7250 Nucleic Acids Research, 2008, Vol. 36, No. 22 RNA chaperones in S. coelicolor The regulatory activity of many trans-acting sRNAs is mediated through base-pairing with their mRNA targets, and the stability of these interactions depends upon the RNA chaperone Hfq. In 2002, a thorough phylogenetic analysis revealed Hfq to be conspicuously absent from three bacterial clades, one of which included the strepto- mycetes and all other actinomycetes (24). Hfq is structu- rally, and functionally, analogous to the Sm-like proteins of eukaryotes: both proteins have important roles in RNA metabolism, and share a common fold consisting of an N-terminal helix followed by ﬁve b-strands (47,48). They do, however, have limited similarity at a sequence level. As BLAST searches rely upon sequence similarity and do not take protein structure into account, we wanted to determine whether an Hfq/Sm-equivalent protein could be identiﬁed in S. coelicolor using a structure-based approach to surveying the genome. We examined the sec- ondary structure of all proteins smaller than 130 amino acids that were conserved in multiple Streptomyces spe- cies, using the JPRED program (49). An Hfq-like fold was not predicted for any of the proteins examined, suggesting that if S. coelicolor encodes a protein with a function analogous to that of Hfq, it is likely to have a unique sequence and structure. We predict that some proportion of the sRNAs identiﬁed here will interact with trans-encoded mRNA targets, and therefore it will be interesting to determine whether additional compo- nents are required to stabilize these interactions. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS We are extremely grateful to Stephen Miller for his com- putational expertise and assistance, and Mark Buttner, Turlough Finan, David Capstick and Andrew Duong for helpful discussions and/or comments on the manuscript. FUNDING National Institutes of Health grant (R15-GM078080 to B.T.); the Grant Agency of the Czech Republic (No. 204/07/P361 to J.B.); the Canada Research Chairs programme (to M.A.E.); a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant (No. 312495 to M.A.E.). Funding for open access charge: McMaster University. Conﬂict of interest statement. None declared. REFERENCES 1. McAdams,H.H., Srinivasan,B. and Arkin,A.P. (2004) The evolution of genetic regulatory systems in bacteria. Nat. Rev. Genet., 5, 169–178. 2. Bentley,S.D., Chater,K.F., Cerdeno-Tarraga,A.M., Challis,G.L., Thomson,N.R., James,K.D., Harris,D.E., Quail,M.A., Kieser,H., Harper,D. et al. 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