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Nucleic Acids Research Advance Access published online on September 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm660
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates

Nikolai B. Ulyanov1,*, Kinneret Shefer2, Thomas L. James1 and Yehuda Tzfati2

1Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and 2Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel

*To whom correspondence should be addressed. Tel: +1 415 476 0707; Fax: +1 415 502 8298; Email: ulyanov{at}picasso.ucsf.edu Correspondence may also be addressed to Yehuda Tzfati. Tel: +972 2 6584902; Fax: +972 2 6586975; Email: tzfati{at}cc.huji.ac.il

Received July 1, 2007. Revised August 9, 2007. Accepted August 9, 2007.

Telomerase maintains the integrity of telomeres, the ends of linear chromosomes, by adding G-rich repeats to their 3'-ends. Telomerase RNA is an integral component of telomerase. It contains a template for the synthesis of the telomeric repeats by the telomerase reverse transcriptase. Although telomerase RNAs of different organisms are very diverse in their sequences, a functional non-template element, a pseudoknot, was predicted in all of them. Pseudoknot elements in human and the budding yeast Kluyveromyces lactis telomerase RNAs contain unusual triple-helical segments with AUU base triples, which are critical for telomerase function. Such base triples in ciliates have not been previously reported. We analyzed the pseudoknot sequences in 28 ciliate species and classified them in six different groups based on the lengths of the stems and loops composing the pseudoknot. Using miniCarlo, a helical parameter-based modeling program, we calculated 3D models for a representative of each morphological group. In all cases, the predicted structure contains at least one AUU base triple in stem 2, except for that of Colpidium colpoda, which contains unconventional GCG and AUA triples. These results suggest that base triples in a pseudoknot element are a conserved feature of all telomerases.


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