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

ABSTRACT 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.

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Available from: Yuh Min Chook, Dec 21, 2014
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    • "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. "
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    • "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]. "
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    • "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. "
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