ZBP1 recognition of beta-actin zipcode induces RNA looping.

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
Genes & development (Impact Factor: 12.64). 01/2010; 24(2):148-58. DOI: 10.1101/gad.1862910
Source: PubMed

ABSTRACT ZBP1 (zipcode-binding protein 1) was originally discovered as a trans-acting factor for the "zipcode" in the 3' untranslated region (UTR) of the beta-actin mRNA that is important for its localization and translational regulation. Subsequently, ZBP1 has been found to be a multifunctional regulator of RNA metabolism that controls aspects of localization, stability, and translation for many mRNAs. To reveal how ZBP1 recognizes its RNA targets, we biochemically characterized the interaction between ZBP1 and the beta-actin zipcode. The third and fourth KH (hnRNP K homology) domains of ZBP1 specifically recognize a bipartite RNA element located within the first 28 nucleotides of the zipcode. The spacing between the RNA sequences is consistent with the structure of IMP1 KH34, the human ortholog of ZBP1, that we solved by X-ray crystallography. The tandem KH domains are arranged in an intramolecular anti-parallel pseudodimer conformation with the canonical RNA-binding surfaces at opposite ends of the molecule. This orientation of the KH domains requires that the RNA backbone must undergo an approximately 180 degrees change in direction in order for both KH domains to contact the RNA simultaneously. The RNA looping induced by ZBP1 binding provides a mechanism for specific recognition and may facilitate the assembly of post-transcriptional regulatory complexes by remodeling the bound transcript.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Corneodesmosin is a protein in humans encoded by the Corneodesmosin (CDSN) gene on chromosome 6p21.3 and is localized to human epidermis and other cells like squamous epithelia reported for psoriasis, a common ch0ronic disfiguring skin disease. As no 3D structure reported in public database, 3D structure is modeled using in-silico modeling approach. The protein exhibits most favorable regions up to 87.1% with a minimum disallowed region of 3.2% and simulated under hydrophilic environment. Molecular interaction study is carried out with several traditional phytochemicals. The binding interactions analysis was carried out using Genetic algorithm. Several phytochemicals/plant extracts were reported to exhibit better interactions with in the protein binding sites.
  • [Show abstract] [Hide abstract]
    ABSTRACT: ZBP1-modulated localization of β-actin mRNA enables a cell to establish polarity and structural asymmetry. While the mechanism of β-actin mRNA localization has been well revealed, the underlying mechanism of how a specific molecular motor contributes to transport of the ZBP1 complex in non-neuronal cells remains elusive. In this study, we report the isolation and identification of KIF11, a microtubule motor, which physically interacts with ZBP1 and is a component of β-actin mRNP. We show that KIF11 co-localizes with the β-actin mRNA and the ability of KIF11 to transport β-actin mRNA is ZBP1-dependent. We characterize the corresponding regions of ZBP1 and KIF11, which mediate the two protein's interaction in vitro and in vivo. Disruption of the in vivo interaction of KIF11 with ZBP1 delocalizes β-actin mRNA and affects cell migration. Our study reveals a molecular mechanism that a particular microtubule motor mediates the transport of an mRNP through the direct interaction with an mRNA-binding protein.
    Journal of Cell Science 01/2015; DOI:10.1242/jcs.161679 · 5.33 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The ability of its four heterogeneous nuclear ribonucleoprotein-K-homology (KH) domains to physically associate with oncogenic mRNAs is a major criterion for the function of Coding Region Determinant-Binding Protein (CRD-BP). However, the particular RNA binding role of each of the KH domains remains largely unresolved. Here, we mutated the first glycine to an aspartate in the universally conserved Glycine-X-X-Glycine (GXXG) motif of the KH domain as an approach to investigate their role. Our results show that mutation of a single GXXG motif generally had no effect on binding but the mutation in any two KH domains, with the exception of the combination of KH3 and KH4 domains, completely abrogated RNA-binding in vitro and significantly retarded granule formation in zebrafish embryos, suggesting that any combination of at least two KH domains cooperate in tandem to bind RNA efficiently. Interestingly, we found that any single point mutation in one of the four KH domains significantly impacted CRD-BP binding to mRNAs in HeLa cells, suggesting that the dynamics of CRD-BP-mRNA interaction vary over time in vivo. Furthermore, our results suggest that different mRNAs bind preferentially to distinct CRD-BP KH domains. The novel insights revealed in this study have important implications on the understanding of the oncogenic mechanism of CRD-BP a well as in the future design of inhibitors against CRD-BP function.
    Journal of Biological Chemistry 11/2014; 290(1). DOI:10.1074/jbc.M114.614735 · 4.60 Impact Factor


Available from