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

• Published in: Biochimica et biophysica acta. Proteins and proteomics 2017-01, Vol.1865 (1), p.65-75
• Main Authors: Kim, Do-Hee, Kang, Su-Jin, Lee, Ki-Young, Jang, Sun-Bok, Kang, Sung-Min, Lee, Bong-Jin
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - ultrastructure; Binding Sites; IF1; Magnetic Resonance Spectroscopy; NMR; Nuclear Magnetic Resonance, Biomolecular; OB-fold; Peptide Chain Initiation, Translational; Prokaryotic Initiation Factors - chemistry; Prokaryotic Initiation Factors - genetics; Prokaryotic Initiation Factors - ultrastructure; Protein Binding; Protein Structure, Secondary; RNA, Bacterial - chemistry; RNA-binding protein; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - ultrastructure; Sequence Alignment; Staphylococcus aureus - genetics; Staphylococcus aureus - metabolism; Staphylococcus aureus Mu50; Translation
• ISSN: 1570-9639; 1878-1454
• DOI: 10.1016/j.bbapap.2016.10.009

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 (IF1Sa) by NMR spectroscopy. First, the NMR-derived solution structure of IF1Sa revealed that IF1Sa 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 15N NMR relaxation data for IF1Sa indicated the flexible nature of the α-helix and the following loop region of IF1Sa. Third, RNA-binding properties were studied using FP assays and NMR titrations. FP binding assays revealed that IF1Sa 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 IF1Sa binds RNAs with moderate binding affinity via the residues that occupy the large surface area of its β-barrel. These findings suggest that IF1Sa is likely to bind RNA in various conformations rather than only at a specific site and indicate that the flexible RNA binding mode of IF1Sa is necessary for its interaction with various RNA substrates. •Structure and RNA-binding properties of IF1Sa are proposed.•The flexibility of the α-helix region of IF1Sa affects the RNA binding.•IF1Sa binds RNAs with moderate binding affinity via the large surface area of its β-barrel.