1
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Rubtsova M, Dontsova O. How Structural Features Define Biogenesis and Function of Human Telomerase RNA Primary Transcript. Biomedicines 2022; 10:biomedicines10071650. [PMID: 35884955 PMCID: PMC9313293 DOI: 10.3390/biomedicines10071650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
Telomerase RNA has been uncovered as a component of the telomerase enzyme, which acts as a reverse transcriptase and maintains the length of telomeres in proliferated eukaryotic cells. Telomerase RNA is considered to have major functions as a template for telomeric repeat synthesis and as a structural scaffold for telomerase. However, investigations of its biogenesis and turnover, as well as structural data, have provided evidence of functions of telomerase RNA that are not associated with telomerase activity. The primary transcript produced from the human telomerase RNA gene encodes for the hTERP protein, which presents regulatory functions related to autophagy, cellular proliferation, and metabolism. This review focuses on the specific features relating to the biogenesis and structure of human telomerase RNA that support the existence of an isoform suitable for functioning as an mRNA. We believe that further investigation into human telomerase RNA biogenesis mechanisms will provide more levels for manipulating cellular homeostasis, survival, and transformation mechanisms, and may contribute to a deeper understanding of the mechanisms of aging.
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Affiliation(s)
- Maria Rubtsova
- Department of Chemistry, A.N. Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence:
| | - Olga Dontsova
- Department of Chemistry, A.N. Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
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2
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Palka C, Forino NM, Hentschel J, Das R, Stone MD. Folding heterogeneity in the essential human telomerase RNA three-way junction. RNA (NEW YORK, N.Y.) 2020; 26:1787-1800. [PMID: 32817241 PMCID: PMC7668248 DOI: 10.1261/rna.077255.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Telomeres safeguard the genome by suppressing illicit DNA damage responses at chromosome termini. To compensate for incomplete DNA replication at telomeres, most continually dividing cells, including many cancers, express the telomerase ribonucleoprotein (RNP) complex. Telomerase maintains telomere length by catalyzing de novo synthesis of short DNA repeats using an internal telomerase RNA (TR) template. TRs from diverse species harbor structurally conserved domains that contribute to RNP biogenesis and function. In vertebrate TRs, the conserved regions 4 and 5 (CR4/5) fold into a three-way junction (TWJ) that binds directly to the telomerase catalytic protein subunit and is required for telomerase function. We have analyzed the structural properties of the human TR (hTR) CR4/5 domain using a combination of in vitro chemical mapping, secondary structural modeling, and single-molecule structural analysis. Our data suggest the essential P6.1 stem-loop within CR4/5 is not stably folded in the absence of the telomerase reverse transcriptase in vitro. Rather, the hTR CR4/5 domain adopts a heterogeneous ensemble of conformations. Finally, single-molecule FRET measurements of CR4/5 and a mutant designed to stabilize the P6.1 stem demonstrate that TERT binding selects for a structural conformation of CR4/5 that is not the dominant state of the TERT-free in vitro RNA ensemble.
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Affiliation(s)
- Christina Palka
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Nicholas M Forino
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | - Jendrik Hentschel
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, California 94305, USA
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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3
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Wang Y, Sušac L, Feigon J. Structural Biology of Telomerase. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032383. [PMID: 31451513 DOI: 10.1101/cshperspect.a032383] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Telomerase is a DNA polymerase that extends the 3' ends of chromosomes by processively synthesizing multiple telomeric repeats. It is a unique ribonucleoprotein (RNP) containing a specialized telomerase reverse transcriptase (TERT) and telomerase RNA (TER) with its own template and other elements required with TERT for activity (catalytic core), as well as species-specific TER-binding proteins important for biogenesis and assembly (core RNP); other proteins bind telomerase transiently or constitutively to allow association of telomerase and other proteins with telomere ends for regulation of DNA synthesis. Here we describe how nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography of TER and protein domains helped define the structure and function of the core RNP, laying the groundwork for interpreting negative-stain and cryo electron microscopy (cryo-EM) density maps of Tetrahymena thermophila and human telomerase holoenzymes. As the resolution has improved from ∼30 Å to ∼5 Å, these studies have provided increasingly detailed information on telomerase architecture and mechanism.
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Affiliation(s)
- Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Los Angeles, California 90095-1569
| | - Lukas Sušac
- Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Los Angeles, California 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Los Angeles, California 90095-1569
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4
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Lessons learned from a lncRNA odyssey for two genes with vascular functions, DLL4 and TIE1. Vascul Pharmacol 2019; 114:103-109. [PMID: 30910126 DOI: 10.1016/j.vph.2018.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/24/2018] [Accepted: 06/13/2018] [Indexed: 01/30/2023]
Abstract
Pervasive transcription is a feature of the human genome that requires better understanding. Over the last decade or so, RNA species longer than 200 nucleotides-dubbed long non-coding RNA (lncRNAs)-had been found in sense or anti-sense orientation within or outside of genes that encode proteins. Importantly, lncRNA-mediated gene regulation and the elements that control lncRNA expression are a source of fascination among molecular biologists. In vascular biology, a dozen or so lncRNAs had been identified, and progress occurs each day. In this review, we highlighted our laboratories' contribution to the lncRNA field by discussing lessons learned from two lncRNAs in the tyrosine kinase containing immunoglobulin and epidermal growth factor homology1 (Tie1) and delta-like 4 (Dll4) loci. These genes are responsible for basic vascular patterning and pathophysiological remodeling in angiogenesis.
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5
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An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. Cell 2018; 174:218-230.e13. [PMID: 29804836 DOI: 10.1016/j.cell.2018.04.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/22/2018] [Accepted: 04/27/2018] [Indexed: 12/24/2022]
Abstract
Ribonucleoprotein enzymes require dynamic conformations of their RNA constituents for regulated catalysis. Human telomerase employs a non-coding RNA (hTR) with a bipartite arrangement of domains-a template-containing core and a distal three-way junction (CR4/5) that stimulates catalysis through unknown means. Here, we show that telomerase activity unexpectedly depends upon the holoenzyme protein TCAB1, which in turn controls conformation of CR4/5. Cells lacking TCAB1 exhibit a marked reduction in telomerase catalysis without affecting enzyme assembly. Instead, TCAB1 inactivation causes unfolding of CR4/5 helices that are required for catalysis and for association with the telomerase reverse-transcriptase (TERT). CR4/5 mutations derived from patients with telomere biology disorders provoke defects in catalysis and TERT binding similar to TCAB1 inactivation. These findings reveal a conformational "activity switch" in human telomerase RNA controlling catalysis and TERT engagement. The identification of two discrete catalytic states for telomerase suggests an intramolecular means for controlling telomerase in cancers and progenitor cells.
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6
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Martin WJ, Reiter NJ. Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes. Biochemistry 2016; 56:3-13. [PMID: 27935277 DOI: 10.1021/acs.biochem.6b01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Over billions of years of evolution, nature has embraced proteins as the major workhorse molecules of the cell. However, nearly every aspect of metabolism is dependent upon how structured RNAs interact with proteins, ligands, and other nucleic acids. Key processes, including telomere maintenance, RNA processing, and protein synthesis, require large RNAs that assemble into elaborate three-dimensional shapes. These RNAs can (i) act as flexible scaffolds for protein subunits, (ii) participate directly in substrate recognition, and (iii) serve as catalytic components. Here, we juxtapose the near atomic level interactions of three ribonucleoprotein complexes: ribonuclease P (involved in 5' pre-tRNA processing), the spliceosome (responsible for pre-mRNA splicing), and telomerase (an RNA-directed DNA polymerase that extends the ends of chromosomes). The focus of this perspective is profiling the structural and dynamic roles of RNAs at the core of these enzymes, highlighting how large RNAs contribute to molecular recognition and catalysis.
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Affiliation(s)
- William J Martin
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Nicholas J Reiter
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
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7
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Cash DD, Feigon J. Structure and folding of the Tetrahymena telomerase RNA pseudoknot. Nucleic Acids Res 2016; 45:482-495. [PMID: 27899638 PMCID: PMC5224487 DOI: 10.1093/nar/gkw1153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/26/2016] [Accepted: 11/03/2016] [Indexed: 12/21/2022] Open
Abstract
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot. Here, we describe in detail the structure and folding of the isolated pseudoknot, which forms a compact structure with major groove U•A-U and novel C•G-A+ base triples. Base substitutions that disrupt the base triples reduce telomerase activity in vitro. NMR studies also reveal that the pseudoknot does not form in the context of full-length TER in the absence of TERT, due to formation of a competing structure that sequesters pseudoknot residues. The residues around the TBE remain unpaired, potentially providing access by TERT to this high affinity binding site during an early step in TERT-TER assembly. A model for the assembly pathway of the catalytic core is proposed.
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Affiliation(s)
- Darian D Cash
- Department of Chemistry and Biochemistry, and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
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8
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Zemora G, Handl S, Waldsich C. Human telomerase reverse transcriptase binds to a pre-organized hTR in vivo exposing its template. Nucleic Acids Res 2015; 44:413-25. [PMID: 26481359 PMCID: PMC4705647 DOI: 10.1093/nar/gkv1065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/05/2015] [Indexed: 01/08/2023] Open
Abstract
Telomerase is a specialized reverse transcriptase that is responsible for telomere length maintenance. As in other organisms, the minimal components required for an active human telomerase are the template-providing telomerase RNA (hTR) and the enzymatic entity telomerase reverse transcriptase (hTERT). Here, we explored the structure of hTR and the hTERT-induced conformational changes within hTR in living cells. By employing an in vivo DMS chemical probing technique, we showed that the pseudoknot and associated triple helical scaffold form stably in vivo independently of hTERT. In fact, the dimethyl-sulfate (DMS) modification pattern suggests that hTR alone is capable of adopting a conformation that is suited to interact with hTERT. However, in the absence of hTERT the template region of hTR is only weakly accessible to DMS-modifications. The predominant change after binding of hTERT to hTR is the exposure of the template region.
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Affiliation(s)
- Georgeta Zemora
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria
| | - Stefan Handl
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria
| | - Christina Waldsich
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria
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9
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Blythe AJ, Fox AH, Bond CS. The ins and outs of lncRNA structure: How, why and what comes next? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:46-58. [PMID: 26325022 DOI: 10.1016/j.bbagrm.2015.08.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 12/20/2022]
Abstract
The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Amanda J Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Archa H Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
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10
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Niederer RO, Zappulla DC. Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE. RNA (NEW YORK, N.Y.) 2015; 21:254-261. [PMID: 25512567 PMCID: PMC4338352 DOI: 10.1261/rna.048959.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Telomerase catalyzes the addition of nucleotides to the ends of chromosomes to complete genomic DNA replication in eukaryotes and is implicated in multiple diseases, including most cancers. The core enzyme is composed of a reverse transcriptase and an RNA subunit, which provides the template for DNA synthesis. Despite extensive divergence at the sequence level, telomerase RNAs share several structural features within the catalytic core, suggesting a conserved enzyme mechanism. We have investigated the structure of the core of the human and yeast telomerase RNAs using SHAPE, which interrogates flexibility of each nucleotide. We present improved secondary-structure models, refined by addition of five base triples within the yeast pseudoknot and an alternate pairing within the human-specific element J2a.1 in the human pseudoknot, both of which have implications for thermodynamic stability. We also identified a potentially structured CCC region within the template that may facilitate substrate binding and enzyme mechanism. Overall, the SHAPE findings reveal multiple similarities between the Saccharomyces cerevisiae and Homo sapiens telomerase RNA cores.
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Affiliation(s)
- Rachel O Niederer
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David C Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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11
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Eichhorn CD, Al-Hashimi HM. Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA (NEW YORK, N.Y.) 2014; 20:782-91. [PMID: 24742933 PMCID: PMC4024633 DOI: 10.1261/rna.043711.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3' end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, (13)C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A6-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA-helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition.
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Affiliation(s)
- Catherine D. Eichhorn
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Corresponding authorE-mail
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12
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Progress in structural studies of telomerase. Curr Opin Struct Biol 2014; 24:115-24. [PMID: 24508601 DOI: 10.1016/j.sbi.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/01/2014] [Accepted: 01/08/2014] [Indexed: 02/01/2023]
Abstract
Telomerase is the ribonucleoprotein (RNP) reverse transcriptase responsible for synthesizing the 3' ends of linear chromosomes. It plays critical roles in tumorigenesis, cellular aging, and stem cell renewal. The past two years have seen exciting progress in determining telomerase holoenzyme architecture and the structural basis of telomerase activity. Notably, the first electron microscopy structures of telomerase were reported, of the Tetrahymena thermophila telomerase holoenzyme and a human telomerase dimer. In addition to new structures of TERT and TER domains, the first structures of telomerase protein domains beyond TERT, and their complexes with TER or telomeric single-stranded DNA, were reported. Together these studies provide the first glimpse into the organization of the proteins and RNA in the telomerase RNP.
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13
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Kim NK, Zhang Q, Feigon J. Structure and sequence elements of the CR4/5 domain of medaka telomerase RNA important for telomerase function. Nucleic Acids Res 2013; 42:3395-408. [PMID: 24335084 PMCID: PMC3950677 DOI: 10.1093/nar/gkt1276] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Telomerase is a unique reverse transcriptase that maintains the 3' ends of eukaryotic chromosomes by adding tandem telomeric repeats. The RNA subunit (TR) of vertebrate telomerase provides a template for reverse transcription, contained within the conserved template/pseudoknot domain, and a conserved regions 4 and 5 (CR4/5) domain, all essential for catalytic activity. We report the nuclear magnetic resonance (NMR) solution structure of the full-length CR4/5 domain from the teleost fish medaka (Oryzias latipes). Three helices emanate from a structured internal loop, forming a Y-shaped structure, where helix P6 stacks on P5 and helix P6.1 points away from P6. The relative orientations of the three helices are Mg2+ dependent and dynamic. Although the three-way junction is structured and has unexpected base pairs, telomerase activity assays with nucleotide substitutions and deletions in CR4/5 indicate that none of these are essential for activity. The results suggest that the junction is likely to change conformation in complex with telomerase reverse transcriptase and that it provides a flexible scaffold that allows P6 and P6.1 to correctly fold and interact with telomerase reverse transcriptase.
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Affiliation(s)
- Nak-Kyoon Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 136-791, Republic of Korea and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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14
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Sekaran V, Soares J, Jarstfer MB. Telomere Maintenance as a Target for Drug Discovery. J Med Chem 2013; 57:521-38. [DOI: 10.1021/jm400528t] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vijay Sekaran
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joana Soares
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael B. Jarstfer
- Division of Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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15
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Rubtsova M, Vasilkova D, Malyavko A, Naraikina Y, Zvereva M, Dontsova O. Telomere lengthening and other functions of telomerase. Acta Naturae 2012; 4:44-61. [PMID: 22872811 PMCID: PMC3408703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Telomerase is an enzyme that maintains the length of the telomere. The telomere length specifies the number of divisions a cell can undergo before it finally dies (i.e. the proliferative potential of cells). For example, telomerase is activated in embryonic cell lines and the telomere length is maintained at a constant level; therefore, these cells have an unlimited fission potential. Stem cells are characterized by a lower telomerase activity, which enables only partial compensation for the shortening of telomeres. Somatic cells are usually characterized by the absence of telomerase activity. Telomere shortening leads to the attainment of the Hayflick limit, the transition of cells to a state of senescence. The cells subsequently enter a state of crisis, accompanied by massive cell death. The surviving cells become cancer cells, which are capable both of dividing indefinitely and maintaining telomere length (usually with the aid of telomerase). Telomerase is a reverse transcriptase. It consists of two major components: telomerase RNA (TER) and reverse transcriptase (TERT). TER is a non-coding RNA, and it contains the region which serves as a template for telomere synthesis. An increasing number of articles focussing on the alternative functions of telomerase components have recently started appearing. The present review summarizes data on the structure, biogenesis, and functions of telomerase.
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Affiliation(s)
- M.P. Rubtsova
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
| | | | - A.N. Malyavko
- Lomonosov Moscow State University, Chemistry Department
| | - Yu.V. Naraikina
- Lomonosov Moscow State University, Faculty of Bioengineering and
Bioinformatics
| | - M.I. Zvereva
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
| | - O.A. Dontsova
- Lomonosov Moscow State University, Chemistry Department
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State
University
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16
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Abstract
Telomerase is a specialized reverse transcriptase containing an intrinsic telomerase RNA (TR) which provides the template for telomeric DNA synthesis. Distinct from conventional reverse transcriptases, telomerase has evolved a unique TR-binding domain (TRBD) in the catalytic telomerase reverse transcriptase (TERT) protein, integral for ribonucleoprotein assembly. Two structural elements in the vertebrate TR, the pseudoknot and CR4/5, bind TERT independently and are essential for telomerase enzymatic activity. However, the details of the TR-TERT interaction have remained elusive. In this study, we employed a photoaffinity cross-linking approach to map the CR4/5-TRBD RNA-protein binding interface by identifying RNA and protein residues in close proximity. Photoreactive 5-iodouridines were incorporated into the medaka CR4/5 RNA fragment and UV cross-linked to the medaka TRBD protein fragment. The cross-linking RNA residues were identified by alkaline partial hydrolysis and cross-linked protein residues were identified by mass spectrometry. Three CR4/5 RNA residues (U182, U187, and U205) were found cross-linking to TRBD amino acids Tyr503, Phe355, and Trp477, respectively. This CR4/5 binding pocket is distinct and separate from the previously proposed T pocket in the Tetrahymena TRBD. Based on homologous structural models, our cross-linking data position the essential loop L6.1 adjacent to the TERT C-terminal extension domain. We thus propose that stem-loop 6.1 facilitates proper TERT folding by interacting with both TRBD and C-terminal extension. Revealing the telomerase CR4/5-TRBD binding interface with single-residue resolution provides important insights into telomerase ribonucleoprotein architecture and the function of the essential CR4/5 domain.
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17
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Hengesbach M, Akiyama BM, Stone MD. Single-molecule analysis of telomerase structure and function. Curr Opin Chem Biol 2011; 15:845-52. [PMID: 22057212 DOI: 10.1016/j.cbpa.2011.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/05/2011] [Accepted: 10/17/2011] [Indexed: 02/06/2023]
Abstract
The telomerase ribonucleoprotein is a specialized reverse transcriptase required to maintain protective chromosome end-capping structures called telomeres. In most cells, telomerase is not active and the natural shortening of telomeres with each round of DNA replication ultimately triggers cell growth arrest. In contrast, the presence of telomerase confers a high level of renewal capacity upon rapidly dividing cells. Telomerase is aberrantly activated in 90% of human cancers and thus represents an important target for anticancer therapeutics. However, the naturally low abundance of telomerase has hampered efforts to obtain high-resolution models for telomerase structure and function. To circumvent these challenges, single-molecule techniques have recently been employed to investigate telomerase assembly, structure, and catalysis.
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Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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18
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Zvereva MI, Shcherbakova DM, Dontsova OA. Telomerase: structure, functions, and activity regulation. BIOCHEMISTRY (MOSCOW) 2011; 75:1563-83. [PMID: 21417995 DOI: 10.1134/s0006297910130055] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Telomerase is the enzyme responsible for maintenance of the length of telomeres by addition of guanine-rich repetitive sequences. Telomerase activity is exhibited in gametes and stem and tumor cells. In human somatic cells proliferation potential is strictly limited and senescence follows approximately 50-70 cell divisions. In most tumor cells, on the contrary, replication potential is unlimited. The key role in this process of the system of the telomere length maintenance with involvement of telomerase is still poorly studied. No doubt, DNA polymerase is not capable to completely copy DNA at the very ends of chromosomes; therefore, approximately 50 nucleotides are lost during each cell cycle, which results in gradual telomere length shortening. Critically short telomeres cause senescence, following crisis, and cell death. However, in tumor cells the system of telomere length maintenance is activated. Besides catalytic telomere elongation, independent telomerase functions can be also involved in cell cycle regulation. Inhibition of the telomerase catalytic function and resulting cessation of telomere length maintenance will help in restriction of tumor cell replication potential. On the other hand, formation of temporarily active enzyme via its intracellular activation or due to stimulation of expression of telomerase components will result in telomerase activation and telomere elongation that can be used for correction of degenerative changes. Data on telomerase structure and function are summarized in this review, and they are compared for evolutionarily remote organisms. Problems of telomerase activity measurement and modulation by enzyme inhibitors or activators are considered as well.
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Affiliation(s)
- M I Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, Russia.
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19
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Abstract
Telomerase is a unique reverse transcriptase that catalyzes the addition of telomere DNA repeats onto the 3' ends of linear chromosomes and plays a critical role in maintaining genome stability. Unlike other reverse transcriptases, telomerase is unique in that it is a ribonucleoprotein complex, where the RNA component [telomerase RNA (TR)] not only provides the template for the synthesis of telomere DNA repeats but also plays essential roles in catalysis, accumulation, TR 3'-end processing, localization, and holoenzyme assembly. Biochemical studies have identified TR elements essential for catalysis that share remarkably conserved secondary structures across different species as well as species-specific domains for other functions, paving the way for high-resolution structure determination of TRs. Over the past decade, structures of key elements from the core, conserved regions 4 and 5, and small Cajal body specific RNA domains of human TR have emerged, providing significant insights into the roles of these RNA elements in telomerase function. Structures of all helical elements of the core domain have been recently reported, providing the basis for a high-resolution model of the complete core domain. We review this progress to determine the overall architecture of human telomerase RNA.
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Abstract
Ribonucleoproteins (RNPs) play key roles in many cellular processes and often function as RNP enzymes. Similar to proteins, some of these RNPs exist and function as multimers, either homomeric or heteromeric. While in some cases the mechanistic function of multimerization is well understood, the functional consequences of multimerization of other RNPs remain enigmatic. In this review we will discuss the function and organization of small RNPs that exist as stable multimers, including RNPs catalyzing RNA chemical modifications, telomerase RNP, and RNPs involved in pre-mRNA splicing.
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21
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Sekaran VG, Soares J, Jarstfer MB. Structures of telomerase subunits provide functional insights. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1190-201. [PMID: 19665593 DOI: 10.1016/j.bbapap.2009.07.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/09/2009] [Accepted: 07/28/2009] [Indexed: 01/14/2023]
Abstract
BACKGROUND Telomerase continues to generate substantial attention both because of its pivotal roles in cellular proliferation and aging and because of its unusual structure and mechanism. By replenishing telomeric DNA lost during the cell cycle, telomerase overcomes one of the many hurdles facing cellular immortalization. Functionally, telomerase is a reverse transcriptase, and it shares structural and mechanistic features with this class of nucleotide polymerases. Telomerase is a very unusual reverse transcriptase because it remains stably associated with its template and because it reverse transcribes multiple copies of its template onto a single primer in one reaction cycle. SCOPE OF REVIEW Here, we review recent findings that illuminate our understanding of telomerase. Even though the specific emphasis is on structure and mechanism, we also highlight new insights into the roles of telomerase in human biology. GENERAL SIGNIFICANCE Recent advances in the structural biology of telomerase, including high resolution structures of the catalytic subunit of a beetle telomerase and two domains of a ciliate telomerase catalytic subunit, provide new perspectives into telomerase biochemistry and reveal new puzzles.
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Affiliation(s)
- Vijay G Sekaran
- Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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22
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Zheng S, Chen Y, Donahue CP, Wolfe MS, Varani G. Structural basis for stabilization of the tau pre-mRNA splicing regulatory element by novantrone (mitoxantrone). ACTA ACUST UNITED AC 2009; 16:557-66. [PMID: 19477420 DOI: 10.1016/j.chembiol.2009.03.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/20/2009] [Accepted: 03/11/2009] [Indexed: 10/20/2022]
Abstract
Some familial neurodegenerative diseases are associated with mutations that destabilize a putative stem-loop structure within an intronic region of the tau pre-messenger RNA (mRNA) and alter the production of tau protein isoforms by alternative splicing. Because stabilization of the stem loop reverses the splicing pattern associated with neurodegeneration, small molecules that stabilize this stem loop would provide new ways to dissect the mechanism of neurodegeneration and treat tauopathies. The anticancer drug mitoxantrone was recently identified in a high throughput screen to stabilize the tau pre-mRNA stem loop. Here we report the solution structure of the tau mRNA-mitoxantrone complex, validated by the structure-activity relationship of existing mitoxantrone analogs. The structure describes the molecular basis for their interaction with RNA and provides a rational basis to optimize the activity of this new class of RNA-binding molecules.
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Affiliation(s)
- Suxin Zheng
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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23
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Abraham M, Dror O, Nussinov R, Wolfson HJ. Analysis and classification of RNA tertiary structures. RNA (NEW YORK, N.Y.) 2008; 14:2274-89. [PMID: 18824509 PMCID: PMC2578864 DOI: 10.1261/rna.853208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 07/05/2008] [Indexed: 05/19/2023]
Abstract
There is a fast growing interest in noncoding RNA transcripts. These transcripts are not translated into proteins, but play essential roles in many cellular and pathological processes. Recent efforts toward comprehension of their function has led to a substantial increase in both the number and the size of solved RNA structures. With the aim of addressing questions relating to RNA structural diversity, we examined RNA conservation at three structural levels: primary, secondary, and tertiary structure. Additionally, we developed an automated method for classifying RNA structures based on spatial (three-dimensional [3D]) similarity. Applying the method to all solved RNA structures resulted in a classified database of RNA tertiary structures (DARTS). DARTS embodies 1333 solved RNA structures classified into 94 clusters. The classification is hierarchical, reflecting the structural relationship between and within clusters. We also developed an application for searching DARTS with a new structure. The search is fast and its performance was successfully tested on all solved RNA structures since the creation of DARTS. A user-friendly interface for both the database and the search application is available online. We show intracluster and intercluster similarities in DARTS and demonstrate the usefulness of the search application. The analysis reveals the current structural repertoire of RNA and exposes common global folds and local tertiary motifs. Further study of these conserved substructures may suggest possible RNA domains and building blocks. This should be beneficial for structure prediction and for gaining insights into structure-function relationships.
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Affiliation(s)
- Mira Abraham
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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24
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Cevec M, Thibaudeau C, Plavec J. Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucleic Acids Res 2008; 36:2330-7. [PMID: 18296482 PMCID: PMC2367737 DOI: 10.1093/nar/gkn088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Let-7 microRNA (miRNA) regulates heterochronic genes in developmental timing of the nematode Caenorhabditis elegans. Binding of miRNA to messenger RNA (mRNA) and structural features of the complex are crucial for gene silencing. We herein present the NMR solution structure of a model mimicking the interaction of let-7 miRNA with its complementary site (LCS 2) in the 3' untranslated region (3'-UTR) of the lin-41 mRNA. A structural study was performed by NMR spectroscopy using NOE restraints, torsion angle restraints and residual dipolar couplings. The 33-nt RNA construct folds into a stem-loop structure that features two stem regions which are separated by an asymmetric internal loop. One of the stems comprises a GU wobble base pair, which does not alter its overall A-form RNA conformation. The asymmetric internal loop adopts a single, well-defined structure in which three uracils form a base triple, while two adenines form a base pair. The 3D structure of the construct gives insight into the structural aspects of interactions between let-7 miRNA and lin-41 mRNA.
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Affiliation(s)
- Mirko Cevec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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25
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Abstract
Telomerase is a ribonucleoprotein enzyme that extends DNA at the chromosome ends in most eukaryotes. Since 1985, telomerase has been studied intensively and components of the telomerase complex have been identified from over 160 eukaryotic species. In the last two decades, there has been a growing interest in studying telomerase owing to its vital role in chromosome stability and cellular immortality. To keep up with the remarkable explosion of knowledge about telomerase, we compiled information related to telomerase in an exhaustive database called the Telomerase Database (http://telomerase.asu.edu/). The Telomerase Database provides comprehensive information about (i) sequences of the RNA and protein subunits of telomerase, (ii) sequence alignments based on the phylogenetic relationship and structure, (iii) secondary structures of the RNA component and tertiary structures of various subunits of telomerase, (iv) mutations of telomerase components found in human patients and (v) active researchers who contributed to the wealth of current knowledge on telomerase. The information is hierarchically organized by the components, i.e. the telomerase reverse transcriptase (TERT), telomerase RNA (TR) and other telomerase-associated proteins. The Telomerase Database is a useful resource especially for researchers who are interested in investigating the structure, function, evolution and medical relevance of the telomerase enzyme.
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Affiliation(s)
- Joshua D Podlevsky
- School of Life Sciences and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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26
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Brown Y, Abraham M, Pearl S, Kabaha MM, Elboher E, Tzfati Y. A critical three-way junction is conserved in budding yeast and vertebrate telomerase RNAs. Nucleic Acids Res 2007; 35:6280-9. [PMID: 17855392 PMCID: PMC2094081 DOI: 10.1093/nar/gkm713] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The telomerase ribonucleoprotein copies a short template within its integral RNA moiety onto eukaryotic chromosome ends, compensating for incomplete replication and degradation. Non-template regions of telomerase RNA (TER) are also crucial for telomerase function, yet they are highly divergent in sequence among species and their roles are largely unclear. Using both phylogenetic and mutational analyses, we predicted secondary structures for TERs from Kluyveromyces budding yeast species. A comparison of these secondary structure models with the published model for the Saccharomyces cerevisiae TER reveals a common arrangement into three long arms, a templating domain in the center and several conserved elements in the same positions within the structure. One of them, a three-way junction element, is highly conserved in budding yeast TERs. This element also shows sequence and structure similarity to the critical CR4-CR5 activating domain of vertebrate TERs. Mutational analysis in Kluyveromyces lactis confirmed that this element, and in particular the residues conserved across yeast and vertebrates, is critical for telomerase action both in vivo and in vitro. These findings demonstrate that despite the extreme divergence of TER sequences from different organisms, they do share conserved elements, which presumably carry out common roles in telomerase function.
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Affiliation(s)
| | | | | | | | | | - Yehuda Tzfati
- *To whom correspondence should be addressed. +972 2 6584902+972 2 6586975
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27
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Getz M, Sun X, Casiano-Negroni A, Zhang Q, Al-Hashimi HM. NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 2007; 86:384-402. [PMID: 17594140 DOI: 10.1002/bip.20765] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large-amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified.
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Affiliation(s)
- Melissa Getz
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
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28
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Li X, Nishizuka H, Tsutsumi K, Imai Y, Kurihara Y, Uesugi S. Structure, interactions and effects on activity of the 5'-terminal region of human telomerase RNA. J Biochem 2007; 141:755-65. [PMID: 17387120 DOI: 10.1093/jb/mvm081] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Telomerase is an enzyme that catalyzes addition of telomeric repeat sequences to the 3'-termini of eukaryotic chromosome DNA. The catalytic core of telomerase consists of a protein component, telomerase reverse transcriptase (TERT), for the catalysis and an RNA component, telomerase RNA (TR), containing the template for the sequence. Human telomerase RNA (hTR) consists of 451 nucleotides (nt) and contains consecutive G-stretches in the 5'-terminal region. We examined the effects of the 5'-terminal sequence (nt 1-17) in hTR, which is assumed to be a single-stranded region (region 1), on interaction and telomerase activity in vitro. Mutation and binding experiments for hTR and its variants suggest that region 1 has repressive effects on telomerase activity by interaction with the region(s) in the 3'-half part. We prepared various hTR variants with mutations in region 1 and two possible target regions (region 2: nt 229-244; region 3: nt 284-297). Studies on these variants showed that region 1 can interact with regions 2 and 3 and the interactions between regions 1 and 3 may contribute to the repressive effects of region 1. We found that a mutation in region 2 markedly enhances telomerase activity. We also found that some deletion and sequence mutations in region 1 enhance the activity.
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Affiliation(s)
- Xianglan Li
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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29
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Getz MM, Andrews AJ, Fierke CA, Al-Hashimi HM. Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. RNA (NEW YORK, N.Y.) 2007; 13:251-66. [PMID: 17194721 PMCID: PMC1781369 DOI: 10.1261/rna.264207] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The P4 helix is an essential element of ribonuclease P (RNase P) that is believed to bind catalytically important metals. Here, we applied a combination of NMR residual dipolar couplings (RDCs) and a recently introduced domain-elongation strategy for measuring "motionally decoupled" relaxation data to characterize the structural dynamics of the P4 helix from Bacillus subtilis RNase P. In the absence of divalent ions, the two P4 helical domains undergo small amplitude (approximately 13 degrees) collective motions about an average interhelical angle of 10 degrees. The highly conserved U7 bulge and helical residue C8, which are proposed to be important for substrate recognition and metal binding, are locally mobile at pico- to nanosecond timescales and together form the pivot point for the collective domain motions. Chemical shift mapping reveals significant association of Mg2+ ions at the P4 major groove near the flexible pivot point at residues (A5, G22, G23) previously identified to bind catalytically important metals. The Mg2+ ions do not, however, significantly alter the structure or dynamics of P4. Analysis of results in the context of available X-ray structures of the RNA component of RNase P and structural models that include the pre-tRNA substrate suggest that the internal motions observed in P4 likely facilitate adaptive changes in conformation that take place during folding and substrate recognition, possibly aided by interactions with Mg2+ ions. Our results add to a growing view supporting the existence of functionally important internal motions in RNA occurring at nanosecond timescales.
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Affiliation(s)
- Melissa M Getz
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA
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30
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Legassie JD, Jarstfer MB. The unmasking of telomerase. Structure 2007; 14:1603-9. [PMID: 17098185 DOI: 10.1016/j.str.2006.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 09/01/2006] [Accepted: 09/08/2006] [Indexed: 12/15/2022]
Abstract
Telomerase is a ribonucleoprotein complex that reverse transcribes a portion of its RNA subunit during the synthesis of G-rich DNA at the 3' end of each chromosome in most eukaryotes. This activity compensates for the inability of the normal DNA replication machinery to fully replicate chromosome termini. The roles of telomerase in cellular immortality and tumor biology have catalyzed a significant interest in this unusual polymerase. Recently the first structures of two domains, the CR4/CR5 and pseudoknot, of human telomerase RNA (hTR) were reported, offering a structural basis for interpreting biochemical studies and possible roles of hTR mutations in human diseases. Structures of the stem II and stem IV domains of Tetrahymena thermophila TR as well as the N-terminal domain of the T. thermophila telomerase reverse transcriptase have also been determined. These studies complement previous biochemical studies, providing rich insight into the structural basis for telomerase activity.
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Affiliation(s)
- Jason D Legassie
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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31
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Gavory G, Symmons MF, Ghosh YK, Klenerman D, Balasubramanian S. Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling. Biochemistry 2006; 45:13304-11. [PMID: 17073451 PMCID: PMC2196208 DOI: 10.1021/bi061150a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Telomerase is the ribonucleoprotein reverse transcriptase involved in the maintenance of the telomeres, the termini of eukaryotic chromosomes. The RNA component of human telomerase (hTR) consists of 451 nucleotides with the 5' half folding into a highly conserved catalytic core comprising the template region and an adjacent pseudoknot domain (nucleotides 1-208). While the secondary structure of hTR is established, there is little understanding of its three-dimensional (3D) architecture. Here, we have used fluorescence resonance energy transfer (FRET) between fluorescently labelled peptide nucleic acids, hybridized to defined single stranded regions of full length hTR, to evaluate long-range distances. Using molecular modeling, the distance constraints derived by FRET were subsequently used, together with the known secondary structure, to generate a 3D model of the catalytic core of hTR. An overlay of a large set of models generated has provided a low-resolution structure (6.5-8.0 A) that can readily be refined as new structural information becomes available. A notable feature of the modeled structure is the positioning of the template adjacent to the pseudoknot, which brings a number of conserved nucleotides close in space.
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Affiliation(s)
- Gérald Gavory
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Martyn F. Symmons
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | | | - David Klenerman
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Shankar Balasubramanian
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
- To whom correspondence should be addressed. Tel: +44-1223-336347. Fax: +44-1223-336362. E-mail:
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32
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Nomura Y, Kajikawa M, Baba S, Nakazato S, Imai T, Sakamoto T, Okada N, Kawai G. Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2. Nucleic Acids Res 2006; 34:5184-93. [PMID: 17000640 PMCID: PMC1636434 DOI: 10.1093/nar/gkl664] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3′ tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3′ conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U–U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3′ conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U–U mismatch are required for efficient retrotransposition.
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Affiliation(s)
| | - Masaki Kajikawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | | | | | | | | | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Gota Kawai
- To whom correspondence should be addressed. Tel/Fax: +81 47 478 0425;
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33
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Chen Y, Fender J, Legassie JD, Jarstfer MB, Bryan TM, Varani G. Structure of stem-loop IV of Tetrahymena telomerase RNA. EMBO J 2006; 25:3156-66. [PMID: 16778765 PMCID: PMC1500990 DOI: 10.1038/sj.emboj.7601195] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 05/15/2006] [Indexed: 12/21/2022] Open
Abstract
Conserved domains within the RNA component of telomerase provide the template for reverse transcription, recruit protein components to the holoenzyme and are required for enzymatic activity. Among the functionally essential domains in ciliate telomerase RNA is stem-loop IV, which strongly stimulates telomerase activity and processivity even when provided in trans. The NMR structure of Tetrahymena thermophila stem-loop IV shows a highly structured distal stem-loop linked to a conformationally flexible template-proximal region by a bulge that severely kinks the entire RNA. Through extensive structure-function studies, we identify residues that contribute to both these structural features and to enzymatic activity, with no apparent effect on the binding of TERT protein. We propose that the bending induced by the GA bulge and the flexibility of the template-proximal region allow positioning of the prestructured apical loop during the catalytic cycle.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, University of Washington, Seattle WA, USA
| | - Jessica Fender
- Department of Chemistry, University of Washington, Seattle WA, USA
| | - Jason D Legassie
- Division of Medicinal Chemistry and Natural Products, University of North Carolina, Chapel Hill, NC, USA
| | - Michael B Jarstfer
- Division of Medicinal Chemistry and Natural Products, University of North Carolina, Chapel Hill, NC, USA
| | - Tracy M Bryan
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle WA, USA
- Department of Biochemistry, University of Washington, Seattle WA, USA
- Departments of Chemistry & Biochemistry, University of Washington, Box 351700, Seattle, WA 98185-1700, USA. Tel: +1 206 543 7113; Fax: +1 206 685 8665; E-mail:
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Wu B, Petersen M, Girard F, Tessari M, Wijmenga SS. Prediction of molecular alignment of nucleic acids in aligned media. JOURNAL OF BIOMOLECULAR NMR 2006; 35:103-15. [PMID: 16718586 DOI: 10.1007/s10858-006-9004-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 03/04/2006] [Accepted: 03/14/2006] [Indexed: 05/09/2023]
Abstract
We demonstrate--using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined--that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request.
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Affiliation(s)
- Bin Wu
- Laboratory of Physical Chemistry-Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6225ED, Nijmegen, The Netherlands
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Theimer CA, Feigon J. Structure and function of telomerase RNA. Curr Opin Struct Biol 2006; 16:307-18. [PMID: 16713250 DOI: 10.1016/j.sbi.2006.05.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 04/25/2006] [Accepted: 05/08/2006] [Indexed: 12/21/2022]
Abstract
Maintenance of telomeres by the enzyme telomerase is essential for genomic stability and cell viability in ciliates, vertebrates and yeast. The minimal components of telomerase required for catalytic activity are the telomerase reverse transcriptase (TERT) protein and the template-containing telomerase RNA (TER). Recent studies have afforded significant advances in the biophysical characterization of telomerase RNAs from various species. The first TER structures have been reported, for regions of the catalytically essential pseudoknot and CR4/CR5 domains of human TER, and provide a structural basis for interpretation of mutational and biochemical data. The domains and interactions of the Tetrahymena thermophila telomerase holoenzyme RNA and protein components have been further characterized biochemically, and structures of the TER template boundary element and the N-terminal domain of T. thermophila TERT have been determined. Phylogenetic and biochemical analyses of yeast TERs have revealed core structural elements in common with ciliates and vertebrates, and the minimal domains required for function in vivo.
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Affiliation(s)
- Carla A Theimer
- Department of Chemistry and Biochemistry, and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
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Keppler BR, Jarstfer MB. A high-throughput assay for a human telomerase protein-human telomerase RNA interaction. Anal Biochem 2006; 353:75-82. [PMID: 16620757 DOI: 10.1016/j.ab.2006.03.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 03/08/2006] [Accepted: 03/15/2006] [Indexed: 02/06/2023]
Abstract
The rapid rate at which cancer cells divide necessitates a mechanism for telomere maintenance, and in approximately 90% of all cancer types the enzyme telomerase is used to maintain the length of telomeric DNA. Telomerase is a multi-subunit enzyme that minimally contains a catalytic protein subunit, hTERT, and an RNA subunit, hTR. Proper assembly of telomerase is critical for its enzymatic activity and therefore is a requirement for the proliferation of most cancer cells. We have developed the first high-throughput screen capable of identifying small molecules that specifically perturb human telomerase assemblage. The screen uses a scintillation proximity assay to identify compounds that prevent a specific and required interaction between hTR and hTERT. Rather than attempting to disrupt all of the individual hTR-hTERT interactions, we focused the screen on the interaction of the CR4-CR5 domain of hTR with hTERT. The screen employs a biotin-labeled derivative of the CR4-CR5 domain of hTR that independently binds [(35)S]hTERT in a functionally relevant manner. The complex between hTERT and biotin-labeled RNA can be captured on streptavidin-coated scintillation proximity beads. Use of 96-well filter plates and a vacuum manifold enables rapid purification of the beads. After optimization, statistical evaluation of the screen generated a Z' factor of 0.6, demonstrating the high precision of the assay.
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Affiliation(s)
- Brian R Keppler
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina, Chapel Hill, 27599, USA
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Carothers JM, Davis JH, Chou JJ, Szostak JW. Solution structure of an informationally complex high-affinity RNA aptamer to GTP. RNA (NEW YORK, N.Y.) 2006; 12:567-79. [PMID: 16510427 PMCID: PMC1421093 DOI: 10.1261/rna.2251306] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K(d) = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K(d) of 6 microM are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81%-85%). However, the GTP aptamer is more informationally complex (approximately 45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base-base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in K(d). These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.
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Affiliation(s)
- James M Carothers
- Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center 7215, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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Yingling YG, Shapiro BA. The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation. J Mol Graph Model 2006; 25:261-74. [PMID: 16481205 DOI: 10.1016/j.jmgm.2006.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 01/06/2006] [Accepted: 01/08/2006] [Indexed: 12/31/2022]
Abstract
In this study, the three-dimensional structure of the wild-type human telomerase RNA pseudoknot was predicted via molecular modeling. The wild-type pseudoknot structure is then compared to the recent NMR solution structure of the telomerase pseudoknot, which does not contain the U177 bulge. The removal of the bulge from the pseudoknot structure results in higher stability and significant reduction of activity of telomerase. We show that the effect of the bulge on the structure results in a significant transformation of the pseudoknot junction region where the starting base pairs are disrupted and unique triple base pairs are formed. We found that the formation of the junction region is greatly influenced by interactions of the U177 bulge with loop residues and rotation of residue A174. Moreover, this is the first study to our knowledge where a structure as complex as the pseudoknot has been solved by purely theoretical methods.
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Affiliation(s)
- Yaroslava G Yingling
- Center for Cancer Research Nanobiology Program, National Cancer Institute, NCI-Frederick, National Institutes of Health, Building 469, Room 150, Frederick, MD 21702, United States
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