1
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Závodník M, Pavlištová V, Machelová A, Lyčka M, Mozgová I, Caklová K, Dvořáčková M, Fajkus J. KU70 and CAF-1 in Arabidopsis: Divergent roles in rDNA stability and telomere homeostasis. Plant J 2024. [PMID: 38493352 DOI: 10.1111/tpj.16718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024]
Abstract
Deficiency in chromatin assembly factor-1 (CAF-1) in plants through dysfunction of its components, FASCIATA1 and 2 (FAS1, FAS2), leads to the specific and progressive loss of rDNA and telomere repeats in plants. This loss is attributed to defective repair mechanisms for the increased DNA breaks encountered during replication, a consequence of impaired replication-dependent chromatin assembly. In this study, we explore the role of KU70 in these processes. Our findings reveal that, although the rDNA copy number is reduced in ku70 mutants when compared with wild-type plants, it is not markedly affected by diverse KU70 status in fas1 mutants. This is consistent with our previous characterisation of rDNA loss in fas mutants as a consequence part of the single-strand annealing pathway of homology-dependent repair. In stark contrast to rDNA, KU70 dysfunction fully suppresses the loss of telomeres in fas1 plants and converts telomeres to their elongated and heterogeneous state typical for ku70 plants. We conclude that the alternative telomere lengthening pathway, known to be activated in the absence of KU70, overrides progressive telomere loss due to CAF-1 dysfunction.
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Affiliation(s)
- Michal Závodník
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, CZ-61265, Czech Republic
| | - Veronika Pavlištová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Adéla Machelová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Karolína Caklová
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, CZ-61265, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
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2
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Bozděchová L, Rudolfová A, Hanáková K, Fojtová M, Fajkus J. Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study. Plants (Basel) 2024; 13:850. [PMID: 38592918 PMCID: PMC10975786 DOI: 10.3390/plants13060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Anna Rudolfová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Kateřina Hanáková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
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3
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Rudolf J, Tomovičová L, Panzarová K, Fajkus J, Hejátko J, Skalák J. Epigenetics and plant hormone dynamics - a functional and methodological perspective. J Exp Bot 2024:erae054. [PMID: 38373206 DOI: 10.1093/jxb/erae054] [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: 11/29/2023] [Indexed: 02/21/2024]
Abstract
Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.
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Affiliation(s)
- Jiří Rudolf
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Lucia Tomovičová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Klára Panzarová
- Photon Systems Instruments, Prumyslova 470, CZ-664 24 Drasov, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Hejátko
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Skalák
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
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4
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Bozděchová L, Havlová K, Fajkus P, Fajkus J. Analysis of Telomerase RNA Structure in Physcomitrium patens Indicates Functionally Relevant Transitions Between OPEN and CLOSED Conformations. J Mol Biol 2024; 436:168417. [PMID: 38143018 DOI: 10.1016/j.jmb.2023.168417] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Telomerase RNA (TR) conformation determines its function as a template for telomere synthesis and as a scaffold for the assembly of the telomerase nucleoprotein complex. Experimental analyses of TR secondary structure using DMS-Map Seq and SHAPE-Map Seq techniques show its CLOSED conformation as the consensus structure where the template region cannot perform its function. Our data show that the apparent discrepancy between experimental results and predicted TR functional conformation, mostly ignored in published studies, can be explained using data analysis based on single-molecule structure prediction from individual sequencing reads by the recently established DaVinci method. This method results in several clusters of secondary structures reflecting the structural dynamics of TR, possibly related to its multiple functional states. Interestingly, the presumed active (OPEN) conformation of TR corresponds to a minor fraction of TR under in vivo conditions. Therefore, structural polymorphism and dynamic TR transitions between CLOSED and OPEN conformations may be involved in telomerase activity regulation as a switch that functions independently of total TR transcript levels.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Kateřina Havlová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Institute of Biophysics, Czech Acad Sci, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Institute of Biophysics, Czech Acad Sci, Královopolská 135, 61200 Brno, Czech Republic.
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5
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Lyčka M, Bubeník M, Závodník M, Peska V, Fajkus P, Demko M, Fajkus J, Fojtová M. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Res 2024; 52:D311-D321. [PMID: 37602392 PMCID: PMC10767889 DOI: 10.1093/nar/gkad672] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023] Open
Abstract
Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, 'Telomerase database' and 'Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Bubeník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Závodník
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Faculty of Informatics, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
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6
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Pírek P, Kryštofová K, Kováčová I, Kromerová A, Zachová D, Helia O, Panzarová K, Fajkus J, Zdráhal Z, Lochmanová G, Fojtová M. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. Plants (Basel) 2023; 12:4177. [PMID: 38140504 PMCID: PMC10747063 DOI: 10.3390/plants12244177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.
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Affiliation(s)
- Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Ingrid Kováčová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Anna Kromerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s.r.o., 66424 Drásov, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
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7
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Závodník M, Fajkus P, Franek M, Kopecký D, Garcia S, Dodsworth S, Orejuela A, Kilar A, Ptáček J, Mátl M, Hýsková A, Fajkus J, Peška V. Telomerase RNA gene paralogs in plants - the usual pathway to unusual telomeres. New Phytol 2023; 239:2353-2366. [PMID: 37391893 DOI: 10.1111/nph.19110] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
Telomerase, telomeric DNA and associated proteins together represent a complex, finely tuned and functionally conserved mechanism that ensures genome integrity by protecting and maintaining chromosome ends. Changes in its components can threaten an organism's viability. Nevertheless, molecular innovation in telomere maintenance has occurred multiple times during eukaryote evolution, giving rise to species/taxa with unusual telomeric DNA sequences, telomerase components or telomerase-independent telomere maintenance. The central component of telomere maintenance machinery is telomerase RNA (TR) as it templates telomere DNA synthesis, its mutation can change telomere DNA and disrupt its recognition by telomere proteins, thereby leading to collapse of their end-protective and telomerase recruitment functions. Using a combination of bioinformatic and experimental approaches, we examine a plausible scenario of evolutionary changes in TR underlying telomere transitions. We identified plants harbouring multiple TR paralogs whose template regions could support the synthesis of diverse telomeres. In our hypothesis, formation of unusual telomeres is associated with the occurrence of TR paralogs that can accumulate mutations, and through their functional redundancy, allow for the adaptive evolution of the other telomere components. Experimental analyses of telomeres in the examined plants demonstrate evolutionary telomere transitions corresponding to TR paralogs with diverse template regions.
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Affiliation(s)
- Michal Závodník
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, CZ-62500, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, CZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, CZ-62500, Czech Republic
| | - David Kopecký
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, CZ-779 00, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia S/N, Barcelona, 08038, Catalonia, Spain
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I St., Portsmouth, PO1 2DY, UK
| | - Andrés Orejuela
- Grupo de Investigación en Recursos Naturales Amazónicos - GRAM, Facultad de Ingenierías y Ciencias Básicas and Herbario Etnobotánico del Piedemonte Andino Amazónico (HEAA), Instituto Tecnológico del Putumayo - ITP, Mocoa, Putumayo, Colombia
| | - Agata Kilar
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, CZ-62500, Czech Republic
| | - Jiří Ptáček
- Potato Research Institute Havlíčkův Brod Ltd, Havlíčkův Brod, CZ-58001, Czech Republic
| | - Martin Mátl
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
| | - Anna Hýsková
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, CZ-61137, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, CZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic
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8
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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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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Lyčka M, Barták M, Helia O, Kopriva S, Moravcová D, Hájek J, Fojt L, Čmelík R, Fajkus J, Fojtová M. Sulfate supplementation affects nutrient and photosynthetic status of Arabidopsis thaliana and Nicotiana tabacum differently under prolonged exposure to cadmium. J Hazard Mater 2023; 445:130527. [PMID: 36495640 DOI: 10.1016/j.jhazmat.2022.130527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 09/16/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Hydroponic experiments were performed to examine the effect of prolonged sulfate limitation combined with cadmium (Cd) exposure in Arabidopsis thaliana and a potential Cd hyperaccumulator, Nicotiana tabacum. Low sulfate treatments (20 and 40 µM MgSO4) and Cd stress (4 µM CdCl2) showed adverse effects on morphology, photosynthetic and biochemical parameters and the nutritional status of both species. For example, Cd stress decreased NO3- root content under 20 µM MgSO4 to approximately 50% compared with respective controls. Interestingly, changes in many measured parameters, such as chlorophyll and carotenoid contents, the concentrations of anions, nutrients and Cd, induced by low sulfate supply, Cd exposure or a combination of both factors, were species-specific. Our data showed opposing effects of Cd exposure on Ca, Fe, Mn, Cu and Zn levels in roots of the studied plants. In A. thaliana, levels of glutathione, phytochelatins and glucosinolates demonstrated their distinct involvement in response to sub-optimal growth conditions and Cd stress. In shoot, the levels of phytochelatins and glucosinolates in the organic sulfur fraction were not dependent on sulfate supply under Cd stress. Altogether, our data showed both common and species-specific features of the complex plant response to prolonged sulfate deprivation and/or Cd exposure.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.
| | - Miloš Barták
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanislav Kopriva
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, Germany; Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Josef Hájek
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Lukáš Fojt
- Institute of Biophysics of the Czech Academy of Sciences, 612 00 Brno, Czech Republic
| | - Richard Čmelík
- Institute of Analytical Chemistry of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, 612 00 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
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11
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Dvořáčková M, Fajkus J. Visualization of the Nucleolus Using 5' Ethynyl Uridine. Methods Mol Biol 2023; 2672:377-385. [PMID: 37335490 DOI: 10.1007/978-1-0716-3226-0_24] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Labeling of the nucleolus in Arabidopsis thaliana can be achieved by incorporation of 5'-ethynyl uridine (EU) into bulk RNA. Although EU does not selectively label the nucleolus, the abundance of ribosomal transcripts results in the predominant accumulation of the signal in the nucleolus. Ethynyl uridine has the advantage of being detected via Click-iT chemistry providing a specific signal and low background. While the protocol presented here employs fluorescent dye and allows visualization of the nucleolus by microscopy, this method can also be used for other downstream applications. Though we tested nucleolar labeling only in A. thaliana, in principle it can be applied to other plant species.
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Affiliation(s)
- Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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12
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Kilar AM, Fajkus P, Fajkus J. GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context. Gigascience 2022; 12:giad080. [PMID: 37848616 PMCID: PMC10580375 DOI: 10.1093/gigascience/giad080] [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: 06/08/2023] [Revised: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND While web-based tools such as BLAST have made identifying conserved gene homologs appear easy, genes with variable sequences pose significant challenges. Functionally important noncoding RNAs (ncRNA) often show low sequence conservation due to genetic variations, including insertions and deletions. Rather than conserved sequences, these RNAs possess highly conserved structural features across a broad phylogenetic range. Such features can be identified using the covariance models approach, which combines sequence alignment with a secondary RNA structure consensus. However, running standard implementation of that approach (Infernal) requires advanced bioinformatics knowledge compared to user-friendly web services like BLAST. The issue is partially addressed by RNAcentral, which can be used to search for homologs across a broad range of ncRNA sequence collections from diverse organisms but not across the genome assemblies. RESULTS Here, we present GERONIMO, which conducts evolutionary searches across hundreds of genomes in a fully automated way. It provides results extended with taxonomy context, as summary tables and visualizations, to facilitate analysis for user convenience. Additionally, GERONIMO supplements homologous sequences with genomic regions to analyze promoter motifs or gene collinearity, enhancing the validation of results. CONCLUSION GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.
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Affiliation(s)
- Agata M Kilar
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
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13
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Fajkus P, Adámik M, Nelson ADL, Kilar AM, Franek M, Bubeník M, Frydrychová RČ, Votavová A, Sýkorová E, Fajkus J, Peška V. Telomerase RNA in Hymenoptera (Insecta) switched to plant/ciliate-like biogenesis. Nucleic Acids Res 2022; 51:420-433. [PMID: 36546771 PMCID: PMC9841428 DOI: 10.1093/nar/gkac1202] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
In contrast to the catalytic subunit of telomerase, its RNA subunit (TR) is highly divergent in size, sequence and biogenesis pathways across eukaryotes. Current views on TR evolution assume a common origin of TRs transcribed with RNA polymerase II in Opisthokonta (the supergroup including Animalia and Fungi) and Trypanosomida on one hand, and TRs transcribed with RNA polymerase III under the control of type 3 promoter, found in TSAR and Archaeplastida supergroups (including e.g. ciliates and Viridiplantae taxa, respectively). Here, we focus on unknown TRs in one of the largest Animalia order - Hymenoptera (Arthropoda) with more than 300 available representative genomes. Using a combination of bioinformatic and experimental approaches, we identify their TRs. In contrast to the presumed type of TRs (H/ACA box snoRNAs transcribed with RNA Polymerase II) corresponding to their phylogenetic position, we find here short TRs of the snRNA type, likely transcribed with RNA polymerase III under the control of the type 3 promoter. The newly described insect TRs thus question the hitherto assumed monophyletic origin of TRs across Animalia and point to an evolutionary switch in TR type and biogenesis that was associated with the divergence of Arthropods.
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Affiliation(s)
- Petr Fajkus
- To whom correspondence should be addressed. Tel: +420 41517183;
| | - Matej Adámik
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Andrew D L Nelson
- The Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14850, USA
| | - Agata M Kilar
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
| | - Michal Bubeník
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice CZ-37005, Czech Republic
| | - Alena Votavová
- Agricultural Research, Ltd., Troubsko, CZ-664 41, Czech Republic
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Correspondence may also be addressed to Jiří Fajkus. Tel: +420 549494003;
| | - Vratislav Peška
- Correspondence may also be addressed to Vratislav Peška. Tel: +420 541517183;
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14
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Konečná KP, Kilar A, Kováčiková P, Fajkus J, Sýkorová E, Fojtová M. Compromised function of ARM, the interactor of Arabidopsis telomerase, suggests its role in stress responses. Plant Sci 2022; 325:111453. [PMID: 36087885 DOI: 10.1016/j.plantsci.2022.111453] [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: 06/23/2022] [Revised: 08/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
ARM was identified previously as an interaction partner of the telomerase protein subunit (TERT) in Arabidopsis thaliana. To investigate the interconnection between ARM and telomerase and to identify ARM cellular functions, we analyzed a set of arm mutant lines and arm/tert double mutants. Telomere length was not affected in arm single mutant plants, in contrast to double mutants. In the second generation of homozygous arm-1/tert double mutants following the heterozygous state during the double mutant construction, telomeres shortened dramatically, even below levels in tert plants displaying severe morphological defects. Intriguingly, homozygous arm-1/tert double mutants with short telomeres grew without obvious phenotypic changes for next two generations. Then, in agreement with the onset of phenotypic changes in tert, morphological defects were timed to the 5th arm-1/tert homozygous generation. RNAseq analyses of arm-1/tert and respective single mutants displayed markedly overlapping sets of differentially expressed genes in arm-1/tert double mutant and arm-1 single mutant lines, indicating a dominant effect of the ARM mutation. RNAseq data further implied ARM involvement in circadian rhythms, responses to drugs and to biotic and abiotic stimuli. In agreement with it, we observed sensitivity of arm-1 single mutant to the heat stress during germination. Altogether, our results suggest ARM involvement in crucial cellular processes without evidencing its role in the telomerase canonical function.
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Affiliation(s)
- Klára Přikrylová Konečná
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Kováčiková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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15
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Agrawal R, Sharma M, Dwivedi N, Maji S, Thakur P, Junaid A, Fajkus J, Laxmi A, Thakur JK. MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis. Plant Physiol 2022; 189:2259-2280. [PMID: 35567489 PMCID: PMC9342970 DOI: 10.1093/plphys/kiac220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.
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Affiliation(s)
- Rekha Agrawal
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Mohan Sharma
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Pallabi Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Alim Junaid
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ashverya Laxmi
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Plant Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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16
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Fajkus P, Kilar A, Nelson ADL, Holá M, Peška V, Goffová I, Fojtová M, Zachová D, Fulnečková J, Fajkus J. Evolution of plant telomerase RNAs: farther to the past, deeper to the roots. Nucleic Acids Res 2021; 49:7680-7694. [PMID: 34181710 PMCID: PMC8287931 DOI: 10.1093/nar/gkab545] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
The enormous sequence heterogeneity of telomerase RNA (TR) subunits has thus far complicated their characterization in a wider phylogenetic range. Our recent finding that land plant TRs are, similarly to known ciliate TRs, transcribed by RNA polymerase III and under the control of the type-3 promoter, allowed us to design a novel strategy to characterize TRs in early diverging Viridiplantae taxa, as well as in ciliates and other Diaphoretickes lineages. Starting with the characterization of the upstream sequence element of the type 3 promoter that is conserved in a number of small nuclear RNAs, and the expected minimum TR template region as search features, we identified candidate TRs in selected Diaphoretickes genomes. Homologous TRs were then used to build covariance models to identify TRs in more distant species. Transcripts of the identified TRs were confirmed by transcriptomic data, RT-PCR and Northern hybridization. A templating role for one of our candidates was validated in Physcomitrium patens. Analysis of secondary structure demonstrated a deep conservation of motifs (pseudoknot and template boundary element) observed in all published TRs. These results elucidate the evolution of the earliest eukaryotic TRs, linking the common origin of TRs across Diaphoretickes, and underlying evolutionary transitions in telomere repeats.
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Affiliation(s)
- Petr Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | | | - Marcela Holá
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague CZ-16000, Czech Republic
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Ivana Goffová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Fulnečková
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
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17
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Jernfors T, Danforth J, Kesäniemi J, Lavrinienko A, Tukalenko E, Fajkus J, Dvořáčková M, Mappes T, Watts PC. Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides. Ecol Evol 2021; 11:8754-8767. [PMID: 34257925 PMCID: PMC8258220 DOI: 10.1002/ece3.7684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Altered copy number of certain highly repetitive regions of the genome, such as satellite DNA within heterochromatin and ribosomal RNA loci (rDNA), is hypothesized to help safeguard the genome against damage derived from external stressors. We quantified copy number of the 18S rDNA and a pericentromeric satellite DNA (Msat-160) in bank voles (Myodes glareolus) inhabiting the Chernobyl Exclusion Zone (CEZ), an area that is contaminated by radionuclides and where organisms are exposed to elevated levels of ionizing radiation. We found a significant increase in 18S rDNA and Msat-160 content in the genomes of bank voles from contaminated locations within the CEZ compared with animals from uncontaminated locations. Moreover, 18S rDNA and Msat-160 copy number were positively correlated in the genomes of bank voles from uncontaminated, but not in the genomes of animals inhabiting contaminated, areas. These results show the capacity for local-scale geographic variation in genome architecture and are consistent with the genomic safeguard hypothesis. Disruption of cellular processes related to genomic stability appears to be a hallmark effect in bank voles inhabiting areas contaminated by radionuclides.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - John Danforth
- Department of Biochemistry & Molecular BiologyRobson DNA Science CentreArnie Charbonneau Cancer InstituteCumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Jenni Kesäniemi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anton Lavrinienko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Eugene Tukalenko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- National Research Center for Radiation Medicine of the National Academy of Medical ScienceKyivUkraine
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
- Laboratory of Functional Genomics and ProteomicsNCBRFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Department of Cell Biology and RadiobiologyInstitute of Biophysics of the Czech Academy of SciencesBrnoCzech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Tapio Mappes
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Phillip C. Watts
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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18
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Peska V, Fajkus P, Bubeník M, Brázda V, Bohálová N, Dvořáček V, Fajkus J, Garcia S. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Sci Rep 2021; 11:12784. [PMID: 34140564 PMCID: PMC8211666 DOI: 10.1038/s41598-021-92126-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.
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Affiliation(s)
- Vratislav Peska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.
| | - Petr Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Michal Bubeník
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Vojtěch Dvořáček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain.
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19
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Lyčka M, Peska V, Demko M, Spyroglou I, Kilar A, Fajkus J, Fojtová M. WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics 2021; 22:145. [PMID: 33752601 PMCID: PMC7986547 DOI: 10.1186/s12859-021-04064-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/07/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. RESULTS To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. CONCLUSIONS WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER .
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 612 00, Brno, Czech Republic.
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Faculty of Informatics, Masaryk University, 602 00, Brno, Czech Republic
| | - Ioannis Spyroglou
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 612 00, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
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20
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Fajkus P, Peška V, Fajkus J, Sýkorová E. Origin and Fates of TERT Gene Copies in Polyploid Plants. Int J Mol Sci 2021; 22:1783. [PMID: 33670111 PMCID: PMC7916837 DOI: 10.3390/ijms22041783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
The gene coding for the telomerase reverse transcriptase (TERT) is essential for the maintenance of telomeres. Previously we described the presence of three TERT paralogs in the allotetraploid plant Nicotiana tabacum, while a single TERT copy was identified in the paleopolyploid model plant Arabidopsis thaliana. Here we examine the presence, origin and functional status of TERT variants in allotetraploid Nicotiana species of diverse evolutionary ages and their parental genome donors, as well as in other diploid and polyploid plant species. A combination of experimental and in silico bottom-up analyses of TERT gene copies in Nicotiana polyploids revealed various patterns of retention or loss of parental TERT variants and divergence in their functions. RT-qPCR results confirmed the expression of all the identified TERT variants. In representative plant and green algal genomes, our synteny analyses show that their TERT genes were located in a conserved locus that became advantageous after the divergence of eudicots, and the gene was later translocated in several plant groups. In various diploid and polyploid species, translocation of TERT became fixed in target loci that show ancient synapomorphy.
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Affiliation(s)
- Petr Fajkus
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; (P.F.); (V.P.)
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; (P.F.); (V.P.)
| | - Jiří Fajkus
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; (P.F.); (V.P.)
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; (P.F.); (V.P.)
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21
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Goffová I, Fajkus J. The rDNA Loci-Intersections of Replication, Transcription, and Repair Pathways. Int J Mol Sci 2021; 22:1302. [PMID: 33525595 PMCID: PMC7865372 DOI: 10.3390/ijms22031302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/28/2022] Open
Abstract
Genes encoding ribosomal RNA (rDNA) are essential for cell survival and are particularly sensitive to factors leading to genomic instability. Their repetitive character makes them prone to inappropriate recombinational events arising from collision of transcriptional and replication machineries, resulting in unstable rDNA copy numbers. In this review, we summarize current knowledge on the structure and organization of rDNA, its role in sensing changes in the genome, and its linkage to aging. We also review recent findings on the main factors involved in chromatin assembly and DNA repair in the maintenance of rDNA stability in the model plants Arabidopsis thaliana and the moss Physcomitrella patens, providing a view across the plant evolutionary tree.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
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22
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Konečná K, Sováková PP, Anteková K, Fajkus J, Fojtová M. Distinct Responses of Arabidopsis Telomeres and Transposable Elements to Zebularine Exposure. Int J Mol Sci 2021; 22:ijms22010468. [PMID: 33466545 PMCID: PMC7796508 DOI: 10.3390/ijms22010468] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022] Open
Abstract
Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Karin Anteková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- Correspondence: ; Tel.: +420-54949-8063
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23
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Havlová K, Fajkus J. G4 Structures in Control of Replication and Transcription of rRNA Genes. Front Plant Sci 2020; 11:593692. [PMID: 33133121 PMCID: PMC7579416 DOI: 10.3389/fpls.2020.593692] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were actually shown to affect activity and stability of rDNA. Here, we focus on another phenomenon - the potential of DNA containing shortly spaced oligo-guanine tracts to form quadruplex structures (G4). Interestingly, sites with a high propensity to form G4 were described in yeast, animal, and plant rDNAs, in addition to G4 at telomeres, some gene promoters, and transposons, suggesting the evolutionary ancient origin of G4 as a regulatory module. Here, we present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens. The high G4 potential is balanced by the activity of G4-resolving enzymes. The ability of rDNA to undergo these "structural gymnastics" thus represents another layer of the rich repertoire of epigenetic regulations, which is pronounced in rDNA due to its highly repetitive character.
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Affiliation(s)
- Kateřina Havlová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
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24
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Schrumpfová PP, Fajkus J. Composition and Function of Telomerase-A Polymerase Associated with the Origin of Eukaryotes. Biomolecules 2020; 10:biom10101425. [PMID: 33050064 PMCID: PMC7658794 DOI: 10.3390/biom10101425] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
The canonical DNA polymerases involved in the replication of the genome are unable to fully replicate the physical ends of linear chromosomes, called telomeres. Chromosomal termini thus become shortened in each cell cycle. The maintenance of telomeres requires telomerase—a specific RNA-dependent DNA polymerase enzyme complex that carries its own RNA template and adds telomeric repeats to the ends of chromosomes using a reverse transcription mechanism. Both core subunits of telomerase—its catalytic telomerase reverse transcriptase (TERT) subunit and telomerase RNA (TR) component—were identified in quick succession in Tetrahymena more than 30 years ago. Since then, both telomerase subunits have been described in various organisms including yeasts, mammals, birds, reptiles and fish. Despite the fact that telomerase activity in plants was described 25 years ago and the TERT subunit four years later, a genuine plant TR has only recently been identified by our group. In this review, we focus on the structure, composition and function of telomerases. In addition, we discuss the origin and phylogenetic divergence of this unique RNA-dependent DNA polymerase as a witness of early eukaryotic evolution. Specifically, we discuss the latest information regarding the recently discovered TR component in plants, its conservation and its structural features.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic;
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Correspondence:
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic;
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65 Brno, Czech Republic
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25
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Peska V, Mátl M, Mandáková T, Vitales D, Fajkus P, Fajkus J, Garcia S. Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences. J Exp Bot 2020; 71:5786-5793. [PMID: 32589715 DOI: 10.1093/jxb/eraa293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/01/2020] [Accepted: 06/16/2020] [Indexed: 05/26/2023]
Abstract
A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment such as the loss of stomatal genes, while other functions such as an algal-like cell wall composition were acquired. Beyond these, the genome structure and organization were comparable with those of the majority of plant genomes sequenced, except for one striking feature that went unnoticed at that time: the presence of human-like instead of the expected plant-type telomeric sequences. By using different experimental approaches including fluorescence in situ hybridization (FISH), genome skimming by next-generation sequencing (NGS), and analysis of non-coding transcriptome, we have confirmed its telomeric location in the chromosomes of Z. marina. We have also identified its telomerase RNA (TR) subunit, confirming the presence of the human-type telomeric sequence in the template region. Remarkably, this region was found to be very variable even in clades with a highly conserved telomeric sequence across their species. Based on this observation, we propose that alternative annealing preferences in the template borders can explain the transition between the plant and human telomeric sequences. The further identification of paralogues of TR in several plant genomes led us to the hypothesis that plants may retain an increased ability to change their telomeric sequence. We discuss the implications of this occurrence in the evolution of telomeres while introducing a mechanistic model for the transition from the plant to the human telomeric sequences.
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Affiliation(s)
- Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Martin Mátl
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Terezie Mandáková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Plant Molecular Genetics, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s/n, Barcelona, Catalonia, Spain
| | - Petr Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s/n, Barcelona, Catalonia, Spain
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26
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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27
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Flütsch S, Nigro A, Conci F, Fajkus J, Thalmann M, Trtílek M, Panzarová K, Santelia D. Glucose uptake to guard cells via STP transporters provides carbon sources for stomatal opening and plant growth. EMBO Rep 2020; 21:e49719. [PMID: 32627357 PMCID: PMC7403697 DOI: 10.15252/embr.201949719] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 11/20/2019] [Revised: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 01/16/2023] Open
Abstract
Guard cells on the leaf epidermis regulate stomatal opening for gas exchange between plants and the atmosphere, allowing a balance between photosynthesis and transpiration. Given that guard cells possess several characteristics of sink tissues, their metabolic activities should largely depend on mesophyll-derived sugars. Early biochemical studies revealed sugar uptake into guard cells. However, the transporters that are involved and their relative contribution to guard cell function are not yet known. Here, we identified the monosaccharide/proton symporters Sugar Transport Protein 1 and 4 (STP1 and STP4) as the major plasma membrane hexose sugar transporters in the guard cells of Arabidopsis thaliana. We show that their combined action is required for glucose import to guard cells, providing carbon sources for starch accumulation and light-induced stomatal opening that are essential for plant growth. These findings highlight mesophyll-derived glucose as an important metabolite connecting stomatal movements with photosynthesis.
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Affiliation(s)
- Sabrina Flütsch
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Arianna Nigro
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Franco Conci
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Jiří Fajkus
- Photon Systems Instruments (PSI), Drasov, Czech Republic
| | - Matthias Thalmann
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Martin Trtílek
- Photon Systems Instruments (PSI), Drasov, Czech Republic
| | | | - Diana Santelia
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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28
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Adamusová K, Khosravi S, Fujimoto S, Houben A, Matsunaga S, Fajkus J, Fojtová M. Two combinatorial patterns of telomere histone marks in plants with canonical and non-canonical telomere repeats. Plant J 2020; 102:678-687. [PMID: 31834959 DOI: 10.1111/tpj.14653] [Citation(s) in RCA: 7] [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: 06/28/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 05/24/2023]
Abstract
Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are crucial for the maintenance of genome integrity. In most plants, telomeres consist of conserved tandem repeat units comprising the TTTAGGG motif. Recently, non-canonical telomeres were described in several plants and plant taxons, including the carnivorous plant Genlisea hispidula (TTCAGG/TTTCAGG), the genus Cestrum (Solanaceae; TTTTTTAGGG), and plants from the Asparagales order with either a vertebrate-type telomere repeat TTAGGG or Allium genus-specific CTCGGTTATGGG repeat. We analyzed epigenetic modifications of telomeric histones in plants with canonical and non-canonical telomeres, and further in telomeric chromatin captured from leaves of Nicotiana benthamiana transiently transformed by telomere CRISPR-dCas9-eGFP, and of Arabidopsis thaliana stably transformed with TALE_telo C-3×GFP. Two combinatorial patterns of telomeric histone modifications were identified: (i) an Arabidopsis-like pattern (A. thaliana, G. hispidula, Genlisea nigrocaulis, Allium cepa, Narcissus pseudonarcissus, Petunia hybrida, Solanum tuberosum, Solanum lycopersicum) with telomeric histones decorated predominantly by H3K9me2; (ii) a tobacco-like pattern (Nicotiana tabacum, N. benthamiana, C. elegans) with a strong H3K27me3 signal. Our data suggest that epigenetic modifications of plant telomere-associated histones are related neither to the sequence of the telomere motif nor to the lengths of the telomeres. Nor the phylogenetic position of the species plays the role; representatives of the Solanaceae family are included in both groups. As both patterns of histone marks are compatible with fully functional telomeres in respective plants, we conclude that the described specific differences in histone marks are not critical for telomere functions.
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Affiliation(s)
- Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Solmaz Khosravi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany
| | - Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
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29
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Cai N, Fňašková M, Konečná K, Fojtová M, Fajkus J, Coomber E, Watt S, Soranzo N, Preiss M, Rektor I. No Evidence of Persistence or Inheritance of Mitochondrial DNA Copy Number in Holocaust Survivors and Their Descendants. Front Genet 2020; 11:87. [PMID: 32211017 PMCID: PMC7069217 DOI: 10.3389/fgene.2020.00087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/10/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial DNA copy number has been previously shown to be elevated with severe and chronic stress, as well as stress-related pathology like Major Depressive Disorder (MDD) and post-traumatic stress disorder (PTSD). While experimental data point to likely recovery of mtDNA copy number changes after the stressful event, time needed for full recovery and whether it can be achieved are still unknown. Further, while it has been shown that stress-related mtDNA elevation affects multiple tissues, its specific consequences for oogenesis and maternal inheritance of mtDNA has never been explored. In this study, we used qPCR to quantify mtDNA copy number in 15 Holocaust survivors and 102 of their second- and third-generation descendants from the Czech Republic, many of whom suffer from PTSD, and compared them to controls in the respective generations. We found no significant difference in mtDNA copy number in the Holocaust survivors compared to controls, whether they have PTSD or not, and no significant elevation in descendants of female Holocaust survivors as compared to descendants of male survivors or controls. Our results showed no evidence of persistence or inheritance of mtDNA changes in Holocaust survivors, though that does not rule out effects in other tissues or mitigating mechanism for such changes.
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Affiliation(s)
- Na Cai
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Monika Fňašková
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia.,1st Neurology Department, Hospital St Anne and School of Medicine, Masaryk University, Brno, Czechia
| | - Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eve Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Stephen Watt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Marek Preiss
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia
| | - Ivan Rektor
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia
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30
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Fajkus P, Peška V, Závodník M, Fojtová M, Fulnečková J, Dobias Š, Kilar A, Dvořáčková M, Zachová D, Nečasová I, Sims J, Sýkorová E, Fajkus J. Telomerase RNAs in land plants. Nucleic Acids Res 2019; 47:9842-9856. [PMID: 31392988 PMCID: PMC6765143 DOI: 10.1093/nar/gkz695] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
To elucidate the molecular nature of evolutionary changes of telomeres in the plant order Asparagales, we aimed to characterize telomerase RNA subunits (TRs) in these plants. The unusually long telomere repeat unit in Allium plants (12 nt) allowed us to identify TRs in transcriptomic data of representative species of the Allium genus. Orthologous TRs were then identified in Asparagales plants harbouring telomere DNA composed of TTAGGG (human type) or TTTAGGG (Arabidopsis-type) repeats. Further, we identified TRs across the land plant phylogeny, including common model plants, crop plants, and plants with unusual telomeres. Several lines of functional testing demonstrate the templating telomerase function of the identified TRs and disprove a functionality of the only previously reported plant telomerase RNA in Arabidopsis thaliana. Importantly, our results change the existing paradigm in plant telomere biology which has been based on the existence of a relatively conserved telomerase reverse transcriptase subunit (TERT) associating with highly divergent TRs even between closely related plant taxa. The finding of a monophyletic origin of genuine TRs across land plants opens the possibility to identify TRs directly in transcriptomic or genomic data and/or predict telomere sequences synthesized according to the respective TR template region.
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Affiliation(s)
- Petr Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic
| | - Michal Závodník
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Miloslava Fojtová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Fulnečková
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Šimon Dobias
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Agata Kilar
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ivona Nečasová
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jason Sims
- Max Perutz Labs, University of Vienna, Dr. Bohr Gasse 9, A-1030, Vienna, Austria
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
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31
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Lochmanová G, Ihnatová I, Kuchaříková H, Brabencová S, Zachová D, Fajkus J, Zdráhal Z, Fojtová M. Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications. Int J Mol Sci 2019; 20:ijms20205093. [PMID: 31615119 PMCID: PMC6829310 DOI: 10.3390/ijms20205093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/02/2023] Open
Abstract
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.
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Affiliation(s)
- Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Ivana Ihnatová
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
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32
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Konečná K, Lyčka M, Nohelová L, Petráková M, Fňašková M, Koriťáková E, Sováková PP, Brabencová S, Preiss M, Rektor I, Fajkus J, Fojtová M. Holocaust history is not reflected in telomere homeostasis in survivors and their offspring. J Psychiatr Res 2019; 117:7-14. [PMID: 31255955 DOI: 10.1016/j.jpsychires.2019.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/30/2023]
Abstract
Telomeres, nucleoprotein structures at the ends of eukaryotic chromosomes, are crucial for the maintenance of genome integrity. While the lengths of telomeres at birth are determined genetically, many factors including environmental and living conditions affect the telomere lengths during a lifespan. In this context, extreme and long-term stress has been shown to negatively impact telomeres and their protective function, with even offspring being influenced by the stress experienced by parents. Using quantitative PCR, the relative lengths of telomeres of survivors of the Holocaust during World War II and two generations of their offspring were analyzed. These data were related to those of control groups, persons of comparable age without a strong life stress experience. In contrast to previous studies of other stress-exposed groups, the relative lengths of telomeres were comparable in groups of persons exposed to Holocaust-related stress and their progenies, and in control groups. Interestingly, shorter telomeres of Holocaust survivors of the age under 12 in the year 1945 compared to Holocaust survivors of the age above 12 were detected. Our results are discussed with respect to certain exceptionality of persons having been able to cope with an extreme stress more than 70 years ago and living to a very old age.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Lucie Nohelová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Monika Petráková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Monika Fňašková
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Eva Koriťáková
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic; Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Marek Preiss
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic; National Institute of Mental Health and University of New York in Prague, Czech Republic
| | - Ivan Rektor
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
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33
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Goffová I, Vágnerová R, Peška V, Franek M, Havlová K, Holá M, Zachová D, Fojtová M, Cuming A, Kamisugi Y, Angelis KJ, Fajkus J. Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens. Plant J 2019; 98:1090-1105. [PMID: 30834585 DOI: 10.1111/tpj.14304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 05/11/2023]
Abstract
Telomeres and ribosomal RNA genes (rDNA) are essential for cell survival and particularly sensitive to factors affecting genome stability. Here, we examine the role of RAD51 and its antagonist, RTEL1, in the moss Physcomitrella patens. In corresponding mutants, we analyse their sensitivity to DNA damage, the maintenance of telomeres and rDNA, and repair of double-stranded breaks (DSBs) induced by genotoxins with various modes of action. While the loss of RTEL1 results in rapid telomere shortening, concurrent loss of both RAD51 genes has no effect on telomere lengths. We further demonstrate here the linked arrangement of 5S and 45S rRNA genes in P. patens. The spacer between 5S and 18S rRNA genes, especially the region downstream from the transcription start site, shows conspicuous clustering of sites with a high propensity to form quadruplex (G4) structures. Copy numbers of 5S and 18S rDNA are reduced moderately in the pprtel1 mutant, and significantly in the double pprad51-1-2 mutant, with no progression during subsequent cultivation. While reductions in 45S rDNA copy numbers observed in pprtel1 and pprad51-1-2 plants apply also to 5S rDNA, changes in transcript levels are different for 45S and 5S rRNA, indicating their independent transcription by RNA polymerase I and III, respectively. The loss of SOL (Sog One-Like), a transcription factor regulating numerous genes involved in DSB repair, increases the rate of DSB repair in dividing as well as differentiated tissue, and through deactivation of G2/M cell-cycle checkpoint allows the cell-cycle progression manifested as a phenotype resistant to bleomycin.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Radka Vágnerová
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Vratislav Peška
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michal Franek
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Kateřina Havlová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Marcela Holá
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Dagmar Zachová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Andrew Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karel J Angelis
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
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Schořová Š, Fajkus J, Záveská Drábková L, Honys D, Schrumpfová PP. The plant Pontin and Reptin homologues, RuvBL1 and RuvBL2a, colocalize with TERT and TRB proteins in vivo, and participate in telomerase biogenesis. Plant J 2019; 98:195-212. [PMID: 30834599 DOI: 10.1111/tpj.14306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/26/2018] [Revised: 02/08/2019] [Accepted: 02/26/2019] [Indexed: 05/15/2023]
Abstract
Telomerase maturation and recruitment to telomeres is regulated by several telomerase- and telomere-associated proteins. Among a number of proteins, human Pontin and Reptin play critical roles in telomerase biogenesis. Here we characterized plant orthologues of Pontin and Reptin, RuvBL1 and RuvBL2a, respectively, and show association of Arabidopsis thaliana RuvBL1 (AtRuvBL1) with the catalytic subunit of telomerase (AtTERT) in the nucleolus in vivo. In contrast to mammals, interactions between AtTERT and AtRuvBL proteins in A. thaliana are not direct and they are rather mediated by one of the Arabidopsis thaliana Telomere Repeat Binding (AtTRB) proteins. We further show that plant orthologue of dyskerin, named AtCBF5, is indirectly associated with AtTRB proteins but not with the AtRuvBL proteins in the plant nucleus/nucleolus, and interacts with the Protection of telomere 1 (AtPOT1a) in the nucleolus or cytoplasmic foci. Our genome-wide phylogenetic analyses identify orthologues in RuvBL protein family within the plant kingdom. Dysfunction of AtRuvBL genes in heterozygous T-DNA insertion A. thaliana mutants results in reduced telomerase activity and indicate the involvement of AtRuvBL in plant telomerase biogenesis.
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Affiliation(s)
- Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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Peška V, Mandáková T, Ihradská V, Fajkus J. Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum. Int J Mol Sci 2019; 20:E733. [PMID: 30744119 PMCID: PMC6387171 DOI: 10.3390/ijms20030733] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and complexity. Such studies are particularly fruitful in large genomes, and useful mainly in crop plants where they provide a rich source of molecular markers or information on indispensable genomic components (e.g., telomeres, centromeres, or ribosomal RNA genes). Surprisingly, in Allium species, a comprehensive comparative study of repeats is lacking. Here we provide such a study of two economically important species, Allium cepa (onion), and A. sativum (garlic), and their distantly related A. ursinum (wild garlic). We present an overview and classification of major repeats in these species and have paid specific attention to sequence conservation and copy numbers of major representatives in each type of repeat, including retrotransposons, rDNA, or newly identified satellite sequences. Prevailing repeats in all three studied species belonged to Ty3/gypsy elements, however they significantly diverged and we did not detect them in common clusters in comparative analysis. Actually, only a low number of clusters was shared by all three species. Such conserved repeats were for example 5S and 45S rDNA genes and surprisingly a specific and quite rare Ty1/copia lineage. Species-specific long satellites were found mainly in A. cepa and A. sativum. We also show in situ localization of selected repeats that could potentially be applicable as chromosomal markers, e.g., in interspecific breeding.
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Affiliation(s)
- Vratislav Peška
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Terezie Mandáková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
| | - Veronika Ihradská
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
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Sováková PP, Magdolenová A, Konečná K, Rájecká V, Fajkus J, Fojtová M. Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis. Plant Mol Biol 2018; 98:81-99. [PMID: 30128721 DOI: 10.1007/s11103-018-0765-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 07/23/2018] [Accepted: 08/12/2018] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE Standard pathways involved in the regulation of telomere stability do not contribute to gradual telomere elongation observed in the course of A. thaliana calli propagation. Genetic and epigenetic changes accompanying the culturing of plant cells have frequently been reported. Here we aimed to characterize the telomere homeostasis during long term callus propagation. While in Arabidopsis thaliana calli gradual telomere elongation was observed, telomeres were stable in Nicotiana tabacum and N. sylvestris cultures. Telomere elongation during callus propagation is thus not a general feature of plant cells. The long telomere phenotype in Arabidopsis calli was correlated neither with changes in telomerase activity nor with activation of alternative mechanisms of telomere elongation. The dynamics of telomere length changes was maintained in mutant calli with loss of function of important epigenetic modifiers but compromised in the presence of epigenetically active drug zebularine. To examine whether the cell culture-induced disruption of telomere homeostasis is associated with the modulated structure of chromosome ends, epigenetic properties of telomere chromatin were analysed. Albeit distinct changes in epigenetic modifications of telomere histones were observed, these were broadly stochastic. Our results show that contrary to animal cells, the structure and function of plant telomeres is not determined significantly by the epigenetic character of telomere chromatin. Set of differentially transcribed genes was identified in calli, but considering the known telomere- or telomerase-related functions of respective proteins, none of these changes per se was apparently related to the elongated telomere phenotype. Based on our data, we propose that the disruption in telomere homeostasis in Arabidopsis calli arises from the interplay of multiple factors, as a part of reprogramming of plant cells to long-term culture conditions.
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Affiliation(s)
- Pavla Polanská Sováková
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Alžbeta Magdolenová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Prague, Czech Republic
| | - Klára Konečná
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Veronika Rájecká
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
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Dvořáčková M, Raposo B, Matula P, Fuchs J, Schubert V, Peška V, Desvoyes B, Gutierrez C, Fajkus J. Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression. J Cell Sci 2018; 131:jcs.202416. [PMID: 28483825 DOI: 10.1242/jcs.202416] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
Ribosomal RNA genes (rDNA) have been used as valuable experimental systems in numerous studies. Here, we focus on elucidating the spatiotemporal organisation of rDNA replication in Arabidopsis thaliana To determine the subnuclear distribution of rDNA and the progression of its replication during the S phase, we apply 5-ethynyl-2'-deoxyuridine (EdU) labelling, fluorescence-activated cell sorting, fluorescence in situ hybridization and structured illumination microscopy. We show that rDNA is replicated inside and outside the nucleolus, where active transcription occurs at the same time. Nascent rDNA shows a maximum of nucleolar associations during early S phase. In addition to EdU patterns typical for early or late S phase, we describe two intermediate EdU profiles characteristic for mid S phase. Moreover, the use of lines containing mutations in the chromatin assembly factor-1 gene fas1 and wild-type progeny of fas1xfas2 crosses depleted of inactive copies allows for selective observation of the replication pattern of active rDNA. High-resolution data are presented, revealing the culmination of replication in the mid S phase in the nucleolus and its vicinity. Taken together, our results provide a detailed snapshot of replication of active and inactive rDNA during S phase progression.
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Affiliation(s)
- Martina Dvořáčková
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Berta Raposo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Petr Matula
- Department of Computer Graphics and Design, Faculty of Informatics, Masaryk University, Botanická 554/68a, Brno 60200, Czech Republic
| | - Joerg Fuchs
- Breeding Research Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland D-06466, Germany
| | - Veit Schubert
- Breeding Research Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland D-06466, Germany
| | - Vratislav Peška
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic.,Department of Cell Biology and Radiology, Institute of Biophysics ASCR, v.v.i., Královopolská 135, Brno 61265, Czech Republic
| | - Bénédicte Desvoyes
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Madrid 28049, Spain
| | - Jiří Fajkus
- Laboratory of Molecular Complexes of Chromatin, Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno 62500, Czech Republic .,Department of Cell Biology and Radiology, Institute of Biophysics ASCR, v.v.i., Královopolská 135, Brno 61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno 61137, Czech Republic
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Abstract
Thanks to recent innovative methodologies, key cellular processes such as replication or transcription can be visualized directly in situ in intact tissues. Many studies use so-called click iT chemistry where nascent DNA can be tracked by 5-ethynyl-2'-deoxyuridine (EdU), and nascent RNA by 5-ethynyl uridine (EU). While the labeling of replicating DNA by EdU has already been well established and further exploited in plants, the use of EU to reveal nascent RNA has not been developed to such an extent. In this article, we present a protocol for labeling of nucleolar RNA transcripts using EU and show that EU effectively highlights the nucleolus. The method is advantageous, because the need to prepare transgenic plants expressing fluorescently tagged nucleolar components when the nucleolus has to be visualized can be avoided.
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Affiliation(s)
- Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Martina Dvořáčková, Jiří Fajkus, ;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- *Correspondence: Martina Dvořáčková, Jiří Fajkus, ;
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Jurečková JF, Sýkorová E, Hafidh S, Honys D, Fajkus J, Fojtová M. Tissue-specific expression of telomerase reverse transcriptase gene variants in Nicotiana tabacum. Planta 2017; 245:549-561. [PMID: 27900472 DOI: 10.1007/s00425-016-2624-1] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N. sylvestris genome (TERT_Cs, TERT_D) and one originated from the N. tomentosiformis paternal genome (TERT_Ct). In this work, we analyzed the transcription of TERT variants in correlation with telomerase activity in tobacco tissues. High and approximately comparable levels of TERT_Ct and TERT_Cs transcripts were detected in seedlings, roots, flower buds and leaves, while the transcript of the TERT_D variant was markedly underrepresented. Similarly, in N. sylvestris tissues, TERT_Cs transcript significantly predominated. A specific pattern of TERT transcripts was found in samples of tobacco pollen with the TERT_Cs variant clearly dominating particularly at the early stage of pollen development. Detailed analysis of TERT_C variants representation in functionally distinct fractions of pollen transcriptome revealed their prevalence in large ribonucleoprotein particles encompassing translationally silent mRNA; only a minority of TERT_Ct and TERT_Cs transcripts were localized in actively translated polysomes. Histones of the TERT_C chromatin were decorated predominantly with the euchromatin-specific epigenetic modification in both telomerase-positive and telomerase-negative tobacco tissues. We conclude that the existence and transcription pattern of tobacco TERT paralogs represents an interesting phenomenon and our results indicate its functional significance. Nicotiana species have again proved to be appropriate and useful model plants in telomere biology studies.
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Affiliation(s)
- Jana Fišerová Jurečková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Said Hafidh
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic v.v.i., Rozvojová 263, 165 02, Prague, Czech Republic
| | - David Honys
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic v.v.i., Rozvojová 263, 165 02, Prague, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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Brabencová S, Ihnatová I, Potěšil D, Fojtová M, Fajkus J, Zdráhal Z, Lochmanová G. Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors. Front Plant Sci 2017; 8:2084. [PMID: 29270186 PMCID: PMC5725443 DOI: 10.3389/fpls.2017.02084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/22/2017] [Indexed: 05/07/2023]
Abstract
Inter-individual variability of conspecific plants is governed by differences in their genetically determined growth and development traits, environmental conditions, and adaptive responses under epigenetic control involving histone post-translational modifications. The apparent variability in histone modifications among plants might be increased by technical variation introduced in sample processing during epigenetic analyses. Thus, to detect true variations in epigenetic histone patterns associated with given factors, the basal variability among samples that is not associated with them must be estimated. To improve knowledge of relative contribution of biological and technical variation, mass spectrometry was used to examine histone modification patterns (acetylation and methylation) among Arabidopsis thaliana plants of ecotypes Columbia 0 (Col-0) and Wassilewskija (Ws) homogenized by two techniques (grinding in a cryomill or with a mortar and pestle). We found little difference in histone modification profiles between the ecotypes. However, in comparison of the biological and technical components of variability, we found consistently higher inter-individual variability in histone mark levels among Ws plants than among Col-0 plants (grown from seeds collected either from single plants or sets of plants). Thus, more replicates of Ws would be needed for rigorous analysis of epigenetic marks. Regarding technical variability, the cryomill introduced detectably more heterogeneity in the data than the mortar and pestle treatment, but mass spectrometric analyses had minor apparent effects. Our study shows that it is essential to consider inter-sample variance and estimate suitable numbers of biological replicates for statistical analysis for each studied organism when investigating changes in epigenetic histone profiles.
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Affiliation(s)
- Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ivana Ihnatová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Gabriela Lochmanová,
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Pavlištová V, Dvořáčková M, Jež M, Mozgová I, Mokroš P, Fajkus J. Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes. Plant J 2016; 88:411-424. [PMID: 27377564 DOI: 10.1111/tpj.13257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 02/06/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 05/28/2023]
Abstract
Arabidopsis thaliana mutants dysfunctional in the evolutionarily conserved protein complex chromatin assembly factor-1 (CAF-1), which deposits the canonical histone H3 variant H3.1 during DNA synthesis-dependent chromatin assembly, display complex phenotypic changes including meristem and growth alterations, sensitivity to DNA-damaging agents, and reduced fertility. We reported previously that mutants in the FAS1 subunit of CAF-1 progressively lose telomere and 45S rDNA repeats. Here we show that multiple aspects of the fas phenotype are recovered immediately on expression of a reintroduced FAS1 allele, and are clearly independent of the recovery of rDNA copy-numbers and telomeres. In reverted lines, 45S rDNA genes are recovered to diverse levels with a strikingly different representation of their variants, and the typical association of nucleolar organizing region 4 with the nucleolus is perturbed. One of 45S rDNA variants (VAR1), which is silenced in wild-type (WT) plants without mutation history (Col-0 WT), dominates the expression pattern, whereas VAR2 is dominant in Col-0 WT plants. We propose an explanation for the variability of telomere and 45S rDNA repeats associated with CAF-1 function, suggesting that the differences in nuclear partitioning and expression of the rDNA variants in fas mutants and their revertants provide a useful experimental system to study genetic and epigenetic factors in gene dosage compensation.
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Affiliation(s)
- Veronika Pavlištová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Michal Jež
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Iva Mozgová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Mokroš
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology - CEITEC, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
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Havlová K, Dvořáčková M, Peiro R, Abia D, Mozgová I, Vansáčová L, Gutierrez C, Fajkus J. Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana. Plant Mol Biol 2016; 92:457-471. [PMID: 27531496 DOI: 10.1007/s11103-016-0524-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/03/2016] [Indexed: 05/28/2023]
Abstract
Approximately seven hundred 45S rRNA genes (rDNA) in the Arabidopsis thaliana genome are organised in two 4 Mbp-long arrays of tandem repeats arranged in head-to-tail fashion separated by an intergenic spacer (IGS). These arrays make up 5 % of the A. thaliana genome. IGS are rapidly evolving sequences and frequent rearrangements inside the rDNA loci have generated considerable interspecific and even intra-individual variability which allows to distinguish among otherwise highly conserved rRNA genes. The IGS has not been comprehensively described despite its potential importance in regulation of rDNA transcription and replication. Here we describe the detailed sequence variation in the complete IGS of A. thaliana WT plants and provide the reference/consensus IGS sequence, as well as genomic DNA analysis. We further investigate mutants dysfunctional in chromatin assembly factor-1 (CAF-1) (fas1 and fas2 mutants), which are known to have a reduced number of rDNA copies, and plant lines with restored CAF-1 function (segregated from a fas1xfas2 genetic background) showing major rDNA rearrangements. The systematic rDNA loss in CAF-1 mutants leads to the decreased variability of the IGS and to the occurrence of distinct IGS variants. We present for the first time a comprehensive and representative set of complete IGS sequences, obtained by conventional cloning and by Pacific Biosciences sequencing. Our data expands the knowledge of the A. thaliana IGS sequence arrangement and variability, which has not been available in full and in detail until now. This is also the first study combining IGS sequencing data with RFLP analysis of genomic DNA.
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Affiliation(s)
- Kateřina Havlová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- Institute of Biophysics ASCR, v.v.i., Královopolská 135, 61265, Brno, Czech Republic.
| | - Ramon Peiro
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Madrid, 28049, Spain
| | - David Abia
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Madrid, 28049, Spain
| | - Iva Mozgová
- Faculty of Science, Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Lenka Vansáčová
- Faculty of Science, Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Madrid, 28049, Spain
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- Faculty of Science, Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.
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Awlia M, Nigro A, Fajkus J, Schmoeckel SM, Negrão S, Santelia D, Trtílek M, Tester M, Julkowska MM, Panzarová K. High-Throughput Non-destructive Phenotyping of Traits that Contribute to Salinity Tolerance in Arabidopsis thaliana. Front Plant Sci 2016; 7:1414. [PMID: 27733855 PMCID: PMC5039194 DOI: 10.3389/fpls.2016.01414] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/05/2016] [Indexed: 05/18/2023]
Abstract
Reproducible and efficient high-throughput phenotyping approaches, combined with advances in genome sequencing, are facilitating the discovery of genes affecting plant performance. Salinity tolerance is a desirable trait that can be achieved through breeding, where most have aimed at selecting for plants that perform effective ion exclusion from the shoots. To determine overall plant performance under salt stress, it is helpful to investigate several plant traits collectively in one experimental setup. Hence, we developed a quantitative phenotyping protocol using a high-throughput phenotyping system, with RGB and chlorophyll fluorescence (ChlF) imaging, which captures the growth, morphology, color and photosynthetic performance of Arabidopsis thaliana plants in response to salt stress. We optimized our salt treatment by controlling the soil-water content prior to introducing salt stress. We investigated these traits over time in two accessions in soil at 150, 100, or 50 mM NaCl to find that the plants subjected to 100 mM NaCl showed the most prominent responses in the absence of symptoms of severe stress. In these plants, salt stress induced significant changes in rosette area and morphology, but less prominent changes in rosette coloring and photosystem II efficiency. Clustering of ChlF traits with plant growth of nine accessions maintained at 100 mM NaCl revealed that in the early stage of salt stress, salinity tolerance correlated with non-photochemical quenching processes and during the later stage, plant performance correlated with quantum yield. This integrative approach allows the simultaneous analysis of several phenotypic traits. In combination with various genetic resources, the phenotyping protocol described here is expected to increase our understanding of plant performance and stress responses, ultimately identifying genes that improve plant performance in salt stress conditions.
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Affiliation(s)
- Mariam Awlia
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Arianna Nigro
- Institute of Plant and Microbial Biology, University of ZurichZurich, Switzerland
| | - Jiří Fajkus
- PSI (Photon Systems Instruments)Drásov, Czech Republic
| | - Sandra M. Schmoeckel
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Diana Santelia
- Institute of Plant and Microbial Biology, University of ZurichZurich, Switzerland
| | | | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Magdalena M. Julkowska
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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Peška V, Sitová Z, Fajkus P, Fajkus J. BAL31-NGS approach for identification of telomeres de novo in large genomes. Methods 2016; 114:16-27. [PMID: 27595912 DOI: 10.1016/j.ymeth.2016.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/22/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022] Open
Abstract
This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n=14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples.
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Affiliation(s)
- Vratislav Peška
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Zdeňka Sitová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
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Pontvianne F, Carpentier MC, Durut N, Pavlištová V, Jaške K, Schořová Š, Parrinello H, Rohmer M, Pikaard CS, Fojtová M, Fajkus J, Sáez-Vásquez J. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome. Cell Rep 2016; 16:1574-1587. [PMID: 27477271 PMCID: PMC5279810 DOI: 10.1016/j.celrep.2016.07.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 02/18/2016] [Revised: 05/24/2016] [Accepted: 07/03/2016] [Indexed: 11/27/2022] Open
Abstract
The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Marie-Christine Carpentier
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Nathalie Durut
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Veronika Pavlištová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Karin Jaške
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Šárka Schořová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | | | | | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
| | - Miloslava Fojtová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
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Marecek R, Lamos M, Mikl M, Barton M, Fajkus J, Rektor, Brazdil M. What can be found in scalp EEG spectrum beyond common frequency bands. EEG-fMRI study. J Neural Eng 2016; 13:046026. [PMID: 27432759 DOI: 10.1088/1741-2560/13/4/046026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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]
Abstract
OBJECTIVE The scalp EEG spectrum is a frequently used marker of neural activity. Commonly, the preprocessing of EEG utilizes constraints, e.g. dealing with a predefined subset of electrodes or a predefined frequency band of interest. Such treatment of the EEG spectrum neglects the fact that particular neural processes may be reflected in several frequency bands and/or several electrodes concurrently, and can overlook the complexity of the structure of the EEG spectrum. APPROACH We showed that the EEG spectrum structure can be described by parallel factor analysis (PARAFAC), a method which blindly uncovers the spatial-temporal-spectral patterns of EEG. We used an algorithm based on variational Bayesian statistics to reveal nine patterns from the EEG of 38 healthy subjects, acquired during a semantic decision task. The patterns reflected neural activity synchronized across theta, alpha, beta and gamma bands and spread over many electrodes, as well as various EEG artifacts. MAIN RESULTS Specifically, one of the patterns showed significant correlation with the stimuli timing. The correlation was higher when compared to commonly used models of neural activity (power fluctuations in distinct frequency band averaged across a subset of electrodes) and we found significantly correlated hemodynamic fluctuations in simultaneously acquired fMRI data in regions known to be involved in speech processing. Further, we show that the pattern also occurs in EEG data which were acquired outside the MR machine. Two other patterns reflected brain rhythms linked to the attentional and basal ganglia large scale networks. The other patterns were related to various EEG artifacts. SIGNIFICANCE These results show that PARAFAC blindly identifies neural activity in the EEG spectrum and that it naturally handles the correlations among frequency bands and electrodes. We conclude that PARAFAC seems to be a powerful tool for analysis of the EEG spectrum and might bring novel insight to the relationships between EEG activity and brain hemodynamics.
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Affiliation(s)
- R Marecek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
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Fajkus P, Peška V, Sitová Z, Fulnečková J, Dvořáčková M, Gogela R, Sýkorová E, Hapala J, Fajkus J. Allium telomeres unmasked: the unusual telomeric sequence (CTCGGTTATGGG)n is synthesized by telomerase. Plant J 2016; 85:337-47. [PMID: 26716914 DOI: 10.1111/tpj.13115] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [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: 11/19/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 05/25/2023]
Abstract
Phylogenetic divergence in Asparagales plants is associated with switches in telomere sequences. The last switch occurred with divergence of the genus Allium (Amaryllidaceae) from the other Allioideae (formerly Alliaceae) genera, resulting in uncharacterized telomeres maintained by an unknown mechanism. To characterize the unknown Allium telomeres, we applied a combination of bioinformatic processing of transcriptomic and genomic data with standard approaches in telomere biology such as BAL31 sensitivity tests, terminal restriction fragment analysis, the telomere repeat amplification protocol (TRAP), and fluorescence in situ hybridization (FISH). Using these methods, we characterize the unusual telomeric sequence (CTCGGTTATGGG)n present in Allium species, demonstrate its synthesis by telomerase, and characterize the telomerase reverse transcriptase (TERT) subunit of Allium cepa. Our findings open up the possibility of studying the molecular details of the evolutionary genetic change in Allium telomeres and its possible role in speciation. Experimental studies addressing the implications of this change in terms of the interplay of telomere components may now be designed to shed more light on telomere functions and evolution in general.
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Affiliation(s)
- Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Zdeňka Sitová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Jana Fulnečková
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Roman Gogela
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Jan Hapala
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
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Procházková Schrumpfová P, Schořová Š, Fajkus J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. Front Plant Sci 2016; 7:851. [PMID: 27446102 PMCID: PMC4924339 DOI: 10.3389/fpls.2016.00851] [Citation(s) in RCA: 20] [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] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
Telomeres, as physical ends of linear chromosomes, are targets of a number of specific proteins, including primarily telomerase reverse transcriptase. Access of proteins to the telomere may be affected by a number of diverse factors, e.g., protein interaction partners, local DNA or chromatin structures, subcellular localization/trafficking, or simply protein modification. Knowledge of composition of the functional nucleoprotein complex of plant telomeres is only fragmentary. Moreover, the plant telomeric repeat binding proteins that were characterized recently appear to also be involved in non-telomeric processes, e.g., ribosome biogenesis. This interesting finding was not totally unexpected since non-telomeric functions of yeast or animal telomeric proteins, as well as of telomerase subunits, have been reported for almost a decade. Here we summarize known facts about the architecture of plant telomeres and compare them with the well-described composition of telomeres in other organisms.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Petra Procházková Schrumpfová,
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Brno, Czech Republic
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49
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Schrumpfová PP, Vychodilová I, Hapala J, Schořová Š, Dvořáček V, Fajkus J. Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo. Plant Mol Biol 2016; 90:189-206. [PMID: 26597966 DOI: 10.1007/s11103-015-0409-8] [Citation(s) in RCA: 14] [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: 07/29/2015] [Accepted: 11/16/2015] [Indexed: 05/24/2023]
Abstract
Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically to telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human shelterin proteins TRF1 or TRF2, also possess a histone-like domain which is involved in protein-protein interactions e.g., with POT1b. Here we set out to investigate the genome-wide localization pattern of TRB1 to reveal its preferential sites of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Our results demonstrate that TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis, in addition to its roles at telomeres. This preference coincides with the frequent occurrence of telobox motifs in the upstream regions of genes in this category, but it is not restricted to the presence of a telobox. We conclude that TRB1 shows a specific genome-wide distribution pattern which suggests its role in regulation of genes involved in biogenesis of the translational machinery, in addition to its preferential telomeric localization.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivona Vychodilová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jan Hapala
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Šárka Schořová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vojtěch Dvořáček
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265, Brno, Czech Republic.
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Tran TD, Cao HX, Jovtchev G, Neumann P, Novák P, Fojtová M, Vu GTH, Macas J, Fajkus J, Schubert I, Fuchs J. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J 2015; 84:1087-99. [PMID: 26485466 DOI: 10.1111/tpj.13058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 03/03/2015] [Revised: 10/07/2015] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.
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Affiliation(s)
- Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Miloslava Fojtová
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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