1
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Lash E, Maufrais C, Janbon G, Robbins N, Herzel L, Cowen LE. The spliceosome impacts morphogenesis in the human fungal pathogen Candida albicans. mBio 2024; 15:e0153524. [PMID: 38980041 PMCID: PMC11323467 DOI: 10.1128/mbio.01535-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 07/10/2024] Open
Abstract
At human body temperature, the fungal pathogen Candida albicans can transition from yeast to filamentous morphologies in response to host-relevant cues. Additionally, elevated temperatures encountered during febrile episodes can independently induce C. albicans filamentation. However, the underlying genetic pathways governing this developmental transition in response to elevated temperatures remain largely unexplored. Here, we conducted a functional genomic screen to unravel the genetic mechanisms orchestrating C. albicans filamentation specifically in response to elevated temperature, implicating 45% of genes associated with the spliceosome or pre-mRNA splicing in this process. Employing RNA-Seq to elucidate the relationship between mRNA splicing and filamentation, we identified greater levels of intron retention in filaments compared to yeast, which correlated with reduced expression of the affected genes. Intriguingly, homozygous deletion of a gene encoding a spliceosome component important for filamentation (PRP19) caused even greater levels of intron retention compared with wild type and displayed globally dysregulated gene expression. This suggests that intron retention is a mechanism for fine-tuning gene expression during filamentation, with perturbations of the spliceosome exacerbating this process and blocking filamentation. Overall, this study unveils a novel biological process governing C. albicans filamentation, providing new insights into the complex regulation of this key virulence trait.IMPORTANCEFungal pathogens such as Candida albicans can cause serious infections with high mortality rates in immunocompromised individuals. When C. albicans is grown at temperatures encountered during human febrile episodes, yeast cells undergo a transition to filamentous cells, and this process is key to its virulence. Here, we expanded our understanding of how C. albicans undergoes filamentation in response to elevated temperature and identified many genes involved in mRNA splicing that positively regulate filamentation. Through transcriptome analyses, we found that intron retention is a mechanism for fine-tuning gene expression in filaments, and perturbation of the spliceosome exacerbates intron retention and alters gene expression substantially, causing a block in filamentation. This work adds to the growing body of knowledge on the role of introns in fungi and provides new insights into the cellular processes that regulate a key virulence trait in C. albicans.
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Affiliation(s)
- Emma Lash
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Corinne Maufrais
- Unité Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Université Paris Cité, Paris, France
- HUB Bioinformatique et Biostatistique, Institut Pasteur, Université Paris Cité, Paris, France
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lydia Herzel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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2
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Davis JA, Chakrabarti K. Molecular and Evolutionary Analysis of RNA-Protein Interactions in Telomerase Regulation. Noncoding RNA 2024; 10:36. [PMID: 38921833 PMCID: PMC11206666 DOI: 10.3390/ncrna10030036] [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: 04/08/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Telomerase is an enzyme involved in the maintenance of telomeres. Telomere shortening due to the end-replication problem is a threat to the genome integrity of all eukaryotes. Telomerase inside cells depends on a myriad of protein-protein and RNA-protein interactions to properly assemble and regulate the function of the telomerase holoenzyme. These interactions are well studied in model eukaryotes, like humans, yeast, and the ciliated protozoan known as Tetrahymena thermophila. Emerging evidence also suggests that deep-branching eukaryotes, such as the parasitic protist Trypanosoma brucei require conserved and novel RNA-binding proteins for the assembly and function of their telomerase. In this review, we will discuss telomerase regulatory pathways in the context of telomerase-interacting proteins, with special attention paid to RNA-binding proteins. We will discuss these interactors on an evolutionary scale, from parasitic protists to humans, to provide a broader perspective on the extensive role that protein-protein and RNA-protein interactions play in regulating telomerase activity in eukaryotes.
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Affiliation(s)
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
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3
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Bartle L, Wellinger RJ. Methods that shaped telomerase research. Biogerontology 2024; 25:249-263. [PMID: 37903970 PMCID: PMC10998806 DOI: 10.1007/s10522-023-10073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/30/2023] [Indexed: 11/01/2023]
Abstract
Telomerase, the ribonucleoprotein (RNP) responsible for telomere maintenance, has a complex life. Complex in that it is made of multiple proteins and an RNA, and complex because it undergoes many changes, and passes through different cell compartments. As such, many methods have been developed to discover telomerase components, delve deep into understanding its structure and function and to figure out how telomerase biology ultimately relates to human health and disease. While some old gold-standard methods are still key for determining telomere length and measuring telomerase activity, new technologies are providing promising new ways to gain detailed information that we have never had access to before. Therefore, we thought it timely to briefly review the methods that have revealed information about the telomerase RNP and outline some of the remaining questions that could be answered using new methodology.
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Affiliation(s)
- Louise Bartle
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavilion, 3201 rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavilion, 3201 rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada.
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4
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Neumann H, Bartle L, Bonnell E, Wellinger RJ. Ratcheted transport and sequential assembly of the yeast telomerase RNP. Cell Rep 2023; 42:113565. [PMID: 38096049 DOI: 10.1016/j.celrep.2023.113565] [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: 06/28/2023] [Revised: 10/04/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
The telomerase ribonucleoprotein particle (RNP) replenishes telomeric DNA and minimally requires an RNA component and a catalytic protein subunit. However, telomerase RNP maturation is an intricate process occurring in several subcellular compartments and is incompletely understood. Here, we report how the co-transcriptional association of key telomerase components and nuclear export factors leads to an export-competent, but inactive, RNP. Export is dependent on the 5' cap, the 3' extension of unprocessed telomerase RNA, and protein associations. When the RNP reaches the cytoplasm, an extensive protein swap occurs, the RNA is trimmed to its mature length, and the essential catalytic Est2 protein joins the RNP. This mature and active complex is then reimported into the nucleus as its final destination and last processing steps. The irreversible processing events on the RNA thus support a ratchet-type model of telomerase maturation, with only a single nucleo-cytoplasmic cycle that is essential for the assembly of mature telomerase.
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Affiliation(s)
- Hannah Neumann
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Louise Bartle
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada; Research Center on Aging (CdRV), 1036 rue Belvedere Sud, Sherbrooke, QC J1H 4C4, Canada
| | - Erin Bonnell
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada; Research Center on Aging (CdRV), 1036 rue Belvedere Sud, Sherbrooke, QC J1H 4C4, Canada.
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5
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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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6
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Sanpedro-Luna JA, Jacinto-Vázquez JJ, Anastacio-Marcelino E, Posadas-Gutiérrez CM, Olmos-Pineda I, González-Bernal JA, Carcaño-Montiel M, Vega-Alvarado L, Vázquez-Cruz C, Sánchez-Alonso P. Telomerase RNA plays a major role in the completion of the life cycle in Ustilago maydis and shares conserved domains with other Ustilaginales. PLoS One 2023; 18:e0281251. [PMID: 36952474 PMCID: PMC10035886 DOI: 10.1371/journal.pone.0281251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/18/2023] [Indexed: 03/25/2023] Open
Abstract
The RNA subunit of telomerase is an essential component whose primary sequence and length are poorly conserved among eukaryotic organisms. The phytopathogen Ustilago maydis is a dimorphic fungus of the order Ustilaginales. We analyzed several species of Ustilaginales to computationally identify the TElomere RNA (TER) gene ter1. To confirm the identity of the TER gene, we disrupted the gene and characterized telomerase-negative mutants. Similar to catalytic TERT mutants, ter1Δ mutants exhibit phenotypes of growth delay, telomere shortening and low replicative potential. ter1-disrupted mutants were unable to infect maize seedlings in heterozygous crosses and showed defects such as cell cycle arrest and segregation failure. We concluded that ter1, which encodes the TER subunit of the telomerase of U. maydis, have similar and perhaps more extensive functions than trt1.
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Affiliation(s)
- Juan Antonio Sanpedro-Luna
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - José Juan Jacinto-Vázquez
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Estela Anastacio-Marcelino
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | | | - Iván Olmos-Pineda
- Facultad de Ciencias de la Computación, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Jesús Antonio González-Bernal
- Department of Computer Science and Engineering, The University of Texas Arlington, Arlington, Texas, United States of America
| | - Moisés Carcaño-Montiel
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México, México
| | - Candelario Vázquez-Cruz
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Patricia Sánchez-Alonso
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
- * E-mail:
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7
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Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:ijms24055027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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8
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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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9
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Logeswaran D, Li Y, Akhter K, Podlevsky JD, Olson TL, Forsberg K, Chen JJL. Biogenesis of telomerase RNA from a protein-coding mRNA precursor. Proc Natl Acad Sci U S A 2022; 119:e2204636119. [PMID: 36197996 PMCID: PMC9564094 DOI: 10.1073/pnas.2204636119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
Telomerase is a eukaryotic ribonucleoprotein (RNP) enzyme that adds DNA repeats onto chromosome ends to maintain genomic stability and confer cellular immortality in cancer and stem cells. The telomerase RNA (TER) component is essential for telomerase catalytic activity and provides the template for telomeric DNA synthesis. The biogenesis of TERs is extremely divergent across eukaryotic kingdoms, employing distinct types of transcription machinery and processing pathways. In ciliates and plants, TERs are transcribed by RNA polymerase III (Pol III), while animal and ascomycete fungal TERs are transcribed by RNA Pol II and share biogenesis pathways with small nucleolar RNA (snoRNA) and small nuclear RNA (snRNA), respectively. Here, we report an unprecedented messenger RNA (mRNA)-derived biogenesis pathway for the 1,291 nucleotide TER from the basidiomycete fungus Ustilago maydis. The U. maydis TER (UmTER) contains a 5'-monophosphate, distinct from the 5' 2,2,7-trimethylguanosine (TMG) cap common to animal and ascomycete fungal TERs. The mature UmTER is processed from the 3'-untranslated region (3'-UTR) of a larger RNA precursor that possesses characteristics of mRNA including a 5' 7-methyl-guanosine (m7G) cap, alternative splicing of introns, and a poly(A) tail. Moreover, this mRNA transcript encodes a protein called Early meiotic induction protein 1 (Emi1) that is conserved across dikaryotic fungi. A recombinant UmTER precursor expressed from an mRNA promoter is processed correctly to yield mature UmTER, confirming an mRNA-processing pathway for producing TER. Our findings expand the plethora of TER biogenesis mechanisms and demonstrate a pathway for producing a functional long noncoding RNA from a protein-coding mRNA precursor.
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Affiliation(s)
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
| | - Khadiza Akhter
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
| | | | - Tamara L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
| | | | - Julian J.-L. Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
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10
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Páez-Moscoso DJ, Ho DV, Pan L, Hildebrand K, Jensen KL, Levy MJ, Florens L, Baumann P. A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis. Nat Commun 2022; 13:1067. [PMID: 35217638 PMCID: PMC8881624 DOI: 10.1038/s41467-022-28545-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/13/2022] [Indexed: 01/29/2023] Open
Abstract
Telomerase reverse transcriptase (TERT) and the noncoding telomerase RNA (TR) subunit constitute the core of telomerase. Additional subunits are required for ribonucleoprotein complex assembly and in some cases remain stably associated with the active holoenzyme. Pof8, a member of the LARP7 protein family is such a constitutive component of telomerase in fission yeast. Using affinity purification of Pof8, we have identified two previously uncharacterized proteins that form a complex with Pof8 and participate in telomerase biogenesis. Both proteins participate in ribonucleoprotein complex assembly and are required for wildtype telomerase activity and telomere length maintenance. One factor we named Thc1 (Telomerase Holoenzyme Component 1) shares structural similarity with the nuclear cap binding complex and the poly-adenosine ribonuclease (PARN), the other is the ortholog of the methyl phosphate capping enzyme (Bin3/MePCE) in metazoans and was named Bmc1 (Bin3/MePCE 1) to reflect its evolutionary roots. Thc1 and Bmc1 function together with Pof8 in recognizing correctly folded telomerase RNA and promoting the recruitment of the Lsm2-8 complex and the catalytic subunit to assemble functional telomerase.
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Affiliation(s)
- Diego J Páez-Moscoso
- Faculty of Biology, Johannes Gutenberg University, 55099, Mainz, Germany
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Institute of Molecular Biology, Ackermannweg, 4 55128, Mainz, Germany
| | - David V Ho
- Faculty of Biology, Johannes Gutenberg University, 55099, Mainz, Germany
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Lili Pan
- Faculty of Biology, Johannes Gutenberg University, 55099, Mainz, Germany
| | - Katie Hildebrand
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Transgenic and Gene-Targeting Institutional Facility, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Kristi L Jensen
- Faculty of Biology, Johannes Gutenberg University, 55099, Mainz, Germany
| | - Michaella J Levy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- KCAS, 12400 Shawnee Mission Parkway, Shawnee, KS, 66216, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg University, 55099, Mainz, Germany.
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.
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11
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Hirsch AG, Becker D, Lamping JP, Krebber H. Unraveling the stepwise maturation of the yeast telomerase including a Cse1 and Mtr10 mediated quality control checkpoint. Sci Rep 2021; 11:22174. [PMID: 34773052 PMCID: PMC8590012 DOI: 10.1038/s41598-021-01599-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/29/2021] [Indexed: 01/17/2023] Open
Abstract
Telomerases elongate the ends of chromosomes required for cell immortality through their reverse transcriptase activity. By using the model organism Saccharomyces cerevisiae we defined the order in which the holoenzyme matures. First, a longer precursor of the telomerase RNA, TLC1 is transcribed and exported into the cytoplasm, where it associates with the protecting Sm-ring, the Est and the Pop proteins. This partly matured telomerase is re-imported into the nucleus via Mtr10 and a novel TLC1-import factor, the karyopherin Cse1. Remarkably, while mutations in all known transport factors result in short telomere ends, mutation in CSE1 leads to the amplification of Y′ elements in the terminal chromosome regions and thus elongated telomere ends. Cse1 does not only support TLC1 import, but also the Sm-ring stabilization on the RNA enableling Mtr10 contact and nuclear import. Thus, Sm-ring formation and import factor contact resembles a quality control step in the maturation process of the telomerase. The re-imported immature TLC1 is finally trimmed into the 1158 nucleotides long mature form via the nuclear exosome. TMG-capping of TLC1 finalizes maturation, leading to mature telomerase.
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Affiliation(s)
- Anna Greta Hirsch
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie Und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Daniel Becker
- Philipps-Universität Marburg, Klinik für Dermatologie Und Allergologie, Baldingerstraße, 35043, Marburg, Germany
| | - Jan-Philipp Lamping
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie Und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie Und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany.
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12
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Maturation and shuttling of the yeast telomerase RNP: assembling something new using recycled parts. Curr Genet 2021; 68:3-14. [PMID: 34476547 PMCID: PMC8801399 DOI: 10.1007/s00294-021-01210-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022]
Abstract
As the limiting component of the budding yeast telomerase, the Tlc1 RNA must undergo multiple consecutive modifications and rigorous quality checks throughout its lifecycle. These steps will ensure that only correctly processed and matured molecules are assembled into telomerase complexes that subsequently act at telomeres. The complex pathway of Tlc1 RNA maturation, involving 5'- and 3'-end processing, stabilisation and assembly with the protein subunits, requires at least one nucleo-cytoplasmic passage. Furthermore, it appears that the pathway is tightly coordinated with the association of various and changing proteins, including the export factor Xpo1, the Mex67/Mtr2 complex, the Kap122 importin, the Sm7 ring and possibly the CBC and TREX-1 complexes. Although many of these maturation processes also affect other RNA species, the Tlc1 RNA exploits them in a new combination and, therefore, ultimately follows its own and unique pathway. In this review, we highlight recent new insights in maturation and subcellular shuttling of the budding yeast telomerase RNA and discuss how these events may be fine-tuned by the biochemical characteristics of the varying processing and transport factors as well as the final telomerase components. Finally, we indicate outstanding questions that we feel are important to be addressed for a complete understanding of the telomerase RNA lifecycle and that could have implications for the human telomerase as well.
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13
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Logeswaran D, Li Y, Podlevsky JD, Chen JJL. Monophyletic Origin and Divergent Evolution of Animal Telomerase RNA. Mol Biol Evol 2021; 38:215-228. [PMID: 32770221 PMCID: PMC8480181 DOI: 10.1093/molbev/msaa203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Telomerase RNA (TR) is a noncoding RNA essential for the function of telomerase ribonucleoprotein. TRs from vertebrates, fungi, ciliates, and plants exhibit extreme diversity in size, sequence, secondary structure, and biogenesis pathway. However, the evolutionary pathways leading to such unusual diversity among eukaryotic kingdoms remain elusive. Within the metazoan kingdom, the study of TR has been limited to vertebrates and echinoderms. To understand the origin and evolution of TR across the animal kingdom, we employed a phylogeny-guided, structure-based bioinformatics approach to identify 82 novel TRs from eight previously unexplored metazoan phyla, including the basal-branching sponges. Synthetic TRs from two representative species, a hemichordate and a mollusk, reconstitute active telomerase in vitro with their corresponding telomerase reverse transcriptase components, confirming that they are authentic TRs. Comparative analysis shows that three functional domains, template-pseudoknot (T-PK), CR4/5, and box H/ACA, are conserved between vertebrate and the basal metazoan lineages, indicating a monophyletic origin of the animal TRs with a snoRNA-related biogenesis mechanism. Nonetheless, TRs along separate animal lineages evolved with divergent structural elements in the T-PK and CR4/5 domains. For example, TRs from echinoderms and protostomes lack the canonical CR4/5 and have independently evolved functionally equivalent domains with different secondary structures. In the T-PK domain, a P1.1 stem common in most metazoan clades defines the template boundary, which is replaced by a P1-defined boundary in vertebrates. This study provides unprecedented insight into the divergent evolution of detailed TR secondary structures across broad metazoan lineages, revealing ancestral and later-diversified elements.
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Affiliation(s)
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ
| | | | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ
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14
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Qin J, Autexier C. Regulation of human telomerase RNA biogenesis and localization. RNA Biol 2021; 18:305-315. [PMID: 32813614 PMCID: PMC7954027 DOI: 10.1080/15476286.2020.1809196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/16/2022] Open
Abstract
Maintenance of telomeres is essential for genome integrity and replicative capacity in eukaryotic cells. Telomerase, the ribonucleoprotein complex that catalyses telomere synthesis is minimally composed of a reverse transcriptase and an RNA component. The sequence and structural domains of human telomerase RNA (hTR) have been extensively characterized, while the regulation of hTR transcription, maturation, and localization, is not fully understood. Here, we provide an up-to-date review of hTR, with an emphasis on current breakthroughs uncovering the mechanisms of hTR maturation and localization.
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Affiliation(s)
- Jian Qin
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
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15
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Liu JC, Li QJ, He MH, Hu C, Dai P, Meng FL, Zhou BO, Zhou JQ. Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes. Nucleic Acids Res 2021; 48:12792-12803. [PMID: 33270890 PMCID: PMC7736797 DOI: 10.1093/nar/gkaa1150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and examined 195 strains, in which individual non-essential gene deletion causes telomere shortening. We have identified 24 genes whose deletion results in dramatic failure of Cdc13-Est2 function, including those encoding components of telomerase, Yku, KEOPS and NMD complexes, as well as quite a few whose functions are not obvious in telomerase activity regulation. We have characterized Swc4, a shared subunit of histone acetyltransferase NuA4 and chromatin remodeling SWR1 (SWR1-C) complexes, in telomere length regulation. Deletion of SWC4, but not other non-essential subunits of either NuA4 or SWR1-C, causes significant telomere shortening. Consistently, simultaneous disassembly of NuA4 and SWR1-C does not affect telomere length. Interestingly, inactivation of Swc4 in telomerase null cells accelerates both telomere shortening and senescence rates. Swc4 associates with telomeric DNA in vivo, suggesting a direct role of Swc4 at telomeres. Taken together, our work reveals a distinct role of Swc4 in telomere length regulation, separable from its canonical roles in both NuA4 and SWR1-C.
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Affiliation(s)
- Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian-Jin Li
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Fei-Long Meng
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo O Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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16
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Vasianovich Y, Bajon E, Wellinger RJ. Telomerase biogenesis requires a novel Mex67 function and a cytoplasmic association with the Sm 7 complex. eLife 2020; 9:60000. [PMID: 33095156 PMCID: PMC7644208 DOI: 10.7554/elife.60000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
The templating RNA is the core of the telomerase reverse transcriptase. In Saccharomyces cerevisiae, the complex life cycle and maturation of telomerase includes a cytoplasmic stage. However, timing and reason for this cytoplasmic passage are poorly understood. Here, we use inducible RNA tagging experiments to show that immediately after transcription, newly synthesized telomerase RNAs undergo one round of nucleo-cytoplasmic shuttling. Their export depends entirely on Crm1/Xpo1, whereas re-import is mediated by Kap122 plus redundant, kinetically less efficient import pathways. Strikingly, Mex67 is essential to stabilize newly transcribed RNA before Xpo1-mediated nuclear export. The results further show that the Sm7 complex associates with and stabilizes the telomerase RNA in the cytoplasm and promotes its nuclear re-import. Remarkably, after this cytoplasmic passage, the nuclear stability of telomerase RNA no longer depends on Mex67. These results underscore the utility of inducible RNA tagging and challenge current models of telomerase maturation.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emmanuel Bajon
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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17
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Hyjek‐Składanowska M, Bajczyk M, Gołębiewski M, Nuc P, Kołowerzo‐Lubnau A, Jarmołowski A, Smoliński DJ. Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1155-1173. [PMID: 32369637 PMCID: PMC7540296 DOI: 10.1111/tpj.14792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 05/15/2023]
Abstract
In recent years, research has increasingly focused on the key role of post-transcriptional regulation of messenger ribonucleoprotein (mRNP) function and turnover. As a result of the complexity and dynamic nature of mRNPs, the full composition of a single mRNP complex remains unrevealed and mRNPs are poorly described in plants. Here we identify canonical Sm proteins as part of the cytoplasmic mRNP complex, indicating their function in the post-transcriptional regulation of gene expression in plants. Sm proteins comprise an evolutionarily ancient family of small RNA-binding proteins involved in pre-mRNA splicing. The latest research indicates that Sm could also impact on mRNA at subsequent stages of its life cycle. In this work we show that in the microsporocyte cytoplasm of Larix decidua, the European larch, Sm proteins accumulate within distinct cytoplasmic bodies, also containing polyadenylated RNA. To date, several types of cytoplasmic bodies involved in the post-transcriptional regulation of gene expression have been described, mainly in animal cells. Their role and molecular composition in plants remain less well established, however. A total of 222 mRNA transcripts have been identified as cytoplasmic partners for Sm proteins. The specific colocalization of these mRNAs with Sm proteins within cytoplasmic bodies has been confirmed via microscopic analysis. The results from this work support the hypothesis, that evolutionarily conserved Sm proteins have been adapted to perform a whole repertoire of functions related to the post-transcriptional regulation of gene expression in Eukaryota. This adaptation presumably enabled them to coordinate the interdependent processes of splicing element assembly, mRNA maturation and processing, and mRNA translation regulation, and its degradation.
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Affiliation(s)
- Malwina Hyjek‐Składanowska
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Present address:
Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology4 Trojdena St.02‐109WarsawPoland
| | - Mateusz Bajczyk
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Marcin Gołębiewski
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Department of Plant Physiology and BiotechnologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
| | - Przemysław Nuc
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Agnieszka Kołowerzo‐Lubnau
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
| | - Artur Jarmołowski
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
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18
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Liu J, Liu JP. A method for efficient quantitative analysis of genomic subtelomere Y' element abundance in yeasts. Yeast 2020; 37:373-388. [PMID: 32639041 DOI: 10.1002/yea.3511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/09/2023] Open
Abstract
Subtelomere Y' elements get amplified by homologous recombination in sustaining the survival and division of the budding yeast Saccharomyces cerevisiae. However, current method for measurement of the subtelomere structures uses Southern blotting with labelled specific probes, which is laborious and time-consuming. By multiple sequence alignment analysis of all 19 subtelomere Y' elements across the 13 chromosomes of the sequenced S288C strain deposited in the yeast genome SGD database, we identified 12 consensus and relative longer fragments and 14 pairs of unique primers for real-time quantitative PCR analysis. With a PAC2 or ACT1 located near the centromere of chromosome V and VI as internal controls, these primers were applied to real-time quantitative PCR analysis, so the relative Y' element intensity normalised to that of wild type (WT) cells was calculated for subtelomere Y' element copy numbers across all different chromosomes using the formula: 2^[-((CTmutant Y' - CTmutant control ) - (CTWT Y' - CTWT control ))]. This novel quantitative subtelomere amplification assay across chromosomes by real-time PCR proves to be a much simpler and more sensitive way than the traditional Southern blotting method to analyse the Y' element recombination events in survivors derived from telomerase deficiency or recruitment failure.
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Affiliation(s)
- Jun Liu
- Institute of Ageing Research, College of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jun-Ping Liu
- Institute of Ageing Research, College of Medicine, Hangzhou Normal University, Hangzhou, China
- Department of Immunology, Faculty of Medicine, Monash University, Prahran, Victoria, Australia
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
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19
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Insights into the structure and function of Est3 from the Hansenula polymorpha telomerase. Sci Rep 2020; 10:11109. [PMID: 32632130 PMCID: PMC7338525 DOI: 10.1038/s41598-020-68107-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Telomerase is a ribonucleoprotein enzyme, which maintains genome integrity in eukaryotes and ensures continuous cellular proliferation. Telomerase holoenzyme from the thermotolerant yeast Hansenula polymorpha, in addition to the catalytic subunit (TERT) and telomerase RNA (TER), contains accessory proteins Est1 and Est3, which are essential for in vivo telomerase function. Here we report the high-resolution structure of Est3 from Hansenula polymorpha (HpEst3) in solution, as well as the characterization of its functional relationships with other components of telomerase. The overall structure of HpEst3 is similar to that of Est3 from Saccharomyces cerevisiae and human TPP1. We have shown that telomerase activity in H. polymorpha relies on both Est3 and Est1 proteins in a functionally symmetrical manner. The absence of either Est3 or Est1 prevents formation of a stable ribonucleoprotein complex, weakens binding of a second protein to TER, and decreases the amount of cellular TERT, presumably due to the destabilization of telomerase RNP. NMR probing has shown no direct in vitro interactions of free Est3 either with the N-terminal domain of TERT or with DNA or RNA fragments mimicking the probable telomerase environment. Our findings corroborate the idea that telomerase possesses the evolutionarily variable functionality within the conservative structural context.
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20
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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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21
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Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun 2020; 11:2173. [PMID: 32358529 PMCID: PMC7195438 DOI: 10.1038/s41467-020-15875-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/27/2020] [Indexed: 01/17/2023] Open
Abstract
RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal and tRNAs. Three proteins found in both complexes, Pop1, Pop6, and Pop7 are also telomerase-associated. Here, we determine how temperature sensitive POP1 and POP6 alleles affect yeast telomerase. At permissive temperatures, mutant Pop1/6 have little or no effect on cell growth, global protein levels, the abundance of Est1 and Est2 (telomerase proteins), and the processing of TLC1 (telomerase RNA). However, in pop mutants, TLC1 is more abundant, telomeres are short, and TLC1 accumulates in the cytoplasm. Although Est1/2 binding to TLC1 occurs at normal levels, Est1 (and hence Est3) binding is highly unstable. We propose that Pop-mediated stabilization of Est1 binding to TLC1 is a pre-requisite for formation and nuclear localization of the telomerase holoenzyme. Furthermore, Pop proteins affect TLC1 and the RNA subunits of RNase P/MRP in very different ways.
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Affiliation(s)
- P Daniela Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert W Leach
- Bioinformatics Group, Genomics Core Facility, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, 08544, USA
| | - Gable M Wadsworth
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Krishna Choudhary
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Hua Li
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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22
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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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23
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Nguyen THD, Collins K, Nogales E. Telomerase structures and regulation: shedding light on the chromosome end. Curr Opin Struct Biol 2019; 55:185-193. [PMID: 31202023 DOI: 10.1016/j.sbi.2019.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/28/2019] [Accepted: 04/29/2019] [Indexed: 02/06/2023]
Abstract
During genome replication, telomerase adds repeats to the ends of chromosomes to balance the loss of telomeric DNA. The regulation of telomerase activity is of medical relevance, as it has been implicated in human diseases such as cancer, as well as in aging. Until recently, structural information on this enzyme that would facilitate its clinical manipulation had been lacking due to telomerase very low abundance in cells. Recent cryo-EM structures of both the human and Tetrahymena thermophila telomerases have provided a picture of both the shared catalytic core of telomerase and its interaction with species-specific factors that play different roles in telomerase RNP assembly and function. We discuss also progress toward an understanding of telomerase RNP biogenesis and telomere recruitment from recent studies.
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Affiliation(s)
- Thi Hoang Duong Nguyen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA.
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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24
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Viviescas MA, Cano MIN, Segatto M. Chaperones and Their Role in Telomerase Ribonucleoprotein Biogenesis and Telomere Maintenance. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180713103133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Telomere length maintenance is important for genome stability and cell division. In most
eukaryotes, telomeres are maintained by the telomerase ribonucleoprotein (RNP) complex, minimally
composed of the Telomerase Reverse Transcriptase (TERT) and the telomerase RNA (TER) components.
In addition to TERT and TER, other protein subunits are part of the complex and are involved in
telomerase regulation, assembly, disassembly, and degradation. Among them are some molecular
chaperones such as Hsp90 and its co-chaperone p23 which are found associated with the telomerase
RNP complex in humans, yeast and probably in protozoa. Hsp90 and p23 are necessary for the telomerase
RNP assembly and enzyme activity. In budding yeast, the Hsp90 homolog (Hsp82) is also responsible
for the association and dissociation of telomerase from the telomeric DNA by its direct interaction
with a telomere end-binding protein (Cdc13), responsible for regulating telomerase access to telomeres.
In addition, AAA+ ATPases, such as Pontin and Reptin, which are also considered chaperone-
like proteins, associate with the human telomerase complex by the direct interaction of Pontin with
TERT and dyskerin. They are probably responsible for telomerase RNP assembly since their depletion
impairs the accumulation of the complex. Moreover, various RNA chaperones, are also pivotal in the
assembly and migration of the mature telomerase complex and complex intermediates. In this review,
we will focus on the importance of molecular chaperones for telomerase RNP biogenesis and how they
impact telomere length maintenance and cellular homeostasis.
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Affiliation(s)
- Maria Alejandra Viviescas
- Genetics Department, Biosciences Institute, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Marcela Segatto
- Genetics Department, Biosciences Institute, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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25
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Abstract
Viruses masterfully regulate host gene expression during infection. Many do so, in part, by expressing non-coding RNAs. Recent work has shown that HSUR 2, a viral non-coding RNA expressed by the oncogenic Herpesvirus saimiri, regulates mRNA expression through a novel mechanism. HSUR 2 base pairs with both target mRNAs and host miRNAs in infected cells. This results in HSUR 2-dependent recruitment of host miRNAs and associated Ago proteins to target mRNAs, and the subsequent destabilization of target mRNAs. Using this mechanism, this virus regulates key cellular pathways during viral infection. Here I discuss the evolution of our thinking about HSUR function and explore the implications of recent findings in relation to the current views on the functions of interactions between miRNAs and other classes of non-coding RNAs, the potential advantages of this mechanism of regulation of gene expression, and the evolutionary origin of HSUR 2.
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Affiliation(s)
- Demián Cazalla
- a Department of Biochemistry , University of Utah School of Medicine , Salt Lake City , UT , USA
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26
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Páez-Moscoso DJ, Pan L, Sigauke RF, Schroeder MR, Tang W, Baumann P. Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast. Nat Commun 2018; 9:587. [PMID: 29422664 PMCID: PMC5805746 DOI: 10.1038/s41467-017-02284-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/17/2017] [Indexed: 01/06/2023] Open
Abstract
Telomerase reverse transcriptase (TERT) and the non-coding telomerase RNA subunit (TR) constitute the core of telomerase. Here we now report that the putative F-box protein Pof8 is also a constitutive component of active telomerase in fission yeast. Pof8 functions in a hierarchical assembly pathway by promoting the binding of the Lsm2-8 complex to telomerase RNA, which in turn promotes binding of the catalytic subunit. Loss of Pof8 reduces TER1 stability, causes a severe assembly defect, and results in critically short telomeres. Structure profile searches identified similarities between Pof8 and telomerase subunits from ciliated protozoa, making Pof8 next to TERT the most widely conserved telomerase subunits identified to date.
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Affiliation(s)
| | - Lili Pan
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | | | - Wen Tang
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Peter Baumann
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Howard Hughes Medical Institute, Kansas City, MO, 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, MO, 66160, USA. .,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099, Mainz, Germany.
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27
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Current Perspectives of Telomerase Structure and Function in Eukaryotes with Emerging Views on Telomerase in Human Parasites. Int J Mol Sci 2018; 19:ijms19020333. [PMID: 29364142 PMCID: PMC5855555 DOI: 10.3390/ijms19020333] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/10/2018] [Accepted: 01/17/2018] [Indexed: 12/11/2022] Open
Abstract
Replicative capacity of a cell is strongly correlated with telomere length regulation. Aberrant lengthening or reduction in the length of telomeres can lead to health anomalies, such as cancer or premature aging. Telomerase is a master regulator for maintaining replicative potential in most eukaryotic cells. It does so by controlling telomere length at chromosome ends. Akin to cancer cells, most single-cell eukaryotic pathogens are highly proliferative and require persistent telomerase activity to maintain constant length of telomere and propagation within their host. Although telomerase is key to unlimited cellular proliferation in both cases, not much was known about the role of telomerase in human parasites (malaria, Trypanosoma, etc.) until recently. Since telomerase regulation is mediated via its own structural components, interactions with catalytic reverse transcriptase and several factors that can recruit and assemble telomerase to telomeres in a cell cycle-dependent manner, we compare and discuss here recent findings in telomerase biology in cancer, aging and parasitic diseases to give a broader perspective of telomerase function in human diseases.
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Using Separation-of-Function Mutagenesis To Define the Full Spectrum of Activities Performed by the Est1 Telomerase Subunit in Vivo. Genetics 2017; 208:97-110. [PMID: 29187507 PMCID: PMC5753878 DOI: 10.1534/genetics.117.300145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/15/2017] [Indexed: 01/04/2023] Open
Abstract
A leading objective in biology is to identify the complete set of activities performed by each gene. Identification of a comprehensive set of separation... A leading objective in biology is to identify the complete set of activities that each gene performs in vivo. In this study, we have asked whether a genetic approach can provide an efficient means of achieving this goal, through the identification and analysis of a comprehensive set of separation-of-function (sof−) mutations in a gene. Toward this goal, we have subjected the Saccharomyces cerevisiae EST1 gene, which encodes a regulatory subunit of telomerase, to intensive mutagenesis (with an average coverage of one mutation for every 4.5 residues), using strategies that eliminated those mutations that disrupted protein folding/stability. The resulting set of sof− mutations defined four biochemically distinct activities for the Est1 telomerase protein: two temporally separable steps in telomerase holoenzyme assembly, a telomerase recruitment activity, and a fourth newly discovered regulatory function. Although biochemically distinct, impairment of each of these four different activities nevertheless conferred a common phenotype (critically short telomeres) comparable to that of an est1-∆ null strain. This highlights the limitations of gene deletions, even for nonessential genes; we suggest that employing a representative set of sof− mutations for each gene in future high- and low-throughput investigations will provide deeper insights into how proteins interact inside the cell.
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29
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Beletsky AV, Malyavko AN, Sukhanova MV, Mardanova ES, Zvereva MI, Petrova OA, Parfenova YY, Rubtsova MP, Mardanov AV, Lavrik OI, Dontsova OA, Ravin NV. The genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1. BMC Genomics 2017; 18:492. [PMID: 28659185 PMCID: PMC5490237 DOI: 10.1186/s12864-017-3889-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 06/21/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity. RESULTS Mutant strain of H. polymorpha carrying a disrupted telomerase RNA gene was produced, grown to senescence and analyzed by RNA-seq along with wild type strain. Telomere shortening induced a transcriptional response involving genes relevant to telomere structure and maintenance, DNA damage response, information processing, and some metabolic pathways. Genes involved in DNA replication and repair, response to environmental stresses and intracellular traffic were up-regulated in senescent H. polymorpha cells, while strong down-regulation was observed for genes involved in transcription and translation, as well as core histones. CONCLUSIONS Comparison of the telomerase deletion transcription responses by Saccharomyces cerevisiae and H. polymorpha demonstrates that senescence makes different impact on the main metabolic pathways of these yeast species but induces similar changes in processes related to nucleic acids metabolism and protein synthesis. Up-regulation of a subunit of the TORC1 complex is clearly relevant for both types of yeast.
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Affiliation(s)
- Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Alexander N Malyavko
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Eugenia S Mardanova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Olga A Petrova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia
| | - Yulia Yu Parfenova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Maria P Rubtsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia.
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30
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Vasianovich Y, Wellinger RJ. Life and Death of Yeast Telomerase RNA. J Mol Biol 2017; 429:3242-3254. [PMID: 28115201 DOI: 10.1016/j.jmb.2017.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/14/2017] [Indexed: 12/20/2022]
Abstract
Telomerase reverse transcriptase elongates telomeres to overcome their natural attrition and allow unlimited cellular proliferation, a characteristic shared by stem cells and the majority of malignant cancerous cells. The telomerase holoenzyme comprises a core RNA molecule, a catalytic protein subunit, and other accessory proteins. Malfunction of certain telomerase components can cause serious genetic disorders including dyskeratosis congenita and aplastic anaemia. A hierarchy of tightly regulated steps constitutes the process of telomerase biogenesis, which, if interrupted or misregulated, can impede the production of a functional enzyme and severely affect telomere maintenance. Here, we take a closer look at the budding yeast telomerase RNA component, TLC1, in its long lifetime journey around the cell. We review the extensive knowledge on TLC1 transcription and processing. We focus on exciting recent studies on telomerase assembly, trafficking, and nuclear dynamics, which for the first time unveil striking similarities between the yeast and human telomerase ribonucleoproteins. Finally, we identify questions yet to be answered and new directions to be followed, which, in the future, might improve our knowledge of telomerase biology and trigger the development of new therapies against cancer and other telomerase-related diseases.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
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31
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Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu XH, Yu YT, Isobe T, Takahashi N, Min J. Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes Dev 2016; 30:2376-2390. [PMID: 27881600 PMCID: PMC5131778 DOI: 10.1101/gad.288340.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/26/2016] [Indexed: 12/26/2022]
Abstract
Xu et al. show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs. They also determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA. In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4–6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.
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Affiliation(s)
- Chao Xu
- Hefei National Laboratory for Physical Sciences at Microscale, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hideaki Ishikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Keiichi Izumikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hao He
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yuko Nobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Hanief M Shahjee
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Xian-Hui Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Toshiaki Isobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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32
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MacNeil DE, Bensoussan HJ, Autexier C. Telomerase Regulation from Beginning to the End. Genes (Basel) 2016; 7:genes7090064. [PMID: 27649246 PMCID: PMC5042394 DOI: 10.3390/genes7090064] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
The vast body of literature regarding human telomere maintenance is a true testament to the importance of understanding telomere regulation in both normal and diseased states. In this review, our goal was simple: tell the telomerase story from the biogenesis of its parts to its maturity as a complex and function at its site of action, emphasizing new developments and how they contribute to the foundational knowledge of telomerase and telomere biology.
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Affiliation(s)
- Deanna Elise MacNeil
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Hélène Jeanne Bensoussan
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
| | - Chantal Autexier
- Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montréal, QC H3T 1E2, Canada.
- Room M-29, Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, QC H3A 0C7, Canada.
- Department of Experimental Medicine, McGill University, 1110 Pins Avenue West, Room 101, Montréal, QC H3A 1A3, Canada.
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33
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Laprade H, Lalonde M, Guérit D, Chartrand P. Live-cell imaging of budding yeast telomerase RNA and TERRA. Methods 2016; 114:46-53. [PMID: 27474163 DOI: 10.1016/j.ymeth.2016.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/11/2016] [Accepted: 07/23/2016] [Indexed: 02/02/2023] Open
Abstract
In most eukaryotes, the ribonucleoprotein complex telomerase is responsible for maintaining telomere length. In recent years, single-cell microscopy techniques such as fluorescent in situ hybridization and live-cell imaging have been developed to image the RNA subunit of the telomerase holoenzyme. These techniques are now becoming important tools for the study of telomerase biogenesis, its association with telomeres and its regulation. Here, we present detailed protocols for live-cell imaging of the Saccharomyces cerevisiae telomerase RNA subunit, called TLC1, and also of the non-coding telomeric repeat-containing RNA TERRA. We describe the approach used for genomic integration of MS2 stem-loops in these transcripts, and provide information for optimal live-cell imaging of these non-coding RNAs.
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Affiliation(s)
- Hadrien Laprade
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - Maxime Lalonde
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - David Guérit
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada.
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Abstract
Telomerase is the eukaryotic solution to the ‘end-replication problem’ of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes.
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Affiliation(s)
- Joshua D Podlevsky
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
| | - Julian J-L Chen
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
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35
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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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36
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Podlevsky JD, Li Y, Chen JJL. Structure and function of echinoderm telomerase RNA. RNA (NEW YORK, N.Y.) 2016; 22:204-215. [PMID: 26598712 PMCID: PMC4712671 DOI: 10.1261/rna.053280.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms-marine invertebrates closely related to vertebrates-determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function.
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Affiliation(s)
- Joshua D Podlevsky
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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37
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Lin KW, Zakian VA. 21st Century Genetics: Mass Spectrometry of Yeast Telomerase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:111-6. [PMID: 26763982 PMCID: PMC5441543 DOI: 10.1101/sqb.2015.80.027656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Telomerase is a specialized reverse transcriptase that maintains the ends of chromosomes in almost all eukaryotes. The core of telomerase consists of telomerase RNA and the reverse transcriptase that uses a short segment without the RNA to template the addition of telomeric repeats. In addition, one or more accessory proteins are required for telomerase action in vivo. The best-studied accessory protein is Est1, which is conserved from yeasts to humans. In budding yeast, Est1 has two critical in vivo functions: By interaction with Cdc13, a telomere-binding protein, it recruits telomerase to telomeres, and it also increases telomerase activity. Although budding yeast telomerase is highly regulated by the cell cycle, Est1 is the only telomerase subunit whose abundance is cell cycle-regulated. Close to 400 yeast genes are reported to affect telomere length, although the specific function of most of them is unknown. With the goal of identifying novel telomerase regulators by mass spectrometry, we developed methods for purifying yeast telomerase and its associated proteins. We summarize the methods we used and describe the experiments that show that four telomerase-associated proteins identified by mass spectrometry, none of which had been linked previously to telomeres, affect telomere length and cell cycle regulation of telomerase by controlling Est1 abundance.
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Affiliation(s)
- Kah Wai Lin
- Department of Molecular Biology, Lewis Thomas Labs, Princeton University, Princeton, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Labs, Princeton University, Princeton, New Jersey 08544
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38
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Tseng CK, Wang HF, Burns A, Schroeder M, Gaspari M, Baumann P. Human Telomerase RNA Processing and Quality Control. Cell Rep 2015; 13:2232-43. [DOI: 10.1016/j.celrep.2015.10.075] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/02/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
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39
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Physical Connectivity Mapping by Circular Permutation of Human Telomerase RNA Reveals New Regions Critical for Activity and Processivity. Mol Cell Biol 2015; 36:251-61. [PMID: 26503788 DOI: 10.1128/mcb.00794-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
Telomerase is a specialized ribonucleoprotein complex that extends the 3' ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5' and 3' ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3' of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics.
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Lin KW, McDonald KR, Guise AJ, Chan A, Cristea IM, Zakian VA. Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nat Commun 2015; 6:8290. [PMID: 26365526 PMCID: PMC4579843 DOI: 10.1038/ncomms9290] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022] Open
Abstract
Almost 400 genes affect yeast telomere length, including Est1, which is critical for recruitment and activation of telomerase. Here we use mass spectrometry to identify novel telomerase regulators by their co-purification with the telomerase holoenzyme. In addition to all known subunits, over 100 proteins are telomerase associated, including all three subunits of the essential Cdc48-Npl4-Ufd1 complex as well as three E3 ubiquitin ligases. The Cdc48 complex is evolutionarily conserved and targets ubiquitinated proteins for degradation. Est1 levels are ∼40-fold higher in cells with reduced Cdc48, yet, paradoxically, telomeres are shorter. Furthermore, Est1 is ubiquitinated and its cell cycle-regulated abundance is lost in Cdc48-deficient cells. Deletion of the telomerase-associated E3 ligase, Ufd4, in cdc48-3 cells further increases Est1 abundance but suppresses the telomere length phenotype of the single mutant. These data argue that, in concert with Ufd4, the Cdc48 complex regulates telomerase by controlling the level and activity of Est1.
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Affiliation(s)
- Kah-Wai Lin
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Karin R McDonald
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Amanda J Guise
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
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Abstract
In this review, Schmidt and Cech cover human telomerase biogenesis, trafficking, and activation, comparing key aspects with the analogous events in other species. Telomerase is the ribonucleoprotein enzyme that catalyzes the extension of telomeric DNA in eukaryotes. Recent work has begun to reveal key aspects of the assembly of the human telomerase complex, its intracellular trafficking involving Cajal bodies, and its recruitment to telomeres. Once telomerase has been recruited to the telomere, it appears to undergo a separate activation step, which may include an increase in its repeat addition processivity. This review covers human telomerase biogenesis, trafficking, and activation, comparing key aspects with the analogous events in other species.
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Affiliation(s)
- Jens C Schmidt
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, USA
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Vogan JM, Collins K. Dynamics of Human Telomerase Holoenzyme Assembly and Subunit Exchange across the Cell Cycle. J Biol Chem 2015; 290:21320-35. [PMID: 26170453 DOI: 10.1074/jbc.m115.659359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 01/04/2023] Open
Abstract
Human telomerase acts on telomeres during the genome synthesis phase of the cell cycle, accompanied by its concentration in Cajal bodies and transient colocalization with telomeres. Whether the regulation of human telomerase holoenzyme assembly contributes to the cell cycle restriction of telomerase function is unknown. We investigated the steady-state levels, assembly, and exchange dynamics of human telomerase subunits with quantitative in vivo cross-linking and other methods. We determined the physical association of telomerase subunits in cells blocked or progressing through the cell cycle as synchronized by multiple protocols. The total level of human telomerase RNA (hTR) was invariant across the cell cycle. In vivo snapshots of telomerase holoenzyme composition established that hTR remains bound to human telomerase reverse transcriptase (hTERT) throughout all phases of the cell cycle, and subunit competition assays suggested that hTERT-hTR interaction is not readily exchangeable. In contrast, the telomerase holoenzyme Cajal body-associated protein, TCAB1, was released from hTR in mitotic cells coincident with TCAB1 delocalization from Cajal bodies. This telomerase holoenzyme disassembly was reversible with cell cycle progression without any change in total TCAB1 protein level. Consistent with differential cell cycle regulation of hTERT-hTR and TCAB1-hTR protein-RNA interactions, overexpression of hTERT or TCAB1 had limited if any influence on hTR assembly of the other subunit. Overall, these findings revealed a cell cycle regulation that disables human telomerase association with telomeres while preserving the co-folded hTERT-hTR ribonucleoprotein catalytic core. Studies here, integrated with previous work, led to a unifying model for telomerase subunit assembly and trafficking in human cells.
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Affiliation(s)
- Jacob M Vogan
- From the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720
| | - Kathleen Collins
- From the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720
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Kwapisz M, Ruault M, van Dijk E, Gourvennec S, Descrimes M, Taddei A, Morillon A. Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae. Noncoding RNA 2015; 1:94-126. [PMID: 29861418 PMCID: PMC5932542 DOI: 10.3390/ncrna1020094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 11/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in S. cerevisiae of several lncRNAs within Y′ subtelomeric regions. We have called them subTERRA. These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. subTERRA transcription, carried out mainly by RNAPII, is initiated within the subtelomeric Y’ element and occurs in both directions, towards telomeres as well as centromeres. We show that subTERRA are distinct from TERRA and are mainly degraded by the general cytoplasmic and nuclear 5′- and 3′- RNA decay pathways in a transcription-dependent manner. subTERRA accumulates preferentially during the G1/S transition and in C-terminal rap1 mutant but independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomeres, loss of telomeric clustering in mitotic cells and changes in silencing of subtelomeric regions. Our data suggest that subtelomeric RNAs expression links telomere maintenance to RNA degradation pathways.
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Affiliation(s)
- Marta Kwapisz
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
- Authors to whom correspondence should be addressed; E-Mails: (M.K.); (A.M.); Tel.: +33-561-335-824 (M.K.); +33-(0)-156-246-515 (A.M.); Fax: +33-524-335-886 (M.K.); +33-(0)-156-246-674 (A.M.)
| | - Myriam Ruault
- Nuclear Dynamics, Institut Curie, PSL Research University, CNRS UMR3664, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mails: (M.R.); (A.T.)
| | - Erwin van Dijk
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Stephanie Gourvennec
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Marc Descrimes
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Angela Taddei
- Nuclear Dynamics, Institut Curie, PSL Research University, CNRS UMR3664, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mails: (M.R.); (A.T.)
| | - Antonin Morillon
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
- Authors to whom correspondence should be addressed; E-Mails: (M.K.); (A.M.); Tel.: +33-561-335-824 (M.K.); +33-(0)-156-246-515 (A.M.); Fax: +33-524-335-886 (M.K.); +33-(0)-156-246-674 (A.M.)
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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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The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets. Life (Basel) 2015; 5:1264-81. [PMID: 25905548 PMCID: PMC4500138 DOI: 10.3390/life5021264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2015] [Accepted: 04/15/2015] [Indexed: 12/04/2022] Open
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by an RNA-associated molecular assembly built on Sm proteins. Despite the availability of several 3D-structures of Sm-like archaeal proteins (SmAPs), their function has remained elusive. The aim of this study was to shed light on the function of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso). Using co-purification followed by RNASeq different classes of non-coding RNAs and mRNAs were identified that co-purified either with both paralogues or solely with Sso-SmAP1 or Sso-SmAP2. The large number of associated intron-containing tRNAs and tRNA/rRNA modifying RNAs may suggest a role of the two Sso-SmAPs in tRNA/rRNA processing. Moreover, the 3D structure of Sso-SmAP2 was elucidated. Like Sso-SmAP1, Sso-SmAP2 forms homoheptamers. The binding of both proteins to distinct RNA substrates is discussed in terms of surface conservation, structural differences in the RNA binding sites and differences in the electrostatic surface potential of the two Sso-SmAP proteins. Taken together, this study may hint to common and different functions of both Sso-SmAPs in Sso RNA metabolism.
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Prevalent and distinct spliceosomal 3'-end processing mechanisms for fungal telomerase RNA. Nat Commun 2015; 6:6105. [PMID: 25598218 PMCID: PMC4299825 DOI: 10.1038/ncomms7105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/15/2014] [Indexed: 11/19/2022] Open
Abstract
Telomerase RNA (TER) is an essential component of the telomerase ribonucleoprotein complex. The mechanism for TER 3′-end processing is highly divergent among different organisms. Here we report a unique spliceosome-mediated TER 3′-end cleavage mechanism in Neurospora crassa which is distinct from that found specifically in the fission yeast Schizosaccharomyces pombe. While the S. pombe TER intron contains the canonical 5′-splice site GUAUGU, the N. crassa TER intron contains a non-canonical 5′-splice site AUAAGU that alone prevents the second step of splicing and promotes spliceosomal cleavage. The unique N. crassa TER 5′-splice site sequence is evolutionarily conserved in TERs from Pezizomycotina and early branching Taphrinomycotina species. This suggests that the widespread and basal N. crassa-type spliceosomal cleavage mechanism is more ancestral than the S. pombe-type. The discovery of a prevalent, yet distinct, spliceosomal cleavage mechanism throughout diverse fungal clades furthers our understanding of TER evolution and non-coding RNA processing.
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Wu H, Becker D, Krebber H. Telomerase RNA TLC1 shuttling to the cytoplasm requires mRNA export factors and is important for telomere maintenance. Cell Rep 2014; 8:1630-1638. [PMID: 25220466 DOI: 10.1016/j.celrep.2014.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/09/2014] [Accepted: 08/08/2014] [Indexed: 12/23/2022] Open
Abstract
Telomerases protect the ends of linear chromosomes from shortening. They are composed of an RNA (TLC1 in S. cerevisiae) and several proteins. TLC1 undergoes several maturation steps before it is exported into the cytoplasm to recruit the Est proteins for complete assembly. The mature telomerase is subsequently reimported into the nucleus, where it fulfills its function on telomeres. Here, we show that TLC1 export into the cytoplasm requires not only the Ran GTPase-dependent karyopherin Crm1/Xpo1 but also the mRNA export machinery. mRNA export factor mutants accumulate mature and export-competent TLC1 RNAs in their nuclei. Moreover, TLC1 physically interacts with the mRNA transport factors Mex67 and Dbp5/Rat8. Most importantly, we show that the nuclear export of TLC1 is an essential step for the formation of the functional RNA containing enzyme, because blocking TLC1 export in the mex67-5 xpo1-1 double mutant prevents its cytoplasmic maturation and leads to telomere shortening.
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Affiliation(s)
- Haijia Wu
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany
| | - Daniel Becker
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, 37077 Göttingen, Germany.
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48
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Abstract
In budding yeast, telomerase consists of the catalytic Est2 protein and two regulatory subunits (Est1 and Est3) in association with the TLC1 RNA, with each of the four subunits essential for in vivo telomerase function. Tucey and Lundblad show that a hierarchy of assembly and disassembly results in limiting amounts of the quaternary complex late in the cell cycle, following completion of DNA replication. Telomerase disassembles due to dissociation of the catalytic subunit from the complex in every cell cycle. The enzyme telomerase, which elongates chromosome termini, is a critical factor in determining long-term cellular proliferation and tissue renewal. Hence, even small differences in telomerase levels can have substantial consequences for human health. In budding yeast, telomerase consists of the catalytic Est2 protein and two regulatory subunits (Est1 and Est3) in association with the TLC1 RNA, with each of the four subunits essential for in vivo telomerase function. We show here that a hierarchy of assembly and disassembly results in limiting amounts of the quaternary complex late in the cell cycle, following completion of DNA replication. The assembly pathway, which is driven by interaction of the Est3 telomerase subunit with a previously formed Est1–TLC1–Est2 preassembly complex, is highly regulated, involving Est3-binding sites on both Est2 and Est1 as well as an interface on Est3 itself that functions as a toggle switch. Telomerase subsequently disassembles by a mechanistically distinct pathway due to dissociation of the catalytic subunit from the complex in every cell cycle. The balance between the assembly and disassembly pathways, which dictate the levels of the active holoenzyme in the cell, reveals a novel mechanism by which telomerase (and hence telomere homeostasis) is regulated.
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Affiliation(s)
- Timothy M Tucey
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA; Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Victoria Lundblad
- Salk Institute for Biological Studies, La Jolla, California 92037, USA
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Quality control of assembly-defective U1 snRNAs by decapping and 5'-to-3' exonucleolytic digestion. Proc Natl Acad Sci U S A 2014; 111:E3277-86. [PMID: 25071210 DOI: 10.1073/pnas.1412614111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The accurate biogenesis of RNA-protein complexes is a key aspect of eukaryotic cells. Defects in Sm protein complex binding to snRNAs are known to reduce levels of snRNAs, suggesting an unknown quality control system for small nuclear ribonucleoprotein (snRNP) assembly. snRNA quality control may also be relevant in spinal muscular atrophy, which is caused by defects in the survival motor neuron (SMN)1 gene, an assembly factor for loading the Sm complex on snRNAs and, when severely reduced, can lead to reduced levels of snRNAs and splicing defects. To determine how assembly-defective snRNAs are degraded, we first demonstrate that yeast U1 Sm-mutant snRNAs are degraded either by Rrp6- or by Dcp2-dependent decapping/5'-to-3' decay. Knockdown of the decapping enzyme DCP2 in mammalian cells also increases the levels of assembly-defective snRNAs and suppresses some splicing defects seen in SMN-deficient cells. These results identify a conserved mechanism of snRNA quality control, and also suggest a general paradigm wherein the phenotype of an "RNP assembly disease" might be suppressed by inhibition of a competing RNA quality control mechanism.
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50
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Normal telomere length maintenance in Saccharomyces cerevisiae requires nuclear import of the ever shorter telomeres 1 (Est1) protein via the importin alpha pathway. EUKARYOTIC CELL 2014; 13:1036-50. [PMID: 24906415 DOI: 10.1128/ec.00115-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Est1 (ever shorter telomeres 1) protein is an essential component of yeast telomerase, a ribonucleoprotein complex that restores the repetitive sequences at chromosome ends (telomeres) that would otherwise be lost during DNA replication. Previous work has shown that the telomerase RNA component (TLC1) transits through the cytoplasm during telomerase biogenesis, but mechanisms of protein import have not been addressed. Here we identify three nuclear localization sequences (NLSs) in Est1p. Mutation of the most N-terminal NLS in the context of full-length Est1p reduces Est1p nuclear localization and causes telomere shortening-phenotypes that are rescued by fusion with the NLS from the simian virus 40 (SV40) large-T antigen. In contrast to that of the TLC1 RNA, Est1p nuclear import is facilitated by Srp1p, the yeast homolog of importin α. The reduction in telomere length observed at the semipermissive temperature in a srp1 mutant strain is rescued by increased Est1p expression, consistent with a defect in Est1p nuclear import. These studies suggest that at least two nuclear import pathways are required to achieve normal telomere length homeostasis in yeast.
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