Annotation and evolutionary relationships of a small regulatory RNA gene <it>micF </it>and its target <it>ompF </it>in <it>Yersinia </it>species

<p>Abstract</p> <p>Background</p> <p><it>micF </it>RNA, a small regulatory RNA found in bacteria, post-transcriptionally regulates expression of outer membrane protein F (OmpF) by interaction with the <it>ompF </it>mRNA 5'UTR. Phylogenetic data can be useful for RNA/RNA duplex structure analyses and aid in elucidation of mechanism of regulation. However <it>micF </it>and associated genes, <it>ompF </it>and <it>ompC </it>are difficult to annotate because of either similarities or divergences in nucleotide sequence. We report by using sequences that represent "gene signatures" as probes, e.g., mRNA 5'UTR sequences, closely related genes can be accurately located in genomic sequences.</p> <p>Results</p> <p>Alignment and search methods using NCBI BLAST programs have been used to identify <it>micF</it>, <it>ompF </it>and <it>ompC </it>in <it>Yersinia pestis </it>and <it>Yersinia enterocolitica</it>. By alignment with DNA sequences from other bacterial species, 5' start sites of genes and upstream transcriptional regulatory sites in promoter regions were predicted. Annotated genes from <it>Yersinia </it>species provide phylogenetic information on the <it>micF </it>regulatory system. High sequence conservation in binding sites of transcriptional regulatory factors are found in the promoter region upstream of <it>micF </it>and conservation in blocks of sequences as well as marked sequence variation is seen in segments of the <it>micF </it>RNA gene. Unexpected large differences in rates of evolution were found between the interacting RNA transcripts, <it>micF </it>RNA and the 5' UTR of the <it>ompF </it>mRNA. <it>micF </it>RNA/<it>ompF </it>mRNA 5' UTR duplex structures were modeled by the mfold program. Functional domains such as RNA/RNA interacting sites appear to display a minimum of evolutionary drift in sequence with the exception of a significant change in <it>Y. enterocolitica micF </it>RNA.</p> <p>Conclusions</p> <p>Newly annotated <it>Yersinia micF </it>and <it>ompF </it>genes and the resultant RNA/RNA duplex structures add strong phylogenetic support for a generalized duplex model. The alignment and search approach using 5' UTR signatures may be a model to help define other genes and their start sites when annotated genes are available in well-defined reference organisms.</p>