title: A single spacer nucleotide determines the specificities of two mRNA regulatory proteins.
abstract: Regulation of messenger RNA is crucial in many contexts, including development, memory and cell growth. The 3' untranslated region is a rich repository of regulatory elements that bind proteins and microRNAs. Here we focus on PUF proteins, an important family of mRNA regulatory proteins crucial in stem-cell proliferation, pattern formation and synaptic plasticity. We show that two Caenorhabditis elegans PUF proteins, FBF and PUF-8, differ in RNA-binding specificity. FBF requires the presence of a single 'extra' nucleotide in the middle of an eight-nucleotide site, whereas PUF-8 requires its absence. A discrete protein segment is responsible for the difference. We propose that a structural distortion in the central region of FBF imposes the requirement for the additional nucleotide and that this mode of PUF specificity may be common. We suggest that new specificities can be designed and selected using the PUF scaffold.
authors.affiliation: Department of Biochemistry, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Opperman
authors.forename: Brad
authors.initials: B
authors.lastname: Hook
authors.forename: Mia
authors.initials: M
authors.lastname: DeFino
authors.forename: David S
authors.initials: DS
authors.lastname: Bernstein
authors.forename: Marvin
authors.initials: M
authors.lastname: Wickens
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D005786:Gene Expression Regulation / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D020798:Two-Hybrid System Techniques; D015003:Yeasts
chemical_list: D029742:Caenorhabditis elegans Proteins; D009711:Nucleotides; C510538:PUF-8 protein, C elegans; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C109286:fem-3-binding protein, C elegans