Functional proteomics mapping of a human signaling pathway.
Access to the human genome facilitates extensive functional proteomics studies. Here, we present an integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway. As a proof of principle, we studied the Smad signaling system, which is regulated by members of the transforming growth factor beta (TGFbeta) superfamily. We used two-hybrid screening to map Smad signaling protein-protein interactions and to establish a network of 755 interactions, involving 591 proteins, 179 of which were poorly or not annotated. The exploration of such complex interaction databases is improved by the use of PIMRider, a dedicated navigation tool accessible through the Web. The biological meaning of this network is illustrated by the presence of 18 known Smad-associated proteins. Functional assays performed in mammalian cells including siRNA knock-down experiments identified eight novel proteins involved in Smad signaling, thus validating this integrated functional proteomics approach.
Colland
Frédéric
F
Hybrigenics SA, 75014 Paris, France. fcolland@hybrigenics.fr
Jacq
Xavier
X
Trouplin
Virginie
V
Mougin
Christelle
C
Groizeleau
Caroline
C
Hamburger
Alexandre
A
Meil
Alain
A
Wojcik
Jérôme
J
Legrain
Pierre
P
Gauthier
Jean-Michel
JM
D048868:Adaptor Proteins, Signal Transducing; D006528:Carcinoma, Hepatocellular / Q000235:genetics / Q000473:pathology; D002352:Carrier Proteins / Q000502:physiology; D002460:Cell Line; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D015723:Gene Library; D018398:Homeodomain Proteins / Q000502:physiology; D006801:Humans; D007668:Kidney / Q000737:chemistry / Q000166:cytology / Q000196:embryology / Q000378:metabolism; D060588:LIM Domain Proteins; D008113:Liver Neoplasms / Q000235:genetics / Q000473:pathology; D008565:Membrane Proteins / Q000502:physiology; D010920:Placenta / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D015534:Trans-Activators / Q000502:physiology; D014157:Transcription Factors / Q000502:physiology; D016212:Transforming Growth Factor beta / Q000502:physiology; D020798:Two-Hybrid System Techniques
D048868:Adaptor Proteins, Signal Transducing; D002352:Carrier Proteins; D018398:Homeodomain Proteins; D060588:LIM Domain Proteins; C114905:LMO4 protein, human; D008565:Membrane Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D016212:Transforming Growth Factor beta; C100848:LAPTM5 protein, human