Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2

Area of Science:

• Molecular Biology
• Gene Regulation
• RNA Surveillance

Background:

• Nonsense-mediated mRNA decay (NMD) is a crucial pathway for regulating gene expression by degrading aberrant mRNAs.
• Core NMD factors UPF1, UPF2, and UPF3B are essential for identifying and degrading mRNAs with premature stop codons.
• While UPF2's interactions with UPF1 and UPF3B are known, its direct association with RNA is poorly understood.

Purpose of the Study:

• To investigate the RNA-binding properties and functions of the NMD factor UPF2.
• To characterize the specific domains and activities of UPF2 involved in nucleic acid interactions.
• To elucidate how UPF2's RNA binding contributes to the overall NMD mechanism.

Main Methods:

• Analysis of nucleic acid binding using biochemical assays.
• Identification of RNA/DNA-binding modules within UPF2.
• Characterization of UPF2's RNA annealing and unfolding activities.
• Assessment of UPF2's conformational changes upon single-stranded RNA (ss-RNA) binding.

Main Results:

• The first and third MIF4G domains of UPF2 were identified as the primary RNA/DNA-binding modules.
• UPF2's MIF4G domain-3 exhibits RNA annealing activity, and full-length UPF2 can unfold hairpin RNA structures.
• UPF2 preferentially binds and stabilizes ss-RNA in a sequence-independent manner, inducing conformational changes.
• UPF2's RNA binding and unfolding activities are linked to its dynamic structural properties.

Conclusions:

• UPF2 directly interacts with and modulates RNA structures, particularly ss-RNA.
• These RNA-binding and unfolding activities of UPF2 likely contribute to UPF1's helicase and mRNP remodeling functions.
• UPF2's RNA interactions, in conjunction with UPF3B, may stabilize UPF1's association with target nonsense mRNAs, facilitating NMD.