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Kusová A, Steinbachová L, Přerovská T, Drábková LZ, Paleček J, Khan A, Rigóová G, Gadiou Z, Jourdain C, Stricker T, Schubert D, Honys D, Schrumpfová PP. Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. PLANT MOLECULAR BIOLOGY 2023; 112:61-83. [PMID: 37118559 PMCID: PMC10167121 DOI: 10.1007/s11103-023-01348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/02/2023] [Indexed: 05/09/2023]
Abstract
Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) from Arabidopsis thaliana have already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as one telo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2.
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Affiliation(s)
- Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Paleček
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahamed Khan
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Gabriela Rigóová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Zuzana Gadiou
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Claire Jourdain
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tino Stricker
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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2
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Zhou Q, Sun Y, Zhao X, Yu Y, Cheng W, Lu L, Chu Z, Chen X. Bromodomain-containing factor GTE4 regulates Arabidopsis immune response. BMC Biol 2022; 20:256. [DOI: 10.1186/s12915-022-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Plants are continuously challenged with biotic stress from environmental pathogens, and precise regulation of defense responses is critical for plant survival. Defense systems require considerable amounts of energy and resources, impairing plant growth, and plant hormones controlling transcriptional regulation play essential roles in establishing the appropriate balance between defense response to pathogens and growth. Chromatin regulators modulating gene transcription are broadly involved in regulating stress-responsive genes. However, which chromatin factors are involved in coordinating hormone signaling and immune responses in plants, and their functional mechanisms, remains unclear. Here, we identified a role of bromodomain-containing protein GTE4 in negatively regulating defense responses in Arabidopsis thaliana.
Results
GTE4 mainly functions as activator of gene expression upon infection with Pseudomonas syringe. Genome-wide profiling of GTE4 occupancy shows that GTE4 tends to bind to active genes, including ribosome biogenesis related genes and maintains their high expression levels during pathogen infection. However, GTE4 is also able to repress gene expression. GTE4 binds to and represses jasmonate biosynthesis gene OPR3. Disruption of GTE4 results in overaccumulation of jasmonic acid (JA) and enhanced JA-responsive gene expression. Unexpectedly, over-accumulated JA content in gte4 mutant is coupled with downregulation of JA-mediated immune defense genes and upregulation of salicylic acid (SA)-mediated immune defense genes, and enhanced resistance to Pseudomonas, likely through a noncanonical pathway.
Conclusions
Overall, we identified a new role of the chromatin factor GTE4 as negative regulator of plant immune response through inhibition of JA biosynthesis, which in turn noncanonically activates the defense system against Pseudomonas. These findings provide new knowledge of chromatic regulation of plant hormone signaling during defense responses.
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Peska V, Garcia S. Origin, Diversity, and Evolution of Telomere Sequences in Plants. FRONTIERS IN PLANT SCIENCE 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] [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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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Necasová I, Janoušková E, Klumpler T, Hofr C. Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 2017; 45:12170-12180. [PMID: 28981702 PMCID: PMC5716094 DOI: 10.1093/nar/gkx812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/09/2017] [Indexed: 01/06/2023] Open
Abstract
Telomeric repeat binding factor 2 (TRF2) folds human telomeres into loops to prevent unwanted DNA repair and chromosome end-joining. The N-terminal basic domain of TRF2 (B-domain) protects the telomeric displacement loop (D-loop) from cleavage by endonucleases. Repressor activator protein 1 (Rap1) binds TRF2 and improves telomeric DNA recognition. We found that the B-domain of TRF2 stabilized the D-loop and thus reduced unwinding by BLM and RPA, whereas the formation of the Rap1–TRF2 complex restored DNA unwinding. To understand how the B-domain of TRF2 affects DNA binding and D-loop processing, we analyzed DNA binding of full-length TRF2 and a truncated TRF2 construct lacking the B-domain. We quantified how the B-domain improves TRF2’s interaction with DNA via enhanced long-range electrostatic interactions. We developed a structural envelope model of the B-domain bound on DNA. The model revealed that the B-domain is flexible in solution but becomes rigid upon binding to telomeric DNA. We proposed a mechanism for how the B-domain stabilizes the D-loop.
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Affiliation(s)
- Ivona Necasová
- LifeB, Chromatin Molecular Complexes, CEITEC and Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Eliška Janoušková
- LifeB, Chromatin Molecular Complexes, CEITEC and Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Tomáš Klumpler
- Structural Biology of Gene Regulation, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ctirad Hofr
- LifeB, Chromatin Molecular Complexes, CEITEC and Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
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6
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Fulcher N, Riha K. Using Centromere Mediated Genome Elimination to Elucidate the Functional Redundancy of Candidate Telomere Binding Proteins in Arabidopsis thaliana. Front Genet 2016; 6:349. [PMID: 26779251 PMCID: PMC4700174 DOI: 10.3389/fgene.2015.00349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/29/2015] [Indexed: 12/23/2022] Open
Abstract
Proteins that bind to telomeric DNA form the key structural and functional constituents of telomeres. While telomere binding proteins have been described in the majority of organisms, their identity in plants remains unknown. Several protein families containing a telomere binding motif known as the telobox have been previously described in Arabidopsis thaliana. Nonetheless, functional evidence for their involvement at telomeres has not been obtained, likely due to functional redundancy. Here we performed genetic analysis on the TRF-like family consisting of six proteins (TRB1, TRP1, TRFL1, TRFL2, TRFL4, and TRF9) which have previously shown to bind telomeric DNA in vitro. We used haploid genetics to create multiple knock-out plants deficient for all six proteins of this gene family. These plants did not exhibit changes in telomere length, or phenotypes associated with telomere dysfunction. This data demonstrates that this telobox protein family is not involved in telomere maintenance in Arabidopsis. Phylogenetic analysis in major plant lineages revealed early diversification of telobox proteins families indicating that telomere function may be associated with other telobox proteins.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Austria
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 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. FRONTIERS IN PLANT SCIENCE 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] [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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8
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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 MOLECULAR BIOLOGY 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] [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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9
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Dvořáčková M, Fojtová M, Fajkus J. Chromatin dynamics of plant telomeres and ribosomal genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:18-37. [PMID: 25752316 DOI: 10.1111/tpj.12822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 05/03/2023]
Abstract
Telomeres and genes encoding 45S ribosomal RNA (rDNA) are frequently located adjacent to each other on eukaryotic chromosomes. Although their primary roles are different, they show striking similarities with respect to their features and additional functions. Both genome domains have remarkably dynamic chromatin structures. Both are hypersensitive to dysfunctional histone chaperones, responding at the genomic and epigenomic levels. Both generate non-coding transcripts that, in addition to their epigenetic roles, may induce gross chromosomal rearrangements. Both give rise to chromosomal fragile sites, as their replication is intrinsically problematic. However, at the same time, both are essential for maintenance of genomic stability and integrity. Here we discuss the structural and functional inter-connectivity of telomeres and rDNA, with a focus on recent results obtained in plants.
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Affiliation(s)
- Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
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10
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Janoušková E, Nečasová I, Pavloušková J, Zimmermann M, Hluchý M, Marini V, Nováková M, Hofr C. Human Rap1 modulates TRF2 attraction to telomeric DNA. Nucleic Acids Res 2015; 43:2691-700. [PMID: 25675958 PMCID: PMC4357705 DOI: 10.1093/nar/gkv097] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
More than two decades of genetic research have identified and assigned main biological functions of shelterin proteins that safeguard telomeres. However, a molecular mechanism of how each protein subunit contributes to the protecting function of the whole shelterin complex remains elusive. Human Repressor activator protein 1 (Rap1) forms a multifunctional complex with Telomeric Repeat binding Factor 2 (TRF2). Rap1–TRF2 complex is a critical part of shelterin as it suppresses homology-directed repair in Ku 70/80 heterodimer absence. To understand how Rap1 affects key functions of TRF2, we investigated full-length Rap1 binding to TRF2 and Rap1–TRF2 complex interactions with double-stranded DNA by quantitative biochemical approaches. We observed that Rap1 reduces the overall DNA duplex binding affinity of TRF2 but increases the selectivity of TRF2 to telomeric DNA. Additionally, we observed that Rap1 induces a partial release of TRF2 from DNA duplex. The improved TRF2 selectivity to telomeric DNA is caused by less pronounced electrostatic attractions between TRF2 and DNA in Rap1 presence. Thus, Rap1 prompts more accurate and selective TRF2 recognition of telomeric DNA and TRF2 localization on single/double-strand DNA junctions. These quantitative functional studies contribute to the understanding of the selective recognition of telomeric DNA by the whole shelterin complex.
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Affiliation(s)
- Eliška Janoušková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ivona Nečasová
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Pavloušková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Michal Zimmermann
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Milan Hluchý
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Victoria Marini
- Department of Biology, Faculty of Medicine, Masaryk University, Brno CZ-62500, Czech Republic
| | - Monika Nováková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ctirad Hofr
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
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11
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Procházková Schrumpfová P, Vychodilová I, Dvořáčková M, Majerská J, Dokládal L, Schořová Š, Fajkus J. Telomere repeat binding proteins are functional components of Arabidopsis telomeres and interact with telomerase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:770-81. [PMID: 24397874 PMCID: PMC4282523 DOI: 10.1111/tpj.12428] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/06/2013] [Accepted: 12/23/2013] [Indexed: 05/19/2023]
Abstract
Although telomere-binding proteins constitute an essential part of telomeres, in vivo data indicating the existence of a structure similar to mammalian shelterin complex in plants are limited. Partial characterization of a number of candidate proteins has not identified true components of plant shelterin or elucidated their functional mechanisms. Telomere repeat binding (TRB) proteins from Arabidopsis thaliana bind plant telomeric repeats through a Myb domain of the telobox type in vitro, and have been shown to interact with POT1b (Protection of telomeres 1). Here we demonstrate co-localization of TRB1 protein with telomeres in situ using fluorescence microscopy, as well as in vivo interaction using chromatin immunoprecipitation. Classification of the TRB1 protein as a component of plant telomeres is further confirmed by the observation of shortening of telomeres in knockout mutants of the trb1 gene. Moreover, TRB proteins physically interact with plant telomerase catalytic subunits. These findings integrate TRB proteins into the telomeric interactome of A. thaliana.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Functional Genomics and Proteomics, CEITEC National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- *For correspondence (e-mails or )
| | - Ivona Vychodilová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Functional Genomics and Proteomics, CEITEC National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republicv.v.i, Královopolská 135, Brno, CZ, 61265, Czech Republic
| | - Jana Majerská
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- †Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de LausanneStation 19, 1015, Lausanne, Switzerland
| | - Ladislav Dokládal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republicv.v.i, Královopolská 135, Brno, CZ, 61265, Czech Republic
| | - Šárka Schořová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Functional Genomics and Proteomics, CEITEC National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Functional Genomics and Proteomics, CEITEC National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityKamenice 5, Brno, CZ, 62500, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republicv.v.i, Královopolská 135, Brno, CZ, 61265, Czech Republic
- *For correspondence (e-mails or )
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Visacka K, Hofr C, Willcox S, Necasova I, Pavlouskova J, Sepsiova R, Wimmerova M, Simonicova L, Nosek J, Fajkus J, Griffith JD, Tomaska L. Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres. J Biol Chem 2012; 287:32206-15. [PMID: 22815473 DOI: 10.1074/jbc.m112.385591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Double-stranded regions of the telomeres are recognized by proteins containing Myb-like domains conferring specificity toward telomeric repeats. Although biochemical and structural studies revealed basic molecular principles involved in DNA binding, relatively little is known about evolutionary pathways leading to various types of Myb domain-containing proteins in divergent species of eukaryotes. Recently we identified a novel type of telomere-binding protein YlTay1p from the yeast Yarrowia lipolytica containing two Myb domains (Myb1, Myb2) very similar to the Myb domain of mammalian TRF1 and TRF2. In this study we prepared mutant versions of YlTay1p lacking Myb1, Myb2, or both Myb domains and found that YlTay1p carrying either Myb domain exhibits preferential affinity to both Y. lipolytica (GGGTTAGTCA)(n) and human (TTAGGG)(n) telomeric sequences. Quantitative measurements of the protein binding to telomeric DNA revealed that the presence of both Myb domains is required for a high affinity of YlTay1p to either telomeric repeat. Additionally, we performed detailed thermodynamic analysis of the YlTay1p interaction with its cognate telomeric DNA, which is to our knowledge the first energetic description of a full-length telomeric-protein binding to DNA. Interestingly, when compared with human TRF1 and TRF2 proteins, YlTay1p exhibited higher affinity not only for Y. lipolytica telomeres but also for human telomeric sequences. The duplication of the Myb domain region in YlTay1p thus produces a synergistic effect on its affinity toward the cognate telomeric sequence, alleviating the need for homodimerization observed in TRF-like proteins possessing a single Myb domain.
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Affiliation(s)
- Katarina Visacka
- Department of Genetics and Biochemistry, Comenius University, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava, Slovakia
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O'Neill JS, van Ooijen G, Le Bihan T, Millar AJ. Circadian clock parameter measurement: characterization of clock transcription factors using surface plasmon resonance. J Biol Rhythms 2011; 26:91-8. [PMID: 21454289 DOI: 10.1177/0748730410397465] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To refine mathematical models of the transcriptional/translational feedback loop in the clockwork of Arabidopsis thaliana, the investigators sought to determine the affinity of the transcription factors LHY, CCA1, and CHE for their cognate DNA target sequences in vitro. Steady-state dissociation constants were observed to lie in the low nanomolar range. Furthermore, the data suggest that the LHY/CCA1 heterodimer binds more tightly than either homodimer and that DNA binding of these complexes is temperature compensated. Finally, it was found that LHY binding to the evening element in vitro is enhanced by both molecular crowding effects and by casein kinase 2-mediated phosphorylation.
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Affiliation(s)
- John S O'Neill
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
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Dvorácková M, Rossignol P, Shaw PJ, Koroleva OA, Doonan JH, Fajkus J. AtTRB1, a telomeric DNA-binding protein from Arabidopsis, is concentrated in the nucleolus and shows highly dynamic association with chromatin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:637-49. [PMID: 19947985 DOI: 10.1111/j.1365-313x.2009.04094.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
AtTRB1, 2 and 3 are members of the SMH (single Myb histone) protein family, which comprises double-stranded DNA-binding proteins that are specific to higher plants. They are structurally conserved, containing a Myb domain at the N-terminus, a central H1/H5-like domain and a C-terminally located coiled-coil domain. AtTRB1, 2 and 3 interact through their Myb domain specifically with telomeric double-stranded DNA in vitro, while the central H1/H5-like domain interacts non-specifically with DNA sequences and mediates protein-protein interactions. Here we show that AtTRB1, 2 and 3 preferentially localize to the nucleus and nucleolus during interphase. Both the central H1/H5-like domain and the Myb domain from AtTRB1 can direct a GFP fusion protein to the nucleus and nucleolus. AtTRB1-GFP localization is cell cycle-regulated, as the level of nuclear-associated GFP diminishes during mitotic entry and GFP progressively re-associates with chromatin during anaphase/telophase. Using fluorescence recovery after photobleaching and fluorescence loss in photobleaching, we determined the dynamics of AtTRB1 interactions in vivo. The results reveal that AtTRB1 interaction with chromatin is regulated at two levels at least, one of which is coupled with cell-cycle progression, with the other involving rapid exchange.
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Affiliation(s)
- Martina Dvorácková
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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