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Frydrychová RČ, Konopová B, Peska V, Brejcha M, Sábová M. Telomeres and telomerase: active but complex players in life-history decisions. Biogerontology 2024; 25:205-226. [PMID: 37610666 DOI: 10.1007/s10522-023-10060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Studies on human telomeres have established that telomeres exert a significant influence on lifespan and health of organisms. However, recent research has indicated that the original idea that telomeres affect lifespan in a universal and central manner across all eukaryotic species is an oversimplification. Indeed, findings from a variety of animal species revealed that the role of telomere biology in aging is more subtle and intricate than previously recognized. Here, we show how telomere biology varies depending on the taxon. We also show how telomere biology corresponds to basic life history traits and affects the life table of a species and investments in growth, body size, reproduction, and lifespan; telomeres are hypothesized to shape evolutionary perspectives for species in an active but complex manner. Our evaluation is based on telomere biology data from many examples from throughout the animal kingdom that vary according to the degree of organismal complexity and life history strategies.
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Affiliation(s)
- Radmila Čapková Frydrychová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.
| | - Barbora Konopová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Miloslav Brejcha
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic
| | - Michala Sábová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
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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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Brejcha M, Prušáková D, Sábová M, Peska V, Černý J, Kodrík D, Konopová B, Čapková Frydrychová R. Seasonal changes in ultrastructure and gene expression in the fat body of worker honey bees. J Insect Physiol 2023; 146:104504. [PMID: 36935036 DOI: 10.1016/j.jinsphys.2023.104504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/19/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
The anatomical, physiological, and behavioral characteristics of honey bees are affected by the season as well as division of labor. In this study, we examined the structure, ultrastructure, and gene expression of fat body cells in both long-lived winter and short-lived summer worker bees (the youngest stage of hive bees and forager bees). In contrast to hive bees, foragers and winter bees have a higher metabolism due to intensive muscle activity during their flight (foragers) or endothermic heat production (winter bees). These workers differ from hive bees in the biology of their mitochondria, peroxisomes, and lysosomes as well as in the expression of the genes involved in lipid, carbohydrate, amino acid metabolism, insulin, and TGF- β signaling. Additionally, the expression of genes related to phospholipid metabolism was higher in the hive bees. However, we found no differences between workers in the expression of genes controlling cell organelles, such as the Golgi apparatus, endoplasmic reticulum, ribosomes, nucleus, and vacuoles, as well as genes for DNA replication, cell cycle control, and autophagy. Furthermore, lysosomes, autophagic processes and lipofuscin particles were more frequently observed in winter bees using electron microscopy.
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Affiliation(s)
- Miloslav Brejcha
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Daniela Prušáková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Michala Sábová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Černý
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Dalibor Kodrík
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Barbora Konopová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic.
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Lyčka M, Fajkus P, Jenner LP, Sýkorová E, Fojtová M, Peska V. Identification of the Sequence and the Length of Telomere DNA. Methods Mol Biol 2023; 2672:285-302. [PMID: 37335484 DOI: 10.1007/978-1-0716-3226-0_18] [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
Telomeres are essential nucleoprotein structures at the very ends of linear eukaryote chromosomes. They shelter the terminal genome territories against degradation and prevent the natural chromosome ends from being recognized by repair mechanisms as double-strand DNA breaks.There are two basic characteristics of telomeric DNA, its sequence and its length. The telomere sequence is important as a "landing area" for specific telomere-binding proteins, which function as signals and moderate the interactions required for correct telomere function. While the sequence forms the proper "landing surface" of telomeric DNA, its length is similarly important. Too short or exceptionally long telomere DNA cannot perform its function properly. In this chapter, methods for the investigation of these two basic telomere DNA characteristics are described, namely, telomere motif identification and telomere length measurement.
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Affiliation(s)
- Martin Lyčka
- 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
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Leon P Jenner
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the 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.
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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Čapková Frydrychová R, Mason JM, Peska V. Editorial: Telomere Flexibility and Versatility: A Role of Telomeres in Adaptive Potential. Front Genet 2021; 12:771938. [PMID: 34671387 PMCID: PMC8520972 DOI: 10.3389/fgene.2021.771938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Radmila Čapková Frydrychová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
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Prušáková D, Peska V, Pekár S, Bubeník M, Čížek L, Bezděk A, Čapková Frydrychová R. Telomeric DNA sequences in beetle taxa vary with species richness. Sci Rep 2021; 11:13319. [PMID: 34172809 PMCID: PMC8233369 DOI: 10.1038/s41598-021-92705-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Telomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.
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Affiliation(s)
- Daniela Prušáková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Michal Bubeník
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Lukáš Čížek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Bezděk
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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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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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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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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Baránková S, Pascual-Díaz JP, Sultana N, Alonso-Lifante MP, Balant M, Barros K, D'Ambrosio U, Malinská H, Peska V, Pérez Lorenzo I, Kovařík A, Vyskot B, Janoušek B, Garcia S. Sex-chrom, a database on plant sex chromosomes. New Phytol 2020; 227:1594-1604. [PMID: 32357248 DOI: 10.1111/nph.16635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 05/15/2023]
Affiliation(s)
- Simona Baránková
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Joan Pere Pascual-Díaz
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Nusrat Sultana
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Botany, Faculty of Life and Earth Sciences, Jagannath University, Dhaka, 1100, Bangladesh
| | - Maria Pilar Alonso-Lifante
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Manica Balant
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Karina Barros
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ugo D'Ambrosio
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Hana Malinská
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, 400 96, Ústí nad Labem, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Iván Pérez Lorenzo
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Bohuslav Janoušek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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Peska V, Garcia S. Origin, Diversity, and Evolution of Telomere Sequences in Plants. Front Plant Sci 2020; 11:117. [PMID: 32153618 PMCID: PMC7046594 DOI: 10.3389/fpls.2020.00117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 05/18/2023]
Abstract
Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (TxAyGz)n. Although they are well conserved across large groups of organisms, recent findings in plants imply that their diversity has been underestimated. Changes in telomeres are of enormous evolutionary importance as they can affect whole-genome stability. Even a small change in the telomere motif of each repeat unit represents an important interference in the system of sequence-specific telomere binding proteins. Here, we provide an overview of telomere sequences, considering the latest phylogenomic evolutionary framework of plants in the broad sense (Archaeplastida), in which new telomeric sequences have recently been found in diverse and economically important families such as Solanaceae and Amaryllidaceae. In the family Lentibulariaceae and in many groups of green algae, deviations from the typical plant telomeric sequence have also been detected recently. Ancestry and possible homoplasy in telomeric motifs, as well as extant gaps in knowledge are discussed. With the increasing availability of genomic approaches, it is likely that more telomeric diversity will be uncovered in the future. We also discuss basic methods used for telomere identification and we explain the implications of the recent discovery of plant telomerase RNA on further research about the role of telomerase in eukaryogenesis or on the molecular causes and consequences of telomere variability.
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Affiliation(s)
- Vratislav Peska
- Department of Cell Biology and Radiobiology, The Czech Academy of Sciences, Institute of Biophysics, Brno, Czechia
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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Peska V, Prochazkova Schrumpfova P, Fajkus J. Using the Telobox to Search for Plant Telomere Binding Proteins. Curr Protein Pept Sci 2011. [DOI: 10.2174/1389211213488502037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Peska V, Sýkorová E, Fajkus J. Two faces of Solanaceae telomeres: a comparison between Nicotiana and Cestrum telomeres and telomere-binding proteins. Cytogenet Genome Res 2009; 122:380-7. [PMID: 19188709 DOI: 10.1159/000167826] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2008] [Indexed: 11/19/2022] Open
Abstract
While most Solanaceae genera (e.g.Solanum, Nicotiana) possess Arabidopsis-type telomeres of (TTTAGGG)n maintained by telomerase, the genera Cestrum, Vestia and Sessea (Cestrum group) lack these telomeres. Here we show that in the Cestrum-group the activity of telomerase has been lost. Nevertheless, proteins binding the single-stranded G-rich strand of the Arabidopsis-type and related human-type (TTAGGG)n telomeric sequences are present in nuclear extracts of both Nicotiana and Cestrum species. These proteins may have a role in telomere function or other cellular activities. In addition to characterizing DNA binding specificity and molecular weights of these proteins, we searched in both N. tabacum (tobacco) and C. parqui for the presence of POT1-like proteins, involved in telomere capping and telomerase regulation. Analysis of POT1-like proteins available on public databases and cloned by us from C. parqui, revealed the N-terminal OB folds typical for this protein family and a novel, plant-specific conserved C-terminal OB-fold domain (CTOB). We propose that CTOB is involved in protein-protein interactions.
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Affiliation(s)
- V Peska
- Institute of Biophysics, Czech Academy of Sciences, Masaryk University, Brno, Czech Republic
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