Machado de Amorim, A. | Search bioRxiv

bioRxiv2025

Molecular mechanisms of recruitment, function and regulation of UPF1 in histone mRNA decay

Animal replication-dependent histone mRNAs end in a conserved stem loop (SL) instead of the canonical poly(A) tail present in all other eukaryotic mRNAs. Degradation of the histone SL at the end of the S-phase is initiated by the stem-loop binding protein SLBP and its interplay with the RNA helicase UPF1 and the exoribonuclease 3hExo. We report direct interactions between SLBP and UPF1 and show that the unstructured SLBP N-terminus wraps around the UPF1 helicase core, contacting it at multiple sites. Although binding of SLBP to UPF1 impedes unwinding activity, it is critical for efficient histone mRNA decay in cells, as unwinding of the SL facilitates degradation by 3hExo. Here we show that the UPF1-activator, UPF2, binds 3hExo, and that UPF2-mediated activation of UPF1 overrides the inhibitory effect of SLBP. Our results highlight the intricate network of UPF1-centric protein-protein and protein/RNA interactions that fine-tunes its unwinding activity and orchestrates timely and efficient degradation of histone mRNA.

biochemistry↗

bioRxiv2022

Modulation of RNA binding properties of the RNA helicase UPF1 by its activator UPF2

The NMD helicase UPF1 is a prototype of the superfamily 1 (SF1) of RNA helicases that bind RNA with high affinity and translocate on it in an ATP-dependent manner. Previous studies showed that UPF1 has a low basal catalytic activity that is greatly enhanced upon binding of its interaction partner, UPF2. Activation of UPF1 by UPF2 entails a large conformational change that switches the helicase from an RNA-clamping mode to an RNA-unwinding mode. The ability of UPF1 to bind RNA was expected to be unaffected by this activation mechanism. Here we show, using a combination of biochemical and biophysical methods, that binding of UPF2 to UPF1 drastically reduces the affinity of UPF1 for RNA, leading to a release of the bound RNA. Although UPF2 is capable of binding RNA in vitro, our results suggest that dissociation of the UPF1-RNA complex is not a consequence of direct competition in RNA binding but rather an allosteric effect that is likely mediated by the conformational change induced by binding of the helicase to its activator. We discuss these results in light of transient interactions forged during mRNP assembly, particularly in the UPF1-dependent mRNA decay pathways.

biochemistry↗