Secondary Structure of Vertebrate Telomerase RNA

Telomerase is a ribonucleoprotein enzyme that maintains telomere length by adding telomeric sequence repeats onto chromosome ends. The essential RNA component of telomerase provides the template for telomeric repeat synthesis. To determine the secondary structure of vertebrate telomerase RNA, 32 new telomerase RNA genes were cloned and sequenced from a variety of vertebrate species including 18 mammals, 2 birds, 1 reptile, 7 amphibians, and 4 fishes. Using phylogenetic comparative analysis, we propose a secondary structure that contains four structural domains conserved in all vertebrates. Ten helical regions of the RNA are universally conserved while other regions vary significantly in length and sequence between different classes of vertebrates. The proposed vertebrate telomerase RNA structure displays a strikingly similar topology to the previously determined ciliate telomerase RNA structure, implying an evolutionary conservation of the global architecture of telomerase RNA.

[1]  D. Romero,et al.  Ciliate telomerase RNA structural features. , 1995, Nucleic acids research.

[2]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[3]  D. Gottschling,et al.  TLC1: template RNA component of Saccharomyces cerevisiae telomerase. , 1994, Science.

[4]  N. Pace,et al.  Comparative photocross‐linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs , 1998, The EMBO journal.

[5]  R. Terns,et al.  Nucleolar localization signals of Box H/ACA small nucleolar RNAs , 1999, The EMBO journal.

[6]  K. Ríha,et al.  Disruption of the telomerase catalytic subunit gene from Arabidopsis inactivates telomerase and leads to a slow loss of telomeric DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[7]  K. Collins,et al.  The reverse transcriptase component of the Tetrahymena telomerase ribonucleoprotein complex. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  K. Pleij,et al.  A conserved pseudoknot in telomerase RNA. , 1991, Nucleic acids research.

[9]  N. Pace,et al.  Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. , 1989, Gene.

[10]  E. Blackburn,et al.  The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Gutell,et al.  Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. , 1983, Microbiological reviews.

[12]  H. Noller,et al.  Secondary structure of 16S ribosomal RNA. , 1981, Science.

[13]  Tamás Kiss,et al.  Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs , 1997, Cell.

[14]  Carol W. Greider,et al.  The telomere terminal transferase of tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity , 1987, Cell.

[15]  et al.,et al.  The RNA component of human telomerase , 1995, Science.

[16]  Gregg B. Morin,et al.  Reconstitution of human telomerase with the template RNA component hTR and the catalytic protein subunit hTRT , 1997, Nature Genetics.

[17]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[18]  E. Dam,et al.  Structural and functional aspects of RNA pseudoknots. , 1992, Biochemistry.

[19]  T. Cech,et al.  Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle , 1999, Nature.

[20]  Y. S. Lin,et al.  Molecular cloning of bovine telomerase RNA. , 1998, Gene.

[21]  James W. Brown,et al.  Phylogenetic analysis and evolution of RNase P RNA in proteobacteria , 1991, Journal of bacteriology.

[22]  Jeffrey B. Cheng,et al.  A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3′ End , 1999, Molecular and Cellular Biology.

[23]  W. Herr,et al.  The mouse telomerase RNA 5"-end lies just upstream of the telomerase template sequence. , 1998, Nucleic acids research.

[24]  M. Goodman,et al.  Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences. , 1990, Methods in enzymology.

[25]  K. Tamura,et al.  Molecular cloning and characterization of AtTERT, a telomerase reverse transcriptase homolog in Arabidopsis thaliana , 1999, FEBS letters.

[26]  T. Cech,et al.  Telomerase reverse transcriptase genes identified in Tetrahymena thermophila and Oxytricha trifallax. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[27]  M. Blasco,et al.  Functional characterization and developmental regulation of mouse telomerase RNA , 1995, Science.

[28]  K. Collins,et al.  Ciliate telomerase biochemistry. , 1999, Annual review of biochemistry.

[29]  T R Hughes,et al.  Reverse transcriptase motifs in the catalytic subunit of telomerase. , 1997, Science.

[30]  C. Autexier,et al.  Mutational analysis of the Tetrahymena telomerase RNA: identification of residues affecting telomerase activity in vitro. , 1998, Nucleic acids research.

[31]  Laurie Smith,et al.  The RNA World of the Nucleolus: Two Major Families of Small RNAs Defined by Different Box Elements with Related Functions , 1996, Cell.

[32]  C. Autexier,et al.  Boundary elements of the Tetrahymena telomerase RNA template and alignment domains. , 1995, Genes & development.

[33]  A. Weiner,et al.  Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. , 1986, Annual review of biochemistry.

[34]  Bryan Frank,et al.  Two Inactive Fragments of the Integral RNA Cooperate To Assemble Active Telomerase with the Human Protein Catalytic Subunit (hTERT) In Vitro , 1999, Molecular and Cellular Biology.

[35]  E. Blackburn,et al.  Runaway telomere elongation caused by telomerase RNA gene mutations , 1995, Nature.

[36]  M. Kindruk,et al.  On a method for determining the , 1973 .

[37]  C B Harley,et al.  Telomerase catalytic subunit homologs from fission yeast and human. , 1997, Science.

[38]  R. Weinberg,et al.  hEST2, the Putative Human Telomerase Catalytic Subunit Gene, Is Up-Regulated in Tumor Cells and during Immortalization , 1997, Cell.

[39]  L. Chin,et al.  Expression of mouse telomerase reverse transcriptase during development, differentiation and proliferation , 1998, Oncogene.

[40]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[41]  R. Gutell,et al.  Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. , 1994, Microbiological reviews.

[42]  D. Tollervey,et al.  Function and synthesis of small nucleolar RNAs. , 1997, Current opinion in cell biology.

[43]  E. Blackburn,et al.  In vivo alteration of telomere sequences and senescence caused by mutated Tetrahymena telomerase RNAs , 1990, Nature.

[44]  C. Autexier,et al.  Reconstitution of human telomerase activity and identification of a minimal functional region of the human telomerase RNA. , 1996, The EMBO journal.

[45]  N. Larsen,et al.  SRP-RNA sequence alignment and secondary structure. , 1991, Nucleic acids research.

[46]  T. Kiss,et al.  The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. , 1997, Genes & development.

[47]  E. Blackburn,et al.  Altering specific telomerase RNA template residues affects active site function. , 1995, Genes & development.

[48]  E. Blackburn,et al.  A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis , 1989, Nature.

[49]  D Gautheret,et al.  A major family of motifs involving G.A mismatches in ribosomal RNA. , 1994, Journal of molecular biology.

[50]  Daniel P. Romero,et al.  A conserved secondary structure for telomerase RNA , 1991, Cell.

[51]  James W. Brown,et al.  Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[52]  J. Ofengand,et al.  The pseudouridine residues of ribosomal RNA. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[53]  T. Cech,et al.  Method for determining RNA 3' ends and application to human telomerase RNA. , 1996, Nucleic acids research.

[54]  E. Blackburn,et al.  Specific RNA residue interactions required for enzymatic functions of Tetrahymena telomerase , 1996, Molecular and cellular biology.

[55]  R. Weinberg,et al.  The catalytic subunit of yeast telomerase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[56]  B. Ganem.  RNA world , 1987, Nature.

[57]  J. Licht,et al.  Telomerase RNA function in recombinant Tetrahymena telomerase. , 1999, Genes & development.

[58]  D. Bartel,et al.  Phylogenetic analysis of tmRNA secondary structure. , 1996, RNA.

[59]  V A Zakian,et al.  Structure, function, and replication of Saccharomyces cerevisiae telomeres. , 1996, Annual review of genetics.

[60]  T. Cech,et al.  Telomerase RNAs of different ciliates have a common secondary structure and a permuted template. , 1994, Genes & development.

[61]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[62]  C. Pleij,et al.  RNA pseudoknots: structure, detection, and prediction. , 1989, Methods in enzymology.

[63]  S. Lukyanov,et al.  An improved PCR method for walking in uncloned genomic DNA. , 1995, Nucleic acids research.

[64]  E. Vanin,et al.  Processed pseudogenes: characteristics and evolution. , 1984, Annual review of genetics.

[65]  Carol W. Greider,et al.  Identification of a specific telomere terminal transferase activity in tetrahymena extracts , 1985, Cell.

[66]  M. Robinson,et al.  Reconstitution of human telomerase activity in vitro , 1998, Current Biology.

[67]  N. Pace,et al.  The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme , 1988, Cell.