Staufen-mediated mRNA decay

Abstract

Staufen1 (STAU1)-mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1-binding site (SBS) within the 3'-untranslated region (3'-UTR) of target mRNAs. During SMD, STAU1, a double-stranded (ds) RNA-binding protein, recognizes dsRNA structures formed either by intramolecular base pairing of 3'-UTR sequences or by intermolecular base pairing of 3'-UTR sequences with a long-noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP-dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain-swapping. Because both SMD and the mechanistically related nonsense-mediated mRNA decay (NMD) employ UPF1; SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms.

Figure 1. Diagrams of human STAU1 and STAU2 isoforms

Superscript numbers approximate the mass (kD) of the isoform; boxes represent functional and/or structural domains. 1, N-terminal amino acid; RBD, dsRNA-binding domain (bold RBDs are able to bind dsRNA); TBD, tubulin-binding domain (where hatched STAU2 TBDs are ~18% identical to STAU1 TBDs); SSM, Staufen-swapping motif; aa, amino acids.

Figure 2. Features of STAU1-binding sites

A. A STAU1-binding site (SBS) that triggers SMD can be a stem-loop structure formed by intramolecular base-paring within an mRNA 3'UTR. (A)n, mRNA poly(A) tail. B. The SBS within ARF1 mRNA provides an example of intramolecular base-paired SBS. Enlarged sequences include the 19-bp stem that largely defines the STAU1-binding sequence. ORF, open reading frame. C. Alternatively, an SBS can be formed by intermolecular base-pairing between a 3'UTR Alu element and a partially complementary Alu element within a long non-coding (lnc) RNA, which we call a ½sbs-RNA. D. Predicted intermolecular base-pairing between the 3'UTR Alu element within SERPINE1 mRNA and the Alu element within ½-sbsRNA1 that forms a functional SBS. Cap, 5' mRNA cap structure, AUG, translation initiation codon; Ter, translation termination codon; (A)n, poly(A) tail.

Figure 3. Tethering transiently expressed MS2-tagged STAU1 or MS2-tagged STAU2 to an mRNA 3'UTR triggers SMD in a mechanism that involves interactions with cellular STAU1 and/or cellular STAU2

A. Tethering of STAU1 or STAU2, fused to the viral MS2 coat protein (MS2), to eight tandem repeats of the MS2 coat protein-binding site (MS2bs) inserted into the 3'UTR of a firefly luciferase (FLUC) reporter mRNA triggers mRNA decay by recruiting cellular STAU1 and/or STAU2. ORF, open translational reading frame; (A)n, poly(A). B. Knock-down of cellular STAU1 or STAU2 using STAU1 siRNA or STAU2 siRNA, respectively, inhibits mRNA decay brought about by tethering MS2-STAU1 or MS2-STAU2.

Figure 4. Model for homodimeric and heterodimeric interactions between STAU1 and/or STAU2 via domain swapping

Simplified diagram of homo- or hetero-dimerization of STAU molecules via domain-swapping between the STAU-swapping motif (SSM) of one molecule and the dsRBD5 of another molecule. Yellow circle, SSM; green rectangle, dsRBD5; red oval; rest of STAU molecule. Enlarged box shows the crystal structure of the interaction, detailing that the two α-helices of the SSM of one STAU molecule interdigitate with the two α-helices of the dsRBD5 of another STAU molecule. Notably, the smallest isoform of STAU2 lacks the C-terminal α-helix of dsRBD5, and only the N-terminal α-helix of dsRBD5 is necessary for the interaction.

Figure 5. Model for the mechanism of SMD

STAU1 and/or STAU2, either individually (as shown for simplicity) or more likely as homo- or hetero-dimers if not multimers, bind to a 3'UTR SBS that can be formed by either intramolecular or intermolecular base-pairing^,. During protein synthesis, when ribosomes reach a termination codon that resides sufficiently upstream of an SBS so that bound STAU1 and/or STAU2 is not removed by the terminating ribosome, UPF1, which is recruited by SBS-bound STAU(s), is activated. Taking cues from the related pathway, NMD, translation termination may facilitate the loading of UPF1 onto the mRNA 3'UTR, as may SBS-bound STAU1. Activation of mRNA decay may involve UPF1 phosphorylation, possibly by SMG1: it has been reported that UPF1 phosphorylation enhances the co-IP of UPF1 with STAU1. STAU promotes a conformational change in UPF1, thereby enhancing UPF1 helicase activity without concomitantly enhancing UPF1 ATPase activity. That noted, however, ATP hydrolysis is required for helicase activity, which may be required for mRNP remodeling, as is the case for NMD. Cap, 5' mRNA cap structure; SBS, STAU-binding site; Ter, termination codon; (A)n, poly(A) tail, orange ovals, 80S translationally active ribosome; purple UPF1, inactive form; blue UPF1, conformationally changed and active UPF1.

Figure 6. Model for competition between SMD and NMD

SMD and NMD compete with one another since STAU1 and STAU2, which function in SMD, compete with UPF2, which functions in NMD, for binding to UPF1, which functions in both pathways. Notably, the STAU paralogs function when bound to an intramolecular (shown) or intermolecular (not shown) STAU-binding site (SBS) that is situated sufficiently downstream of a termination codon that is usually the normal termination codon (Ter). In contrast, UPF2 generally functions as a constituent of an exon-junction complex (EJC) that is situated sufficiently downstream of a termination codon that is usually a premature termination codon (PTC). AUG, translation initiation codon; (A)n, poly(A) tail.