Suel, K. E., Gu, H. & Chook, Y. M. Modular organization and combinatorial energetics of proline-tyrosine nuclear localization signals. PLoS Biol. 6, e137

Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America.
PLoS Biology (Impact Factor: 9.34). 07/2008; 6(6):e137. DOI: 10.1371/journal.pbio.0060137
Source: PubMed


Proline-tyrosine nuclear localization signals (PY-NLSs) are recognized and transported into the nucleus by human Karyopherin (Kap) beta2/Transportin and yeast Kap104p. Multipartite PY-NLSs are highly diverse in sequence and structure, share a common C-terminal R/H/KX2-5PY motif, and can be subdivided into hydrophobic and basic subclasses based on loose N-terminal sequence motifs. PY-NLS variability is consistent with weak consensus motifs, but such diversity potentially renders comprehensive genome-scale searches intractable. Here, we use yeast Kap104p as a model system to understand the energetic organization of this NLS. First, we show that Kap104p substrates contain PY-NLSs, demonstrating their generality across eukaryotes. Previously reported Kapbeta2-NLS structures explain Kap104p specificity for the basic PY-NLS. More importantly, thermodynamic analyses revealed physical properties that govern PY-NLS binding affinity: (1) PY-NLSs contain three energetically significant linear epitopes, (2) each epitope accommodates substantial sequence diversity, within defined limits, (3) the epitopes are energetically quasi-independent, and (4) a given linear epitope can contribute differently to total binding energy in different PY-NLSs, amplifying signal diversity through combinatorial mixing of energetically weak and strong motifs. The modular organization of the PY-NLS coupled with its combinatorial energetics lays a path to decode this diverse and evolvable signal for future comprehensive genome-scale identification of nuclear import substrates.

Download full-text


Available from: Yuh Min Chook, Dec 21, 2014
  • Source
    • "One transport signal that has emerged from such an approach is termed a Proline Tyrosine (PY)-NLS, which is found in a number of RNA binding proteins [33]. Interestingly, the PY-NLS is defined not so much by the primary amino acid sequence but more by general structural features, making this motif challenging to identify by simple sequence analysis [34]. An ongoing goal for the field is to continue to define multiple cargo proteins that interact with specific transport receptors as well as to provide atomic level insight into mechanisms of recognition. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18-23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
    Full-text · Article · Aug 2014 · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
  • Source
    • "However, a more specific approach might be to target the non-canonical mechanism of translocation, which seems to act within a limited number of distinct proteins upon stimulation. In this direction, efforts were made to develop a blocking peptide for importin-2 [81,82]. This peptide is able to compete with natural substrates and is resistant to Ran-mediated release in the nucleus [83], therefore specifically inhibiting this process [81]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Classic nuclear shuttling is mediated by an importin-α∙β heterodimer that binds to cargoes containing a nuclear localization signal, and shuttles most nuclear proteins immediately after their translation. Aside from this canonical mechanism, kariopheryn-βs or β-like importins operate by binding to non-canonical nuclear localization signals to mediate translocation without the assistance of importin-α. The mechanism by which these components operate is much less understood and is currently under investigation. Recently, several β-like importins have been implicated in the stimulated nuclear translocation of signaling proteins. Here, we propose that this group of importins might be responsible for the swift nuclear shuttling of many proteins following various stimuli.
    Full-text · Article · Oct 2013 · F1000 Prime Reports
  • Source
    • "Further experiments are needed to test this proposed mechanism of FUS polymerization. The majority of ALS-linked FUS mutations cluster at the extreme C-terminal region (Da Cruz and Cleveland, 2011; Kwiatkowski et al., 2009; Vance et al., 2009) and many of these are predicted to disrupt a conserved PY-nuclear localization signal (NLS), which is decoded by karyopherin beta2 (Lee et al., 2006; Suel et al., 2008). Indeed, nuclear localization of FUS is disrupted by some of these mutations, (e.g. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Prions are self-templating protein conformers that are naturally transmitted between individuals and promote phenotypic change. In yeast, prion-encoded phenotypes can be beneficial, neutral or deleterious depending upon genetic background and environmental conditions. A distinctive and portable 'prion domain' enriched in asparagine, glutamine, tyrosine and glycine residues unifies the majority of yeast prion proteins. Deletion of this domain precludes prionogenesis and appending this domain to reporter proteins can confer prionogenicity. An algorithm designed to detect prion domains has successfully identified 19 domains that can confer prion behavior. Scouring the human genome with this algorithm enriches a select group of RNA-binding proteins harboring a canonical RNA recognition motif (RRM) and a putative prion domain. Indeed, of 210 human RRM-bearing proteins, 29 have a putative prion domain, and 12 of these are in the top 60 prion candidates in the entire genome. Startlingly, these RNA-binding prion candidates are inexorably emerging, one by one, in the pathology and genetics of devastating neurodegenerative disorders, including: amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), Alzheimer's disease and Huntington's disease. For example, FUS and TDP-43, which rank 1st and 10th among RRM-bearing prion candidates, form cytoplasmic inclusions in the degenerating motor neurons of ALS patients and mutations in TDP-43 and FUS cause familial ALS. Recently, perturbed RNA-binding proteostasis of TAF15, which is the 2nd ranked RRM-bearing prion candidate, has been connected with ALS and FTLD-U. We strongly suspect that we have now merely reached the tip of the iceberg. We predict that additional RNA-binding prion candidates identified by our algorithm will soon surface as genetic modifiers or causes of diverse neurodegenerative conditions. Indeed, simple prion-like transfer mechanisms involving the prion domains of RNA-binding proteins could underlie the classical non-cell-autonomous emanation of neurodegenerative pathology from originating epicenters to neighboring portions of the nervous system. This article is part of a Special Issue entitled RNA-Binding Proteins.
    Full-text · Article · Jan 2012 · Brain research
Show more