NESdb: a database of NES-containing CRM1 cargoes

Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390 Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390.
Molecular biology of the cell (Impact Factor: 4.47). 07/2012; 23(18):3673-6. DOI: 10.1091/mbc.E12-01-0045
Source: PubMed


The leucine-rich nuclear export signal (NES) is the only known class of targeting signal that directs macromolecules out of the cell nucleus. NESs are short stretches of 8-15 amino acids with regularly spaced hydrophobic residues that bind the export karyopherin CRM1. NES-containing proteins are involved in numerous cellular and disease processes. We compiled a database named NESdb that contains 221 NES-containing CRM1 cargoes that were manually curated from the published literature. Each NESdb entry is annotated with information about sequence and structure of both the NES and the cargo protein, as well as information about experimental evidence of NES-mapping and CRM1-mediated nuclear export. NESdb will be updated regularly and will serve as an important resource for nuclear export signals. NESdb is freely available to nonprofit organizations at


Available from: Yuh Min Chook, Dec 21, 2014
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    • "This malfunction is often directly attributed to the over expression or increased activity of exportin 1 (XPO1/CRM1) [2]. XPO1 serves as the nuclear export chaperone for over 200 different cargo proteins [3, 4]. The interaction between XPO1 and the activated small G-protein Ran (Ran-GTP) in the nucleus facilitates the binding to cargo proteins containing a short amino acid sequence of hydrophobic residues called a nuclear export signal (NES). "
    [Show abstract] [Hide abstract] ABSTRACT: Selective Inhibitor of Nuclear Export (SINE) compounds are a family of small-molecules that inhibit nuclear export through covalent binding to cysteine 528 (Cys528) in the cargo-binding pocket of Exportin 1 (XPO1/CRM1) and promote cancer cell death. Selinexor is the lead SINE compound currently in phase I and II clinical trials for advanced solid and hematological malignancies. In an effort to understand selinexor-XPO1 interaction and to establish whether cancer cell response is a function of drug-target engagement, we developed a quantitative XPO1 occupancy assay. Biotinylated leptomycin B (b-LMB) was utilized as a tool compound to measure SINE-free XPO1. Binding to XPO1 was quantitated from SINE compound treated adherent and suspension cells in vitro, dosed ex vivo human peripheral blood mononuclear cells (PBMCs), and PBMCs from mice dosed orally with drug in vivo. Evaluation of a panel of selinexor sensitive and resistant cell lines revealed that resistance was not attributed to XPO1 occupancy by selinexor. Administration of a single dose of selinexor bound XPO1 for minimally 72 hours both in vitro and in vivo. While XPO1 inhibition directly correlates with selinexor pharmacokinetics, the biological outcome of this inhibition depends on modulation of pathways downstream of XPO1, which ultimately determines cancer cell responsiveness.
    Preview · Article · Dec 2015 · Oncotarget
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    • "Since XLG2 and XLG3 also show both nuclear and extranuclear localization, we analyzed these sequences in search of a nuclear export signal (NES). We did not find a direct match to the classic consensus pattern for a Leu-rich NES (Xu et al., 2012); therefore, we used computational regular expression to search the set of validated NESs identified by Kosugi et al. (2008). Our analyses based on hydrophobic residue spacing identified a potential unconventional class 2 NES in XLG3 (LELRILKL;Fig. "
    [Show abstract] [Hide abstract] ABSTRACT: Heterotrimeric G proteins, consisting of Gα, Gβ and Gγ subunits, are a conserved signal transduction mechanism in eukaryotes. However, G protein subunit numbers in diploid plant genomes are greatly reduced as compared to animals, and do not correlate with the diversity of functions and phenotypes in which heterotrimeric G proteins have been implicated. In addition to GPA1, the sole canonical Arabidopsis thaliana Gα subunit, Arabidopsis has three related proteins: the extra-large GTP-binding proteins XLG1, XLG2 and XLG3. We demonstrate that the XLGs can bind Gβγ dimers (AGB1 plus a Gγ subunit: AGG1, AGG2, or AGG3) with differing specificity, in yeast 3-hybrid assays. Our in silico structural analysis shows that XLG3 aligns closely to the crystal structure of GPA1, and XLG3 also competes with GPA1 for Gβγ binding in yeast. We observed interaction of the XLGs with all three Gβγ dimers at the plasma membrane in planta by BiFC. Bioinformatic and localization studies identified and confirmed nuclear localization signals in XLG2 and XLG3, and a nuclear export signal in XLG3, which may facilitate intracellular shuttling. We found that tunicamycin, salt, and glucose hypersensitivity, and increased stomatal density are agb1 specific phenotypes that are not observed in gpa1 mutants but are recapitulated in xlg mutants. Thus, XLG-Gβγ heterotrimers provide additional signaling modalities for tuning plant G protein responses, and increase the repertoire of G protein heterotrimer combinations from three to twelve. The potential for signal partitioning and competition between the XLGs and GPA1 is a new paradigm for plant-specific cell signaling. Copyright © 2015, Plant Physiology.
    Full-text · Article · Jul 2015 · Plant physiology
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    • "CRM1 is among seven exportins, and the only one that mediates the transport of over 230 proteins including tumor suppressors (e.g., p53, p73, and FOXO1), growth regulator/pro-inflammatory (e.g., IkB, Rb, p21, p27, BRCA1, and APC), and anti-apoptotic proteins (e.g., NPM and AP-1) (Table 1, the aforementioned proteins are part of a comprehensive list appearing on the web page: Academics/IndexFiles/names.php) (Kau et al., 2004; Turner et al., 2012; Xu et al., 2012). CRM1 is also required for the transport of several mRNAs, proteins, and rRNAs that are essential for ribosomal biogenesis (Thomas & Kutay, 2003; Golomb et al., 2012; Bai et al., 2013; Tabe et al., 2013). "
    [Show abstract] [Hide abstract] ABSTRACT: Nucleocytoplasmic trafficking of proteins/RNAs is essential to normal cellular function. Indeed, accumulating evidence suggests that cancer cells escape anti-neoplastic mechanisms and benefit from pro-survival signals via the dysregulation of this system. The nuclear exporter chromosome region maintenance 1 (CRM1) protein is the only protein in the karyopherin-β protein family that contributes to the trafficking of numerous proteins and RNAs from the nucleus. It is considered to be an oncogenic, anti-apoptotic protein in transformed cells, since it reportedly functions as a gatekeeper for cell survival, including affecting p53 function, and ribosomal biogenesis. Furthermore, abnormally high expression of CRM1 is correlated with poor patient prognosis in various malignancies. Therapeutic targeting of CRM1 has emerged as a novel cancer treatment strategy, starting with a clinical trial with leptomycin B, the original specific inhibitor of CRM1, followed by development of several next-generation small molecules. KPT-330, a novel member of the CRM1-selective inhibitors of nuclear export (SINE) class of compounds, is currently undergoing clinical evaluation for the therapy of various malignancies. Results from these trials suggest that SINE compounds may be particularly useful against hematological malignancies, which often become refractory to standard chemotherapeutic agents. Copyright © 2015. Published by Elsevier Inc.
    Full-text · Article · Jun 2015 · Pharmacology [?] Therapeutics
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