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Lebo KJ, Zappulla DC. Inverse-Folding Design of Yeast Telomerase RNA Increases Activity In Vitro. Noncoding RNA 2023; 9:51. [PMID: 37736897 PMCID: PMC10514824 DOI: 10.3390/ncrna9050051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/19/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Saccharomyces cerevisiae telomerase RNA, TLC1, is an 1157 nt non-coding RNA that functions as both a template for DNA synthesis and a flexible scaffold for telomerase RNP holoenzyme protein subunits. The tractable budding yeast system has provided landmark discoveries about telomere biology in vivo, but yeast telomerase research has been hampered by the fact that the large TLC1 RNA subunit does not support robust telomerase activity in vitro. In contrast, 155-500 nt miniaturized TLC1 alleles comprising the catalytic core domain and lacking the RNA's long arms do reconstitute robust activity. We hypothesized that full-length TLC1 is prone to misfolding in vitro. To create a full-length yeast telomerase RNA, predicted to fold into its biologically relevant structure, we took an inverse RNA-folding approach, changing 59 nucleotides predicted to increase the energetic favorability of folding into the modeled native structure based on the p-num feature of Mfold software. The sequence changes lowered the predicted ∆G of this "determined-arm" allele, DA-TLC1, by 61 kcal/mol (-19%) compared to wild-type. We tested DA-TLC1 for reconstituted activity and found it to be ~5-fold more robust than wild-type TLC1, suggesting that the inverse-folding design indeed improved folding in vitro into a catalytically active conformation. We also tested if DA-TLC1 functions in vivo, discovering that it complements a tlc1∆ strain, allowing cells to avoid senescence and maintain telomeres of nearly wild-type length. However, all inverse-designed RNAs that we tested had reduced abundance in vivo. In particular, inverse-designing nearly all of the Ku arm caused a profound reduction in telomerase RNA abundance in the cell and very short telomeres. Overall, these results show that the inverse design of S. cerevisiae telomerase RNA increases activity in vitro, while reducing abundance in vivo. This study provides a biochemically and biologically tested approach to inverse-design RNAs using Mfold that could be useful for controlling RNA structure in basic research and biomedicine.
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Affiliation(s)
- Kevin J. Lebo
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David C. Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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2
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Lebo KJ, Zappulla DC. Inverse-folding design of yeast telomerase RNA increases activity in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527468. [PMID: 36798419 PMCID: PMC9934677 DOI: 10.1101/2023.02.08.527468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Saccharomyces cerevisiae telomerase RNA, TLC1, is an 1157 nt non-coding RNA that functions as both a template for DNA synthesis and a flexible scaffold for telomerase RNP holoenzyme protein subunits. The tractable budding yeast system has provided landmark discoveries about telomere biology in vivo , but yeast telomerase research has been hampered by the fact that the large TLC1 RNA subunit does not support robust telomerase activity in vitro . In contrast, 155-500 nt miniaturized TLC1 alleles comprising the catalytic core domain and lacking the RNA's long arms do reconstitute robust activity. We hypothesized that full-length TLC1 is prone to misfolding in vitro . To create a full-length yeast telomerase RNA predicted to fold into its biological relevant structure, we took an inverse RNA folding approach, changing 59 nucleotides predicted to increase the energetic favorability of folding into the modeled native structure based on the p-num feature of Mfold software. The sequence changes lowered the predicted ∆G in this "determined-arm" allele, DA-TLC1, by 61 kcal/mol (-19%) compared to wild type. We tested DA-TLC1 for reconstituted activity and found it to be ∼5-fold more robust than wild-type TLC1, suggesting that the inverse-folding design indeed improved folding in vitro into a catalytically active conformation. We also tested if DA-TLC1 functions in vivo and found that it complements a tlc1 ∆ strain, allowing cells to avoid senescence and maintain telomeres of nearly wild-type length. However, all inverse-designed RNAs that we tested had reduced abundance in vivo . In particular, inverse-designing nearly all of the Ku arm caused a profound reduction in telomerase RNA abundance in the cell and very short telomeres. Overall, these results show that inverse design of S. cerevisiae telomerase RNA increases activity in vitro , while reducing abundance in vivo . This study provides a biochemically and biologically tested approach to inverse-design RNAs using Mfold that could be useful for controlling RNA structure in basic research and biomedicine.
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Affiliation(s)
- Kevin J. Lebo
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - David C. Zappulla
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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3
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Zappulla DC. Yeast Telomerase RNA Flexibly Scaffolds Protein Subunits: Results and Repercussions. Molecules 2020; 25:E2750. [PMID: 32545864 PMCID: PMC7356895 DOI: 10.3390/molecules25122750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/25/2022] Open
Abstract
It is said that "hindsight is 20-20", so, given the current year, it is an opportune time to review and learn from experiences studying long noncoding RNAs. Investigation of the Saccharomyces cerevisiae telomerase RNA, TLC1, has unveiled striking flexibility in terms of both structural and functional features. Results support the "flexible scaffold" hypothesis for this 1157-nt telomerase RNA. This model describes TLC1 acting as a tether for holoenzyme protein subunits, and it also may apply to a plethora of RNAs beyond telomerase, such as types of lncRNAs. In this short perspective review, I summarize findings from studying the large yeast telomerase ribonucleoprotein (RNP) complex in the hope that this hindsight will sharpen foresight as so many of us seek to mechanistically understand noncoding RNA molecules from vast transcriptomes.
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Affiliation(s)
- David C Zappulla
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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4
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Hass EP, Zappulla DC. Repositioning the Sm-Binding Site in Saccharomyces cerevisiae Telomerase RNA Reveals RNP Organizational Flexibility and Sm-Directed 3'-End Formation. Noncoding RNA 2020; 6:ncrna6010009. [PMID: 32121425 PMCID: PMC7151599 DOI: 10.3390/ncrna6010009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 01/10/2023] Open
Abstract
Telomerase RNA contains a template for synthesizing telomeric DNA and has been proposed to act as a flexible scaffold for holoenzyme protein subunits in the RNP. In Saccharomyces cerevisiae, the telomerase RNA, TLC1, is bound by the Sm7 protein complex, which is required for stabilization of the predominant, non-polyadenylated (poly(A)–) TLC1 isoform. However, it remains unclear (1) whether Sm7 retains this function when its binding site is repositioned within TLC1, as has been shown for other TLC1-binding telomerase subunits, and (2) how Sm7 stabilizes poly(A)– TLC1. Here, we first show that Sm7 can stabilize poly(A)– TLC1 even when its binding site is repositioned via circular permutation to several different positions within TLC1, further supporting the conclusion that the telomerase holoenzyme is organizationally flexible. Next, we show that when an Sm site is inserted 5′ of its native position and the native site is mutated, Sm7 stabilizes shorter forms of poly(A)– TLC1 in a manner corresponding to how far upstream the new site was inserted, providing strong evidence that Sm7 binding to TLC1 controls where the mature poly(A)– 3′ is formed by directing a 3′-to-5′ processing mechanism. In summary, our results show that Sm7 and the 3′ end of yeast telomerase RNA comprise an organizationally flexible module within the telomerase RNP and provide insights into the mechanistic role of Sm7 in telomerase RNA biogenesis.
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Affiliation(s)
- Evan P. Hass
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - David C. Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA;
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
- Correspondence: ; Tel.:+1-(610)-758-5088
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Long Noncoding RNAs in the Yeast S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:119-132. [PMID: 28815538 DOI: 10.1007/978-981-10-5203-3_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Long noncoding RNAs have recently been discovered to comprise a sizeable fraction of the RNA World. The scope of their functions, physical organization, and disease relevance remain in the early stages of characterization. Although many thousands of lncRNA transcripts recently have been found to emanate from the expansive DNA between protein-coding genes in animals, there are also hundreds that have been found in simple eukaryotes. Furthermore, lncRNAs have been found in the bacterial and archaeal branches of the tree of life, suggesting they are ubiquitous. In this chapter, we focus primarily on what has been learned so far about lncRNAs from the greatly studied single-celled eukaryote, the yeast Saccharomyces cerevisiae. Most lncRNAs examined in yeast have been implicated in transcriptional regulation of protein-coding genes-often in response to forms of stress-whereas a select few have been ascribed yet other functions. Of those known to be involved in transcriptional regulation of protein-coding genes, the vast majority function in cis. There are also some yeast lncRNAs identified that are not directly involved in regulation of transcription. Examples of these include the telomerase RNA and telomere-encoded transcripts. In addition to its role as a template-encoding telomeric DNA synthesis, telomerase RNA has been shown to function as a flexible scaffold for protein subunits of the RNP holoenzyme. The flexible scaffold model provides a specific mechanistic paradigm that is likely to apply to many other lncRNAs that assemble and orchestrate large RNP complexes, even in humans. Looking to the future, it is clear that considerable fundamental knowledge remains to be obtained about the architecture and functions of lncRNAs. Using genetically tractable unicellular model organisms should facilitate lncRNA characterization. The acquired basic knowledge will ultimately translate to better understanding of the growing list of lncRNAs linked to human maladies.
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Singh J, Sikand K, Conrad H, Will CL, Komar AA, Shukla GC. U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III. Sci Rep 2016; 6:31393. [PMID: 27510544 PMCID: PMC4980772 DOI: 10.1038/srep31393] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/06/2016] [Indexed: 12/11/2022] Open
Abstract
Formation of catalytic core of the U12-dependent spliceosome involves U6atac and U12 interaction with the 5′ splice site and branch site regions of a U12-dependent intron, respectively. Beyond the formation of intermolecular helix I region between U6atac and U12 snRNAs, several other regions within these RNA molecules are predicted to form stem-loop structures. Our previous work demonstrated that the 3′ stem-loop region of U6atac snRNA contains a U12-dependent spliceosome-specific targeting activity. Here, we show a detailed structure-function analysis and requirement of a substructure of U6atac 3′ stem-loop in U12-dependent in vivo splicing. We show that the C-terminal RNA recognition motif of p65, a U12 snRNA binding protein, also binds to the distal 3′ stem-loop of U6atac. By using a binary splice site mutation suppressor assay we demonstrate that p65 protein-binding apical stem-loop of U12 snRNA can be replaced by this U6atac distal 3′ stem-loop. Furthermore, we tested the compatibility of the U6atac 3′ end from phylogenetically distant species in a human U6atac background, to establish the evolutionary relatedness of these structures and in vivo function. In summary, we demonstrate that RNA-RNA and RNA-protein interactions in the minor spliceosome are highly plastic as compared to the major spliceosome.
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Affiliation(s)
- Jagjit Singh
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Kavleen Sikand
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Heike Conrad
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Girish C Shukla
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
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Lemieux B, Laterreur N, Perederina A, Noël JF, Dubois ML, Krasilnikov AS, Wellinger RJ. Active Yeast Telomerase Shares Subunits with Ribonucleoproteins RNase P and RNase MRP. Cell 2016; 165:1171-1181. [PMID: 27156450 DOI: 10.1016/j.cell.2016.04.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/20/2016] [Accepted: 04/01/2016] [Indexed: 01/01/2023]
Abstract
Telomerase is the ribonucleoprotein enzyme that replenishes telomeric DNA and maintains genome integrity. Minimally, telomerase activity requires a templating RNA and a catalytic protein. Additional proteins are required for activity on telomeres in vivo. Here, we report that the Pop1, Pop6, and Pop7 proteins, known components of RNase P and RNase MRP, bind to yeast telomerase RNA and are essential constituents of the telomerase holoenzyme. Pop1/Pop6/Pop7 binding is specific and involves an RNA domain highly similar to a protein-binding domain in the RNAs of RNase P/MRP. The results also show that Pop1/Pop6/Pop7 function to maintain the essential components Est1 and Est2 on the RNA in vivo. Consistently, addition of Pop1 allows for telomerase activity reconstitution with wild-type telomerase RNA in vitro. Thus, the same chaperoning module has allowed the evolution of functionally and, remarkably, structurally distinct RNPs, telomerase, and RNases P/MRP from unrelated progenitor RNAs.
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Affiliation(s)
- Bruno Lemieux
- Department of Microbiology and Infectious Diseases, Center of Excellence in RNA Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Nancy Laterreur
- Department of Microbiology and Infectious Diseases, Center of Excellence in RNA Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Anna Perederina
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-François Noël
- Department of Microbiology and Infectious Diseases, Center of Excellence in RNA Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Marie-Line Dubois
- Department of Anatomy and Cellular Biology,Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Andrey S Krasilnikov
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Center of Excellence in RNA Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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Hass EP, Zappulla DC. The Ku subunit of telomerase binds Sir4 to recruit telomerase to lengthen telomeres in S. cerevisiae. eLife 2015. [PMID: 26218225 PMCID: PMC4547093 DOI: 10.7554/elife.07750] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In Saccharomyces cerevisiae and in humans, the telomerase RNA subunit is bound by Ku, a ring-shaped protein heterodimer best known for its function in DNA repair. Ku binding to yeast telomerase RNA promotes telomere lengthening and telomerase recruitment to telomeres, but how this is achieved remains unknown. Using telomere-length analysis and chromatin immunoprecipitation, we show that Sir4 – a previously identified Ku-binding protein that is a component of telomeric silent chromatin – is required for Ku-mediated telomere lengthening and telomerase recruitment. We also find that specifically tethering Sir4 directly to Ku-binding-defective telomerase RNA restores otherwise-shortened telomeres to wild-type length. These findings suggest that Sir4 is the telomere-bound target of Ku-mediated telomerase recruitment and provide one mechanism for how the Sir4-competing Rif1 and Rif2 proteins negatively regulate telomere length in yeast. DOI:http://dx.doi.org/10.7554/eLife.07750.001 Inside a cell's nucleus, DNA is packaged into structures called chromosomes. The ends of every chromosome are capped by repeating sequences of DNA known as telomeres, which protect the chromosomes from damage. Every time a cell divides, the telomeres shorten. If telomere length falls below a critical level, the cell can die or enter a state in which it can no longer divide. During cell division, an enzyme called telomerase normally restores telomeres to their original length. Telomerase is made up of several proteins and an RNA molecule. In yeast and humans, a protein called Ku is one part of the telomerase enzyme. Ku binds to the RNA subunit of telomerase and helps the enzyme find and interact with the telomeres. Previous research has shown that Ku is unable to work alone to recruit telomerase to the chromosome. A protein called Sir4 binds to telomeres and cells lacking it have short telomeres, but the reason behind this was not known. Hass and Zappulla confirmed previous reports that Ku binds to Sir4 using a biochemical approach. Additional experiments provided genetic evidence that this binding interaction is important for telomerase to lengthen telomeres appropriately. Cells in which the RNA subunit of telomerase is unable to bind effectively to Ku have short telomeres. Hass and Zappulla directly tethered Sir4 to this defective RNA and found this restored the shortened telomeres to a normal length, indicating that Sir4 normally binds Ku to recruit telomerase. Discovering this mode of recruitment also helps to explain how two other telomeric proteins (Rif1 and 2) limit telomere lengthening; they compete with Ku-Sir4 recruitment to form a length-regulating system. Taken together, Hass and Zappulla's results provide strong evidence that Sir4 cooperates with Ku to control the lengthening of chromosome ends. Future research will hopefully reveal the precise space and time requirements for this telomerase-controlling system in yeast. Additionally, because Ku has been reported to be a subunit of human telomerase, future studies could also explore whether human cells use a similar strategy. DOI:http://dx.doi.org/10.7554/eLife.07750.002
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Affiliation(s)
- Evan P Hass
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - David C Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, United States
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9
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Lebo KJ, Niederer RO, Zappulla DC. A second essential function of the Est1-binding arm of yeast telomerase RNA. RNA (NEW YORK, N.Y.) 2015; 21:862-876. [PMID: 25737580 PMCID: PMC4408794 DOI: 10.1261/rna.049379.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
The enzymatic ribonucleoprotein telomerase maintains telomeres in many eukaryotes, including humans, and plays a central role in aging and cancer. Saccharomyces cerevisiae telomerase RNA, TLC1, is a flexible scaffold that tethers telomerase holoenzyme protein subunits to the complex. Here we test the hypothesis that a lengthy conserved region of the Est1-binding TLC1 arm contributes more than simply Est1-binding function. We separated Est1 binding from potential other functions by tethering TLC1 to Est1 via a heterologous RNA-protein binding module. We find that Est1-tethering rescues in vivo function of telomerase RNA alleles missing nucleotides specifically required for Est1 binding, but not those missing the entire conserved region. Notably, however, telomerase function is restored for this condition by expressing the arm of TLC1 in trans. Mutational analysis shows that the Second Essential Est1-arm Domain (SEED) maps to an internal loop of the arm, which SHAPE chemical mapping and 3D modeling suggest could be regulated by conformational change. Finally, we find that the SEED has an essential, Est1-independent role in telomerase function after telomerase recruitment to the telomere. The SEED may be required for establishing telomere extendibility or promoting telomerase RNP holoenzyme activity.
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Affiliation(s)
- Kevin J Lebo
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218-2685, USA
| | - Rachel O Niederer
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218-2685, USA
| | - David C Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218-2685, USA
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10
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Niederer RO, Zappulla DC. Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE. RNA (NEW YORK, N.Y.) 2015; 21:254-261. [PMID: 25512567 PMCID: PMC4338352 DOI: 10.1261/rna.048959.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Telomerase catalyzes the addition of nucleotides to the ends of chromosomes to complete genomic DNA replication in eukaryotes and is implicated in multiple diseases, including most cancers. The core enzyme is composed of a reverse transcriptase and an RNA subunit, which provides the template for DNA synthesis. Despite extensive divergence at the sequence level, telomerase RNAs share several structural features within the catalytic core, suggesting a conserved enzyme mechanism. We have investigated the structure of the core of the human and yeast telomerase RNAs using SHAPE, which interrogates flexibility of each nucleotide. We present improved secondary-structure models, refined by addition of five base triples within the yeast pseudoknot and an alternate pairing within the human-specific element J2a.1 in the human pseudoknot, both of which have implications for thermodynamic stability. We also identified a potentially structured CCC region within the template that may facilitate substrate binding and enzyme mechanism. Overall, the SHAPE findings reveal multiple similarities between the Saccharomyces cerevisiae and Homo sapiens telomerase RNA cores.
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Affiliation(s)
- Rachel O Niederer
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David C Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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11
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Rath AK, Kellermann SJ, Rentmeister A. Programmable Design of Functional Ribonucleoprotein Complexes. Chem Asian J 2014; 9:2045-51. [DOI: 10.1002/asia.201402220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/14/2014] [Indexed: 12/26/2022]
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12
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Mefford MA, Rafiq Q, Zappulla DC. RNA connectivity requirements between conserved elements in the core of the yeast telomerase RNP. EMBO J 2013; 32:2980-93. [PMID: 24129512 DOI: 10.1038/emboj.2013.227] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022] Open
Abstract
Telomerase is a specialized chromosome end-replicating enzyme required for genome duplication in many eukaryotes. An RNA and reverse transcriptase protein subunit comprise its enzymatic core. Telomerase is evolving rapidly, particularly its RNA component. Nevertheless, nearly all telomerase RNAs, including those of H. sapiens and S. cerevisiae, share four conserved structural elements: a core-enclosing helix (CEH), template-boundary element, template, and pseudoknot, in this order along the RNA. It is not clear how these elements coordinate telomerase activity. We find that although rearranging the order of the four conserved elements in the yeast telomerase RNA subunit, TLC1, disrupts activity, the RNA ends can be moved between the template and pseudoknot in vitro and in vivo. However, the ends disrupt activity when inserted between the other structured elements, defining an Area of Required Connectivity (ARC). Within the ARC, we find that only the junction nucleotides between the pseudoknot and CEH are essential. Integrating all of our findings provides a basic map of functional connections in the core of the yeast telomerase RNP and a framework to understand conserved element coordination in telomerase mechanism.
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Affiliation(s)
- Melissa A Mefford
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
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13
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Dionne I, Larose S, Dandjinou AT, Abou Elela S, Wellinger RJ. Cell cycle-dependent transcription factors control the expression of yeast telomerase RNA. RNA (NEW YORK, N.Y.) 2013; 19:992-1002. [PMID: 23690630 PMCID: PMC3683933 DOI: 10.1261/rna.037663.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/12/2013] [Indexed: 06/02/2023]
Abstract
Telomerase is a specialized ribonucleoprotein that adds repeated DNA sequences to the ends of eukaryotic chromosomes to preserve genome integrity. Some secondary structure features of the telomerase RNA are very well conserved, and it serves as a central scaffold for the binding of associated proteins. The Saccharomyces cerevisiae telomerase RNA, TLC1, is found in very low copy number in the cell and is the limiting component of the known telomerase holoenzyme constituents. The reasons for this low abundance are unclear, but given that the RNA is very stable, transcriptional control mechanisms must be extremely important. Here we define the sequences forming the TLC1 promoter and identify the elements required for its low expression level, including enhancer and repressor elements. Within an enhancer element, we found consensus sites for Mbp1/Swi4 association, and chromatin immunoprecipitation (ChIP) assays confirmed the binding of Mbp1 and Swi4 to these sites of the TLC1 promoter. Furthermore, the enhancer element conferred cell cycle-dependent regulation to a reporter gene, and mutations in the Mbp1/Swi4 binding sites affected the levels of telomerase RNA and telomere length. Finally, ChIP experiments using a TLC1 RNA-binding protein as target showed cell cycle-dependent transcription of the TLC1 gene. These results indicate that the budding yeast TLC1 RNA is transcribed in a cell cycle-dependent fashion late in G1 and may be part of the S phase-regulated group of genes involved in DNA replication.
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14
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Geiss BJ, Wilusz J. Ring around the Ro-sie: RNA-mediated alterations of PNPase activity. Cell 2013; 153:12-4. [PMID: 23540686 DOI: 10.1016/j.cell.2013.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chen et al. demonstrate a new way by which noncoding RNAs tailor the function of multicomponent complexes. They show that a noncoding RNA interacts with an exoribonuclease, altering its substrate specificity and enzymatic activity by serving as a ribonucleoprotein scaffold and, perhaps, a gate for entry of the RNA substrate.
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Affiliation(s)
- Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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15
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Gupta SK, Kolet L, Doniger T, Biswas VK, Unger R, Tzfati Y, Michaeli S. The Trypanosoma brucei
telomerase RNA (TER) homologue binds core proteins of the C/D snoRNA family. FEBS Lett 2013; 587:1399-404. [DOI: 10.1016/j.febslet.2013.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 12/16/2022]
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16
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Nandakumar J, Cech TR. Finding the end: recruitment of telomerase to telomeres. Nat Rev Mol Cell Biol 2013; 14:69-82. [PMID: 23299958 DOI: 10.1038/nrm3505] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Telomeres, the ends of linear eukaryotic chromosomes, are characterized by the presence of multiple repeats of a short DNA sequence. This telomeric DNA is protected from illicit repair by telomere-associated proteins, which in mammals form the shelterin complex. Replicative polymerases are unable to synthesize DNA at the extreme ends of chromosomes, but in unicellular eukaryotes such as yeast and in mammalian germ cells and stem cells, telomere length is maintained by a ribonucleoprotein enzyme known as telomerase. Recent work has provided insights into the mechanisms of telomerase recruitment to telomeres, highlighting the contribution of telomere-associated proteins, including TPP1 in humans, Ccq1 in Schizosaccharomyces pombe and Cdc13 and Ku70-Ku80 in Saccharomyces cerevisiae.
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Affiliation(s)
- Jayakrishnan Nandakumar
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309-0596, USA
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