Biology subjects

Axhemi, A.

Publications and source records attributed to Axhemi, A..

2 recordsLinked to original sources

bioRxiv2026

Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing

Argonaute (Ago) proteins associate with 20-22 nucleotide (nt) long microRNAs (miRNAs) to constitute the functional RISC core and downregulate mRNAs containing complementarity to the seed sequence1-3. Target RNA engagement in RISC stimulates CK1-mediated phosphorylation of the conserved eukaryotic insertion (EI) in Ago, releasing the target and enabling the RISC complex to suppress additional target sites for efficient miRNA-mediated silencing4-6. Here, we provide a complete structural view of miRNA guide and target binding to human Ago2, showing Ago2 holding the double-stranded guide-target RNA in an untwisted conformation at its center. We visualize the dynamic changes that RISC undergoes as the guide supplementary region progressively base pairs with the target, enabling CK1 binding. Following seed-helix assembly, initial supplementary pairing restricts RISC to a "closed" form, while with half-supplementary pairing, the PAZ domain moves to open RISC to become receptive to CK1, exhibiting an initial increase in Ago2 phosphorylation. Complete supplementary pairing supports a full PAZ-CK1 interface, allowing for hierarchical phosphorylation of the EI. The combination of target repulsion by EI phosphorylation with an unwound guide-target enables efficient target release to promote RISC turnover.

biochemistry↗

bioRxiv2021

A shape-shifting nuclease unravels structured RNA

RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts that may otherwise interfere with cellular programs. The enzyme Dis3-like protein 2 (Dis3L2) is a 3-5 exoribonuclease that, through its RNA turnover activity, plays a critical role in human development1. Dis3L2 can independently degrade structured substrates and its targets include many coding and non-coding 3-uridylated RNAs1-5. While the basis for Dis3L2s substrate recognition has been well-characterized6, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining electron cryo-microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for single-stranded (ss) and double-stranded (ds) RNA processing. We discovered a dramatic conformational change that is triggered by the dsRNA, involving repositioning of two cold shock domains by 70 [A]. This movement exposes a trihelix-linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not ssRNA, degradation. These findings reveal the conformational plasticity of this enzyme, and detail a novel mechanism of structured RNA degradation.

biochemistry↗