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Yu J, Wang Y, Bai H, Zhang X, Wang R. Genome-wide identification and expressional analysis of carotenoid cleavage oxygenase (CCO) gene family in Betula platyphylla under abiotic stress. BMC Genomics 2024; 25:872. [PMID: 39294571 PMCID: PMC11409583 DOI: 10.1186/s12864-024-10777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Carotenoid cleavage oxygenases (CCOs) are a group of enzymes that catalyze the oxidative cleavage of carotenoid molecules. These enzymes widely exist in plants, fungi, and certain bacteria, and are involved in various biological processes. It would be of great importance and necessity to identify CCO members in birch and characterize their responses upon abiotic stresses. RESULTS A total of 16 BpCCOs, including 8 BpCCDs and 8 BpNCEDs were identified in birch, and phylogenetic tree analysis showed that they could be classified into six subgroups. Collinearity analysis revealed that BpCCOs have the largest number of homologous genes in Gossypium hirsutum and also have more homologous genes in other dicotyledons. In addition, promoter analysis revealed that the promoter regions of BpCCOs contained many abiotic stress-related and hormone-responsive elements. The results of qRT-PCR showed that most of the BpCCOs were able to respond significantly to ABA, PEG, salt and cold stresses. Finally, the prediction of the interacting proteins of BpCCOs by STRING revealed several proteins that may interact with BpCCOs and be involved in plant growth and development/abiotic stress processes, such as HEC1 (bHLH), ATABA1, ATVAMP714, etc. CONCLUSION: In this study, the CCO members were identified in birch in a genome-wide scale. These results indicate that BpCCO genes may play important roles in the abiotic stress responses of birch plants.
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Affiliation(s)
- Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, China
| | - Heming Bai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, China
| | - Xiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, China.
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Zhang F, Liu Y, Ma J, Su S, Chen L, Cheng Y, Buter S, Zhao X, Yi L, Lu Z. Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data. PLANTS (BASEL, SWITZERLAND) 2024; 13:710. [PMID: 38475556 DOI: 10.3390/plants13050710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.
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Affiliation(s)
- Fan Zhang
- School of Life Science, Inner Mongolia University, Hohhot 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Ying Liu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Shaofeng Su
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Liyu Chen
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Siqin Buter
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Liuxi Yi
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
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Kim MJ, Ko YJ, Yun JH, Lee W. Solution structure of the Myb domain of Terfa derived from Zebrafish interacting with both human and plant telomeric DNA. Biochem Biophys Res Commun 2021; 559:252-258. [PMID: 33984809 DOI: 10.1016/j.bbrc.2021.04.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Telomeric repeat binding factor a (Terfa) derived from zebrafish is a homologous protein with human telomeric repeat binding factor 2 (TRF2). Terfa is known as a senescence-associated biomarker in various research through the zebrafish animal model. In addition, according to the findings so far, it has been confirmed that human or plant telomere binding proteins bind to telomeric DNA specialized for each species, but, in our result, Terfa shows it strongly binds to both human or plant type telomeric DNA. Here we characterized the DNA binding properties and demonstrate the solution structure of Terfa and identified residues participating in the interaction with both human and plant telomeric DNA. In DNA recognition of human and plant telomere binding proteins, the N-terminal loop and the α-helix 3 part of Myb domain were bound majorly, whereas, in the case of Terfa, the N-terminal loop, the α-helix 1-2 loop, and α-helix 2 of the Myb domain were dominantly bound. Therefore, when Terfa recognizes DNA, it was found that the binding module differs from previously known telomere binding proteins. The comparison of the structure of the telomere binding proteins provides an opportunity to understand more specifically how the structural properties of each telomere binding protein are associated with telomeric DNA binding from an evolutionary point of view.
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Affiliation(s)
- Min-Jung Kim
- PCG-Biotech, Ltd., Yonsei Engineering Research Park, Yonsei University, Seoul, 120-749, Republic of Korea
| | - Yoon-Joo Ko
- Nuclear Magnetic Resonance Laboratory, National Center for Inter-University Research Facilities, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, South Korea
| | - Ji-Hye Yun
- PCG-Biotech, Ltd., Yonsei Engineering Research Park, Yonsei University, Seoul, 120-749, Republic of Korea.
| | - Weontae Lee
- PCG-Biotech, Ltd., Yonsei Engineering Research Park, Yonsei University, Seoul, 120-749, Republic of Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Republic of Korea.
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Maintaining Genome Integrity during Seed Development in Phaseolus vulgaris L.: Evidence from a Transcriptomic Profiling Study. Genes (Basel) 2018; 9:genes9100463. [PMID: 30241355 PMCID: PMC6209899 DOI: 10.3390/genes9100463] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/01/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
The maintenance of genome integrity is crucial in seeds, due to the constant challenge of several endogenous and exogenous factors. The knowledge concerning DNA damage response and chromatin remodeling during seed development is still scarce, especially in Phaseolus vulgaris L. A transcriptomic profiling of the expression of genes related to DNA damage response/chromatin remodeling mechanisms was performed in P. vulgaris seeds at four distinct developmental stages, spanning from late embryogenesis to seed desiccation. Of the 14,001 expressed genes identified using massive analysis of cDNA ends, 301 belong to the DNA MapMan category. In late embryogenesis, a high expression of genes related to DNA damage sensing and repair suggests there is a tight control of DNA integrity. At the end of filling and the onset of seed dehydration, the upregulation of genes implicated in sensing of DNA double-strand breaks suggests that genome integrity is challenged. The expression of chromatin remodelers seems to imply a concomitant action of chromatin remodeling with DNA repair machinery, maintaining genome stability. The expression of genes related to nucleotide excision repair and chromatin structure is evidenced during the desiccation stage. An overview of the genes involved in DNA damage response and chromatin remodeling during P. vulgaris seed development is presented, providing insights into the mechanisms used by developing seeds to cope with DNA damage.
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Interaction studies of carbon nanomaterials and plasma activated carbon nanomaterials solution with telomere binding protein. Sci Rep 2017; 7:2636. [PMID: 28572671 PMCID: PMC5454022 DOI: 10.1038/s41598-017-02690-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/13/2017] [Indexed: 11/21/2022] Open
Abstract
Most cancer cells have telomerase activity because they can express the human telomerase reverse transcriptase (hTERT) gene. Therefore, the inhibition of the hTERT expression can play an important role in controlling cancer cell proliferation. Our current study aims to inhibit hTERT expression. For this, we synthesized graphene oxide (GO) and a functionalized multiwall carbon nanotube (f-MWCNT), latter treated them with cold atmospheric pressure plasma for further analysis of the hTERT expression. The inhibition of hTERT expression by GO, f-MWCNT, plasma activated GO solution (PGOS), and plasma activated f-MWCNT solution (PCNTS), was studied using two lung cancer cell lines, A549 and H460. The hTERT experimental results revealed that GO and PGOS sufficiently decreased the hTERT concentration, while f-MWCNT and PCNTS were unable to inhibit the hTERT concentration. Therefore, to understand the inhibition mechanism of hTERT, we studied the binding properties of GO and PGOS with telomere binding protein (AtTRB2). The interaction studies were carried out using circular dichroism, fluorescence, 1H-15N NMR spectroscopy, and size-exclusion chromatography (SEC) binding assay. We also used docking simulation to have an better understanding of the interactions between GO nanosheets and AtTRB2 protein. Our results may provide new insights that can benefit in biomedical treatments.
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Lee I, Kim H, Ko YJ, Lee W. NMR Characterization of the DNA-binding Domain of Arabidopsis thalianaTelomere Repeat Factor. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Inhwan Lee
- Department of Biochemistry, College of Life Science and Biotechnology; Yonsei University; Seoul 120-749 Korea
| | - Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology; Yonsei University; Seoul 120-749 Korea
| | - Yoon-Joo Ko
- National Center for Inter-University Research Facilities; Seoul National University; Seoul 151-747 Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology; Yonsei University; Seoul 120-749 Korea
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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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Amiard S, Olivier M, Allain E, Choi K, Smith-Unna R, Henderson IR, White CI, Gallego ME. Telomere stability and development of ctc1 mutants are rescued by inhibition of EJ recombination pathways in a telomerase-dependent manner. Nucleic Acids Res 2014; 42:11979-91. [PMID: 25274733 PMCID: PMC4231758 DOI: 10.1093/nar/gku897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 12/11/2022] Open
Abstract
The telomeres of linear eukaryotic chromosomes are protected by caps consisting of evolutionarily conserved nucleoprotein complexes. Telomere dysfunction leads to recombination of chromosome ends and this can result in fusions which initiate chromosomal breakage-fusion-bridge cycles, causing genomic instability and potentially cell death or cancer. We hypothesize that in the absence of the recombination pathways implicated in these fusions, deprotected chromosome ends will instead be eroded by nucleases, also leading to the loss of genes and cell death. In this work, we set out to specifically test this hypothesis in the plant, Arabidopsis. Telomere protection in Arabidopsis implicates KU and CST and their absence leads to chromosome fusions, severe genomic instability and dramatic developmental defects. We have analysed the involvement of end-joining recombination pathways in telomere fusions and the consequences of this on genomic instability and growth. Strikingly, the absence of the multiple end-joining pathways eliminates chromosome fusion and restores normal growth and development to cst ku80 mutant plants. It is thus the chromosomal fusions, per se, which are the underlying cause of the severe developmental defects. This rescue is mediated by telomerase-dependent telomere extension, revealing a competition between telomerase and end-joining recombination proteins for access to deprotected telomeres.
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Affiliation(s)
- Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Elisabeth Allain
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
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Yun JH, Lee WK, Kim H, Kim E, Cheong C, Cho MH, Lee W. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana. Biochem Biophys Res Commun 2014; 452:436-42. [DOI: 10.1016/j.bbrc.2014.08.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
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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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Yang Q, Zhao J, Zhou N, Ye Z, Li G. Electrochemical sensing telomere-bending motions caused by hTRF1. Biosens Bioelectron 2011; 26:2228-31. [DOI: 10.1016/j.bios.2010.09.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/06/2010] [Accepted: 09/21/2010] [Indexed: 01/29/2023]
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Bowen AJ, Gonzalez D, Mullins JGL, Bhatt AM, Martinez A, Conlan RS. PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors. J Mol Biol 2010; 395:937-49. [PMID: 19962994 DOI: 10.1016/j.jmb.2009.11.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 09/25/2009] [Accepted: 11/29/2009] [Indexed: 11/17/2022]
Abstract
The eukaryotic SIN3 protein is the central component of the evolutionarily conserved multisubunit SIN3 complex that has roles in regulating gene expression and genome stability. Here we characterise the structure of the SIN3 protein in higher plants through the analysis of SNL1 (SIN3-LIKE1), SNL2, SNL3, SNL4, SNL5 and SNL6, a family of six SIN3 homologues in Arabidopsis thaliana. In an Arabidopsis-protoplast beta-glucuronidase reporter gene assay, as well as in a heterologous yeast repression assay, full-length SNL1 was shown to repress transcription in a histone-deacetylase-dependent manner, demonstrating the conserved nature of SIN3 function. Yeast two-hybrid screening identified a number of DNA binding proteins each containing a single Myb domain that included the Arabidopsis ALWAYS EARLY proteins AtALY2 and AtALY3, and two telomere binding proteins AtTBP1 and AtTRP2/TRFL1 as SNL1 partners, suggesting potential functions for SNL1 in development and telomere maintenance. The interaction with telomere-binding protein 1 was found to be mediated through the well-defined paired amphipathic helix domain PAH2. In contrast, the AtALY2 interaction was mediated through the PAH3 domain of SNL1, which is structurally distinct from PAH1 and PAH2, suggesting that evolution of this domain to a more novel structural motif has occurred. These findings support a diverse role of SNL1 in the regulation of transcription and genome stability.
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Affiliation(s)
- Adam J Bowen
- Institute of Life Science, School of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, 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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14
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Mozgová I, Schrumpfová PP, Hofr C, Fajkus J. Functional characterization of domains in AtTRB1, a putative telomere-binding protein in Arabidopsis thaliana. PHYTOCHEMISTRY 2008; 69:1814-9. [PMID: 18479720 DOI: 10.1016/j.phytochem.2008.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 03/24/2008] [Accepted: 04/01/2008] [Indexed: 05/24/2023]
Abstract
Telomeres are nucleoprotein structures ensuring the stability of eukaryotic chromosome ends. Two protein families, TRFL (TFL-Like) and SMH (Single-Myb-Histone), containing a specific telobox motif in their Myb domain, have been identified as potential candidates involved in a functional nucleoprotein structure analogous to human "shelterin" at plant telomeres. We analyze the DNA-protein interaction of the full-length and truncated variants of AtTRB1, a SMH-family member with a typical structure: N-terminal Myb domain, central H1/5 domain and C-terminal coiled-coil. We show that preferential interaction of AtTRB1 with double-stranded telomeric DNA is mediated by the Myb domain, while the H1/5 domain is involved in non-specific DNA-protein interaction and in the multimerization of AtTRB1.
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Affiliation(s)
- Iva Mozgová
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
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15
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Zellinger B, Riha K. Composition of plant telomeres. ACTA ACUST UNITED AC 2007; 1769:399-409. [PMID: 17383025 DOI: 10.1016/j.bbaexp.2007.02.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 02/01/2007] [Accepted: 02/09/2007] [Indexed: 12/15/2022]
Abstract
Telomeres are essential elements of eukaryotic chromosomes that differentiate native chromosome ends from deleterious DNA double-strand breaks (DSBs). This is achieved by assembling chromosome termini in elaborate high-order nucleoprotein structures that in most organisms encompass telomeric DNA, specific telomere-associated proteins as well as general chromatin and DNA repair factors. Although the individual components of telomeric chromatin are evolutionary highly conserved, cross species comparisons have revealed a remarkable flexibility in their utilization at telomeres. This review outlines the strategies used for chromosome end protection and maintenance in mammals, yeast and flies and discusses current progress in deciphering telomere structure in plants.
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Affiliation(s)
- Barbara Zellinger
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, A-1030 Vienna, Austria
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Hwang MG, Cho MH. Arabidopsis thaliana telomeric DNA-binding protein 1 is required for telomere length homeostasis and its Myb-extension domain stabilizes plant telomeric DNA binding. Nucleic Acids Res 2007; 35:1333-42. [PMID: 17272298 PMCID: PMC1851659 DOI: 10.1093/nar/gkm043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Telomeres are specific protein–DNA complexes that protect the ends of eukaryotic chromosomes from fusion and degradation and are maintained by a specialized mechanism exerted by telomerase and telomere-binding proteins (TBPs), which are evolutionarily conserved. AtTBP1 is an Arabidopsis thaliana protein that binds plant telomeric DNA in vitro. Here, we demonstrated that lack of AtTBP1 results in a deregulation of telomere length control, with mutant telomeres expanding steadily by the fourth generation. DNA-binding studies with mutant AtTBP1 proteins showed that the Myb-extension domain of AtTBP1 is required for binding to plant telomeric DNA. Our results suggest that AtTBP1 is involved in the telomere length mechanism in A. thaliana and that the Myb-extension domain of AtTBP1 may stabilize plant telomeric DNA binding.
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Affiliation(s)
| | - Myeon Haeng Cho
- *To whom correspondence should be addressed. Tel: +82 2 2123 4460; Fax: +82 2 312 5657;
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