ZBP1 recognition of -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: 10.8). 01/2010; 24(2):148-58. DOI: 10.1101/gad.1862910
Source: PubMed


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.

18 Reads
  • Source
    • "Biochemical characterization of the ZBP1 recognition motif reveals that the ZBP1 KH34 region functions as a single unit to interact with the zipcode of b-actin mRNA (Chao et al., 2010). Knockdown of ZBP1 by small interfering (si)RNA impairs cellular adhesion, motility and invadopodia formation (Vikesaa et al., 2006; Gu et al., 2012; Katz et al., 2012). "
    [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; 128(5). DOI:10.1242/jcs.161679 · 5.43 Impact Factor
  • Source
    • "The C-terminal KH domains of the IGF2BPs are essential for RNA-binding and thereby determine subcellular localization of all three family members, which is typically characterized by a mainly cytoplasmic, granular distribution [11]. Based on crystal structures as well as NMR studies of the C-terminal KH-3,4 didomain of IGF2BP1, also termed ZBP1, the current view suggests an anti-parallel pseudo-dimer formation of the two KH domains interacting with two appropriately spaced RNA motifs [12] [13]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The post-transcriptional control of gene expression mediated by RNA-binding proteins (RBPs), long non-coding RNAs (lncRNAs) as well as miRNAs is essential to determine tumor cell fate and thus is a major determinant in cancerogenesis. The IGF2 mRNA binding protein family (IGF2BPs) comprises three RBPs. Two members of the family, IGF2BP1 and IGF2BP3, are bona fide oncofetal proteins, which are de novo synthesized in various human cancers. In vitro studies revealed that IGF2BPs serve as post-transcriptional fine-tuners modulating the expression of genes implicated in the control of tumor cell proliferation, survival, chemo-resistance and metastasis. Consistently, the expression of both IGF2BP family members was reported to correlate with an overall poor prognosis and metastasis in various human cancers. Due to the fact that most reports used a pan-IGF2BP antibody for studying IGF2BP expression in cancer, paralogue-specific functions can barely be evaluated at present. Nonetheless, the accordance of IGF2BPs’ role in promoting an aggressive phenotype of tumor-derived cells in vitro and their upregulated expression in aggressive malignancies provides strong evidence that IGF2BPs are powerful post-transcriptional oncogenes enhancing tumor growth, drug-resistance and metastasis. This suggests IGF2BPs as powerful biomarkers and candidate targets for cancer therapy.
    Seminars in Cancer Biology 12/2014; 29. DOI:10.1016/j.semcancer.2014.07.006 · 9.33 Impact Factor
  • Source
    • "The coding region determinant-binding protein (CRD-BP), also commonly known as insulin-like growth factor II mRNA-binding protein 1 (IMP1), is a member of the conserved VICKZ family of RNA-binding proteins that are characterized by the presence of two N-terminal RNA-recognition motifs (RRMs) followed by four C-terminal KH [hnRNP (heterogenous nuclear ribonucleoprotein) K-homology] domains [1]–[4]. CRD-BP has about 95% protein sequence identity to the chicken zipcode-binding protein 1 (ZBP1) [2] that associates with β–actin mRNA [5], [6]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Studies on Coding Region Determinant-Binding Protein (CRD-BP) and its orthologs have confirmed their functional role in mRNA stability and localization. CRD-BP is present in extremely low levels in normal adult tissues, but it is over-expressed in many types of aggressive human cancers and in neonatal tissues. Although the exact role of CRD-BP in tumour progression is unclear, cumulative evidence suggests that its ability to physically associate with target mRNAs is an important criterion for its oncogenic role. CRD-BP has high affinity for the 3'UTR of the oncogenic CD44 mRNA and depletion of CRD-BP in cells led to destabilization of CD44 mRNA, decreased CD44 expression, reduced adhesion and disruption of invadopodia formation. Here, we further characterize the CRD-BP-CD44 RNA interaction and assess specific antisense oligonucleotides and small molecule antibiotics for their ability to inhibit the CRD-BP-CD44 RNA interaction. CRD-BP has a high affinity for binding to CD44 RNA nts 2862-3055 with a Kd of 645 nM. Out of ten antisense oligonucleotides spanning nts 2862-3055, only three antisense oligonucleotides (DD4, DD7 and DD10) were effective in competing with CRD-BP for binding to 32P-labeled CD44 RNA. The potency of DD4, DD7 and DD10 in inhibiting the CRD-BP-CD44 RNA interaction in vitro correlated with their ability to specifically reduce the steady-state level of CD44 mRNA in cells. The aminoglycoside antibiotics neomycin, paramomycin, kanamycin and streptomycin effectively inhibited the CRD-BP-CD44 RNA interaction in vitro. Assessing the potential inhibitory effect of aminoglycoside antibiotics including neomycin on the CRD-BP-CD44 mRNA interaction in cells proved difficult, likely due to their propensity to non-specifically bind nucleic acids. Our results have important implications for future studies in finding small molecules and nucleic acid-based inhibitors that interfere with protein-RNA interactions.
    PLoS ONE 03/2014; 9(3):e91585. DOI:10.1371/journal.pone.0091585 · 3.23 Impact Factor
Show more


18 Reads
Available from