Structural study of elements of Tetrahymena telomerase RNA stem-loop IV domain important for function

RNA

Volumn 12, Issue 8, 2006, Pages 1475-1485

  Richards, Rebecca J ^a   Wu, Haihong ^a   Trantirek, Lukas ^a,c   O'Connor, Catherine M ^b   Collins, Kathleen ^b   Feigon, Juli ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

Author keywords

GA bulge; NMR; p65; Structure; TER; TERT

Indexed keywords

CURVED DNA; HOLOENZYME; RIBONUCLEOPROTEIN; RNA; SYNAPTOTAGMIN; TELOMERASE; TELOMERASE REVERSE TRANSCRIPTASE;

ARTICLE; BASE PAIRING; BINDING SITE; BIOCHEMISTRY; ENZYME STRUCTURE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; STEM LOOP IV DOMAIN; TETRAHYMENA;

ANIMALS; BASE PAIRING; BASE SEQUENCE; BINDING SITES; CATALYSIS; HOLOENZYMES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; RNA; RNA, PROTOZOAN; TELOMERASE; TEMPLATES, GENETIC; TETRAHYMENA THERMOPHILA;

TETRAHYMENA;

EID: 33746483846     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.112306     Document Type: Article

References (49)

1. Al-Hashimi, H.M., Gosser, Y., Gorin, A., Hu, W.D., Majumdar, A., and Patel, D.J. 2002. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol. 315: 95-102.
2. Allain, F.H.-T. and Varani, G. 1995. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250: 333-353.
3. Autexier, C. and Greider, C.W. 1995. Boundary elements of the Tetrahymena telomerase RNA template and alignment domains. Genes & Dev. 9: 2227-2239.
4. _. 1998. Mutational analysis of the Tetrahymena telomerase RNA: Identification of residues affecting telomerase activity in vitro. Nucleic Acids Res. 26: 787-795.
5. Bhattacharyya, A. and Blackburn, E.H. 1994. Architecture of telomerase RNA. EMBO J. 13: 5721-5731.
6. Brunger, A.T. 1992. X-PLOR, version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.
7. Chan, S.R.W.L. and Blackburn, E.H. 2004. Telomeres and telomerase. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359: 109-121.
8. Chen, J.L. and Greider, C.W. 2004. Telomerase RNA structure and function: Implications for dyskeratosis congenita. Trends Biochem. Sci. 29: 183-192.
9. Cromsigt, J., van Buuren, B., Schleucher, J., and Wijmenga, S.S. 2001. Resonance assignment and structure determination for RNA. In Methods in enzymology (eds. T. James et al.), pp. 371-399. Academic Press, San Diego, CA.
10. Dayie, K.T., Brodsky, A.S., and Williamson, J.R. 2002. Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation. J. Mol. Biol. 317: 263-278.
11. Dieckmann, T. and Feigon, J. 1997. Assignment methodology for larger oligonucleotides: Application to an ATP-binding RNA aptamer. J. Biomol. NMR 9: 259-272.
12. Dosset, P., Hus, J.C., Marion, D., and Blackledge, M. 2001. A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J. Biomol. NMR 20: 223-231.
13. Gilley, D. and Blackburn, E.H. 1999. The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein. Proc. Natl. Acad. Sci. 96: 6621-6625.
14. Greider, C.W. 1991. Telomerase is processive. Mol. Cell. Biol. 11: 4572-4580.
15. Greider, C.W. and Blackburn, E.H. 1985. Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell 43: 405-413.
16. _. 1989. A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis. Nature 337: 331-337.
17. Harrington, L 2003. Biochemical aspects of telomerase function. Cancer Lett. 194: 139-154.
18. Jacobs, S.A., Podell, E.R., and Cech, T.R. 2006. Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase. Nat. Struct. Mol. Biol. 13: 218-225.
19. Kelleher, C., Teixeira, M.T., Forstemann, K., and Lingner, J. 2002. Telomerase: Biochemical considerations for enzyme and substrate. Trends Biochem. Sci. 27: 572-579.
20. Kolk, M.H., Wijmenga, S.S., Heus, H.A., and Hilbers, C.W. 1998. On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints. J. Biomol. NMR 12: 423-433.
21. Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL - A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
22. Lai, C.K., Mitchell, J.R., and Collins, K. 2001. RNA binding domain of telomerase reverse transcriptase. Mol. Cell. Biol. 21: 990-1000.
23. Lai, C.K., Miller, M.C., and Collins, K. 2002. Template boundary definition in Tetrahymena telomerase. Genes & Dev. 16: 415-420.
24. _. 2003. Roles for RNA in telomerase nucleotide and repeat addition processivity. Mol. Cell 11: 1673-1683.
25. Legault, P., Jucker, F.M., and Pardi, A. 1995. Improved measurement of C-13, P-31 J coupling constants in isotopically labeled RNA. FEBS Lett. 362: 156-160.
26. Licht, J.D. and Collins, K. 1999. Telomerase RNA function in recombinant Tetrahymena telomerase. Genes & Dev. 13: 1116-1125.
27. Lingner, J., Hendrick, L.L., and Cech, T.R. 1994. Telomerase RNAs of different ciliates have a common secondary structure and a permuted template. Genes & Dev. 8: 1984-1998.
28. Lingner, J., Hughes, T.R., Shevchenko, A., Mann, M., Lundblad, V., and Cech, T.R. 1997. Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 276: 561-567.
29. Losonczi, J.A., Andrec, M., Fischer, M.W.F., and Prestegard, J.H. 1999. Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Reson. 138: 334-342.
30. Lu, X.J. and Olson, W.K. 2003. 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31: 5108-5121.
31. Lue, N.F. 2004. Adding to the ends: What makes telomerase processive and how important is it? Bioessays 26: 955-962.
32. Luy, B. and Marino, J.P. 2000. Direct evidence for Watson-Crick base pairs in a dynamic region of RNA structure. J. Am. Chem. Soc. 122: 8095-8096.
33. Mason, D.X., Goneska, E., and Greider, C.W. 2003. Stem-loop IV of Tetrahymena telomerase RNA stimulates processivity in trans. Mol. Cell. Biol. 23: 5606-5613.
34. McCormick-Graham, M. and Romero, D.P. 1995. Ciliate telomerase RNA structural features. Nucleic Acids Res. 23: 1091-1097.
35. Miller, M.C. and Collins, K. 2002. Telomerase recognizes its template by using an adjacent RNA motif. Proc. Natl. Acad. Sci. 99: 6585-6590.
36. Nakamura, T.M. and Cech, T.R. 1998. Reversing time: Origin of telomerase. Cell 92: 587-590.
37. O'Connor, C.M. and Collins, K. 2006. A novel RNA binding domain in tetrahymena telomerase p65 initiates hierarchical assembly of telomerase holoenzyme. Mol. Cell. Biol. 26: 2029-2036.
38. O'Connor, C.M., Lai, C.K., and Collins, K. 2005. Two purified domains of telomerase reverse transcriptase reconstitute sequence-specific interactions with RNA. J. Biol. Chem. 280: 17533-17539.
39. Prathapam, R., Witkin, K.L., O'Connor, C.M., and Collins, K. 2005. A telomerase holoenzyme protein enhances telomerase RNA assembyl with telomerase reverse transcriptase. Nat. Struct. Mol. Biol. 12: 252-257.
40. Richards, R.J., Theimer, C.A., Finger, L.D., and Feigon, J. 2006. Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element. Nucleic Acids Res. 34: 816-825.
41. Romero, D.P. and Blackburn, E.H. 1991. A conserved secondary structure for telomerase RNA. Cell 67: 343-353.
42. Rückert, M. and Otting, G. 2000. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J. Am. Chem. Soc. 122: 7793-7797.
43. Schwieters, C.D., Kuszewski, J.J., Tjandra, N., and Clore, G.M. 2003. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160: 65-73.
44. Sperger, J.M. and Cech, T.R. 2001. A stem-loop of Tetrahymena telomerase RNA distant from the template potentiates RNA folding and telomerase activity. Biochemistry 40: 7005-7016.
45. Tolman, J.R., Al-Hashimi, H.M., Kay, L.E., and Prestegard, J.H. 2001. Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc. 123: 1416-1424.
46. Valafar, H. and Prestegard, J.H. 2003. REDCAT: A residual dipolar coupling analysis tool. J. Magn. Reson. 167: 228-241.
47. Varani, G., Aboul-ela, F., and Allain, F.H.-T. 1996. NMR investigation of RNA structure. Prog. NMR Spectrosc. 29: 51-127.
48. Witkin, K.L. and Collins, K. 2004. Holoenzyme proteins required for the physiological assembly and activity of telomerase. Genes & Dev. 18: 1107-1118.
49. Ye, A.J. and Romero, D.P. 2002. Phylogenetic relationships amongst tetrahymenine ciliates inferred by a comparison of telomerase RNAs. Int. J. Syst. Evol. Microbiol. 52: 2297-2302.