Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition

Area of Science:

• Molecular Biology
• Structural Biology
• RNA Biology

Background:

• Staufen1 (STAU1) is a double-stranded RNA (dsRNA) binding protein involved in mRNA transport, localization, translational control, and STAU1-mediated mRNA decay (SMD).
• STAU1 binds to specific sites on target mRNAs, such as the STAU1 binding site (SBS) in the human ADP-ribosylation factor 1 (ARF1) 3'UTR, leading to downregulation of ARF1 cytoplasmic mRNA levels via SMD.
• The precise mechanism by which STAU1 recognizes its specific mRNA targets has remained an area of investigation.

Purpose of the Study:

• To elucidate the structural basis of target recognition by Staufen1 (STAU1).
• To understand how STAU1 distinguishes and binds to specific double-stranded RNA (dsRNA) sequences within mRNA targets.

Main Methods:

• X-ray crystallography was used to determine the structure of the complex formed between STAU1 and the ARF1 SBS.
• Biochemical assays were employed to assess in vitro binding affinities.
• In vivo experiments were conducted to evaluate the impact of mutations on STAU1-mediated mRNA decay (SMD).

Main Results:

• The crystal structure revealed that STAU1's dsRNA binding domain (dsRBD) 4 interacts with the minor groove of the dsRNA, recognizing specific pyrimidine and purine bases.
• Helix α1 of dsRBD 4 engages the minor groove, the β1-β2 loop anchors the domain to the dsRNA terminus, and helix α2 interacts with the phosphodiester backbone from the major groove side.
• STAU1 dsRBD 3 also participates in binding, with a specific recognition of a guanine base.
• Mutations designed to disrupt minor groove recognition impaired in vitro binding and reduced SMD in vivo.

Conclusions:

• STAU1 recognizes specific mRNA targets through detailed interactions with the minor groove of dsRNA.
• The findings reveal a mechanism for STAU1 target selection based on the recognition of specific dsRNA structural features.
• This structural understanding provides insights into the regulation of gene expression by STAU1-mediated mRNA decay.