title: Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1.
abstract: Interactions of RNA-binding proteins (RBPs) with their target transcripts are essential for regulating gene expression at the posttranscriptional level including mRNA export/localization, stability, and translation. ZBP1 and HuD are RBPs that play pivotal roles in mRNA transport and local translational control in neuronal processes. While HuD possesses three RNA recognition motifs (RRMs), ZBP1 contains two RRMs and four K homology (KH) domains that either increase target specificity or provide a multi-target binding capability. Here we used isolated cis-element sequences of the target mRNA to examine directly protein-RNA interactions in cell-free systems. We found that both ZBP1 and HuD bind the zipcode element in rat β-actin mRNA's 3' UTR. Differences between HuD and ZBP1 were observed in their binding preference to the element. HuD showed a binding preference for U-rich sequence. In contrast, ZBP1 binding to the zipcode RNA depended more on the structural level, as it required the proper spatial organization of a stem-loop that is mainly determined by the U-rich element juxtaposed to the 3' end of a 5'-ACACCC-3' motif. On the basis of this work, we propose that ZBP1 and HuD bind to overlapping sites in the β-actin zipcode, but they recognize different features of this target sequence.
authors.affiliation: Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA.
authors.forename: Hak Hee
authors.initials: HH
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Seung Joon
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
authors.forename: Amy S
authors.initials: AS
authors.lastname: Gardiner
authors.affiliation: Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
authors.forename: Nora I
authors.initials: NI
authors.lastname: Perrone-Bizzozero
authors.affiliation: Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA yoo@medsci.udel.edu.
authors.forename: Soonmoon
authors.initials: S
authors.lastname: Yoo
mesh_terms: D020413:3' Untranslated Regions; D000199:Actins / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D000067779:ELAV-Like Protein 4 / Q000378:metabolism*; D009474:Neurons / Q000737:chemistry; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011485:Protein Binding; D020871:RNA Stability; D012333:RNA, Messenger / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*; D051381:Rats
chemical_list: D020413:3' Untranslated Regions; D000199:Actins; D000067779:ELAV-Like Protein 4; C000594136:Elavl4 protein, rat; C498634:Igf2bp1 protein, rat; D012333:RNA, Messenger; D016601:RNA-Binding Proteins