Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
BACKGROUND
Several protein-protein interaction studies have been performed for the yeast Saccharomyces cerevisiae using different high-throughput experimental techniques. All these results are collected in the BioGRID database and the SGD database provide detailed annotation of the different proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives.


RESULTS
Here we describe an annotated reconstruction of the protein-protein interactions around four key nutrient-sensing and metabolic regulatory signal transduction pathways (STP) operating in Saccharomyces cerevisiae. The reconstructed STP network includes a full protein-protein interaction network including the key nodes Snf1, Tor1, Hog1 and Pka1. The network includes a total of 623 structural open reading frames (ORFs) and 779 protein-protein interactions. A number of proteins were identified having interactions with more than one of the protein kinases. The fully reconstructed interaction network includes all the information available in separate databases for all the proteins included in the network (nodes) and for all the interactions between them (edges). The annotated information is readily available utilizing the functionalities of network modelling tools such as Cytoscape and CellDesigner.


CONCLUSIONS
The reported fully annotated interaction model serves as a platform for integrated systems biology studies of nutrient sensing and regulation in S. cerevisiae. Furthermore, we propose this annotated reconstruction as a first step towards generation of an extensive annotated protein-protein interaction network of signal transduction and metabolic regulation in this yeast.
Nandy
Subir K
SK
Systems Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
Jouhten
Paula
P
Nielsen
Jens
J
D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
D020928:Mitogen-Activated Protein Kinases; D019869:Phosphatidylinositol 3-Kinases; D017346:Protein Serine-Threonine Kinases; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C071570:SNF1-related protein kinases; C083324:TOR1 protein, S cerevisiae; C088589:HOG1 protein, S cerevisiae