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Published online on December 12, 2006, 10.1073/pnas.0607493103
PNAS | December 19, 2006 | vol. 103 | no. 51 | 19490-19495


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BIOLOGICAL SCIENCES / MICROBIOLOGY
Identification of a large noncoding RNA in extremophilic eubacteria

Elena Puerta-Fernandez*, Jeffrey E. Barrick{dagger},{ddagger}, Adam Roth{ddagger}, and Ronald R. Breaker*,{dagger},{ddagger},§

Departments of *Molecular, Cellular, and Developmental Biology and {dagger}Molecular Biophysics and Biochemistry, and {ddagger}Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103

Edited by Sidney Altman, Yale University, New Haven, CT, and approved October 19, 2006 (received for review August 30, 2006)

We have discovered a large and highly conserved RNA motif that typically resides in a noncoding section of a multigene messenger RNA in extremophilic Gram-positive eubacteria. RNAs of this class adopt an ornate secondary structure, are large compared with most other noncoding RNAs, and have been identified only in certain extremophilic bacteria. These ornate, large, extremophilic (OLE) RNAs have a length of {approx}610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. Structural probing of the OLE RNA from Bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. The patterns of structural conservation, and its unique phylogenetic distribution, suggest that OLE RNA carries out a complex and critical function only in certain extremophilic bacteria.

isoprenoid | riboswitch | ribozyme | superoperon

Author contributions: E.P.-F. and R.R.B. designed research; E.P.-F., J.E.B., and A.R. performed research; E.P.-F., J.E.B., A.R., and R.R.B. analyzed data; and E.P.-F. and R.R.B. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS direct submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0607493103/DC1.

§To whom correspondence should be addressed. E-mail: ronald.breaker{at}yale.edu

© 2006 by The National Academy of Sciences of the USA


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