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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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2
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The inhibitory effects of Dulaglutide on cellular senescence against high glucose in human retinal endothelial cells. Hum Cell 2022; 35:995-1004. [PMID: 35583801 DOI: 10.1007/s13577-022-00703-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/13/2022] [Indexed: 01/25/2023]
Abstract
Diabetic nephropathy is one of the most important chronic microvascular complications of diabetes, and its main feature is diabetic glomerulosclerosis. Endothelial sirtuin 1 (SIRT1) expression is related to aging, and reducing SIRT1 expression promotes endothelial cell aging. Plasminogen activator inhibitor-1 (PAI-1) can be synthesized in a variety of cells, such as endothelial cells. Dulaglutide is a glucagon-like peptide-1 (GLP-1) drug, and it can activate the GLP-1 receptor and promote the conversion of intracellular adenosine triphosphate to adenylate cyclase, thereby activating phosphokinase A, and regulating blood glucose levels effectively in the body. We analyzed the effects of Dulaglutide on inhibiting cell senescence by studying the effects of its different concentrations on telomerase activity and senescence-related gene expression. Our results suggest that Dulaglutide can alleviate high-glucose-induced oxidative stress in human retinal endothelial cells by restoring the expressions of SIRT1 and endothelial nitric oxide synthase (eNOS), thereby inhibiting the expression of PAI-1, and restoring telomerase activity. This suggests that the activity of retinal endothelial cells can be controlled by regulating the expression of SIRT1, so as to achieve the effect of treating diabetic retinopathy.
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3
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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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4
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Fujimoto K, Watanabe N. Fluorescence In Situ Hybridization of 16S rRNA in
Escherichia coli
Using Multiple Photo‐Cross‐Linkable Probes. ChemistrySelect 2020. [DOI: 10.1002/slct.202003343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kenzo Fujimoto
- School of Advanced Science and Technology Japan Advanced Institute of Science and Technology Asahidai 1–1, Nomi Ishikawa 923-1292 Japan
| | - Nanami Watanabe
- School of Advanced Science and Technology Japan Advanced Institute of Science and Technology Asahidai 1–1, Nomi Ishikawa 923-1292 Japan
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5
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Song J, Logeswaran D, Castillo-González C, Li Y, Bose S, Aklilu BB, Ma Z, Polkhovskiy A, Chen JJL, Shippen DE. The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans. Proc Natl Acad Sci U S A 2019; 116:24542-24550. [PMID: 31754031 PMCID: PMC6900512 DOI: 10.1073/pnas.1915312116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Telomerase is essential for maintaining telomere integrity. Although telomerase function is widely conserved, the integral telomerase RNA (TR) that provides a template for telomeric DNA synthesis has diverged dramatically. Nevertheless, TR molecules retain 2 highly conserved structural domains critical for catalysis: a template-proximal pseudoknot (PK) structure and a downstream stem-loop structure. Here we introduce the authentic TR from the plant Arabidopsis thaliana, called AtTR, identified through next-generation sequencing of RNAs copurifying with Arabidopsis TERT. This RNA is distinct from the RNA previously described as the templating telomerase RNA, AtTER1. AtTR is a 268-nt Pol III transcript necessary for telomere maintenance in vivo and sufficient with TERT to reconstitute telomerase activity in vitro. Bioinformatics analysis identified 85 AtTR orthologs from 3 major clades of plants: angiosperms, gymnosperms, and lycophytes. Through phylogenetic comparisons, a secondary structure model conserved among plant TRs was inferred and verified using in vitro and in vivo chemical probing. The conserved plant TR structure contains a template-PK core domain enclosed by a P1 stem and a 3' long-stem P4/5/6, both of which resemble a corresponding structural element in ciliate and vertebrate TRs. However, the plant TR contains additional stems and linkers within the template-PK core, allowing for expansion of PK structure from the simple PK in the smaller ciliate TR during evolution. Thus, the plant TR provides an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates.
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Affiliation(s)
- Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | | | | | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Sreyashree Bose
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Behailu Birhanu Aklilu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Zeyang Ma
- National Maize Improvement Center of China, China Agricultural University, 100193 Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, 100193 Beijing, China
| | - Alexander Polkhovskiy
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russian Federation
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287;
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843;
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6
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Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes (Basel) 2018; 9:genes9080372. [PMID: 30049970 PMCID: PMC6115765 DOI: 10.3390/genes9080372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/20/2022] Open
Abstract
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.
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Affiliation(s)
- Maria Waldl
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Bernhard C Thiel
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Roman Ochsenreiter
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Alexander Holzenleiter
- BioInformatics Group, Fakultät CB Hochschule Mittweida, Technikumplatz 17, D-09648 Mittweida, Germany.
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
| | - João Victor de Araujo Oliveira
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário⁻Asa Norte, Brasília, DF CEP: 70910-900, Brazil.
| | - Maria Emília M T Walter
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário⁻Asa Norte, Brasília, DF CEP: 70910-900, Brazil.
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
- Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria.
| | - Peter F Stadler
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Universität Leipzig, D-04107 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.
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7
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Wu RA, Tam J, Collins K. DNA-binding determinants and cellular thresholds for human telomerase repeat addition processivity. EMBO J 2017; 36:1908-1927. [PMID: 28495680 PMCID: PMC5494469 DOI: 10.15252/embj.201796887] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
The reverse transcriptase telomerase adds telomeric repeats to chromosome ends. Purified human telomerase catalyzes processive repeat synthesis, which could restore the full ~100 nucleotides of (T2AG3)n lost from replicated chromosome ends as a single elongation event. Processivity inhibition is proposed to be a basis of human disease, but the impacts of different levels of processivity on telomere maintenance have not been examined. Here, we delineate side chains in the telomerase active-site cavity important for repeat addition processivity, determine how they contribute to duplex and single-stranded DNA handling, and test the cellular consequences of partial or complete loss of repeat addition processivity for telomere maintenance. Biochemical findings oblige a new model for DNA and RNA handling dynamics in processive repeat synthesis. Biological analyses implicate repeat addition processivity as essential for telomerase function. However, telomeres can be maintained by telomerases with lower than wild-type processivity. Furthermore, telomerases with low processivity dramatically elongate telomeres when overexpressed. These studies reveal distinct consequences of changes in telomerase repeat addition processivity and expression level on telomere elongation and length maintenance.
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Affiliation(s)
- Robert Alexander Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jane Tam
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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8
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Long noncoding RNAs in the progression, metastasis, and prognosis of osteosarcoma. Cell Death Dis 2016; 7:e2389. [PMID: 27685633 PMCID: PMC5059871 DOI: 10.1038/cddis.2016.272] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a class of non-protein-coding molecules longer than 200 nucleotides that are involved in the development and progression of many types of tumors. Numerous lncRNAs regulate cell proliferation, metastasis, and chemotherapeutic drug resistance. Osteosarcoma is one of the main bone tumor subtypes that poses a serious threat to adolescent health. We summarized how lncRNAs regulate osteosarcoma progression, invasion, and drug resistance, as well as how lncRNAs can function as biomarkers or independent prognostic indicators with respect to osteosarcoma therapy.
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9
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Podlevsky JD, Li Y, Chen JJL. The functional requirement of two structural domains within telomerase RNA emerged early in eukaryotes. Nucleic Acids Res 2016; 44:9891-9901. [PMID: 27378779 PMCID: PMC5175330 DOI: 10.1093/nar/gkw605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022] Open
Abstract
Telomerase emerged during evolution as a prominent solution to the eukaryotic linear chromosome end-replication problem. Telomerase minimally comprises the catalytic telomerase reverse transcriptase (TERT) and telomerase RNA (TR) that provides the template for telomeric DNA synthesis. While the TERT protein is well-conserved across taxa, TR is highly divergent amongst distinct groups of species. Herein, we have identified the essential functional domains of TR from the basal eukaryotic species Trypanosoma brucei, revealing the ancestry of TR comprising two distinct structural core domains that can assemble in trans with TERT and reconstitute active telomerase enzyme in vitro. The upstream essential domain of T. brucei TR, termed the template core, constitutes three short helices in addition to the 11-nt template. Interestingly, the trypanosome template core domain lacks the ubiquitous pseudoknot found in all known TRs, suggesting later evolution of this critical structural element. The template-distal domain is a short stem-loop, termed equivalent CR4/5 (eCR4/5). While functionally similar to vertebrate and fungal CR4/5, trypanosome eCR4/5 is structurally distinctive, lacking the essential P6.1 stem-loop. Our functional study of trypanosome TR core domains suggests that the functional requirement of two discrete structural domains is a common feature of TRs and emerged early in telomerase evolution.
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Affiliation(s)
- Joshua D Podlevsky
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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10
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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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11
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Abstract
The addition of telomeric DNA to chromosome ends is an essential cellular activity that compensates for the loss of genomic DNA that is due to the inability of the conventional DNA replication apparatus to duplicate the entire chromosome. The telomerase reverse transcriptase and its associated RNA bind to the very end of the telomere via a sequence in the RNA and specific protein-protein interactions. Telomerase RNA also provides the template for addition of new telomeric repeats by the reverse-transcriptase protein subunit. In addition to the template, there are 3 other conserved regions in telomerase RNA that are essential for normal telomerase activity. Here we briefly review the conserved core regions of telomerase RNA and then focus on a recent study in fission yeast that determined the function of another conserved region in telomerase RNA called the Stem Terminus Element (STE). (1) The STE is distant from the templating core of telomerase in both the linear and RNA secondary structure, but, nonetheless, affects the fidelity of telomere sequence addition and, in turn, the ability of telomere binding proteins to bind and protect chromosome ends. We will discuss possible mechanisms of STE action and the suitability of the STE as an anti-cancer target.
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Affiliation(s)
- Christopher J Webb
- a Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Virginia A Zakian
- a Department of Molecular Biology , Princeton University , Princeton , NJ , USA
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