Design of Peptide Inhibitors for the Importin α/β Nuclear Import Pathway by Activity-Based Profiling

Kosugi, Shunichi; Hasebe, Masako; Entani, Tetsuyuki; Takayama, Seiji; Tomita, Masaru; Yanagawa, Hiroshi

doi:10.1016/j.chembiol.2008.07.019

Cited by 201 publications

(193 citation statements)

References 43 publications

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“…The amino acid substitution analyses of importin-␣-dependent NLSs in our previous and present studies have demonstrated that the contribution of each residue to the overall NLS activity is, in most cases, independent and additive (14). Fig.…”

Section: Accurate Prediction Of Nls Activity By Scoring With the Nls mentioning

confidence: 99%

“…We have recently shown that, even within the same NLS class, the level of NLS activity varies depending on the NLS sequence (5,14). To assess the functional contribution of various amino acids at every position in each of 3 monopartite NLS classes (classes 2-4) (5), all of the amino acid residues of the template NLSs, as representatives of these classes, were serially replaced with Ϸ20 other amino acid residues.…”

Section: Activity-based Profiles Of Different Classes Of Importin-␣-dmentioning

confidence: 99%

“…The relative nuclear import activities of these altered sequences were assayed in yeast and ranked in 1 of the 10 levels based on the localization phenotype of the GFP reporter [see supporting information (SI) Fig. S1 for details], as described previously (14). The profiles of the 3 classes of NLSs are represented as scoring matrices based on the relative NLS activities (Fig. …”

Section: Activity-based Profiles Of Different Classes Of Importin-␣-dmentioning

confidence: 99%

“…It has been shown that acidic amino acids adjacent to the basic core of an importin-␣-dependent NLS inhibit the NLS activity (5,14). Phosphorylation around an NLS mimics the inhibitory effect of acidic amino acids.…”

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confidence: 99%

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Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Kosugi

Hasebe

Tomita

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-␣-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-␣/␤ pathway-specific NLSs (cNLS Mapper, available at http//nls-mapper.iab.keio.ac.jp/) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1-and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1-phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein-protein networks.CDK ͉ computational method ͉ nuclear localization signal ͉ nuclear import ͉ phosphorylation R egulated nuclear import controls the nuclear function of many proteins that shuttle between the nucleus and cytoplasm or other cellular compartments in response to certain physiological conditions or extracellular stimuli (1). Nucleocytoplasmic shuttling comprises both nuclear import and nuclear export activities. Nuclear import is mediated by the interaction of nuclear localization signals (NLSs) with transport receptor importins, among which the importin-␣ family recognizes most major classes of NLSs with 1 or 2 basic stretches, called the classical NLSs (2-4). Six different classes of monopartite and bipartite NLSs bind to distinct binding grooves of importin-␣ (5-7). Nuclear export is mediated by nuclear export signals (NESs), which are recognized by Crm1/exportin or Msn5 in yeast (1, 8). The regulation of these 2 antagonistic activities directs a protein to either the nucleus or the cytoplasm. In general, these activities are regulated by the modification of the NLSs/NESs, by intermolecular or intramolecular interactions that lead to the structural masking of NLSs/NESs, or by the supply of an NLS/NES by another protein (9).Phosphorylation within or around an NLS is the usual strategy for the regulated nuclear transport of a protein (4, 10-13). It has been shown that acidic amino acids adjacent to the basic core ...

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Section: Accurate Prediction Of Nls Activity By Scoring With the Nls mentioning

confidence: 99%

Section: Activity-based Profiles Of Different Classes Of Importin-␣-dmentioning

confidence: 99%

Section: Activity-based Profiles Of Different Classes Of Importin-␣-dmentioning

confidence: 99%

mentioning

confidence: 99%

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Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Kosugi

Hasebe

Tomita

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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1,094

1,028

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“…Analysis of the NOCT orthologs in Fig. 3 using NucPred [96], cNLS Mapper [97–99], and SeqNLS [100] tools did not predict nuclear localization, whereas PSORTII [101,102] predicted nuclear localization for Drosophila, X. laevis , and D. rerio NOCTB orthologs. Mitochondrial localization is predicted for several NOCT orthologs.…”

Section: Is Noct Activity Spatially Restricted?mentioning

confidence: 99%

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

2018

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Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3′ poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin’s involvement in these processes; however, a full understanding of its molecular function remains elusive. Recent studies have provided new insights by identifying putative Nocturnin-regulated mRNAs in mice and by determining the structure and regulatory activities of human Nocturnin. This review seeks to integrate these new discoveries into our understanding of Nocturnin’s regulatory functions and highlight the important remaining unanswered questions surrounding its regulation, biochemical activities, protein partners, and target mRNAs.

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Glucagon‐like peptide‐1 receptor undergoes importin‐α‐dependent nuclear localization in rat aortic smooth muscle cells

et al. 2020

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Edited by Lukas Alfons HuberGlucagon-like peptide 1 receptor (GLP-1R) belongs to the family B of G protein-coupled receptors (GPCRs) and has antidiabetic and cardioprotective effects. Classical GLP-1R at the plasma membrane undergoes desensitization and internalization and is recycled back to the plasma membrane under the control of GLP-1 in islet b-cells. However, the subcellular localization of GLP-1R in the vascular system remains unclear. Here, we find that GLP-1R is localized in the nucleus of rat aortic smooth muscle cells (RASMCs) and in the tunica media. We identify a functional nuclear localization signal (NLS; 412-442aa) at the C-terminal region of GLP-1R. Nuclear import of GLP-1R is mediated by an importin-a-dependent pathway and regulated by phosphorylation of Ser416 in the NLS. Upon leaving the nucleus, GLP-1R promotes cell proliferation in RASMCs. These findings may provide insights into the cardiovascular functions of GLP-1R.

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Design of Peptide Inhibitors for the Importin α/β Nuclear Import Pathway by Activity-Based Profiling

Cited by 201 publications

References 43 publications

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

Glucagon‐like peptide‐1 receptor undergoes importin‐α‐dependent nuclear localization in rat aortic smooth muscle cells

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