Published online 5 July 2006
© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri
Department of Physics, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA 1 Department of Biological Sciences, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA
*To whom correspondence should be addressed. Tel: +1 540 231 3332; Fax: +1 540 231 7511; Email: kulkarni{at}phys.vt.edu
Received April 18, 2006. Revised June 3, 2006. Accepted June 5, 2006.
The role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which control the activity of the global regulator CsrA. Given the critical role played by CsrA in several bacterial species, an important problem is the identification of CsrA-regulating small RNAs. In this paper, we develop a computer program (CSRNA_FIND) designed to locate potential CsrA-regulating small RNAs in bacteria. Using CSRNA_FIND to search the genomes of bacteria having homologs of CsrA, we identify all the experimentally known CsrA-regulating small RNAs and also make predictions for several novel small RNAs. We have verified experimentally our predictions for two CsrA-regulating small RNAs in Vibrio fischeri. As more genomes are sequenced, CSRNA_FIND can be used to locate the corresponding small RNAs that regulate CsrA homologs. This work thus opens up several avenues of research in understanding the mode of CsrA regulation through small RNAs in bacteria.
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