RNA as a flexible scaffold for proteins: Yeast telomerase and beyond

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 71, Issue , 2006, Pages 217-224

  Zappulla, D C ^a   Cech, T R ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBONUCLEASE P; RNA; SCAFFOLD PROTEIN; SIGNAL RECOGNITION PARTICLE; SMALL NUCLEOLAR RIBONUCLEOPROTEIN; TELOMERASE; TRANSFER MESSENGER RNA; UNCLASSIFIED DRUG; FUNGAL RNA; RIBONUCLEOPROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; TELOMERASE RNA;

ARTICLE; CATALYSIS; CHROMATIN STRUCTURE; DNA SYNTHESIS; FLEXIBLE SCAFFOLD MODEL; GENE EXPRESSION REGULATION; HUMAN; INTERNAL RIBOSOME ENTRY SITE; NONBIOLOGICAL MODEL; NONHUMAN; PRIORITY JOURNAL; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION; YEAST; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; MACROMOLECULE; METABOLISM; SACCHAROMYCES CEREVISIAE;

BINDING SITES; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEINS; RNA; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERASE;

EID: 34250619257     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2006.71.011     Document Type: Conference Paper

References (59)

1. Achsel T., Ahrens, K., Brahms H., Teigelkamp S., and Luhrmann R. 1998. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Mol. Cell. Biol. 18: 6756.
2. Batey R.T. 2006. Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol. 16: 299.
3. Boehringer D., Thermann R., Ostareck-Lederer A., Lewis J.D., and Stark H. 2005. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: Remodeling of the HCV IRES. Structure 13: 1695.
4. Brodersen D.E., Clemons W.M., Jr., Carter A.P., Wimberly B.T., and Ramakrishnan V. 2002. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 S RNA. J. Mol. Biol. 316: 725.
5. Burks J., Zwieb C., Muller F., Wower I., and Wower J. 2005. Comparative 3-D modeling of tmRNA. BMC Mol. Biol. 6: 14.
6. Chappell A.S. and Lundblad V. 2004. Structural elements required for association of the Saccharomyces cerevisiae telomerase RNA with the Est2 reverse transcriptase. Mol. Cell. Biol. 24: 7720.
7. Chen J.L., Blasco M.A., and Greider C.W. 2000. Secondary structure of vertebrate telomerase RNA. Cell 100: 503.
8. Dandjinou A.T., Levesque N., Larose S., Lucier J.F., Abou Elela S., and Wellinger R.J. 2004. A phylogenetically based secondary structure for the yeast telomerase RNA. Curr. Biol. 14: 1148.
9. Egea P.F., Stroud R.M., and Walter P. 2005. Targeting proteins to membranes: Structure of the signal recognition particle. Curr. Opin. Struct. Biol. 15: 213.
10. Ganot P., Bortolin M.L., and Kiss T. 1997. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799.
11. Golas M.M., Sander B., Will C.L., Luhrmann R., and Stark H. 2005. Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol. Cell 17: 869.
12. Greider C.W. and Blackburn E.H. 1989. A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis. Nature 337: 331.
13. Haebel P.W., Gutmann S., and Ban N. 2004. Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs. Curr. Opin. Struct. Biol. 14: 58.
14. Halic M., Becker T., Pool M.R., Spahn C.M., Grassucci R.A., Frank J., and Beckmann R. 2004. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427: 808.
15. Igel A.H. and Ares M., Jr. 1988. Internal sequences that distinguish yeast from metazoan U2 snRNA are unnecessary for pre-mRNA splicing. Nature 334: 450.
16. Kachouri R., Stribinskis V., Zhu Y., Ramos K.S., Westhof E., and Li Y. 2005. A surprisingly large RNase P RNA in Candida glabrata. RNA 11: 1064.
17. Karzai A.W. and Sauer R.T. 2001. Protein factors associated with the SsrA•SmpB tagging and ribosome rescue complex. Proc. Natl. Acad. Sci. 98: 3040.
18. Kiss-Laszlo Z., Henry Y., Bachellerie J.P., Caizergues-Ferrer M., and Kiss T. 1996. Site-specific ribose methylation of pre-ribosomal RNA: A novel function for small nucleolar RNAs. Cell 85: 1077.
19. Klein D.J., Moore P.B., and Steitz T.A. 2004. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol. 340: 141.
20. 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.
21. 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.
22. Livengood A.J., Zaug A.J., and Cech T.R. 2002. Essential regions of Saccharomyces cerevisiae telomerase RNA: Separate elements for Est1p and Est2p interaction. Mol. Cell. Biol. 22: 2366.
23. Meier U.T. 2006. How a single protein complex accommodates many different H/ACA RNAs. Trends Biochem. Sci. 31: 311.
24. Mitchell J.R., Cheng J., and Collins K. 1999. A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3′ end. Mol. Cell. Biol. 19: 567.
25. Mozdy A.D. and Cech T.R. 2006. Low abundance of telomerase in yeast: Implications for telomerase haploinsufficiency. RNA 12: 1721.
26. Mura C., Cascio D., Sawaya M.R., and Eisenberg D.S. 2001. The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core. Proc. Natl. Acad. Sci. 98: 5532.
27. Nakamura T.M., Wang Y.H., Zaug A.J., Griffith J.D., and Cech T.R. 1995. Relative orientation of RNA helices in a group 1 ribozyme determined by helix extension electron microscopy. EMBO J. 14: 4849.
28. Noller H.F. 1993. On the origin of the ribosome: Coevolution of subdomains of tRNA and rRNA. In The RNA world (ed. R.F. Gesteland and J.F. Atkins), p. 137. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
29. Omer A.D., Ziesche S., Ebhardt H., and Dennis P.P. 2002. In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc. Natl. Acad. Sci. 99: 5289.
30. Park S.H., Zarrinpar A., and Lim W.A. 2003. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299: 1061.
31. Peterson S.E., Stellwagen A.E., Diede S.J., Singer M. S., Haimberger Z.W., Johnson C.O., Tzoneva M., and Gottschling, D.E. 2001. The function of a stem-loop in telomerase RNA is linked to the DNA repair protein Ku. Nat. Genet. 27: 64.
32. Piccinelli P., Rosenblad M.A., and Samuelsson T. 2005. Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 33: 4485.
33. Rashid R., Liang B., Baker D.L., Youssef O.A., He Y., Phipps K., Terns R.M., Terns M.P., and Li H. 2006. Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol. Cell 21: 249.
34. Romero D.P. and Blackburn E.H. 1991. A conserved secondary structure for telomerase RNA. Cell 67: 343.
35. Seto A.G., Livengood A.J., Tzfati Y., Blackburn E., and Cech T.R. 2002. A bulged stem tethers Est1p to telomerase RNA in budding yeasts. Genes Dev. 16: 2800.
36. Seto A.G., Zaug A.J., Sobel S.G., Wolin S.L., and Cech T.R. 1999. Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature 401: 177.
37. Shuster E.O. and Guthrie C. 1988. Two conserved domains of yeast U2 snRNA are separated by 945 nonessential nucleotides. Cell 55: 41.
38. Siliciano P.G., Kivens W.J., and Guthrie C. 1991. More than half of yeast U1 snRNA is dispensable for growth. Nucleic Acids Res. 19: 6367.
39. Siridechadilok B., Fraser C.S., Hall R.J., Doudna J.A., and Nogales E. 2005. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310: 1513.
40. Spahn C.M., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., and Frank J. 2001. Structure of the 80S ribosome from Saccharomyces cerevisiae - tRNA-ribosome and subunit-subunit interactions. Cell 107: 373.
41. 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.
42. Stark H., Dube P., Luhrmann R., and Kastner B. 2001. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409: 539.
43. Stuckenholz C., Meller V.H., and Kuroda M.I. 2003. Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster. Genetics 164: 1003.
44. ten Dam E., van Belkum A., and Pleij K. 1991. A conserved pseudoknot in telomerase RNA. Nucleic Acids Res. 19: 6951.
45. Theimer C.A., Blois C.A., and Feigon J. 2005. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17: 671.
46. Tollervey D., Lehtonen H., Jansen R., Kern H., and Hurt E.C. 1993. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72: 443.
47. Tzfati Y., Fulton T.B., Roy J., and Blackburn E.H. 2000. Template boundary in a yeast telomerase specified by RNA structure. Science 288: 863.
48. Tzfati Y., Knight Z., Roy J., and Blackburn E.H. 2003. A novel pseudoknot element is essential for the action of a yeast telomerase. Genes Dev. 17: 1779.
49. Van Nues R.W. and Brown J.D. 2004. Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain. RNA 10: 75.
50. Walker J.R., Corpina R.A., and Goldberg J. 2001. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412: 607.
51. Wang H., Boisvert D., Kim K.K., Kim R., and Kim S.H. 2000. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution. EMBO J. 19: 317.
52. Will C.L. and Luhrmann R. 2006. Spliceosome structure and function. In The RNA world (ed. R.F. Gesteland et al.), p.369. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
53. Willingham A.T., Orth A.P., Batalov S., Peters E.C., Wen B.G., Aza-Blanc P., Hogenesch J.B., and Schultz P.G. 2005. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309: 1570.
54. Wutz A. 2003. RNAs templating chromatin structure for dosage compensation in animals. Bioessays 25: 434.
55. Wutz A., Rasmussen T.P., and Jaenisch R. 2002. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat. Genet. 30: 167.
56. Yu G.L., Bradley J.D., Attardi L.D., and Blackburn E.H. 1990. In vivo alteration of telomere sequences and senescence caused by mutated Tetrahymena telomerase RNAs. Nature 344: 126.
57. Zappulla D.C. and Cech T.R. 2004. Yeast telomerase RNA: A flexible scaffold for protein subunits. Proc. Natl. Acad. Sci. 101: 10024.
58. Zappulla D.C., Goodrich K., and Cech T.R. 2005. A miniature yeast telomerase RNA functions in vivo and reconstitutes activity in vitro. Nat. Struct. Mol. Biol. 12: 1072.
59. Zebarjadian Y., King T., Fournier M.J., Clarke L., and Carbon J. 1999. Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol. Cell. Biol. 19: 7461.