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Elife. 2019 Aug 9;8. pii: e48968. doi: 10.7554/eLife.48968.

A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity.

Author information

1
Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States.
2
Department of Biological Sciences, University of Texas at Dallas, Richardson, United States.
#
Contributed equally

Abstract

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 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.

KEYWORDS:

C. elegans; PUF protein; RNA; RNA-binding protein; X-ray crystallography; developmental biology; molecular biophysics; structural biology

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