1
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Bozděchová L, Havlová K, Fajkus P, Fajkus J. Analysis of Telomerase RNA Structure in Physcomitrium patens Indicates Functionally Relevant Transitions Between OPEN and CLOSED Conformations. J Mol Biol 2024; 436:168417. [PMID: 38143018 DOI: 10.1016/j.jmb.2023.168417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Telomerase RNA (TR) conformation determines its function as a template for telomere synthesis and as a scaffold for the assembly of the telomerase nucleoprotein complex. Experimental analyses of TR secondary structure using DMS-Map Seq and SHAPE-Map Seq techniques show its CLOSED conformation as the consensus structure where the template region cannot perform its function. Our data show that the apparent discrepancy between experimental results and predicted TR functional conformation, mostly ignored in published studies, can be explained using data analysis based on single-molecule structure prediction from individual sequencing reads by the recently established DaVinci method. This method results in several clusters of secondary structures reflecting the structural dynamics of TR, possibly related to its multiple functional states. Interestingly, the presumed active (OPEN) conformation of TR corresponds to a minor fraction of TR under in vivo conditions. Therefore, structural polymorphism and dynamic TR transitions between CLOSED and OPEN conformations may be involved in telomerase activity regulation as a switch that functions independently of total TR transcript levels.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Kateřina Havlová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Institute of Biophysics, Czech Acad Sci, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Institute of Biophysics, Czech Acad Sci, Královopolská 135, 61200 Brno, Czech Republic.
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2
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Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Cech TR, Rouskin S, Stone MD. Dissecting telomerase RNA structural heterogeneity in living human cells with DMS-MaPseq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560962. [PMID: 37873413 PMCID: PMC10592977 DOI: 10.1101/2023.10.04.560962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features required for hTERT binding. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.
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Affiliation(s)
- Nicholas M Forino
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Jia Zheng Woo
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Arthur J Zaug
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | | | - Thomas R Cech
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
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3
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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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4
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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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5
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Chen X, Tang WJ, Shi JB, Liu MM, Liu XH. Therapeutic strategies for targeting telomerase in cancer. Med Res Rev 2019; 40:532-585. [PMID: 31361345 DOI: 10.1002/med.21626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Telomere and telomerase play important roles in abnormal cell proliferation, metastasis, stem cell maintenance, and immortalization in various cancers. Therefore, designing of drugs targeting telomerase and telomere is of great significance. Over the past two decades, considerable knowledge regarding telomere and telomerase has been accumulated, which provides theoretical support for the design of therapeutic strategies such as telomere elongation. Therefore, the development of telomere-based therapies such as nucleoside analogs, non-nucleoside small molecules, antisense technology, ribozymes, and dominant negative human telomerase reverse transcriptase are being prioritized for eradicating a majority of tumors. While the benefits of telomere-based therapies are obvious, there is a need to address the limitations of various therapeutic strategies to improve the possibility of clinical applications. In this study, current knowledge of telomere and telomerase is discussed, and therapeutic strategies based on recent research are reviewed.
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Affiliation(s)
- Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Wen-Jian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Jing Bo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Xin-Hua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
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6
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Mitchell D, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA (NEW YORK, N.Y.) 2019; 25:147-157. [PMID: 30341176 PMCID: PMC6298566 DOI: 10.1261/rna.067868.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/18/2018] [Indexed: 05/09/2023]
Abstract
Many biological functions performed by RNAs arise from their in vivo structures. The structure of the same RNA can differ in vitro and in vivo owing in part to the influence of molecules ranging from protons to secondary metabolites to proteins. Chemical reagents that modify the Watson-Crick (WC) face of unprotected RNA bases report on the absence of base-pairing and so are of value to determining structures adopted by RNAs. Reagents have thus been sought that can report on the native RNA structures that prevail in living cells. Dimethyl sulfate (DMS) and glyoxal penetrate cell membranes and inform on RNA secondary structure in vivo through modification of adenine (A), cytosine (C), and guanine (G) bases. Uracil (U) bases, however, have thus far eluded characterization in vivo. Herein, we show that the water-soluble carbodiimide 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is capable of modifying the WC face of U and G in vivo, favoring the former nucleobase by a factor of ∼1.5, and doing so in the eukaryote rice, as well as in the Gram-negative bacterium Escherichia coli While both EDC and glyoxal target Gs, EDC reacts with Gs in their typical neutral state, while glyoxal requires Gs to populate the rare anionic state. EDC may thus be more generally useful; however, comparison of the reactivity of EDC and glyoxal may allow the identification of Gs with perturbed pKas in vivo and genome-wide. Overall, use of EDC with DMS allows in vivo probing of the base-pairing status of all four RNA bases.
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MESH Headings
- Base Pairing
- Base Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Ethyldimethylaminopropyl Carbodiimide
- Glyoxal
- Guanine/chemistry
- Indicators and Reagents
- Molecular Probe Techniques
- Molecular Probes
- Molecular Structure
- Nucleic Acid Conformation
- Oryza/chemistry
- Oryza/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Uracil/chemistry
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Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew J Renda
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Catherine A Douds
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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7
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Assani G, Xiong Y, Zhou F, Zhou Y. Effect of therapies-mediated modulation of telomere and/or telomerase on cancer cells radiosensitivity. Oncotarget 2018; 9:35008-35025. [PMID: 30405890 PMCID: PMC6201854 DOI: 10.18632/oncotarget.26150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 12/11/2022] Open
Abstract
Cancer is one of the leading causes of death in the world. Many strategies of cancer treatment such as radiotherapy which plays a key role in cancer treatment are developed and used nowadays. However, the side effects post-cancer radiotherapy and cancer radioresistance are two major causes of the limitation of cancer radiotherapy effectiveness in the cancer patients. Moreover, reduction of the limitation of cancer radiotherapy effectiveness by reducing the side effects post-cancer radiotherapy and cancer radioresistance is the aim of several radiotherapy-oncologic teams. Otherwise, Telomere and telomerase are two cells components which play an important role in cancer initiation, cancer progression and cancer therapy resistance such as radiotherapy resistance. For resolving the problems of the limitation of cancer radiotherapy effectiveness especially the cancer radio-resistance problems, the radio-gene-therapy strategy which is the use of gene-therapy via modulation of gene expression combined with radiotherapy was developed and used as a new strategy to treat the patients with cancer. In this review, we summarized the information concerning the implication of telomere and telomerase modulation in cancer radiosensitivity.
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Affiliation(s)
- Ganiou Assani
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biology Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yudi Xiong
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biology Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biology Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biology Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
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8
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Mitchell D, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA (NEW YORK, N.Y.) 2018; 24:114-124. [PMID: 29030489 PMCID: PMC5733565 DOI: 10.1261/rna.064014.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/10/2017] [Indexed: 05/09/2023]
Abstract
Elucidation of the folded structures that RNA forms in vivo is vital to understanding its functions. Chemical reagents that modify the Watson-Crick (WC) face of unprotected nucleobases are particularly useful in structure elucidation. Dimethyl sulfate penetrates cell membranes and informs on RNA base-pairing and secondary structure but only modifies the WC face of adenines and cytosines. We present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the WC face of guanines as well as cytosines and adenines. Tests on rice (Oryza sativa) 5.8S rRNA in vitro read out by reverse transcription and gel electrophoresis demonstrate specific modification of almost all guanines in a time- and pH-dependent manner. Subsequent in vivo tests on rice, a eukaryote, and Bacillus subtilis and Escherichia coli, Gram-positive and Gram-negative bacteria, respectively, showed that all three reagents enter living cells without prior membrane permeabilization or pH adjustment of the surrounding media and specifically modify solvent-exposed guanine, cytosine, and adenine residues.
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Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Laura E Ritchey
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hongmarn Park
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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9
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Foley SW, Kramer MC, Gregory BD. RNA structure, binding, and coordination in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28660659 DOI: 10.1002/wrna.1426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 11/05/2022]
Abstract
From the moment of transcription, up through degradation, each RNA transcript is bound by an ever-changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as well as the intramolecular RNA folding, or secondary structure, of the transcript. Thus, RNA secondary structure regulates many post-transcriptional processes. With the advent of next generation sequencing, several techniques have been developed to generate global landscapes of both RNA-protein interactions and RNA secondary structure. In this review, we describe the current state of the field detailing techniques to globally interrogate RNA secondary structure and/or RNA-protein interaction sites, as well as our current understanding of these features in the transcriptome of the model plant Arabidopsis thaliana. WIREs RNA 2017, 8:e1426. doi: 10.1002/wrna.1426 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Shawn W Foley
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Marianne C Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
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10
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Vandivier LE, Anderson SJ, Foley SW, Gregory BD. The Conservation and Function of RNA Secondary Structure in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:463-88. [PMID: 26865341 PMCID: PMC5125251 DOI: 10.1146/annurev-arplant-043015-111754] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance (NMR) imaging to chemical and nuclease probing methods. Combining these latter methods with high-throughput sequencing has enabled them to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure.
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Affiliation(s)
- Lee E Vandivier
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | | | - Shawn W Foley
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Brian D Gregory
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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11
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Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD. Genome-Wide Approaches for RNA Structure Probing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:29-59. [PMID: 27256381 DOI: 10.1007/978-3-319-29073-7_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA molecules of all types fold into complex secondary and tertiary structures that are important for their function and regulation. Structural and catalytic RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA) are central players in protein synthesis, and only function through their proper folding into intricate three-dimensional structures. Studies of messenger RNA (mRNA) regulation have also revealed that structural elements embedded within these RNA species are important for the proper regulation of their total level in the transcriptome. More recently, the discovery of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) has shed light on the importance of RNA structure to genome, transcriptome, and proteome regulation. Due to the relatively small number, high conservation, and importance of structural and catalytic RNAs to all life, much early work in RNA structure analysis mapped out a detailed view of these molecules. Computational and physical methods were used in concert with enzymatic and chemical structure probing to create high-resolution models of these fundamental biological molecules. However, the recent expansion in our knowledge of the importance of RNA structure to coding and regulatory RNAs has left the field in need of faster and scalable methods for high-throughput structural analysis. To address this, nuclease and chemical RNA structure probing methodologies have been adapted for genome-wide analysis. These methods have been deployed to globally characterize thousands of RNA structures in a single experiment. Here, we review these experimental methodologies for high-throughput RNA structure determination and discuss the insights gained from each approach.
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Affiliation(s)
- Ian M Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan D Berkowitz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sager J Gosai
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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12
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Incarnato D, Neri F, Anselmi F, Oliviero S. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol 2015; 15:491. [PMID: 25323333 PMCID: PMC4220049 DOI: 10.1186/s13059-014-0491-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Indexed: 12/21/2022] Open
Abstract
Background The understanding of RNA structure is a key feature toward the comprehension of RNA functions and mechanisms of action. In particular, non-coding RNAs are thought to exert their functions by specific secondary structures, but an efficient annotation on a large scale of these structures is still missing. Results By using a novel high-throughput method, named chemical inference of RNA structures, CIRS-seq, that uses dimethyl sulfate, and N-cyclohexyl- N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate to modify RNA residues in single-stranded conformation within native deproteinized RNA secondary structures, we investigate the structural features of mouse embryonic stem cell transcripts. Our analysis reveals an unexpected higher structuring of the 5′ and 3′ untranslated regions compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observe that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we find that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation. Conclusions This work defines for the first time the complete RNA structurome of mouse embryonic stem cells, revealing an extremely distinct RNA structural landscape. These results demonstrate that CIRS-seq constitutes an important tool for the identification of native deproteinized RNA structures. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0491-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino 10126, Italy
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13
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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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14
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Kellermann G, Kaiser M, Dingli F, Lahuna O, Naud-Martin D, Mahuteau-Betzer F, Loew D, Ségal-Bendirdjian E, Teulade-Fichou MP, Bombard S. Identification of human telomerase assembly inhibitors enabled by a novel method to produce hTERT. Nucleic Acids Res 2015; 43:e99. [PMID: 25958399 PMCID: PMC4551907 DOI: 10.1093/nar/gkv425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/20/2015] [Indexed: 01/23/2023] Open
Abstract
Telomerase is the enzyme that maintains the length of telomeres. It is minimally constituted of two components: a core reverse transcriptase protein (hTERT) and an RNA (hTR). Despite its significance as an almost universal cancer target, the understanding of the structure of telomerase and the optimization of specific inhibitors have been hampered by the limited amount of enzyme available. Here, we present a breakthrough method to produce unprecedented amounts of recombinant hTERT and to reconstitute human telomerase with purified components. This system provides a decisive tool to identify regulators of the assembly of this ribonucleoprotein complex. It also enables the large-scale screening of small-molecules capable to interfere with telomerase assembly. Indeed, it has allowed us to identify a compound that inhibits telomerase activity when added prior to the assembly of the enzyme, while it has no effect on an already assembled telomerase. Therefore, the novel system presented here may accelerate the understanding of human telomerase assembly and facilitate the discovery of potent and mechanistically unique inhibitors.
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Affiliation(s)
- Guillaume Kellermann
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
| | - Markus Kaiser
- Institut Curie, CMIB, CNRS UMR 9187- INSERM U1196, Orsay, France
| | - Florent Dingli
- Institut Curie/laboratoire de spectrométrie de masse protéomique, Paris, France
| | | | | | | | - Damarys Loew
- Institut Curie/laboratoire de spectrométrie de masse protéomique, Paris, France
| | - Evelyne Ségal-Bendirdjian
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
| | | | - Sophie Bombard
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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15
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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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16
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Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:867-81. [PMID: 25132067 DOI: 10.1002/wrna.1253] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 12/19/2022]
Abstract
RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2'-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base-pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2' hydroxyl group reactivity. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (selective 2'- hydroxyl acylation and primer extension). Herein, we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being applied to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merging of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function.
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Affiliation(s)
- Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
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17
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Kwok CK, Ding Y, Tang Y, Assmann SM, Bevilacqua PC. Determination of in vivo RNA structure in low-abundance transcripts. Nat Commun 2013; 4:2971. [DOI: 10.1038/ncomms3971] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/19/2013] [Indexed: 01/19/2023] Open
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18
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Vasilkova DV, Azhibek DM, Zatsepin TS, Naraikina YV, Prassolov VS, Prokofjeva MM, Zvereva MI, Rubtsova MP. Dynamics of human telomerase RNA structure revealed by antisense oligonucleotide technique. Biochimie 2013; 95:2423-8. [PMID: 24035778 DOI: 10.1016/j.biochi.2013.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 09/02/2013] [Indexed: 11/17/2022]
Abstract
Telomeres are the nucleoprotein complexes that cap the linear chromosome ends. Telomerase is a ribonucleoprotein that maintains telomere length in stem, embryonic and cancer cells. Somatic cells don't contain active telomerase and telomere function as mitotic clock and telomere length determines the number of cell divisions. Telomerase RNA (TER) contains the template for telomere synthesis and serves as a structural scaffold for holoenzyme assembly. We compared different oligonucleotide based methods for telomerase RNA inhibition, such as antisense oligonucleotides, knockdown by transient siRNA transfection and silencing by miRNA derived from short expressed RNA hairpin in HEK293 cells. All of these methods were applied to different TER regions. Our results revealed that CR2/CR3 domain of TER is accessible in vitro and in vivo and could serve as an optimal site for oligonucleotide-based telomerase silencing.
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Affiliation(s)
- Daria V Vasilkova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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19
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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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20
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Gude L, Berkovitch SS, Santos WL, Kutchukian PS, Pawloski AR, Kuimelis R, McGall G, Verdine GL. Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays. J Biol Chem 2012; 287:18843-53. [PMID: 22451672 DOI: 10.1074/jbc.m111.316596] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Most cellular RNAs engage in intrastrand base-pairing that gives rise to complex three-dimensional folds. This self-pairing presents an impediment toward binding of the RNA by nucleic acid-based ligands. An important step in the discovery of RNA-targeting ligands is therefore to identify those regions in a folded RNA that are accessible toward the nucleic acid-based ligand. Because the folding of RNA targets can involve interactions between nonadjacent regions and employ both Watson-Crick and non-Watson-Crick base-pairing, screening of candidate binder ensembles is typically necessary. Microarray-based screening approaches have shown great promise in this regard and have suggested that achieving complete sequence coverage would be a valuable attribute of a next generation system. Here, we report a custom microarray displaying a library of RNA-interacting polynucleotides comprising all possible 2'-OMe RNA sequences from 4- to 8-nucleotides in length. We demonstrate the utility of this array in identifying RNA-interacting polynucleotides that bind tightly and specifically to the highly conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhibit telomerase function in vitro.
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Affiliation(s)
- Lourdes Gude
- Departmens of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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21
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Cao S, Chen SJ. A domain-based model for predicting large and complex pseudoknotted structures. RNA Biol 2012; 9:200-11. [PMID: 22418848 DOI: 10.4161/rna.18488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Pseudoknotted structures play important structural and functional roles in RNA cellular functions at the level of transcription, splicing and translation. However, the problem of computational prediction for large pseudoknotted folds remains. Here we develop a domain-based method for predicting complex and large pseudoknotted structures from RNA sequences. The model is based on the observation that large RNAs can be separated into different structural domains. The basic idea is to first identify the domains and then predict the structures for each domain. Assembly of the domain structures gives the full structure. The use of the domain-based approach leads to a reduction of computational time by a factor of about ~N ( 2) for an N-nt sequence. As applications of the model, we predict structures for a variety of RNA systems, such as regions in human telomerase RNA (hTR), internal ribosome entry site (IRES) and HIV genome. The lengths of these sequences range from 200-nt to 400-nt. The results show good agreements with the experiments.
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Affiliation(s)
- Song Cao
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, MO, USA
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22
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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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23
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Denesyuk NA, Thirumalai D. Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA. J Am Chem Soc 2011; 133:11858-61. [DOI: 10.1021/ja2035128] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalia A. Denesyuk
- Department of Chemistry and Biochemistry and Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - D. Thirumalai
- Department of Chemistry and Biochemistry and Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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24
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Liang XH, Vickers TA, Guo S, Crooke ST. Efficient and specific knockdown of small non-coding RNAs in mammalian cells and in mice. Nucleic Acids Res 2011; 39:e13. [PMID: 21062825 PMCID: PMC3035437 DOI: 10.1093/nar/gkq1121] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hundreds of small nuclear non-coding RNAs, including small nucleolar RNAs (snoRNAs), have been identified in different organisms, with important implications in regulating gene expression and in human diseases. However, functionalizing these nuclear RNAs in mammalian cells remains challenging, due to methodological difficulties in depleting these RNAs, especially snoRNAs. Here we report a convenient and efficient approach to deplete snoRNA, small Cajal body RNA (scaRNA) and small nuclear RNA in human and mouse cells by conventional transfection of chemically modified antisense oligonucleotides (ASOs) that promote RNaseH-mediated cleavage of target RNAs. The levels of all seven tested snoRNA/scaRNAs and four snRNAs were reduced by 80-95%, accompanied by impaired endogenous functions of the target RNAs. ASO-targeting is highly specific, without affecting expression of the host genes where snoRNAs are embedded in the introns, nor affecting the levels of snoRNA isoforms with high sequence similarities. At least five snoRNAs could be depleted simultaneously. Importantly, snoRNAs could be dramatically depleted in mice by systematic administration of the ASOs. Together, our findings provide a convenient and efficient approach to characterize nuclear non-coding RNAs in mammalian cells, and to develop antisense drugs against disease-causing non-coding RNAs.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 1896 Rutherford Rd. Carlsbad, CA 92008, USA.
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25
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The 5' guanosine tracts of human telomerase RNA are recognized by the G-quadruplex binding domain of the RNA helicase DHX36 and function to increase RNA accumulation. Mol Cell Biol 2010; 31:736-43. [PMID: 21149580 DOI: 10.1128/mcb.01033-10] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Telomerase promotes telomere maintenance by copying a template within its integral RNA subunit to elongate chromosome ends with new telomeric repeats. Motifs have been defined within the telomerase RNA that contribute to mature RNA accumulation, holoenzyme catalytic activity, or enzyme recruitment to telomeres. Here, we describe a motif of human telomerase RNA (hTR), not previously characterized in a cellular context, comprised of several guanosine tracts near the RNA 5' end. These guanosine tracts together are recognized by the DEXH box RNA helicase DHX36. The helicase domain of DHX36 does not mediate hTR binding; instead, hTR interacts with the N-terminal accessory domain of DHX36 known to bind specifically to the parallel-strand G-quadruplex substrates resolved by the helicase domain. The steady-state level of DHX36-hTR interaction is low, but hTR guanosine tract substitutions substantially reduce mature hTR accumulation and thereby reduce telomere maintenance. These findings suggest that G-quadruplex formation in the hTR precursor improves the escape of immature RNP from degradation, but subsequently the G-quadruplex may be resolved in favor of a longer terminal stem. We conclude that G-quadruplex formation within hTR can stimulate telomerase-mediated telomere maintenance.
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26
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Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA. Proc Natl Acad Sci U S A 2010; 107:18761-8. [PMID: 20966348 DOI: 10.1073/pnas.1013269107] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Telomerase is a unique ribonucleoprotein complex that catalyzes the addition of telomeric DNA repeats onto the 3' ends of linear chromosomes. All vertebrate telomerase RNAs contain a catalytically essential core domain that includes the template and a pseudoknot with extended helical subdomains. Within these helical regions is an asymmetric 5-nt internal bulge loop (J2a/b) flanked by helices (P2a and P2b) that is highly conserved in its location but not sequence. NMR structure determination reveals that J2a/b forms a defined S-shape and creates an ∼90 ° bend with a surprisingly low twist (∼10 °) between the flanking helices. A search of RNA structures revealed only one other example of a 5-nt bulge, from hepatitis C virus internal ribosome entry site, with a different sequence but the same structure. J2a/b is intrinsically flexible but the interhelical motions across the loop are remarkably restricted. Nucleotide substitutions in J2a/b that affect the bend angle, direction, and interhelical dynamics are correlated with telomerase activity. Based on the structures of P2ab (J2a/b and flanking helices), the conserved region of the pseudoknot (P2b/P3, previously determined) and the remaining helical segment (P2a.1-J2a.1 refined using residual dipolar couplings and the modeling program MC-Sym) we have calculated an NMR-based model of the full-length pseudoknot. The model and dynamics analysis show that J2a/b serves as a dominant structural and dynamical element in defining the overall topology of the core domain, and suggest that interhelical motions in P2ab facilitate nucleotide addition along the template and template translocation.
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27
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Specificity and stoichiometry of subunit interactions in the human telomerase holoenzyme assembled in vivo. Mol Cell Biol 2010; 30:2775-86. [PMID: 20351177 DOI: 10.1128/mcb.00151-10] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The H/ACA motif of human telomerase RNA (hTR) directs specific pathways of endogenous telomerase holoenzyme assembly, function, and regulation. Similarities between hTR and other H/ACA RNAs have been established, but differences have not been explored even though unique features of hTR H/ACA RNP assembly give rise to telomerase deficiency in human disease. Here, we define hTR H/ACA RNA and RNP architecture using RNA accumulation, RNP affinity purification, and primer extension activity assays. First, we evaluate alternative folding models for the hTR H/ACA motif 5' hairpin. Second, we demonstrate an unanticipated and surprisingly general asymmetry of 5' and 3' hairpin requirements for H/ACA RNA accumulation. Third, we establish that hTR assembles not one but two sets of all four of the H/ACA RNP core proteins, dyskerin, NOP10, NHP2, and GAR1. Fourth, we address a difference in predicted specificities of hTR association with the holoenzyme subunit WDR79/TCAB1. Together, these results complete the analysis of hTR elements required for active RNP biogenesis and define the interaction specificities and stoichiometries of all functionally essential human telomerase holoenzyme subunits. This study uncovers unexpected similarities but also differences between telomerase and other H/ACA RNPs that allow a unique specificity of telomerase biogenesis and regulation.
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28
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Trahan C, Martel C, Dragon F. Effects of dyskeratosis congenita mutations in dyskerin, NHP2 and NOP10 on assembly of H/ACA pre-RNPs. Hum Mol Genet 2009; 19:825-36. [PMID: 20008900 DOI: 10.1093/hmg/ddp551] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dyskeratosis congenita (DC) is a rare genetic syndrome that gives rise to a variety of disorders in affected individuals. Remarkably, all causative gene mutations identified to date share a link to telomere/telomerase biology. We found that the most prevalent dyskerin mutation in DC (A353V) did not affect formation of the NAF1-dyskerin-NOP10-NHP2 tetramer that normally assembles with nascent H/ACA RNAs in vivo. However, the A353V mutation slightly reduced pre-RNP assembly with the H/ACA-like domain of human telomerase RNA (hTR). In contrast, NHP2 mutations V126M and Y139H impaired association with NOP10, leading to major pre-RNP assembly defects with all H/ACA RNAs tested, including the H/ACA domain of hTR. Mutation R34W in NOP10 caused no apparent defect in protein tetramer formation, but it severely affected pre-RNP assembly with the H/ACA domain of hTR and a subset of H/ACA RNAs. Surprisingly, H/ACA sno/scaRNAs that encode miRNAs were not affected by the mutation R34W, and they were able to form pre-RNPs with NOP10-R34W. This indicates structural differences between H/ACA RNPs that encode miRNAs and those that do not. Altogether, our results suggest that, in addition to major defects in the telomere/telomerase pathways, some of the disorders occurring in DC may be caused by alteration of most H/ACA RNPs, or by only a subset of them.
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Affiliation(s)
- Christian Trahan
- Département des sciences biologiques and Centre de recherche BioMed, Université du Québec à Montréal, Montréal, QC, Canada H3C 3P8
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29
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Bradley RK, Holmes I. Evolutionary triplet models of structured RNA. PLoS Comput Biol 2009; 5:e1000483. [PMID: 19714212 PMCID: PMC2725318 DOI: 10.1371/journal.pcbi.1000483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 07/23/2009] [Indexed: 12/31/2022] Open
Abstract
The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree. This algorithm draws on formal models of computational linguistics as well as the 1985 protosequence algorithm of David Sankoff. The output of the composition algorithm is a multiple-sequence stochastic context-free grammar. We describe dynamic programming algorithms, which are robust to null cycles and empty bifurcations, for parsing this grammar. Example applications include structural alignment of non-coding RNAs, propagation of structural information from an experimentally-characterized sequence to its homologs, and inference of the ancestral structure of a set of diverged RNAs. We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML) alignment of three known RNA structures and a known phylogeny and inference of the common ancestral structure. We compared this ML algorithm to a variety of related, but simpler, techniques, including ML alignment algorithms for simpler models that omitted various aspects of the full model and also a posterior-decoding alignment algorithm for one of the simpler models. In our tests, incorporation of basepair structure was the most important factor for accurate alignment inference; appropriate use of posterior-decoding was next; and fine details of the model were least important. Posterior-decoding heuristics can be substantially faster than exact phylogenetic inference, so this motivates the use of sum-over-pairs heuristics where possible (and approximate sum-over-pairs). For more exact probabilistic inference, we discuss the use of transducer composition for ML (or MCMC) inference on phylogenies, including possible ways to make the core operations tractable.
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Affiliation(s)
- Robert K. Bradley
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
| | - Ian Holmes
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- * E-mail:
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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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Chen G, Wen JD, Tinoco I. Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA (NEW YORK, N.Y.) 2007; 13:2175-88. [PMID: 17959928 PMCID: PMC2080604 DOI: 10.1261/rna.676707] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RNA unfolding and folding reactions in physiological conditions can be facilitated by mechanical force one molecule at a time. By using force-measuring optical tweezers, we studied the mechanical unfolding and folding of a hairpin-type pseudoknot in human telomerase RNA in a near-physiological solution, and at room temperature. Discrete two-state folding transitions of the pseudoknot are seen at approximately 10 and approximately 5 piconewtons (pN), with ensemble rate constants of approximately 0.1 sec(-1), by stepwise force-drop experiments. Folding studies of the isolated 5'-hairpin construct suggested that the 5'-hairpin within the pseudoknot forms first, followed by formation of the 3'-stem. Stepwise formation of the pseudoknot structure at low forces are in contrast with the one-step unfolding at high forces of approximately 46 pN, at an average rate of approximately 0.05 sec(-1). In the constant-force folding trajectories at approximately 10 pN and approximately 5 pN, transient formation of nonnative structures were observed, which is direct experimental evidence that folding of both the hairpin and pseudoknot takes complex pathways. Possible nonnative structures and folding pathways are discussed.
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Affiliation(s)
- Gang Chen
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
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Davis C, Barvish Z, Gitelman I. A method for the construction of equalized directional cDNA libraries from hydrolyzed total RNA. BMC Genomics 2007; 8:363. [PMID: 17925018 PMCID: PMC2134933 DOI: 10.1186/1471-2164-8-363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 10/09/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The transcribed sequences of a cell, the transcriptome, represent the trans-acting fraction of the genetic information, yet eukaryotic cDNA libraries are typically made from only the poly-adenylated fraction. The non-coding or translated but non-polyadenylated RNAs are therefore not represented. The goal of this study was to develop a method that would more completely represent the transcriptome in a useful format, avoiding over-representation of some of the abundant, but low-complexity non-translated transcripts. RESULTS We developed a combination of self-subtraction and directional cloning procedures for this purpose. Libraries were prepared from partially degraded (hydrolyzed) total RNA from three different species. A restriction endonuclease site was added to the 3' end during first-strand synthesis using a directional random-priming technique. The abundant non-polyadenylated rRNA and tRNA sequences were largely removed by using self-subtraction to equalize the representation of the various RNA species. Sequencing random clones from the libraries showed that 87% of clones were in the forward orientation with respect to known or predicted transcripts. 70% matched identified or predicted translated RNAs in the sequence databases. Abundant mRNAs were less frequent in the self-subtracted libraries compared to a non-subtracted mRNA library. 3% of the sequences were from known or hypothesized ncRNA loci, including five matches to miRNA loci. CONCLUSION We describe a simple method for making high-quality, directional, random-primed, cDNA libraries from small amounts of degraded total RNA. This technique is advantageous in situations where a cDNA library with complete but equalized representation of transcribed sequences, whether polyadenylated or not, is desired.
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Affiliation(s)
- Claytus Davis
- Department of Virology and Developmental Genetics, Faculty of Health Science, Ben Gurion University of the Negev, Beer Sheva, Israel.
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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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34
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Tárkányi I, Aradi J. Pharmacological intervention strategies for affecting telomerase activity: future prospects to treat cancer and degenerative disease. Biochimie 2007; 90:156-72. [PMID: 17945408 DOI: 10.1016/j.biochi.2007.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 09/04/2007] [Indexed: 12/20/2022]
Abstract
Telomerase enzyme is a ribonucleoprotein maintaining the length of the telomeres by adding G-rich repeats to the end of the eukaryotic chromosomes. Normal human somatic cells, cultured in vitro, have a strictly limited proliferative potential undergoing senescence after about 50-70 population doublings. In contrast, most of the tumor cells have unlimited replicative potential. Although the mechanisms of immortalization are not understood completely at a genetic level, the key role of the telomere/telomerase system in the process is clear. The DNA replication machinery is not able to replicate fully the DNA at the very end of the chromosomes; therefore, about 50-200 nucleotides are lost during each of the replication cycles resulting in a gradual decrease of telomere length. Critically short telomere induces senescence, subsequent crisis and cell death. In tumor cells, however, the telomerase enzyme prevents the formation of critically short telomeres, adding GGTTAG repeats to the 3' end of the chromosomes immortalizing the cells. Immortality is one of the hallmarks of cancer. Besides the catalytic activity dependent telomere maintenance, catalytic activity-independent effects of telomerase may also be involved in the regulation of cell cycle. The telomere/telomerase system offers two possibilities to intervene the proliferative activity of the cell: (1) inhibition the telomere maintenance by inhibiting the telomerase activity; (2) activating the residual telomerase enzyme or inducing telomerase expression. Whilst the former approach could abolish the limitless replicative potential of malignant cells, the activation of telomerase might be utilized for treating degenerative diseases. Here, we review the current status of telomerase therapeutics, summarizing the activities of those pharmacological agents which either inhibit or activate the enzyme. We also discuss the future opportunities and challenges of research on pharmacological intervention of telomerase activity.
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Affiliation(s)
- I Tárkányi
- 3rd Department of Internal Medicine, University of Debrecen, 22 Moricz Zsigmond Krt., Debrecen 4004, Hungary
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35
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Ulyanov NB, Shefer K, James TL, Tzfati Y. Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucleic Acids Res 2007; 35:6150-60. [PMID: 17827211 PMCID: PMC2094054 DOI: 10.1093/nar/gkm660] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Telomerase maintains the integrity of telomeres, the ends of linear chromosomes, by adding G-rich repeats to their 3′-ends. Telomerase RNA is an integral component of telomerase. It contains a template for the synthesis of the telomeric repeats by the telomerase reverse transcriptase. Although telomerase RNAs of different organisms are very diverse in their sequences, a functional non-template element, a pseudoknot, was predicted in all of them. Pseudoknot elements in human and the budding yeast Kluyveromyces lactis telomerase RNAs contain unusual triple-helical segments with AUU base triples, which are critical for telomerase function. Such base triples in ciliates have not been previously reported. We analyzed the pseudoknot sequences in 28 ciliate species and classified them in six different groups based on the lengths of the stems and loops composing the pseudoknot. Using miniCarlo, a helical parameter-based modeling program, we calculated 3D models for a representative of each morphological group. In all cases, the predicted structure contains at least one AUU base triple in stem 2, except for that of Colpidium colpoda, which contains unconventional GCG and AUA triples. These results suggest that base triples in a pseudoknot element are a conserved feature of all telomerases.
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Affiliation(s)
- Nikolai B. Ulyanov
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
- *To whom correspondence should be addressed. +1 415 476 0707+1 415 502 8298 Correspondence may also be addressed to Yehuda Tzfati. +972 2 6584902+972 2 6586975
| | - Kinneret Shefer
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Thomas L. James
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Yehuda Tzfati
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
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36
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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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37
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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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38
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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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39
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Garforth S, Wu Y, Prasad V. Structural features of mouse telomerase RNA are responsible for the lower activity of mouse telomerase versus human telomerase. Biochem J 2006; 397:399-406. [PMID: 16669789 PMCID: PMC1533308 DOI: 10.1042/bj20060456] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human and mouse telomerases show a high degree of similarity in both the protein and RNA components. Human telomerase is more active and more processive than the mouse telomerase. There are two key differences between hTR [human TR (telomerase RNA)] and mTR (mouse TR) structures. First, the mouse telomerase contains only 2 nt upstream of its template region, whereas the human telomerase contains 45 nt. Secondly, the template region of human telomerase contains a 5-nt alignment domain, whereas that of mouse has only 2 nt. We hypothesize that these differences are responsible for the differential telomerase activities. Mutations were made in both the hTR and mTR, changing the template length and the length of the RNA upstream of the template, and telomerase was reconstituted in vitro using mouse telomerase reverse transcriptase generated by in vitro translation. We show that the sequences upstream of the template region, with a potential to form a double-stranded helix (the P1 helix) as in hTR, increase telomerase activity. The longer alignment domain increases telomerase activity only in the context of the P1 helix. Thus the TR contributes to regulating the level of activity of mammalian telomerases.
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Affiliation(s)
- Scott J. Garforth
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, GB401, Bronx, NY 10461, U.S.A
| | - Yan Yun Wu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, GB401, Bronx, NY 10461, U.S.A
| | - Vinayaka R. Prasad
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, GB401, Bronx, NY 10461, U.S.A
- To whom correspondence should be addressed (email )
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40
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Shin JS, Hong A, Solomon MJ, Lee CS. The role of telomeres and telomerase in the pathology of human cancer and aging. Pathology 2006; 38:103-13. [PMID: 16581649 DOI: 10.1080/00313020600580468] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cellular senescence, the state of permanent growth arrest, is the inevitable fate of replicating normal somatic cells. Postulated to underlie this finite replicative span is the physiology of telomeres, which constitute the ends of chromosomes. The repetitive sequences of these DNA-protein complexes progressively shorten with each mitosis. When the critical length is bridged, telomeres trigger DNA repair and cell cycle checkpoint mechanisms that result in chromosomal fusions, cell cycle arrest, senescence and/or apoptosis. Should senescence be bypassed at such time, continued cell divisions in the face of dysfunctional telomeres and activated DNA repair machinery can result in the genomic instability favourable for oncogenesis. The longevity and malignant progression of the thus transformed cell requires coincident telomerase expression or other means to negate the constitutional telomeric loss. Practically then, telomeres and telomerase may represent plausible prognostic and screening cancer markers. Furthermore, if the argument is extended, with assumptions that telomeric attrition is indeed the basis of cellular senescence and that accumulation of the latter equates to aging at the organismal level, then telomeres may well explain the increased incidence of cancer with human aging.
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Affiliation(s)
- Joo-Shik Shin
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, Australia.
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41
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Abstract
Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease.
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Affiliation(s)
| | - Shi-Jie Chen
- To whom correspondence should be addressed. Tel: +1 573 882 6626; Fax: +1 573 882 4195;
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42
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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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43
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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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Kiss T, Fayet E, Jády BE, Richard P, Weber M. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 71:407-17. [PMID: 17381323 DOI: 10.1101/sqb.2006.71.025] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Box C/D and H/ACA snoRNAs represent two abundant groups of small noncoding RNAs. The majority of box C/D and H/ACA snoRNAs function as guide RNAs in the site-specific 2'-O-methylation and pseudouridylation of rRNAs, respectively. The box C/D snoRNAs associate with fibrillarin, Nop56, Nop58, and 15.5K/NHPX proteins to form functional snoRNP particles, whereas all box H/ACA snoRNAs form complexes with the dyskerin, Nop10, Nhp2, and Gar1 snoRNP proteins. Recent studies demonstrate that the biogenesis of mammalian snoRNPs is a complex process that requires numerous trans-acting factors. Most vertebrate snoRNAs are posttranscriptionally processed from pre-mRNA introns, and the early steps of snoRNP assembly are physically and functionally coupled with the synthesis or splicing of the host pre-mRNA. The maturing snoRNPs follow a complicated intranuclear trafficking process that is directed by transport factors also involved in nucleocytoplasmic RNA transport. The human telomerase RNA (hTR) carries a box H/ACA RNA domain that shares a common Cajal-body-specific localization element with a subclass of box H/ACA RNAs, which direct pseudouridylation of spliceosomal snRNAs in the Cajal body. However, besides concentrating in Cajal bodies, hTR also accumulates at a small, structurally distinct subset of telomeres during S phase. This suggests that a cell-cycle-dependent, dynamic localization of hTR to telomeres may play an important regulatory role in human telomere synthesis.
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MESH Headings
- Active Transport, Cell Nucleus
- Coiled Bodies/metabolism
- Humans
- Introns
- Models, Biological
- Nucleic Acid Conformation
- RNA/genetics
- RNA/metabolism
- RNA Polymerase II/metabolism
- RNA Splicing
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Telomerase/genetics
- Telomerase/metabolism
- Transcription, Genetic
- RNA, Small Untranslated
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Affiliation(s)
- T Kiss
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109, Toulouse, France
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45
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Marie-Egyptienne DT, Cerone MA, Londoño-Vallejo JA, Autexier C. A human-Tetrahymena pseudoknot chimeric telomerase RNA reconstitutes a nonprocessive enzyme in vitro that is defective in telomere elongation. Nucleic Acids Res 2005; 33:5446-57. [PMID: 16192571 PMCID: PMC1236975 DOI: 10.1093/nar/gki848] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The phylogenetically-derived secondary structures of telomerase RNAs (TR) from ciliates, yeasts and vertebrates are surprisingly conserved and contain a pseudoknot domain at a similar location downstream of the template. As the pseudoknot domains of Tetrahymena TR (tTR) and human TR (hTR) mediate certain similar functions, we hypothesized that they might be functionally interchangeable. We constructed a chimeric TR (htTR) by exchanging the hTR pseudoknot sequences for the tTR pseudoknot region. The chimeric RNA reconstituted human telomerase activity when coexpressed with hTERT in vitro, but exhibited defects in repeat addition processivity and levels of DNA synthesis compared to hTR. Activity was dependent on tTR sequences within the chimeric RNA. htTR interacted with hTERT in vitro and dimerized predominantly via a region of its hTR backbone, the J7b/8a loop. Introduction of htTR in telomerase-negative cells stably expressing hTERT did not reconstitute an active enzyme able to elongate telomeres. Thus, our results indicate that the chimeric RNA reconstituted a weakly active nonprocessive human telomerase enzyme in vitro that was defective in telomere elongation in vivo. This suggests that there may be species-specific requirements for pseudoknot functions.
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Affiliation(s)
- Delphine T. Marie-Egyptienne
- Department of Anatomy and Cell Biology, Institut Curie26 rue d'Ulm, 75248 Paris, CEDEX 05, France
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General HospitalMontréal, Québec, Canada H3T 1E2
| | - Maria Antonietta Cerone
- Department of Anatomy and Cell Biology, Institut Curie26 rue d'Ulm, 75248 Paris, CEDEX 05, France
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General HospitalMontréal, Québec, Canada H3T 1E2
| | | | - Chantal Autexier
- Department of Anatomy and Cell Biology, Institut Curie26 rue d'Ulm, 75248 Paris, CEDEX 05, France
- Department of Medicine, McGill UniversityMontréal, Québec, Canada H3A 2B2
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General HospitalMontréal, Québec, Canada H3T 1E2
- To whom correspondence should be addressed. Tel: +1 514 340 8260; Fax: +1 514 340 8295;
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Moriarty TJ, Marie-Egyptienne DT, Autexier C. Regulation of 5' template usage and incorporation of noncognate nucleotides by human telomerase. RNA (NEW YORK, N.Y.) 2005; 11:1448-60. [PMID: 16120835 PMCID: PMC1370828 DOI: 10.1261/rna.2910105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Telomerase accurately synthesizes telomeric DNA by reverse transcription of a tightly defined template region in the telomerase RNA (TR). Reverse transcription past the 5' boundary of the template can cause the incorporation of noncognate nucleotides into telomeric DNA, which can result in disruption of normal telomere function. The products synthesized by human telomerase do not contain the nucleotide cytosine, which is encoded by an hTR residue 2 nucleotides (nt) 5' of the template boundary. We examined dCTP incorporation by a series of telomerases reconstituted with N- and C-terminally mutated human telomerase reverse transcriptases (hTERTs). We found that altering sequences in the N-terminal RNA interaction domain 1 (RID1) and C terminus caused dCTP-dependent catalytic phenotypes suggestive of reverse transcription of sequences 5' of the template boundary. A RID1 mutant that exhibited a dCTP-dependent phenotype interacted less efficiently with a human telomerase RNA (hTR) variant in which the 5' template boundary-defining P1b element was disrupted, whereas C-terminal mutations did not alter hTR interactions in a P1b-dependent fashion. Disruption of P1b or template linker sequences between P1b and the 5' template boundary also impaired 5' template usage in RID1 and C-terminal hTERT mutants. These observations identify overlapping roles for hTR sequences and structures 5' of the template in regulating both 5' template boundary definition and 5' template usage, and implicate hTERT N- and C-terminal regions in 5' template usage and suppression of noncognate nucleotide incorporation.
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Affiliation(s)
- Tara J Moriarty
- Lady Davis Institute for Medical Research, 3755 chemin Côte Ste. Catherine, Montréal, QC H3T 1E2, Canada
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Förstemann K, Lingner J. Telomerase limits the extent of base pairing between template RNA and telomeric DNA. EMBO Rep 2005; 6:361-6. [PMID: 15776019 PMCID: PMC1299284 DOI: 10.1038/sj.embor.7400374] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Revised: 02/07/2005] [Accepted: 02/14/2005] [Indexed: 01/18/2023] Open
Abstract
Telomerase is the ribonucleoprotein reverse transcriptase that adds telomeric DNA repeats to the ends of chromosomes. This involves annealing of the telomerase RNA template to the 3' end of the chromosome, reverse transcription of the RNA template by the telomerase reverse transcriptase polypeptide and translocation. Here, we overexpress and partially purify the catalytically active yeast telomerase core in its natural host and probe telomerase RNA base methylation accessibility with dimethyl sulphate in the presence and absence of a DNA substrate and after substrate elongation. The length of the RNA-DNA hybrid is kept constant at seven base pairs after primer binding and elongation. Thus, new base-pair formation at the 3' end of the substrate during elongation coincides with disruption of base-pair interactions at the other side of the template. Presumably, this circumvents the generation of an exceedingly high energy barrier for translocation and dissociation. Our analysis also corroborates recently proposed yeast telomerase RNA secondary structure models.
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Affiliation(s)
- Klaus Förstemann
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), and National Center of Competence in Research ‘Frontiers in Genetics', 1066 Epalinges s/Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), and National Center of Competence in Research ‘Frontiers in Genetics', 1066 Epalinges s/Lausanne, Switzerland
- Tel: +41 21 692 5912; Fax: +41 21 652 6933; E-mail:
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Yingling YG, Shapiro BA. Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita. J Mol Biol 2005; 348:27-42. [PMID: 15808851 DOI: 10.1016/j.jmb.2005.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 01/31/2005] [Accepted: 02/04/2005] [Indexed: 10/25/2022]
Abstract
In this paper, we present the results from a comprehensive study of nanosecond-scale implicit and explicit solvent molecular dynamics simulations of the wild-type telomerase RNA hairpin. The effects of various mutations on telomerase RNA dynamics are also investigated. Overall, we found that the human telomerase hairpin is a very flexible molecule. In particular, periodically the molecule exhibits dramatic structural fluctuations represented by the opening and closing of a non-canonical base-pair region. These structural deviations correspond to significant disruptions of the direct hydrogen bonding network in the helix, widening of the major groove of the hairpin structure, and causing several U and C nucleotides to protrude into the major groove from the helix permitting them to hydrogen bond with, for example, the P3 domain of the telomerase RNA. We suggest that these structural fluctuations expose a nucleation point for pseudoknot formation. We also found that mutations in the pentaloop and non-canonical region stabilize the hairpin. Moreover, our results show that the hairpin with dyskeratosis congenita mutations is more stable and less flexible than the wild-type hairpin due to base stacking in the pentaloop. The results from our molecular dynamics simulations are in agreement with experimental observations. In addition, they suggest a possible mechanism for pseudoknot formation based on the dynamics of the hairpin structure and also may explain the mutational aspects of dyskeratosis congenita.
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Affiliation(s)
- Yaroslava G Yingling
- Laboratory of Experimental and Computational Biology, NCI Center for Cancer Research, NCI-Frederick, National Institutes of Health, Building 469, Room 150, Frederick, MD 21702, USA
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Leeper TC, Varani G. The structure of an enzyme-activating fragment of human telomerase RNA. RNA (NEW YORK, N.Y.) 2005; 11:394-403. [PMID: 15703438 PMCID: PMC1370729 DOI: 10.1261/rna.7222505] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 12/21/2004] [Indexed: 05/21/2023]
Abstract
The ribonucleoprotein enzyme telomerase ensures the stability and fidelity of linear chromosome ends by elongating the telomeric DNA that is lost during each round of DNA replication. All telomerases contain a catalytic protein component homologous to viral reverse transcriptases (TERT) and an RNA (TR) that provides the template sequence, acts as the scaffold for ribonucleoprotein assembly, and activates the enzyme for catalysis. Vertebrate telomerase RNAs contain three highly conserved structural and functional domains: the template domain, the "CR4-CR5" or "activation" domain essential for activation of the enzymatic activity, and a 3'-terminal "box H/ACA"-homology domain responsible for ribonucleprotein assembly and maturation. Here we report the NMR structure of a functionally essential RNA structural element derived from the human telomerase RNA CR4-CR5 domain. This RNA, referred to as hTR J6, forms a stable hairpin interrupted by a single nucleotide bulge and an asymmetric internal loop. Previous work on telomerase has shown that deletion of the hTR J6 asymmetric internal loop results in an RNA incapable of binding the enzymatic protein component of the RNP and therefore an inactive RNP without telomerase activity. We demonstrate here that the J6 internal loop introduces a twist in the RNA structure that may position the entire domain into the catalytic site of the enzyme.
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Affiliation(s)
- Thomas C Leeper
- Department of Biochemistry and Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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Theimer CA, Blois CA, Feigon J. Structure of the Human Telomerase RNA Pseudoknot Reveals Conserved Tertiary Interactions Essential for Function. Mol Cell 2005; 17:671-82. [PMID: 15749017 DOI: 10.1016/j.molcel.2005.01.017] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 01/18/2005] [Accepted: 01/21/2005] [Indexed: 11/27/2022]
Abstract
Human telomerase contains a 451 nt RNA (hTR) and several proteins, including a specialized reverse transcriptase (hTERT). The 5' half of hTR comprises the pseudoknot (core) domain, which includes the RNA template for telomere synthesis and a highly conserved pseudoknot that is required for telomerase activity. The solution structure of this essential pseudoknot, presented here, reveals an extended triple helix surrounding the helical junction. The network of tertiary interactions explains the phylogenetic sequence conservation and existing human and mouse TR functional studies as well as mutations linked to disease. Thermodynamic stability, dimerization potential, and telomerase activity of mutant RNAs that alter the tertiary contacts were investigated. Telomerase activity is strongly correlated with tertiary structure stability, whereas there is no correlation with dimerization potential of the pseudoknot. These studies reveal that a conserved pseudoknot tertiary structure is required for telomerase activity.
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Affiliation(s)
- Carla A Theimer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
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