Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
PLoS Biology (Impact Factor: 9.34). 10/2009; 7(10):e1000218. DOI: 10.1371/journal.pbio.1000218
Source: PubMed


Author Summary
Significant diversity exists in protein structure and function, yet certain structural domains are used repeatedly across species to execute similar functions. The SH3 domain is one such common structural domain. It is found in signaling proteins and mediates protein–protein interactions by binding to short peptide sequences generally composed of proline. To investigate both the generality and selectivity of peptide binding by SH3 domains, we examined peptide specificity for almost all SH3 domains encoded within the proteome of the budding yeast, Saccharomyces cerevisiae, using a range of experimental methods. We found that although most of the intrinsic binding specificity for SH3 domains can be summarized by the two previously described canonical binding modes, each individual SH3 domain that we studied utilizes unique features of its cognate ligand to achieve binding selectivity. Moreover, some domains exhibit binding specificities that are distinct from the two canonical classes. We integrated peptide-SH3 domain binding data from three complementary screening techniques using a Bayesian statistical model to generate a protein–protein interaction network for the budding yeast SH3 domain family. This network was highly enriched in endocytosis proteins and their interactions. By examining these interactions in detail, we show that our SH3 domain network can be used to predict the temporal localization of several previously uncharacterized proteins to dynamic complexes that orchestrate the process of endocytosis.

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Available from: Gianni Cesareni, Oct 04, 2015
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    • "Three mutant forms of Abp1 (N*, C* and both N*C*) were kindly shared by D. Drubin (U.C. Berkeley) for this analysis [31]. In addition Abp1 has a C-terminal SH3 domain demonstrated to bind Ark1, Prk1, Scp1 and Srv2/CAP at endocytic sites [32], [33]. An Abp1 truncation lacking the SH3 domain was also generated. "
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    ABSTRACT: Clathrin-mediated endocytosis (CME) is a well characterized pathway in both yeast and mammalian cells. An increasing number of alternative endocytic pathways have now been described in mammalian cells that can be both clathrin, actin, and Arf6- dependent or independent. In yeast, a single clathrin-mediated pathway has been characterized in detail. However, disruption of this pathway in many mutant strains indicates that other uptake pathways might exist, at least for bulk lipid and fluid internalization. Using a combination of genetics and live cell imaging, here we show evidence for a novel endocytic pathway in S. cerevisiae that does not involve several of the proteins previously shown to be associated with the 'classic' pathway of endocytosis. This alternative pathway functions in the presence of low levels of the actin-disrupting drug latrunculin-A which inhibits movement of the proteins Sla1, Sla2, and Sac6, and is independent of dynamin function. We reveal that in the absence of the 'classic' pathway, the actin binding protein Abp1 is now essential for bulk endocytosis. This novel pathway appears to be distinct from another described alternative endocytic route in S. cerevisiae as it involves at least some proteins known to be associated with cortical actin patches rather than being mediated at formin-dependent endocytic sites. These data indicate that cells have the capacity to use overlapping sets of components to facilitate endocytosis under a range of conditions.
    PLoS ONE 07/2014; 9(7):e103311. DOI:10.1371/journal.pone.0103311 · 3.23 Impact Factor
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    • "Consistent with this, we find that deletion of AIM44 affects the phosphorylation and localization of Hof1p, a protein that localizes to the bud neck, binds to septins and Myo1p, regulates contractile ring closure, and is detected as an Aim44p binding partner in a genome-wide protein interaction screen (Tonikian et al., 2009). We find that cell cycle–regulated changes in Hof1p abundance and phosphorylation are altered in aim44∆ cells. "
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    ABSTRACT: While actomyosin and septin ring organization and function in cytokinesis are thoroughly described, little is known regarding the mechanisms whereby the actomyosin ring interacts with septins and associated proteins to coordinate cell division. Here, we show that the protein product of YPL158C, Aim44p, undergoes septin-dependent recruitment to the site of cell division. Aim44p colocalizes with Myo1p, the type II myosin of the contractile ring, throughout most of the cell cycle. The Aim44p ring does not contract when the actomyosin ring closes. Instead, it forms a double ring that associates with septin rings on mother and daughter cells after cell separation. Deletion of AIM44 results in defects in contractile ring closure. Aim44p coimmunoprecipitates with Hof1p, a conserved F-BAR protein that binds both septins and type II myosins and promotes contractile ring closure. Deletion of AIM44 results in a delay in Hof1p phosphorylation, and altered Hof1p localization. Finally, overexpression of Dbf2p, a kinase that phosphorylates Hof1p and is required for relocalization of Hof1p from septin rings to the contractile ring and for Hof1p-triggered contractile ring closure, rescues the cytokinesis defect observed in aim44 cells. Our studies reveal a novel role for Aim44p in regulating contractile ring closure through effects on Hof1p.
    Molecular biology of the cell 01/2014; 25(6). DOI:10.1091/mbc.E13-06-0317 · 4.47 Impact Factor
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    • "Since these domains usually have many interaction partners, a change in specificity would have very drastic effects by simultaneous disrupting tens to hundreds of interactions. Therefore, specificity changes are expected to be largely driven by divergence after duplication, as it has been observed for SH3 and PDZ domains (Tonikian et al, 2008, 2009; Xin et al, 2013). It is important to note that recognition might be also determined independently from the substrate recognition site by additional factors such as localization, expression or interaction with adaptor proteins. "
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    ABSTRACT: Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post-translational regulation and progress made in the large-scale functional characterization of PTM function.
    Molecular Systems Biology 12/2013; 9(1):714. DOI:10.1002/msb.201304521 · 10.87 Impact Factor
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