Structure and dynamics study of translation initiation factor 1 from Staphylococcus aureus suggests its RNA binding mode.

Translation initiation, the rate-limiting step in the protein synthesis, is tightly regulated. As one of the translation initiation factors, translation initiation factor 1 (IF1) plays crucial roles not only in translation but also in many cellular processes that are important for genomic stability, such as the activity of RNA chaperones. Here, we characterize the RNA interactions and dynamics of IF1 from Staphylococcus aureus Mu50 (IF1) by NMR spectroscopy. First, the NMR-derived solution structure of IF1 revealed that IF1 adopts an oligonucleotide/oligosaccharide binding (OB)-fold. Structural comparisons showed large deviations in the α-helix and the following loop, which are potential RNA-binding regions of the OB-fold, as well as differences in the electrostatic potential surface among bacterial IF1s. Second, the N NMR relaxation data for IF1 indicated the flexible nature of the α-helix and the following loop region of IF1. Third, RNA-binding properties were studied using FP assays and NMR titrations. FP binding assays revealed that IF1 binds to RNAs with moderate affinity. In combination with the structural analysis, the NMR titration results revealed the RNA binding sites. Taken together, these results show that IF1 binds RNAs with moderate binding affinity via the residues that occupy the large surface area of its β-barrel. These findings suggest that IF1 is likely to bind RNA in various conformations rather than only at a specific site and indicate that the flexible RNA binding mode of IF1 is necessary for its interaction with various RNA substrates.