In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat, Qiu, et al. 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
Atomic coordinates and structure factors are deposited under RCSB PDB ID 6PUN. SEQRS sequence data are available through the Dryad Digital Repository, accession number doi:10.5061/dryad.30501q7.
SEQRS data for FBF-2 and SEQRS data for the LST-1 FBF-2 complexDryad Digital Repository, doi:10.5061/dryad.30501q7.
Crystal structure of a ternary complex of FBF-2 with LST-1 (site B) and compact FBE RNAProtein Data Bank, 6PUN.
The PUF binding landscape in metazoan germ cellsSupplemental Table S2.
- Traci M T Tanaka Hall
- Zachary T Campbell
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Timothy W Nilsen, Case Western Reserve University, United States
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