Computer modeling of eubacterial SRP RNA by NMR-based study

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Consisting of 114 nucleotides, 4.5S RNA is structurally homologous to mammalian 7S RNA, and it plays an essential role in targeting proteins containing signal peptide to the membrane by forming an SRP-like particle by binding with Ffh. It also binds independently to protein elongation factor (EF-G) and functions in the translation process. This RNA contains a phylogenetically conserved RNA domain, the predicted secondary structure of which consists of a hairpin motif with two bulges. We examined the binding activity of mutants with systematic deletions to define the minimal functional domain of 4.5S RNA that can interact with EF-G. This domain consisted of 35-nucleotides extending from 36 to 70 nucleotides of mature 4.5S RNA and contained two conserved bulges in which mutations of A47, A60, G61, C62, A63, and A67 diminished binding to EF-G, whereas those at A39, C40, C41, A48, and G49 did not affect binding. These data suggested that the 10 nucleotides in 4.5S RNA, which are conserved between 4.5S RNA and 23S rRNA, have a key role for EF-G biding. Based on the NMR-derived structure of mutant A47U causes striking structure changes and the loss of the symmetrical bulge. These results indicate the mechanism by which EF-G interacts with 4.5S RNA and the importance of the bulge structure for EF-G binding.