Cassandra retrotransposons carry independently transcribed 5S RNA

doi:10.1073/pnas.0709698105

Cassandra retrotransposons carry independently transcribed 5S RNA

*MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN-00014, Helsinki, Finland;
^†Biotechnology and Food Research, MTT Agrifood Research, 31600, Jokioinen, Finland; and
^‡Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel

Edited by Susan R. Wessler, University of Georgia, Athens, GA, and approved February 14, 2008 (received for review October 17, 2007)

Abstract

We report a group of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous retrotransposons. These elements, named Cassandra, universally carry conserved 5S RNA sequences and associated RNA polymerase (pol) III promoters and terminators in their long terminal repeats (LTRs). They were found in all vascular plants investigated. Uniquely for LTR retrotransposons, Cassandra produces noncapped, polyadenylated transcripts from the 5S pol III promoter. Capped, read-through transcripts containing Cassandra sequences can also be detected in RNA and in EST databases. The predicted Cassandra RNA 5S secondary structures resemble those for cellular 5S rRNA, with high information content specifically in the pol III promoter region. Genic integration sites are common for Cassandra, an unusual feature for abundant retrotransposons. The 5S in each LTR produces a tandem 5S arrangement with an inter-5S spacing resembling that of cellular 5S. The distribution of 5S genes is very variable in flowering plants and may be partially explained by Cassandra activity. Cassandra thus appears both to have adapted a ubiquitous cellular gene for ribosomal RNA for use as a promoter and to parasitize an as-yet-unidentified group of retrotransposons for the proteins needed in its lifecycle.

Footnotes

^§To whom correspondence should be addressed at:
MTT/BI Plant Genomics Laboratory, P.O. Box 56, FIN-00014, Helsinki, Finland.
E-mail: alan.schulman{at}helsinki.fi
Author contributions: R.K., W.C., H.S., O.P., and A.H.S. designed research; R.K., J.T., W.C., K.A., and H.S. performed research; J.T., W.C., K.A., H.S., and O.P. contributed new reagents/analytic tools; R.K., J.T., H.S., O.P., and A.H.S. analyzed data; and R.K., J.T., and A.H.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF538603–AF538610, AF538605–AF538618, AY164585, AY271957–AY271963, AY359471, AY603364–AY603377, AY860307–AY860317, AY923749, DQ094839–DQ094843, DQ673669, DQ767972, DQ788719, and EF125870–EF125877).
This article contains supporting information online at www.pnas.org/cgi/content/full/0709698105/DCSupplemental.