Protein roles in group I intron RNA folding: the tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics.
The Neurospora crassa CYT-18 protein is a mitochondrial tyrosyl-tRNA synthetase that also promotes self-splicing of group I intron RNAs by stabilizing the functional structure in the conserved core. CYT-18 binds the core along the same surface as a common peripheral element, P5abc, suggesting that CYT-18 can replace P5abc functionally. In addition to stabilizing structure generally, P5abc stabilizes the native conformation of the Tetrahymena group I intron relative to a globally similar misfolded conformation that has only local differences within the core and is populated significantly at equilibrium by a ribozyme variant lacking P5abc (E(DeltaP5abc)). Here, we show that CYT-18 specifically promotes formation of the native group I intron core from this misfolded conformation. Catalytic activity assays demonstrate that CYT-18 shifts the equilibrium of E(DeltaP5abc) toward the native state by at least 35-fold, and binding assays suggest an even larger effect. Thus, similar to P5abc, CYT-18 preferentially recognizes the native core, despite the global similarity of the misfolded core and despite forming crudely similar complexes, as revealed by dimethyl sulfate footprinting. Interestingly, the effects of CYT-18 and P5abc on folding kinetics differ. Whereas P5abc inhibits refolding of the misfolded conformation by forming peripheral contacts that must break during refolding, CYT-18 does not display analogous inhibition, most likely because it relies to a greater extent on direct interactions with the core. Although CYT-18 does not encounter this RNA in vivo, our results suggest that it stabilizes its cognate group I introns relative to analogous misfolded intermediates. By specifically recognizing native structural features, CYT-18 may also interact with earlier folding intermediates to avoid RNA misfolding or to trap native contacts as they form. More generally, our results highlight the ability of a protein cofactor to stabilize a functional RNA structure specifically without incurring associated costs in RNA folding kinetics.
Chadee
Amanda B
AB
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.
Bhaskaran
Hari
H
Russell
Rick
R
D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D007438:Introns; D007700:Kinetics; D046911:Macromolecular Substances; D008958:Models, Molecular; D009492:Neurospora crassa / Q000201:enzymology; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D020871:RNA Stability; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D013768:Tetrahymena / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics; D014448:Tyrosine-tRNA Ligase / Q000235:genetics / Q000378:metabolism*
D005656:Fungal Proteins; D046911:Macromolecular Substances; D016337:RNA, Catalytic; D016053:RNA, Protozoan; D011994:Recombinant Proteins; D014448:Tyrosine-tRNA Ligase