title: Divergent RNA binding specificity of yeast Puf2p.
abstract: PUF proteins bind mRNAs and regulate their translation, stability, and localization. Each PUF protein binds a selective group of mRNAs, enabling their coordinate control. We focus here on the specificity of Puf2p and Puf1p of Saccharomyces cerevisiae, which copurify with overlapping groups of mRNAs. We applied an RNA-adapted version of the DRIM algorithm to identify putative binding sequences for both proteins. We first identified a novel motif in the 3' UTRs of mRNAs previously shown to associate with Puf2p. This motif consisted of two UAAU tetranucleotides separated by a 3-nt linker sequence, which we refer to as the dual UAAU motif. The dual UAAU motif was necessary for binding to Puf2p, as judged by gel shift, yeast three-hybrid, and coimmunoprecipitation from yeast lysates. The UAAU tetranucleotides are required for optimal binding, while the identity and length of the linker sequences are less critical. Puf1p also binds the dual UAAU sequence, consistent with the prior observation that it associates with similar populations of mRNAs. In contrast, three other canonical yeast PUF proteins fail to bind the Puf2p recognition site. The dual UAAU motif is distinct from previously known PUF protein binding sites, which invariably possess a UGU trinucleotide. This study expands the repertoire of cis elements bound by PUF proteins and suggests new modes by which PUF proteins recognize their mRNA targets.
authors.affiliation: Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Yahav
authors.initials: Y
authors.lastname: Yosefzon
authors.forename: Yvonne Y
authors.initials: YY
authors.lastname: Koh
authors.forename: Jacqueline J
authors.initials: JJ
authors.lastname: Chritton
authors.forename: Avigail
authors.initials: A
authors.lastname: Lande
authors.forename: Limor
authors.initials: L
authors.lastname: Leibovich
authors.forename: Lavi
authors.initials: L
authors.lastname: Barziv
authors.forename: Christine
authors.initials: C
authors.lastname: Petzold
authors.forename: Zohar
authors.initials: Z
authors.lastname: Yakhini
authors.forename: Yael
authors.initials: Y
authors.lastname: Mandel-Gutfreund
authors.forename: Marvin
authors.initials: M
authors.lastname: Wickens
authors.forename: Yoav
authors.initials: Y
authors.lastname: Arava
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D009154:Mutation; D011485:Protein Binding; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: C115277:PUF2 protein, S cerevisiae; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins