04/2023]
Abstract
The maintenance of genome integrity over cell divisions is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is the STRUCTURAL MAINTENANCE OF CHROMOSOME5 (SMC5) and SMC6 (SMC5/6) complex, related to the cohesin and condensin complexes that control sister chromatid alignment and chromosome condensation, respectively. Here, we characterize NON-SMC ELEMENT4 (NSE4) paralogs of the SMC5/6 complex in Arabidopsis (Arabidopsis thaliana). NSE4A is expressed in meristems and accumulates during DNA damage repair. Partial loss-of-function nse4a mutants are viable but hypersensitive to DNA damage induced by zebularine. In addition, nse4a mutants produce abnormal seeds, with noncellularized endosperm and embryos that maximally develop to the heart or torpedo stage. This phenotype resembles the defects in cohesin and condensin mutants and suggests a role for all three SMC complexes in differentiation during seed development. By contrast, NSE4B is expressed in only a few cell types, and loss-of-function mutants do not have any obvious abnormal phenotype. In summary, our study shows that the NSE4A subunit of the SMC5-SMC6 complex is essential for DNA damage repair in somatic tissues and plays a role in plant reproduction.
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Affiliation(s)
- Mariana Díaz
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Petra Pečinková
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Anna Nowicka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
- Polish Academy of Sciences, Franciszek Gorski Institute of Plant Physiology, 30-239 Krakow, Poland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Priscilla Yuliani Gandha
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), 50829 Cologne, Germany
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic
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Vuolo F, Kierzkowski D, Runions A, Hajheidari M, Mentink RA, Gupta MD, Zhang Z, Vlad D, Wang Y, Pecinka A, Gan X, Hay A, Huijser P, Tsiantis M. Corrigendum: LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication. Genes Dev 2019; 33:377. [DOI: 10.1101/gad.323733.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Lazaro A, Zhou Y, Giesguth M, Nawaz K, Bergonzi S, Pecinka A, Coupland G, Albani MC. PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina. J Exp Bot 2019; 70:949-961. [PMID: 30481340 PMCID: PMC6363098 DOI: 10.1093/jxb/ery423] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 09/11/2018] [Accepted: 11/19/2018] [Indexed: 05/04/2023]
Abstract
The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 ortholog in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to control flowering through the vernalization pathway via enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the ortholog of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2, we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here, we demonstrate that PEP2 activity prevents the up-regulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY), and APETALA1 (AaAP1), ensuring floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in axillary branches. These multiple roles of PEP2 in the vernalization response contribute to the A. alpina life cycle.
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Affiliation(s)
- Ana Lazaro
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Yanhao Zhou
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Düsseldorf, Germany
| | - Miriam Giesguth
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Düsseldorf, Germany
| | - Kashif Nawaz
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc, Czech Republic
| | - Sara Bergonzi
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc, Czech Republic
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Maria C Albani
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’, Düsseldorf, Germany
- Correspondence: or
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33
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Vuolo F, Kierzkowski D, Runions A, Hajheidari M, Mentink RA, Gupta MD, Zhang Z, Vlad D, Wang Y, Pecinka A, Gan X, Hay A, Huijser P, Tsiantis M. LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication. Genes Dev 2018; 32:1361-1366. [PMID: 30366902 PMCID: PMC6217736 DOI: 10.1101/gad.318212.118] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/21/2018] [Indexed: 12/16/2022]
Abstract
Here, Vuolo et al. investigated the mechanisms controlling the relative size of leaves compared with their lateral appendages (stipules). Using genetics, live imaging, and modeling, they demonstrate that the LATE MERISTEM IDENTITY1 (LMI1) homeodomain protein regulates stipule proportions via an endoreduplication-dependent trade-off that limits tissue size despite increasing cell growth. How the interplay between cell- and tissue-level processes produces correctly proportioned organs is a key problem in biology. In plants, the relative size of leaves compared with their lateral appendages, called stipules, varies tremendously throughout development and evolution, yet relevant mechanisms remain unknown. Here we use genetics, live imaging, and modeling to show that in Arabidopsis leaves, the LATE MERISTEM IDENTITY1 (LMI1) homeodomain protein regulates stipule proportions via an endoreduplication-dependent trade-off that limits tissue size despite increasing cell growth. LM1 acts through directly activating the conserved mitosis blocker WEE1, which is sufficient to bypass the LMI1 requirement for leaf proportionality.
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Affiliation(s)
- Francesco Vuolo
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Daniel Kierzkowski
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Adam Runions
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mohsen Hajheidari
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Remco A Mentink
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mainak Das Gupta
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Zhongjuan Zhang
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Daniela Vlad
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Yi Wang
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Breeding Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Xiangchao Gan
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Angela Hay
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Peter Huijser
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Deparment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Markus C, Pecinka A, Karan R, Barney JN, Merotto A. Epigenetic regulation - contribution to herbicide resistance in weeds? Pest Manag Sci 2018; 74:275-281. [PMID: 28888062 DOI: 10.1002/ps.4727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 06/02/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 05/10/2023]
Abstract
Continuous use of herbicides has resulted in the evolution of resistance to all major herbicide modes of action worldwide. Besides the well-documented cases of newly acquired resistance through genetic changes, epigenetic regulation may also contribute to herbicide resistance in weeds. Epigenetics involves processes that modify the expression of specific genetic elements without changes in the DNA sequence, and play an important role in re-programming gene expression. Epigenetic modifications can be induced spontaneously, genetically or environmentally. Stress-induced epigenetic changes are normally reverted soon after stress exposure, although in specific cases they can also be carried over multiple generations, thereby having a selective benefit. Here, we provide an overview of the basis of epigenetic regulation in plants and discuss the possible effect of epigenetic changes on herbicide resistance. The understanding of these epigenetic changes would add a new perspective to our knowledge of environmental and management stresses and their effects on the evolution of herbicide resistance in weeds. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Catarine Markus
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ratna Karan
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Jacob N Barney
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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35
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Diaz M, Pecinka A. Scaffolding for Repair: Understanding Molecular Functions of the SMC5/6 Complex. Genes (Basel) 2018; 9:genes9010036. [PMID: 29329249 PMCID: PMC5793187 DOI: 10.3390/genes9010036] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 11/15/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 12/17/2022] Open
Abstract
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex. SMC5/6 complex was originally identified based on the sensitivity of its mutants to genotoxic stress but there is increasing number of studies demonstrating its roles in the control of DNA replication, sister chromatid resolution and genomic location-dependent promotion or suppression of homologous recombination. Some of these functions appear to be due to a very dynamic interaction with cohesin or other repair complexes. Studies in Arabidopsis indicate that, besides its canonical function in repair of damaged DNA, the SMC5/6 complex plays important roles in regulating plant development, abiotic stress responses, suppression of autoimmune responses and sexual reproduction.
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Affiliation(s)
- Mariana Diaz
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc-Holice, Czech Republic.
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36
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Abstract
DNA methylation is an epigenetic modification, which contributes to the regulation of gene expression and chromatin organization, and thus plays a role in many aspects of plant life. Here we present three methods for the detection of DNA methylation in plant tissues: high performance liquid chromatography, methylation-sensitive restriction digest followed by quantitative PCR and bisulfite conversion followed by single read sequencing. These methods are complementary and allow analysis of DNA methylation in samples from both model and non-model plant species.
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Affiliation(s)
- Andreas Finke
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, Technische Universität München, Munich, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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37
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van Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M. Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley. Plant Physiol 2017; 174:2397-2408. [PMID: 28655778 PMCID: PMC5543938 DOI: 10.1104/pp.17.00108] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/25/2017] [Indexed: 05/17/2023]
Abstract
The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.
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Affiliation(s)
- G Wilma van Esse
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Agatha Walla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Andreas Finke
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maria von Korff
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
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38
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Affiliation(s)
- Mariana Diaz
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research
- Max Planck Institute for Plant Breeding Research (MPIPZ)
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research
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39
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Pietzenuk B, Markus C, Gaubert H, Bagwan N, Merotto A, Bucher E, Pecinka A. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biol 2016; 17:209. [PMID: 27729060 PMCID: PMC5059998 DOI: 10.1186/s13059-016-1072-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 04/05/2016] [Accepted: 09/23/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. RESULTS We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A. lyrata and A. thaliana. Heat-responsiveness of COPIA families is correlated with the presence of putative high affinity heat shock factor binding HREs within their long terminal repeats in seven Brassicaceae species. The strong HRE of ONSEN is conserved over millions of years and has evolved by duplication of a proto-HRE sequence, which was already present early in the evolution of the Brassicaceae. However, HREs of most families are species-specific, and in Boechera stricta, the ONSEN HRE accumulated mutations and lost heat-responsiveness. CONCLUSIONS Gain of HREs does not always provide an ultimate selective advantage for TEs, but may increase the probability of their long-term survival during the co-evolution of hosts and genomic parasites.
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Affiliation(s)
- Björn Pietzenuk
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Present address: Department of Plant Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Catarine Markus
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540000, Brazil
| | - Hervé Gaubert
- Department of Plant Biology, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, 1211, Geneva 4, Switzerland
- Present address: The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Navratan Bagwan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Present address: Cardiovascular proteomics, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540000, Brazil
| | - Etienne Bucher
- UMR1345 IRHS, Université d'Angers, INRA, Université Bretagne Loire, SFR4207 QUASAV, 49045, Angers, France
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany.
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40
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Vu GTH, Schmutzer T, Bull F, Cao HX, Fuchs J, Tran TD, Jovtchev G, Pistrick K, Stein N, Pecinka A, Neumann P, Novak P, Macas J, Dear PH, Blattner FR, Scholz U, Schubert I. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus. Plant Genome 2015; 8:eplantgenome2015.04.0021. [PMID: 33228273 DOI: 10.3835/plantgenome2015.04.0021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/19/2015] [Indexed: 06/11/2023]
Abstract
The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.-Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400-800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Fabian Bull
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Institute for Biodiversity and Ecosystem Research, 2 Yurii Gagarin Street, Sofia, 1113, Bulgaria
| | - Klaus Pistrick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Petr Novak
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Jiri Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Paul H Dear
- MRC Lab. of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk Univ., 61137, Brno, Czech Republic
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41
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Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, Pecinka A, Schneeberger K. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One 2015; 10:e0137391. [PMID: 26382944 PMCID: PMC4575116 DOI: 10.1371/journal.pone.0137391] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.
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Affiliation(s)
- Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ahmed Abdelsamad
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Department of Genetics, Cairo University, 12613, Giza, Egypt
| | - Björn Pietzenuk
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Danelle K. Seymour
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Daniel Koenig
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35–39, 72076, Tübingen, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- * E-mail: (KS); (AP)
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- * E-mail: (KS); (AP)
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42
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Piofczyk T, Jeena G, Pecinka A. Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses. Plant Physiol Biochem 2015; 93:34-43. [PMID: 25656510 DOI: 10.1016/j.plaphy.2015.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/21/2015] [Indexed: 05/12/2023]
Abstract
UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Here we studied growth related traits of 345 Arabidopsis thaliana accessions in response to UV radiation stress. We analyzed the genetic basis of this natural variation by genome-wide association studies, which suggested a specific candidate genomic region. RNA-sequencing of three sensitive and three resistant accessions combined with mutant analysis revealed five large effect genes. Mutations in PHE ammonia lyase 1 (PAL1) and putative kinase At1g76360 rendered Arabidopsis hypersensitive to UV stress, while loss of function from putative methyltransferase At4g22530, novel plant snare 12 (NPSN12) and defense gene activated disease resistance 2 (ADR2) conferred higher UV stress resistance. Three sensitive accessions showed strong ADR2 transcriptional activation, accumulation of salicylic acid (SA) and dwarf growth upon UV stress, while these phenotypes were much less affected in resistant plants. The phenotype of sensitive accessions resembles autoimmune reactions due to overexpression of defense related genes, and suggests that natural variation in response to UV radiation stress is driven by pathogen-like responses in Arabidopsis.
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Affiliation(s)
- Thomas Piofczyk
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Ganga Jeena
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany.
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43
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Cao HX, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu GTH. Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front Microbiol 2015; 6:526. [PMID: 26236284 PMCID: PMC4500957 DOI: 10.3389/fmicb.2015.00526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 04/15/2015] [Accepted: 05/12/2015] [Indexed: 01/21/2023] Open
Abstract
In the carnivorous plant genus Genlisea a unique lobster pot trapping mechanism supplements nutrition in nutrient-poor habitats. A wide spectrum of microbes frequently occurs in Genlisea's leaf-derived traps without clear relevance for Genlisea carnivory. We sequenced the metatranscriptomes of subterrestrial traps vs. the aerial chlorophyll-containing leaves of G. nigrocaulis and of G. hispidula. Ribosomal RNA assignment revealed soil-borne microbial diversity in Genlisea traps, with 92 genera of 19 phyla present in more than one sample. Microbes from 16 of these phyla including proteobacteria, green algae, amoebozoa, fungi, ciliates and metazoans, contributed additionally short-lived mRNA to the metatranscriptome. Furthermore, transcripts of 438 members of hydrolases (e.g., proteases, phosphatases, lipases), mainly resembling those of metazoans, ciliates and green algae, were found. Compared to aerial leaves, Genlisea traps displayed a transcriptional up-regulation of endogenous NADH oxidases generating reactive oxygen species as well as of acid phosphatases for prey digestion. A leaf-vs.-trap transcriptome comparison reflects that carnivory provides inorganic P- and different forms of N-compounds (ammonium, nitrate, amino acid, oligopeptides) and implies the need to protect trap cells against oxidative stress. The analysis elucidates a complex food web inside the Genlisea traps, and suggests ecological relationships between this plant genus and its entrapped microbiome.
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Affiliation(s)
- Hieu X. Cao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Thomas Schmutzer
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Uwe Scholz
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ)Köln, Germany
| | - Ingo Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
| | - Giang T. H. Vu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
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44
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Liu CH, Finke A, Díaz M, Rozhon W, Poppenberger B, Baubec T, Pecinka A. Repair of DNA Damage Induced by the Cytidine Analog Zebularine Requires ATR and ATM in Arabidopsis. Plant Cell 2015; 27:1788-800. [PMID: 26023162 PMCID: PMC4498198 DOI: 10.1105/tpc.114.135467] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/11/2015] [Indexed: 05/04/2023]
Abstract
DNA damage repair is an essential cellular mechanism that maintains genome stability. Here, we show that the nonmethylable cytidine analog zebularine induces a DNA damage response in Arabidopsis thaliana, independent of changes in DNA methylation. In contrast to genotoxic agents that induce damage in a cell cycle stage-independent manner, zebularine induces damage specifically during strand synthesis in DNA replication. The signaling of this damage is mediated by additive activity of ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED and ATAXIA TELANGIECTASIA MUTATED kinases, which cause postreplicative cell cycle arrest and increased endoreplication. The repair requires a functional STRUCTURAL MAINTENANCE OF CHROMOSOMES5 (SMC5)-SMC6 complex and is accomplished predominantly by synthesis-dependent strand-annealing homologous recombination. Here, we provide insight into the response mechanism for coping with the genotoxic effects of zebularine and identify several components of the zebularine-induced DNA damage repair pathway.
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Affiliation(s)
- Chun-Hsin Liu
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Andreas Finke
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mariana Díaz
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, Technische Universität München, 85354 Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, Technische Universität München, 85354 Freising, Germany
| | | | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Willing EM, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJV, Becker C, Warthmann N, Chica C, Szarzynska B, Zytnicki M, Albani MC, Kiefer C, Bergonzi S, Castaings L, Mateos JL, Berns MC, Bujdoso N, Piofczyk T, de Lorenzo L, Barrero-Sicilia C, Mateos I, Piednoël M, Hagmann J, Chen-Min-Tao R, Iglesias-Fernández R, Schuster SC, Alonso-Blanco C, Roudier F, Carbonero P, Paz-Ares J, Davis SJ, Pecinka A, Quesneville H, Colot V, Lysak MA, Weigel D, Coupland G, Schneeberger K. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants 2015; 1:14023. [PMID: 27246759 DOI: 10.1038/nplants.2014.23] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/10/2014] [Indexed: 05/10/2023]
Abstract
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
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Affiliation(s)
- Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Terezie Mandáková
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Karl J V Nordström
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Claudia Chica
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Bogna Szarzynska
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Matthias Zytnicki
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Maria C Albani
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Sara Bergonzi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Loren Castaings
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Julieta L Mateos
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Markus C Berns
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Nora Bujdoso
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Thomas Piofczyk
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Laura de Lorenzo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Barrero-Sicilia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Isabel Mateos
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Romy Chen-Min-Tao
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Stephan C Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Martin A Lysak
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
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de Meaux J, Pecinka A. The Arabidopsis genus: An emerging model to elucidate the molecular basis of interspecific differences in transposable element activity. Mob Genet Elements 2014; 2:142-144. [PMID: 23061020 PMCID: PMC3463470 DOI: 10.4161/mge.21111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Arabidopsis thaliana is a model plant species and its molecular dissection has greatly contributed to our understanding of the systems preventing genome invasion by transposable elements (TE). Recent advances suggest that A. thaliana may be more efficient than its congener A. lyrata at controlling TE expression and proliferation. The comparative analysis of TE transcription in A. thaliana and A. lyrata, which differ by 40% in genome size, may help understand how silencing mechanisms contribute to the evolution of transposition rate, an important factor controlling genome size variation in plants and animals.
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Affiliation(s)
- Juliette de Meaux
- Institute for Evolution and Biodiversity; University of Münster; Münster, Germany
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Abdelsamad A, Pecinka A. Pollen-specific activation of Arabidopsis retrogenes is associated with global transcriptional reprogramming. Plant Cell 2014; 26:3299-313. [PMID: 25118244 PMCID: PMC4371830 DOI: 10.1105/tpc.114.126011] [Citation(s) in RCA: 13] [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: 04/03/2014] [Revised: 06/19/2014] [Accepted: 07/25/2014] [Indexed: 05/21/2023]
Abstract
Duplications allow for gene functional diversification and accelerate genome evolution. Occasionally, the transposon amplification machinery reverse transcribes the mRNA of a gene, integrates it into the genome, and forms an RNA-duplicated copy: the retrogene. Although retrogenes have been found in plants, their biology and evolution are poorly understood. Here, we identified 251 (216 novel) retrogenes in Arabidopsis thaliana, corresponding to 1% of protein-coding genes. Arabidopsis retrogenes are derived from ubiquitously transcribed parents and reside in gene-rich chromosomal regions. Approximately 25% of retrogenes are cotranscribed with their parents and 3% with head-to-head oriented neighbors. This suggests transcription by novel promoters for 72% of Arabidopsis retrogenes. Many retrogenes reach their transcription maximum in pollen, the tissue analogous to animal spermatocytes, where upregulation of retrogenes has been found previously. This implies an evolutionarily conserved mechanism leading to this transcription pattern of RNA-duplicated genes. During transcriptional repression, retrogenes are depleted of permissive chromatin marks without an obvious enrichment for repressive modifications. However, this pattern is common to many other pollen-transcribed genes independent of their evolutionary origin. Hence, retroposition plays a role in plant genome evolution, and the developmental transcription pattern of retrogenes suggests an analogous regulation of RNA-duplicated genes in plants and animals.
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Affiliation(s)
- Ahmed Abdelsamad
- Max Planck Institute for Plant Breeding Research, Cologne DE-50829, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research, Cologne DE-50829, Germany
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49
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Baubec T, Finke A, Mittelsten Scheid O, Pecinka A. Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep 2014; 15:446-52. [PMID: 24562611 DOI: 10.1002/embr.201337915] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In plants, transposable elements (TEs) are kept inactive by transcriptional gene silencing (TGS). TGS is established and perpetuated by RNA-directed DNA methylation (RdDM) and maintenance methylation pathways, respectively. Here, we describe a novel RdDM function specific for shoot apical meristems that reinforces silencing of TEs during early vegetative growth. In meristems, RdDM counteracts drug-induced interference with TGS maintenance and consequently prevents TE activation. Simultaneous disturbance of both TGS pathways leads to transcriptionally active states of repetitive sequences that are inherited by somatic tissues and partially by the progeny. This apical meristem-specific mechanism is mediated by increased levels of TGS factors and provides a checkpoint for correct epigenetic inheritance during the transition from vegetative to reproductive phase and to the next generation.
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Affiliation(s)
- Tuncay Baubec
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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50
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Pecinka A, Abdelsamad A, Vu GTH. Hidden genetic nature of epigenetic natural variation in plants. Trends Plant Sci 2013; 18:625-32. [PMID: 23953885 DOI: 10.1016/j.tplants.2013.07.005] [Citation(s) in RCA: 26] [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: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 05/22/2023]
Abstract
Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.
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Affiliation(s)
- Ales Pecinka
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
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