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ZBP1 KH34 consensus RNA‐binding site identifies posttranscriptional regulatory networks
Author(s) -
Chao Jeffrey,
Singer Robert
Publication year - 2012
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.26.1_supplement.949.1
Subject(s) - rna , biology , messenger rna , translation (biology) , rna binding protein , gene , microbiology and biotechnology , genetics
ZBP1 is a multifunctional regulator of RNA metabolism that has been shown to control aspects of localization, stability and translation for many mRNAs. To reveal the basis for ZBP1 recognition of its RNA targets, we have biochemically characterized the interaction between ZBP1 and the β‐actin zipcode. We have determined that ZBP1 KH34 recognizes a bipartite RNA element located within the first 28 nucleotides of the zipcode. The 5′ sequence of the bipartite element was determined to be CGGAC while the 3′ sequence was C/A‐CA‐C/U. The spacing between these RNA sequences is consistent with the structure of KH34 that we solved by X‐ray crystallography where the tandem KH domains are arranged in an anti‐parallel pseudodimer conformation. NMR chemical shift mapping of KH34 in complex with zipcode RNA fragments identified that KH4 recognizes the 5′ region of the bipartite element and KH3 binds to the 3′ region. In order to identify other mRNA targets of ZBP1, the KH34 consensus sequence was used to search the 3′ UTRs of human and mouse and the bipartite element was conserved in 114 mRNAs. Many of the predicted mRNA targets were found to coimmunoprecipitate with ZBP1 from mouse embryonic brain lysate. Gene ontology analysis of the ZBP1 target mRNAs indicated that these mRNAs were significantly enriched in categories involved in cellular development, assembly and motility, which correspond to the known cellular functions of ZBP1.