1
|
Wu Z, Gu X, Zha L, Yang Q, Zhou Y, Zeng Z. Structural and functional insights into yeast Tbf1 as an atypical telomeric repeat-binding factor. Structure 2024:S0969-2126(24)00128-X. [PMID: 38677290 DOI: 10.1016/j.str.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Telomeric repeat-binding factor 1 (Tbf1) has a similar architecture as the TRF family of telomeric proteins and plays important roles in both telomere homeostasis and ribosome regulation. However, the molecular basis of why Tbf1 has such different functions compared to other TRFs remains unclear. Here, we present the crystal structures of the TRF homology (TRFH) and Myb-L domains from Schizosaccharomyces pombe Tbf1 (spTbf1). TRFH-mediated homodimerization is essential for spTbf1 stability. Importantly, spTbf1TRFH lacks the conserved docking motif for interactions with telomeric proteins, explaining why spTbf1 does not participate in the assembly of the shelterin complex. Finally, structural and biochemical analyses demonstrate that TRFH and Myb-L domains as well as the loop region of spTbf1 coordinate to recognize S. pombe telomeric double-stranded DNA. Overall, our findings provide structural and functional insights into how fungi Tbf1 acts as an atypical telomeric repeat-binding factor, which helps to understand the evolution of TRFH-containing telomeric proteins.
Collapse
Affiliation(s)
- Zhenfang Wu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Xin Gu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Zha
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Qingqiu Yang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yuanze Zhou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Zhixiong Zeng
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Byun MY, Cui LH, Lee H, Kim WT. Telomere association of Oryza sativa telomere repeat-binding factor like 1 and its roles in telomere maintenance and development in rice, Oryza sativa L. BMB Rep 2018. [PMID: 29936933 PMCID: PMC6283022 DOI: 10.5483/bmbrep.2018.51.11.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Telomeres are specialized nucleoprotein complexes that function to protect eukaryotic chromosomes from recombination and erosion. Several telomere binding proteins (TBPs) have been characterized in higher plants, but their detailed in vivo functions at the plant level are largely unknown. In this study, we identified and characterized OsTRFL1 (Oryza sativa Telomere Repeat-binding Factor Like 1) in rice, a monocot model crop. Although OsTRFL1 did not directly bind to telomere repeats (TTTAGGG)4in vitro, it was associated with telomeric sequences in planta. OsTRFL1 interacted with rice TBPs, such as OsTRBF1 and RTBP1, in yeast and plant cells as well as in vitro. Thus, it seems likely that the association of OsTRFL1 with other TBPs enables OsTRFL1 to bind to telomeres indirectly. T-DNA inserted OsTRFL1 knock-out mutant rice plants displayed significantly longer telomeres (6–25 kb) than those (5–12 kb) in wild-type plants, indicating that OsTRFL1 is a negative factor for telomere lengthening. The reduced levels of OsTRFL1 caused serious developmental defects in both vegetative and reproductive organs of rice plants. These results suggest that OsTRFL1 is an essential factor for the proper maintenance of telomeres and normal development of rice.
Collapse
Affiliation(s)
- Mi Young Byun
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea
| | - Li Hua Cui
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea
| | - Woo Taek Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
5
|
Jørgensen MM, Ekundayo B, Zaratiegui M, Skriver K, Thon G, Schalch T. Structure of the replication regulator Sap1 reveals functionally important interfaces. Sci Rep 2018; 8:10930. [PMID: 30026545 PMCID: PMC6053445 DOI: 10.1038/s41598-018-29198-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 01/05/2023] Open
Abstract
The mechanism by which specific protein-DNA complexes induce programmed replication fork stalling in the eukaryotic genome remains poorly understood. In order to shed light on this process we carried out structural investigations on the essential fission yeast protein Sap1. Sap1 was identified as a protein involved in mating-type switching in Schizosaccharomyces pombe, and has been shown to be involved in programmed replication fork stalling. Interestingly, Sap1 assumes two different DNA binding modes. At the mating-type locus dimers of Sap1 bind the SAS1 sequence in a head-to-head arrangement, while they bind to replication fork blocking sites at rDNA and Tf2 transposons in a head-to-tail mode. In this study, we have solved the crystal structure of the Sap1 DNA binding domain and we observe that Sap1 molecules interact in the crystal using a head-to-tail arrangement that is compatible with DNA binding. We find that Sap1 mutations which alleviate replication-fork blockage at Tf2 transposons in CENP-B mutants map to the head-to-tail interface. Furthermore, several other mutations introduced in this interface are found to be lethal. Our data suggests that essential functions of Sap1 depend on its head-to-tail oligomerization.
Collapse
Affiliation(s)
- Maria M Jørgensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Babatunde Ekundayo
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, USA
| | - Karen Skriver
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Geneviève Thon
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Thomas Schalch
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland. .,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK.
| |
Collapse
|
6
|
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.
Collapse
|
7
|
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Mukherjee K, Pandey DM, Vidyarthi AS. In Silico Characterization and Analysis of RTBP1 and NgTRF1 Protein Through MD Simulation and Molecular Docking: A Comparative Study. Interdiscip Sci 2015; 7:275-86. [PMID: 26289405 DOI: 10.1007/s12539-015-0268-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/25/2014] [Accepted: 11/04/2014] [Indexed: 10/23/2022]
Abstract
Gaining access to sequence and structure information of telomere-binding proteins helps in understanding the essential biological processes involve in conserved sequence-specific interaction between DNA and the proteins. Rice telomere-binding protein (RTBP1) and Nicotiana glutinosa telomere repeat binding factor (NgTRF1) are helix-turn-helix motif type of proteins that plays role in telomeric DNA protection and length regulation. Both the proteins share same type of domain, but till now there is very less communication on the in silico studies of these complete proteins. Here we intend to do a comparative study between two proteins through modeling of the complete proteins, physiochemical characterization, MD simulation and DNA-protein docking. I-TASSER and CLC protein work bench was performed to find out the protein 3D structure as well as the different parameters to characterize the proteins. MD simulation was completed by GROMOS forcefield of GROMACS for 10 ns of time stretch. The simulated 3D structures were docked with template DNA (3D DNA modeled through 3D-DART) of TTTAGGG conserved sequence motif using HADDOCK Web server. By digging up all the facts about the proteins, it was revealed that around 120 amino acids in the tail part were showing a good sequence similarity between the proteins. Molecular modeling, sequence characterization and secondary structure prediction also indicate the similarity between the protein's structure and sequence. The result of MD simulation highlights on the RMSD, RMSF, Rg, PCA and energy plots which also conveys the similar type of motional behavior between them. The best complex formation for both the proteins in docking result also indicates for the first interaction site which is mainly the helix3 region of the DNA-binding domain. The overall computational analysis reveals that RTBP1 and NgTRF1 proteins display good amount of similarity in their physicochemical properties, structure, dynamics and binding mode.
Collapse
Affiliation(s)
- Koel Mukherjee
- Bioinformatics Laboratory, Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Dev Mani Pandey
- Bioinformatics Laboratory, Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | | |
Collapse
|
11
|
Mukherjee K, Pandey DM, Vidyarthi AS. In silico characterization and analysis of RTBP1 and NgTRF1 protein through MD simulation and molecular docking - A comparative study. Interdiscip Sci 2015. [PMID: 25663113 DOI: 10.1007/s12539-014-0237-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/25/2014] [Accepted: 11/04/2014] [Indexed: 11/30/2022]
Abstract
Gaining access to sequence and structure information of telomere binding proteins helps in understanding the essential biological processes involve in conserved sequence specific interaction between DNA and the proteins. Rice telomere binding protein (RTBP1) and Nicotiana glutinosa telomere repeat binding factor (NgTRF1) are helix turn helix motif type of proteins that plays role in telomeric DNA protection and length regulation. Both the proteins share same type of domain but till now there is very less communication on the in silico studies of these complete proteins.Here we intend to do a comparative study between two proteins through modeling of the complete proteins, physiochemical characterization, MD simulation and DNA-protein docking. I-TASSER and CLC protein work bench was performed to find out the protein 3D structure as well as the different parameters to characterize the proteins. MD simulation was completed by GROMOS forcefield of GROMACS for 10 ns of time stretch. The simulated 3D structures were docked with template DNA (3D DNA modeled through 3D-DART) of TTTAGGG conserved sequence motif using HADDOCK web server.Digging up all the facts about the proteins it was reveled that around 120 amino acids in the tail part was showing a good sequence similarity between the proteins. Molecular modeling, sequence characterization and secondary structure prediction also indicates the similarity between the protein's structure and sequence. The result of MD simulation highlights on the RMSD, RMSF, Rg, PCA and Energy plots which also conveys the similar type of motional behavior between them. The best complex formation for both the proteins in docking result also indicates for the first interaction site which is mainly the helix3 region of the DNA binding domain. The overall computational analysis reveals that RTBP1 and NgTRF1 proteins display good amount of similarity in their physicochemical properties, structure, dynamics and binding mode.
Collapse
Affiliation(s)
- Koel Mukherjee
- Bioinformatics Laboratory, Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | | | | |
Collapse
|
12
|
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]
|
13
|
Lee JY, Lee HS, Song JY, Jung YJ, Reinbothe S, Park YI, Lee SY, Pai HS. Cell growth defect factor1/chaperone-like protein of POR1 plays a role in stabilization of light-dependent protochlorophyllide oxidoreductase in Nicotiana benthamiana and Arabidopsis. THE PLANT CELL 2013; 25:3944-60. [PMID: 24151298 PMCID: PMC3877821 DOI: 10.1105/tpc.113.111096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 09/11/2013] [Accepted: 09/30/2013] [Indexed: 05/20/2023]
Abstract
Angiosperms require light for chlorophyll biosynthesis because one reaction in the pathway, the reduction of protochlorophyllide (Pchlide) to chlorophyllide, is catalyzed by the light-dependent protochlorophyllide oxidoreductase (POR). Here, we report that Cell growth defect factor1 (Cdf1), renamed here as chaperone-like protein of POR1 (CPP1), an essential protein for chloroplast development, plays a role in the regulation of POR stability and function. Cdf1/CPP1 contains a J-like domain and three transmembrane domains, is localized in the thylakoid and envelope membranes, and interacts with POR isoforms in chloroplasts. CPP1 can stabilize POR proteins with its holdase chaperone activity. CPP1 deficiency results in diminished POR protein accumulation and defective chlorophyll synthesis, leading to photobleaching and growth inhibition of plants under light conditions. CPP1 depletion also causes reduced POR accumulation in etioplasts of dark-grown plants and as a result impairs the formation of prolamellar bodies, which subsequently affects chloroplast biogenesis upon illumination. Furthermore, in cyanobacteria, the CPP1 homolog critically regulates POR accumulation and chlorophyll synthesis under high-light conditions, in which the dark-operative Pchlide oxidoreductase is repressed by its oxygen sensitivity. These findings and the ubiquitous presence of CPP1 in oxygenic photosynthetic organisms suggest the conserved nature of CPP1 function in the regulation of POR.
Collapse
Affiliation(s)
- Jae-Yong Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Ho-Seok Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Ji-Young Song
- Department of Biological Science and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Young Jun Jung
- Division of Applied Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Steffen Reinbothe
- Biologie Environnementale et Systémique, Université Joseph Fourier LBFA, BP53F 38041 Grenoble cedex 9 France
| | - Youn-Il Park
- Department of Biological Science and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| |
Collapse
|
14
|
Mukherjee K, Abhipriya, Vidyarthi AS, Pandey DM. SVM based model generation for binding site prediction on helix turn helix motif type of transcription factors in eukaryotes. Bioinformation 2013; 9:500-5. [PMID: 23861565 PMCID: PMC3705624 DOI: 10.6026/97320630009500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 05/17/2013] [Indexed: 12/02/2022] Open
Abstract
Support vector machine is a class of machine learning algorithms which uses a set of related supervised learning methods
for classification and regression. Nowadays this method is vividly applied to many detection problems related with secondary
structure, tumor cell and binding residue prediction. In this work, support vector machines (SVMs) have been trained on 90
sequences of transcription factors with HTH motif. Four sequence features were used as attribute for the prediction of interaction
site in HTH motif. A web page was also developed so that user can easily enter the protein sequence and receive the output as
interaction site predicted or not predicted. The generated model shows a very high amount of accuracy, sensitivity and specificity
which proves to be a good model for the selected case.
Collapse
Affiliation(s)
- Koel Mukherjee
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi-835 215, Jharkhand, India
| | | | | | | |
Collapse
|
15
|
Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | | |
Collapse
|
16
|
Giraud-Panis MJ, Pisano S, Benarroch-Popivker D, Pei B, Le Du MH, Gilson E. One identity or more for telomeres? Front Oncol 2013; 3:48. [PMID: 23509004 PMCID: PMC3598436 DOI: 10.3389/fonc.2013.00048] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 02/23/2013] [Indexed: 12/19/2022] Open
Abstract
A major issue in telomere research is to understand how the integrity of chromosome ends is controlled. The fact that different types of nucleoprotein complexes have been described at the telomeres of different organisms raises the question of whether they have in common a structural identity that explains their role in chromosome protection. We will review here how telomeric nucleoprotein complexes are structured, comparing different organisms and trying to link these structures to telomere biology. It emerges that telomeres are formed by a complex and specific network of interactions between DNA, RNA, and proteins. The fact that these interactions and associated activities are reinforcing each other might help to guarantee the robustness of telomeric functions across the cell cycle and in the event of cellular perturbations. We will also discuss the recent notion that telomeres have evolved specific systems to overcome the DNA topological stress generated during their replication and transcription. This will lead to revisit the way we envisage the functioning of telomeric complexes since the regulation of topology is central to DNA stability, replication, recombination, and transcription as well as to chromosome higher-order organization.
Collapse
Affiliation(s)
- Marie-Josèphe Giraud-Panis
- Faculté de Médecine de Nice, Université de Nice-Sophia Antipolis, Institute for Research on Cancer and Aging Nice, UMR 7284 CNRS, U1081 INSERM Nice, France
| | | | | | | | | | | |
Collapse
|
17
|
Lee WK, Yun JH, Lee W, Cho MH. DNA-binding domain of AtTRB2 reveals unique features of a single Myb histone protein family that binds to both Arabidopsis- and human-type telomeric DNA sequences. MOLECULAR PLANT 2012; 5:1406-1408. [PMID: 22859734 DOI: 10.1093/mp/sss063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
|
18
|
Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
|
19
|
Wei SY, Lou YC, Tsai JY, Ho MR, Chou CC, Rajasekaran M, Hsu HM, Tai JH, Hsiao CD, Chen C. Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal β-hairpin conformation. Nucleic Acids Res 2011; 40:449-60. [PMID: 21908401 PMCID: PMC3245928 DOI: 10.1093/nar/gkr707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Trichomonas vaginalis Myb3 transcription factor (tvMyb3) recognizes the MRE-1 promoter sequence and regulates ap65-1 gene, which encodes a hydrogenosomal malic enzyme that may play a role in the cytoadherence of the parasite. Here, we identified tvMyb353–180 as the essential fragment for DNA recognition and report the crystal structure of tvMyb353–180 bound to MRE-1 DNA. The N-terminal fragment adopts the classical conformation of an Myb DNA-binding domain, with the third helices of R2 and R3 motifs intercalating in the major groove of DNA. The C-terminal extension forms a β-hairpin followed by a flexible tail, which is stabilized by several interactions with the R3 motif and is not observed in other Myb proteins. Interestingly, this unique C-terminal fragment does not stably connect with DNA in the complex structure but is involved in DNA binding, as demonstrated by NMR chemical shift perturbation, 1H-15N heteronuclear-nuclear Overhauser effect and intermolecular paramagnetic relaxation enhancement. Site-directed mutagenesis also revealed that this C-terminal fragment is crucial for DNA binding, especially the residue Arg153 and the fragment K170KRK173. We provide a structural basis for MRE-1 DNA recognition and suggest a possible post-translational regulation of tvMyb3 protein.
Collapse
Affiliation(s)
- Shu-Yi Wei
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
Telomeres are essential structures at the ends of eukaryotic chromosomes. Work on their structure and function began almost 70 years ago in plants and flies, continued through the Nobel Prize winning work on yeast and ciliates, and goes on today in many model and non-model organisms. The basic molecular mechanisms of telomeres are highly conserved throughout evolution, and our current understanding of how telomeres function is a conglomeration of insights gained from many different species. This review will compare the current knowledge of telomeres in plants with other organisms, with special focus on the functional length of telomeric DNA, the search for TRF homologs, the family of POT1 proteins, and the recent discovery of members of the CST complex.
Collapse
Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | | |
Collapse
|
21
|
Giraud-Panis MJ, Pisano S, Poulet A, Le Du MH, Gilson E. Structural identity of telomeric complexes. FEBS Lett 2010; 584:3785-99. [PMID: 20696167 DOI: 10.1016/j.febslet.2010.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/02/2010] [Accepted: 08/02/2010] [Indexed: 02/01/2023]
Abstract
A major issue in telomere research is to understand how the integrity of chromosome ends is controlled. Although several nucleoprotein complexes have been described at the telomeres of different organisms, it is still unclear how they confer a structural identity to chromosome ends in order to mask them from DNA repair and to ensure their proper replication. In this review, we describe how telomeric nucleoprotein complexes are structured, comparing different organisms and trying to link these structures to telomere biology. It emerges that telomeres are formed by a complex and specific network of interactions between DNA, RNA and proteins. The fact that these interactions and associated activities are reinforcing each other might help to guaranty the robustness of telomeric functions across the cell cycle and in the event of cellular perturbations. We propose that telomeric nucleoprotein complexes orient cell fate through dynamic transitions in their structures and their organization.
Collapse
Affiliation(s)
- Marie-Josèphe Giraud-Panis
- University de Nice, Laboratory of Biology and Pathology of Genomes, UMR 6267 CNRS U998 INSERM, Faculté de Médecine, Nice, France
| | | | | | | | | |
Collapse
|
22
|
Watson JM, Riha K. Comparative biology of telomeres: where plants stand. FEBS Lett 2010; 584:3752-9. [PMID: 20580356 PMCID: PMC3767043 DOI: 10.1016/j.febslet.2010.06.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/11/2010] [Accepted: 06/14/2010] [Indexed: 01/02/2023]
Abstract
Telomeres are essential structures at the ends of eukaryotic chromosomes. Work on their structure and function began almost 70 years ago in plants and flies, continued through the Nobel Prize winning work on yeast and ciliates, and goes on today in many model and non-model organisms. The basic molecular mechanisms of telomeres are highly conserved throughout evolution, and our current understanding of how telomeres function is a conglomeration of insights gained from many different species. This review will compare the current knowledge of telomeres in plants with other organisms, with special focus on the functional length of telomeric DNA, the search for TRF homologs, the family of POT1 proteins, and the recent discovery of members of the CST complex.
Collapse
Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | | |
Collapse
|
23
|
Ko S, Yu EY, Shin J, Yoo HH, Tanaka T, Kim WT, Cho HS, Lee W, Chung IK. Solution Structure of the DNA Binding Domain of Rice Telomere Binding Protein RTBP1,. Biochemistry 2009; 48:827-38. [DOI: 10.1021/bi801270g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunggeon Ko
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Eun Young Yu
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Joon Shin
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hyun Hee Yoo
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Toshiyuki Tanaka
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Woo Taek Kim
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hyun-Soo Cho
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Weontae Lee
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - In Kwon Chung
- Departments of Biochemistry and Biology, Protein Network Research Center, Yonsei University, Seoul 120-749, Korea, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| |
Collapse
|
24
|
Identification and characterization of three telomere repeat-binding factors in rice. Biochem Biophys Res Commun 2008; 372:85-90. [PMID: 18477473 DOI: 10.1016/j.bbrc.2008.04.181] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 04/29/2008] [Indexed: 12/16/2022]
Abstract
Telomeres consist of nucleoprotein complexes that protect chromosome end structures. Here, we describe three OsTRBF genes, encoding telomere repeat-binding factors of the single Myb histone family in rice. The predicted proteins contain a Myb DNA-binding motif and a linker histone H1/H5 domain in the N-terminal and central regions, respectively. The OsTRBF transcripts were constitutively detected in rice plants grown under greenhouse conditions. Gel retardation assays showed that these OsTRBF proteins bind specifically to the plant double-stranded telomeric sequence, TTTAGGG, with markedly different binding affinities as judged by their respective dissociation constants. Yeast two-hybrid and in vitro pull-down assays indicated that both OsTRBF1 and OsTRBF2 interact with one another to form homo- and hetero-complexes, while OsTRBF3 appeared to act as a monomer. Our results suggest that OsTRBFs play combinatory roles in the function and structure of telomeres in rice.
Collapse
|