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Nucleic Acids Res. 2019 Sep 19;47(16):8770-8784. doi: 10.1093/nar/gkz583.

Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.

Author information

1
Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
2
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
3
Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
4
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Abstract

PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.

PMID:
31294800
DOI:
10.1093/nar/gkz583
[Indexed for MEDLINE]

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