Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Model of a Pseudoknot Structure with a Triple-helical Stem from the Telomerase RNA of Kluyveromyces lactis

Telomerase RNA is a part of a ribonucleoprotein complex, responsible for the maintenance of telomeres, ends of linear chromosomes. Telomerase RNA in budding yeasts is much longer and has a less conserved sequence than in vertebrates; its secondary structure is still an active area of research (1-4). Analysis of telomerase RNA sequences of six Kluyveromyces budding yeast species revealed a conserved pseudoknot structure essential for the telomerase function (5). Here we present a computer model for the pseudoknot of the K. lactis telomerase RNA, calculated with the miniCarlo program (6). An unusual feature of this pseudoknot is a triple-helical stem, where uridines from the third strand are located in the major groove of the duplex and form Hoogsteen hydrogen bonds with adenines of the duplex. This arrangement is similar to the classical major groove RNA triple helix (7) and not to the more commonly found minor groove triplex motifs of RNA pseudoknots (e.g., (8)). This model of the K. lactis telomerase RNA pseudoknot is confirmed by in vitro gel mobility assays and by a set of designed mutations in vivo, in particular, mutations on all three strands of the triple-helical stem. The K. lactis pseudoknot will be compared with the results of modeling studies for telomerase RNA of other organisms, which are currently in progress, and with the recently solved NMR structure of the human telomerase RNA pseudoknot (9).

References and Footnotes
  1. D.C. Zappulla & T.R. Cech. Proc. Nat. Acad. Sci. 101, 10024-10029 (2004).
  2. A.T. Dandjinou et al., Cur. Biol. 14, 1148-1158 (2004).
  3. A.S. Chappell & V. Lundblad, Mol. Cel. Biol. 24, 7720-7736 (2004).
  4. J. Lin et al., Proc. Nat. Acad. Sci. 101, 14713-14718 (2004).
  5. Y. Tzfati et al., Gen. Dev. 17, 1779-1788 (2003).
  6. V.B. Zhurkin et al., Proc. Nat. Acad. Sci. 88, 7046-7050 (1991).
  7. G. Felsenfeld, D.R. Davies & A. Rich, J. Am. Chem. Soc. 79, 2023-2024 (1957).
  8. L. Su et al., Nat. Struct. Biol. 6, 285-292 (1999).
  9. C.A. Theimer, C.A. Blois & J. Feigon. Mol. Cell 17, 671-682 (2005).

Nikolai B. Ulyanov1*
Kinneret Shefer2
Valentin Gorkovoy2
Tamar Nussbaum2
Yogev Braun2
Mira Abraham2
Sivan Pearl2
Deborah Shalev2
Yehuda Tzfati2

1University of California
San Francisco, CA 94143-2280, U.S.A.
2The Hebrew University of Jerusalem
Jerusalem, 91904, Israel

*Phone: 415-476-0707
Email: ulyanov@picasso.ucsf.edu