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Nucleic Acids Research Advance Access published online on July 9, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm487
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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.

Genomics

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

Zasha Weinberg1,*, Jeffrey E. Barrick2,3, Zizhen Yao4, Adam Roth2, Jane N. Kim1, Jeremy Gore1, Joy Xin Wang1,2, Elaine R. Lee1, Kirsten F. Block1, Narasimhan Sudarsan1, Shane Neph5, Martin Tompa4,5, Walter L. Ruzzo4,5 and Ronald R. Breaker1,2,3

1Department of Molecular, Cellular and Developmental Biology, 2Howard Hughes Medical Institute, 3Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA 4Department of Computer Science and Engineering and 5Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA

*To whom correspondence should be addressed. Tel: (203) 432-6554; Fax: (203) 432-6161; Email: zasha.weinberg{at}yale.edu

Correspondence may also be addressed to Ronald R. Breaker. Tel: (203) 432-9389; Fax: (203) 432-6161; Email: ronald.breaker{at}yale.edu

Received April 25, 2007. Revised June 4, 2007. Accepted June 5, 2007.

We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in {varepsilon}-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.

Present address: Jeffrey E. Barrick, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA


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