Antisense micF RNA and 5'-UTR of the target ompF RNA: phylogenetic conservation of primary and secondary structures

Outer membrane protein F (OmpF) found in E. coli and related bacteria is post-transcriptionally regulated by antisense micF RNA. During down regulation of ompF expression, micF RNA binds to the 5' UTR of ompF mRNA, blocks translation of the message, and also participates in the chemical destabilization of the ompF mRNA. Only about one third of the micF RNA sequence binds the target ompF mRNA. Phylogenetic analyses of micF RNA and ompF mRNA show: 1) a high degree of conservation of nucleotide sequence in regions of both RNAs involved in RNA/RNA interaction, 2) a low nucleotide sequence conservation but high degree of secondary structure conservation in regions of antisense and target RNAs not involved in the RNA/RNA interaction. Whereas conserved sequences are associated with RNA/RNA binding and blockage of translation, conservation of secondary structure may be related to protein interactions associated with chemical destabilization of the message.