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Luo M, Luo H, Li H, Liu D, Lu H. Single-stranded DNA-binding proteins in plant telomeres. Int J Biol Macromol 2020; 165:1463-7. [PMID: 32998016 DOI: 10.1016/j.ijbiomac.2020.09.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 11/21/2022]
Abstract
Telomere single-stranded DNA-binding proteins bind to the terminal single-stranded DNA of telomeres, maintaining and protecting the chromosomal end in eukaryotes. This paper focuses on the protective mechanism of single-stranded DNA-binding proteins in plant telomeres. This review summarizes the roles of plant single-stranded DNA-binding proteins and their influence on telomere length and telomerase. This review provides insights into the mechanism and development of single-stranded DNA-binding proteins in plants.
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2
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Procházková Schrumpfová P, Schořová Š, Fajkus J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. Front Plant Sci 2016; 7:851. [PMID: 27446102 PMCID: PMC4924339 DOI: 10.3389/fpls.2016.00851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
Telomeres, as physical ends of linear chromosomes, are targets of a number of specific proteins, including primarily telomerase reverse transcriptase. Access of proteins to the telomere may be affected by a number of diverse factors, e.g., protein interaction partners, local DNA or chromatin structures, subcellular localization/trafficking, or simply protein modification. Knowledge of composition of the functional nucleoprotein complex of plant telomeres is only fragmentary. Moreover, the plant telomeric repeat binding proteins that were characterized recently appear to also be involved in non-telomeric processes, e.g., ribosome biogenesis. This interesting finding was not totally unexpected since non-telomeric functions of yeast or animal telomeric proteins, as well as of telomerase subunits, have been reported for almost a decade. Here we summarize known facts about the architecture of plant telomeres and compare them with the well-described composition of telomeres in other organisms.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Petra Procházková Schrumpfová,
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Brno, Czech Republic
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3
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He Q, Chen L, Xu Y, Yu W. Identification of centromeric and telomeric DNA-binding proteins in rice. Proteomics 2013; 13:826-32. [PMID: 23303719 DOI: 10.1002/pmic.201100416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/22/2012] [Accepted: 11/25/2012] [Indexed: 12/17/2022]
Abstract
Centromeres and telomeres are DNA/protein complexes and essential functional components of eukaryotic chromosomes. Previous studies have shown that rice centromeres and telomeres are occupied by CentO (rice centromere satellite DNA) satellite and G-rich telomere repeats, respectively. However, the protein components are not fully understood. DNA-binding proteins associated with centromeric or telomeric DNAs will most likely be important for the understanding of centromere and telomere structure and functions. To capture DNA-specific binding proteins, affinity pull-down technique was applied in this study to isolate rice centromeric and telomeric DNA-binding proteins. Fifty-five proteins were identified for their binding affinity to rice CentO repeat, and 80 proteins were identified for their binding to telomere repeat. One CentO-binding protein, Os02g0288200, was demonstrated to bind to CentO specifically by in vitro assay. A conserved domain, DUF573 with unknown functions was identified in this protein, and proven to be responsible for the specific binding to CentO in vitro. Four proteins identified as telomere DNA-binding proteins in this study were reported by different groups previously. These results demonstrate that DNA affinity pull-down technique is effective in the isolation of sequence-specific binding proteins and will be applicable in future studies of centromere and telomere proteins.
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Affiliation(s)
- Qi He
- State Key Laboratory for Agrobiotechnology, Institute of Plant Molecular Biology and Agricultural Biotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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4
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Moriguchi R, Ohata K, Kanahama K, Takahashi H, Nishiyama M, Kanayama Y. Suppression of telomere-binding protein gene expression represses seed and fruit development in tomato. J Plant Physiol 2011; 168:1927-1933. [PMID: 21683470 DOI: 10.1016/j.jplph.2011.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/17/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
Tomato (Solanum lycopersicum L.) plants were transformed with an antisense construct of a cDNA encoding tomato telomere-binding protein (LeTBP1) to describe the role of a telomere-binding protein at the whole plant level. Fruit size decreased corresponding to the degree of suppression of LeTBP1 expression. This inhibition of fruit development was likely due to a decrease in the number of seeds in the LeTBP1 antisense plants. Pollen fertility and pollen germination rate decreased in accordance with the degree of suppression of LeTBP1 expression. Ovule viability was also reduced in the LeTBP1 antisense plants. Although plant height was somewhat reduced in the antisense plants compared to the control plants, the number and weight of leaves were unaffected by LeTBP1 suppression. The number and morphology of flowers were also normal in the antisense plants. These indicate that reduced fertility in the antisense plants is not an indirect effect of altered vegetative growth. LeTBP1 expression was sensitive to temperature stress in wild-type plants. We conclude that LeTBP1 plays a critical role in seed and fruit development rather than vegetative growth and flower formation.
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Affiliation(s)
- Ryo Moriguchi
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
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5
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Abstract
Telomeres define the ends of linear eukaryotic chromosomes and are required for genome maintenance and continued cell proliferation. The extreme ends of telomeres terminate in a single-strand protrusion, termed the G-overhang, which, in vertebrates and fission yeast, is bound by evolutionarily conserved members of the POT1 (protection of telomeres) protein family. Unlike most other model organisms, the flowering plant Arabidopsis thaliana encodes two divergent POT1-like proteins. Here we show that the single-strand telomeric DNA binding activity present in A. thaliana nuclear extracts is not dependent on POT1a or POT1b proteins. Furthermore, in contrast to POT1 proteins from yeast and vertebrates, recombinant POT1a and POT1b proteins from A. thaliana, and from two additional Brassicaceae species, Arabidopsis lyrata and Brassica oleracea (cauliflower), fail to bind single-strand telomeric DNA in vitro under the conditions tested. Finally, although we detected four single-strand telomeric DNA binding activities in nuclear extracts from B. oleracea, partial purification and DNA cross-linking analysis of these complexes identified proteins that are smaller than the predicted sizes of BoPOT1a or BoPOT1b. Taken together, these data suggest that POT1 proteins are not the major single-strand telomeric DNA binding activities in A. thaliana and its close relatives, underscoring the remarkable functional divergence of POT1 proteins from plants and other eukaryotes.
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Affiliation(s)
- Eugene V. Shakirov
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Thomas D. McKnight
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843-3258, USA
| | - Dorothy E. Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
- For correspondence (fax +1 979 845 9274; )
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6
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Ko S, Jun SH, Bae H, Byun JS, Han W, Park H, Yang SW, Park SY, Jeon YH, Cheong C, Kim WT, Lee W, Cho HS. Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins. Nucleic Acids Res 2008; 36:2739-55. [PMID: 18367475 PMCID: PMC2377444 DOI: 10.1093/nar/gkn030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 02/04/2023] Open
Abstract
Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1(561-681)), and was composed of 4 alpha-helices. We also determined the structure of NgTRF1(561-681) bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1(561-681) with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1(561-681), may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)(n).
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Affiliation(s)
- Sunggeon Ko
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Sung-Hoon Jun
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Hansol Bae
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Jung-Sue Byun
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Woong Han
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Heeyoung Park
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Seong Wook Yang
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Sam-Yong Park
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Young Ho Jeon
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Chaejoon Cheong
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Woo Taek Kim
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Weontae Lee
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
| | - Hyun-Soo Cho
- Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea, Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan and Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Korea
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7
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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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8
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Abstract
UV-B radiation causes diverse morphological and physiological responses in plants, but the underlying mechanisms governing these integrated responses are unknown. In this study, we systematically surveyed responses of maize leaves to UV-B radiation using DIGE 2D gels and identified selected proteins by mass spectrometry and immunodetection analysis. To identify changes in protein accumulation in response to UV-B radiation, a line (b, pl W23) deficient in flavonoid sunscreen compounds and hence similar to commercial corn was used. In addition, its proteome in natural UV-B conditions was compared with that of two maize landraces from high altitudes (Cacahuacintle and Confite Puneño) that have improved UV-B tolerance. Protein patterns in adult maize leaves (Zea mays) were documented after growth for 21 days in sunlight depleted of UV-B radiation or growth in sunlight including an 8-h UV-B supplementation during 1 day in the field. We found that there is a very high correlation between previously documented mRNA accumulation assessed by microarray hybridization and quantitative real time reverse transcription-PCR and protein expression after UV-B irradiation in leaves of W23. Multiple isoforms were confirmed for some proteins; at least one protein, pyruvate, phosphate dikinase, is regulated post-translationally by phosphorylation by UV-B exposure. Proteins differentially regulated by UV-B radiation in W23 with higher levels under similar UV-B conditions in high altitude plants were also identified. These could be genetically fixed traits conferring UV-B tolerance and offer clues to specific adaptations to living in high ambient UV-B conditions.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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9
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Schrumpfová P, Kuchar M, Miková G, Skrísovská L, Kubicárová T, Fajkus J. Characterization of two Arabidopsis thaliana myb-like proteins showing affinity to telomeric DNA sequence. Genome 2005; 47:316-24. [PMID: 15060584 DOI: 10.1139/g03-136] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Telomere-binding proteins participate in forming a functional nucleoprotein structure at chromosome ends. Using a genomic approach, two Arabidopsis thaliana genes coding for candidate Myb-like telomere binding proteins were cloned and expressed in E. coli. Both proteins, termed AtTBP2 (accession Nos. T46051 (protein database) and GI:638639 (nucleotide database); 295 amino acids, 32 kDa, pI 9.53) and AtTBP3 (BAB08466, GI:9757879; 299 amino acids, 33 kDa, pI 9.88), contain a single Myb-like DNA-binding domain at the N-terminus, and a histone H1/H5-like DNA-binding domain in the middle of the protein sequence. Both proteins are expressed in various A. thaliana tissues. Using the two-hybrid system interaction between the proteins AtTBP2 and AtTBP3 and self interactions of each of the proteins were detected. Gel-retardation assays revealed that each of the two proteins is able to bind the G-rich strand and double-stranded DNA of plant telomeric sequence with an affinity proportional to a number of telomeric repeats. Substrates bearing a non-telomeric DNA sequence positioned between two telomeric repeats were bound with an efficiency depending on the length of interrupting sequence. The ability to bind variant telomere sequences decreased with sequence divergence from the A. thaliana telomeric DNA. None of the proteins alone or their mixture affects telomerase activity in vitro. Correspondingly, no interaction was observed between any of two proteins and the Arabidopsis telomerase reverse transcriptase catalytic subunit TERT (accession No. AF172097) using two-hybrid assay.
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Affiliation(s)
- Petra Schrumpfová
- Department of Functional Genomics and Proteomics, Masaryk University Brno, Czech Republic
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10
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Abstract
The stability of eukaryotic genomes is provided in part by the integrity of telomeres, the nucleoprotein caps on the ends of chromosome. Recent studies reveal that proper telomere architecture is required for long-term proliferation capacity. Here we describe molecular mechanisms that protect and maintain chromosome ends and discuss why Arabidopsis is emerging as a powerful new model for elucidating fundamental aspects of telomere biology.
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Affiliation(s)
- Karel Riha
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
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11
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Abstract
In this study, we performed gel mobility shift assays using tobacco BY-2 nuclei extracts to identify the plant telomere-binding proteins (TBP). Although no complexes were detected using C-strand as a probe, a single DNA-protein complex was detected using single-stranded 32P-(TTTAGGG)4 as a probe. In competition experiments, formation of the complex was inhibited only when an ssG-strand telomere repeat was used as a competitor. These results indicate that the observed band reflects a G-strand specific single-stranded telomere-binding protein (NtGTBP1). We purified the binding protein and subsequently used RT-PCR to isolate a gene encoding the protein. The sequence reveals that the protein (NtGTBP1) is a novel TBP from a higher plant, and a search for conserved domains showed that NtGTBP1 contains two RNA recognition motifs (RRMs).
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Affiliation(s)
- Yoshinori Hirata
- Laboratory of Plant Physiology, Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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12
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Marian CO, Bordoli SJ, Goltz M, Santarella RA, Jackson LP, Danilevskaya O, Beckstette M, Meeley R, Bass HW. The maize Single myb histone 1 gene, Smh1, belongs to a novel gene family and encodes a protein that binds telomere DNA repeats in vitro. Plant Physiol 2003; 133:1336-50. [PMID: 14576282 PMCID: PMC281628 DOI: 10.1104/pp.103.026856] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2003] [Revised: 06/12/2003] [Accepted: 07/28/2003] [Indexed: 05/19/2023]
Abstract
We screened maize (Zea mays) cDNAs for sequences similar to the single myb-like DNA-binding domain of known telomeric complex proteins. We identified, cloned, and sequenced five full-length cDNAs representing a novel gene family, and we describe the analysis of one of them, the gene Single myb histone 1 (Smh1). The Smh1 gene encodes a small, basic protein with a unique triple motif structure of (a) an N-terminal SANT/myb-like domain of the homeodomain-like superfamily of 3-helical-bundle-fold proteins, (b) a central region with homology to the conserved H1 globular domain found in the linker histones H1/H5, and (c) a coiled-coil domain near the C terminus. The Smh-type genes are plant specific and include a gene family in Arabidopsis and the PcMYB1 gene of parsley (Petroselinum crispum) but are distinct from those (AtTRP1, AtTBP1, and OsRTBP1) recently shown to encode in vitro telomere-repeat DNA-binding activity. The Smh1 gene is expressed in leaf tissue and maps to chromosome 8 (bin 8.05), with a duplicate locus on chromosome 3 (bin 3.09). A recombinant full-length SMH1, rSMH1, was found by band-shift assays to bind double-stranded oligonucleotide probes with at least two internal tandem copies of the maize telomere repeat, TTTAGGG. Point mutations in the telomere repeat residues reduced or abolished the binding, whereas rSMH1 bound nonspecifically to single-stranded DNA probes. The two DNA-binding motifs in SMH proteins may provide a link between sequence recognition and chromatin dynamics and may function at telomeres or other sites in the nucleus.
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Affiliation(s)
- Calin O Marian
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4370, USA
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13
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Fukushi D, Shichiri M, Sugiyama S, Yoshino T, Hagiwara S, Ohtani T. Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit. Exp Cell Res 2003; 289:237-44. [PMID: 14499624 DOI: 10.1016/s0014-4827(03)00259-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence in situ hybridization (FISH) is widely used in molecular biological study. However, high-resolution analysis of fluorescent signals is theoretically limited by the 300-nm resolution optical limit of light microscopy. As an alternative to detection by light microscopy, we used Scanning Near-field Optical/Atomic Force Microscopy (SNOM/AFM), which can simultaneously obtain topographic and fluorescent images with nanometer-scale resolution. In this study, we demonstrated high-resolution SNOM/AFM imaging of barley chromosome (Hordeum vulgare, cv. Minorimugi) FISH signals using telomeric DNA probes. Besides detecting the granular structures on chromosomes in a topographic image, we clearly detected fluorescent signals in telomeric regions with low-magnification imaging. The high-resolution analysis suggested that one of the telomeric signals could be observed by expanded imaging as two fluorescent regions separated by approximately 250 nm. This result indicated that the fluorescent signals beyond the optical limit were detected with higher resolution scanning by SNOM/AFM.
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Affiliation(s)
- Daisuke Fukushi
- National Food Research Institute, Food Engineering Division, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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14
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Yang SW, Kim DH, Lee JJ, Chun YJ, Lee JH, Kim YJ, Chung IK, Kim WT. Expression of the telomeric repeat binding factor gene NgTRF1 is closely coordinated with the cell division program in tobacco BY-2 suspension culture cells. J Biol Chem 2003; 278:21395-407. [PMID: 12646586 DOI: 10.1074/jbc.m209973200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Telomeres are vital for preserving chromosome integrity during cell division. Several genes encoding potential telomere-binding proteins have recently been identified in higher plants, but nothing is known about their function or regulation during cell division. In this study, we have isolated and characterized a cDNA clone, pNgTRF1, encoding a putative double-stranded telomeric repeat binding factor of Nicotiana glutinosa, a diploid tobacco plant. The predicted protein sequence of NgTRF1 (Mr = 75,000) contains a single Myb-like domain with significant homology to a corresponding motif in human TRF1/Pin2 and TRF2. Gel retardation assays revealed that bacterially expressed full-length NgTRF1 was able to form a specific complex only with probes containing three or more contiguous telomeric TTTAGGG repeats. The Myb-like domain of NgTRF1 is essential, but not sufficient, to bind the telomeric repeat sequence. The glutamine-rich extreme C-terminal region, which does not exist in animal proteins, was additionally required to form a specific telomere-protein complex. The dissociation constant (Kd) of the Myb motif plus the glutamine-rich domain of NgTRF1 to the two-telomeric repeat sequence was evaluated to be 4.5 +/- 0.2 x 10-9 m, which is comparable to that of the Myb domain of human TRF1. Expression analysis showed that NgTRF1 gene activity was inversely correlated with the cell division capacity of tobacco root cells and during the 9-day culture period of BY-2 suspension cells, while telomerase activity was positively correlated with cell division. In synchronized BY-2 cells, NgTRF1 was selectively expressed in G1 phase, whereas telomerase activity peaked in S phase. These findings suggest that telomerase activity and NgTRF1 expression are differentially regulated in an opposing fashion during growth and cell division in tobacco plants. The possible physiological functions of NgTRF1 in tobacco cells are also discussed.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Arabidopsis/genetics
- Base Sequence
- Binding, Competitive
- Blotting, Northern
- Blotting, Southern
- Cell Division
- Cell Nucleus/metabolism
- Cloning, Molecular
- DNA/metabolism
- DNA, Complementary/metabolism
- Dose-Response Relationship, Drug
- G1 Phase
- Gene Deletion
- Gene Expression Regulation
- Gene Library
- Green Fluorescent Proteins
- Humans
- Indomethacin/pharmacology
- Kinetics
- Luminescent Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleic Acid Hybridization
- Polymerase Chain Reaction
- Protein Binding
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- S Phase
- Sequence Homology, Amino Acid
- Species Specificity
- Subcellular Fractions
- Telomerase/metabolism
- Telomere/genetics
- Telomere/metabolism
- Telomeric Repeat Binding Protein 1/biosynthesis
- Telomeric Repeat Binding Protein 1/genetics
- Time Factors
- Nicotiana/genetics
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Affiliation(s)
- Seong Wook Yang
- Department of Biology, College of Science, Yonsei University, Seoul 120-749, Korea
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15
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Abstract
We identified and characterized a protein (STB-1) from the nuclear extract of Caenorhabditis elegans that specifically binds single-stranded telomere DNA sequences, but not the corresponding RNA sequences. STB-1 binding activity is specific to the nematode telomere, but not to the human or plant telomere. STB-1 requires the core nucleotides of GCTTAGG and three spacer nucleotides in front of them for binding. While any single nucleotide change in the core sequence abolishes binding, the spacer nucleotides tolerate substitution. STB-1 was determined to be a basic protein of 45 kDa by Southwestern analyses. STB-1 forms a stable complex with DNA once bound to the telomere.
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Affiliation(s)
- S Y Yi
- Department of Biology, Yonsei University, 134 Shinchon-dong, Seodaemun-ku, Seoul 120-749, South Korea
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16
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Kato A, Nishi R, Ozaki M. Isolation and characterization of two genes encoding ubiquitin fused to a ribosomal protein of 53 amino acids in rice. DNA Sequence 2001; 12:53-8. [PMID: 11697144 DOI: 10.3109/10425170109042050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We isolated and determined the nucleotide sequences of two genes encoding ubiquitin fused to a ribosomal protein, Ub-CEP52, from rice (Oryza sativa L.). The deduced amino-acid sequences of the two genes were found to be completely identical. The N-terminal region of 76 residues corresponds to ubiquitin, and the C-terminal region of 53 residues corresponds to ribosomal protein L40. A putative TATA-like sequence, a polypyrimidine sequence, and a similar sequence to telo-box were found in the promoter regions of the two genes. Furthermore, the putative tRNA(Pro) gene was found in the 5'-upstream region of one of them.
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MESH Headings
- Amino Acid Sequence
- Artificial Gene Fusion
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Plant/genetics
- Genes, Plant
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oryza/genetics
- Plant Proteins/genetics
- Protein Precursors/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Transfer, Pro/chemistry
- RNA, Transfer, Pro/genetics
- Ribosomal Proteins/genetics
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Ubiquitin/genetics
- Ubiquitins/genetics
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Affiliation(s)
- A Kato
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.
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17
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Abstract
A gene (AtTRP1) encoding a telomeric repeat-binding protein has been isolated from Arabidopsis thaliana. AtTRP1 is a single copy gene located on chromosome 5 of A. thaliana. The protein AtTRP1 encoded by this gene is not only homologous to the Myb DNA-binding motifs of other telomere-binding proteins but also is similar to several initiator-binding proteins in plants. Gel retardation assay revealed that the 115 residues on the C terminus of this protein, including the Myb motif, are sufficient for binding to the double-stranded plant telomeric sequence. The isolated DNA-binding domain of AtTRP1 recognizes each telomeric repeat centered on the sequence GGTTTAG. The almost full-length protein of AtTRP1 does not form any complex at all with the DNA fragments carrying four or fewer GGTTTAG repeats. However, it forms a complex with the sequence (GGTTTAG)(8) more efficiently than with the sequence (GGTTTAG)(5). These data suggest that the minimum length of a telomeric DNA for AtTRP1 binding consists of five GGTTTAG repeats and that the optimal AtTRP1 binding may require eight or more GGTTTAG repeats. It also implies that this protein AtTRP1 may bind in vivo primarily to the ends of plant chromosomes, which consist of long stretches of telomeric repeats.
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Affiliation(s)
- C M Chen
- Institute of Botany, Academia Sinica, Taipei 115, Taiwan
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18
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Abstract
We have identified a rice gene encoding a DNA-binding protein that specifically recognizes the telomeric repeat sequence TTTAGGG found in plants. This gene, which we refer to as RTBP1 (rice telomere-binding protein 1), encodes a polypeptide with a predicted molecular mass of 70 kDa. RTBP1 is ubiquitously expressed in various organs and binds DNA with two or more duplex TTTAGGG repeats. The predicted protein sequence includes a single domain at the C terminus with extensive homology to Myb-like DNA binding motif. The Myb-like domain of RTBP1 is very closely related to that of other telomere-binding proteins, including TRF1, TRF2, Taz1p, and Tbf1p, indicating that DNA-binding domains of telomere-binding proteins are well conserved among evolutionarily distant species. To obtain precise information on the sequence of the DNA binding site recognized by RTBP1, we analyzed the sequence-specific binding properties of the isolated Myb-like domain of RTBP1. The isolated Myb-like domain was capable of sequence-specific DNA binding as a homodimer. Gel retardation analysis with a series of mutated telomere probes revealed that the internal GGGTTT sequence in the two-telomere repeats is critical for binding of Myb-like domain of RTBP1, which is consistent with the model of the TRF1.DNA complex showing that base-specific contacts are made within the sequence GGGTTA. To the best of our knowledge, RTBP1 is the first cloned gene in which the product is able to bind double-stranded telomeric DNA in plants. Because the Myb-like domain appears to be a significant motif for a large class of proteins that bind the duplex telomeric DNA, RTBP1 may play important roles in plant telomere function in vivo.
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Affiliation(s)
- E Y Yu
- Department of Biology, College of Science, Bioproducts Research Center, Yonsei University, Seoul 120-749, Korea
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19
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Abstract
The activity of telomerase in plant cells is precisely regulated in response to changes in cell division rate. To explore this regulatory mechanism, the effect on telomerase activity of protein extracts from nuclei of telomerase-negative tissues was examined. An inhibition of telomerase activity was found which was species-non-specific. This inhibition was due to proteins which form salt-stable, sequence-specific complexes with the G-rich telomeric strand and reduce its accessibility, as shown by gel retardation and by terminal transferase (TdT) extension of G-rich telomeric and non-telomeric (substrate) primers. A 40 kDa polypeptide was detected by SDS-PAGE after cross-linking the complex formed by extracts from tobacco leaf nuclei. Such proteins may be involved in regulation of telomerase activity in plants.
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Affiliation(s)
- J Fulnecková
- Department of Analysis of Biologically Important Molecular Complexes, Masaryk University Brno, Královopolská 135, CZ-61265, Brno, Czech Republic
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Hemleben V, Zentgraf U, Torres-ruiz RA, Schmidt T. Molecular Cell Biology: Role of Repetitive DNA in Nuclear Architecture and Chromosome Structure. In: Esser K, Kadereit JW, Lüttge U, Runge M, editors. Progress in Botany. Berlin: Springer Berlin Heidelberg; 2000. pp. 91-117. [DOI: 10.1007/978-3-642-57203-6_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
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