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A human MAP kinase interactome.

Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T - Nat. Methods (2010)

Bottom Line: Multiple lines of evidence including conservation with yeast supported a core network of 641 interactions.Using small interfering RNA knockdowns, we observed that approximately one-third of MAPK-interacting proteins modulated MAPK-mediated signaling.We uncovered the Na-H exchanger NHE1 as a potential MAPK scaffold, found links between HSP90 chaperones and MAPK pathways and identified MUC12 as the human analog to the yeast signaling mucin Msb2.

View Article: PubMed Central - PubMed

Affiliation: Departments of Medicine and Bioengineering, University of California at San Diego, La Jolla, California, USA.

ABSTRACT
Mitogen-activated protein kinase (MAPK) pathways form the backbone of signal transduction in the mammalian cell. Here we applied a systematic experimental and computational approach to map 2,269 interactions between human MAPK-related proteins and other cellular machinery and to assemble these data into functional modules. Multiple lines of evidence including conservation with yeast supported a core network of 641 interactions. Using small interfering RNA knockdowns, we observed that approximately one-third of MAPK-interacting proteins modulated MAPK-mediated signaling. We uncovered the Na-H exchanger NHE1 as a potential MAPK scaffold, found links between HSP90 chaperones and MAPK pathways and identified MUC12 as the human analog to the yeast signaling mucin Msb2. This study makes available a large resource of MAPK interactions and clone libraries, and it illustrates a methodology for probing signaling networks based on functional refinement of experimentally derived protein-interaction maps.

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Functional modules in the core network. (a) Bird’s eye view of the core MAPK Y2H network. (b–g) High confidence conserved functional modules. Red edges correspond to core MAPK Y2H interactions which were conserved with yeast. Grey edges indicate core interactions not conserved with yeast. Thickness of the edge increases with the number of observations. (h) AP-1 luciferase activation assay for various siRNAs targeting members of conserved modules. (i) p38 phosphorylation levels are decreased with siRNAs targeting members of conserved modules. (j–l) Novel modules not conserved with yeast.
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Figure 3: Functional modules in the core network. (a) Bird’s eye view of the core MAPK Y2H network. (b–g) High confidence conserved functional modules. Red edges correspond to core MAPK Y2H interactions which were conserved with yeast. Grey edges indicate core interactions not conserved with yeast. Thickness of the edge increases with the number of observations. (h) AP-1 luciferase activation assay for various siRNAs targeting members of conserved modules. (i) p38 phosphorylation levels are decreased with siRNAs targeting members of conserved modules. (j–l) Novel modules not conserved with yeast.

Mentions: To shed further light on the structure and function of the Core MAPK Network (Fig. 3a), we analyzed this network to extract conserved and/or species-specific modules (Methods). To form these modules, we first combined the Core MAPK Network with the Positive Reference Set to capture novel as well as literature-curated MAPK interactions. Network “modules” were identified as all complete interacting triplets of proteins (i.e., triangles) for which at least two interactions were from the Core MAPK Network. Triangles and other dense regions of interactions have been shown to be indicative of protein complexes, signaling pathways, and other functionally cohesive groups of proteins21. In total, 134 triplets were found covering 195 core MAPK Y2H interactions (Supplementary Table 5). We next identified a subset of 19 “Conserved modules”, which were modules for which at least two of the interactions were conserved with yeast. We found that such modules fell into six connected components, highlighting potential conserved mechanisms of signaling and regulation (Fig. 3b–g).


A human MAP kinase interactome.

Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T - Nat. Methods (2010)

Functional modules in the core network. (a) Bird’s eye view of the core MAPK Y2H network. (b–g) High confidence conserved functional modules. Red edges correspond to core MAPK Y2H interactions which were conserved with yeast. Grey edges indicate core interactions not conserved with yeast. Thickness of the edge increases with the number of observations. (h) AP-1 luciferase activation assay for various siRNAs targeting members of conserved modules. (i) p38 phosphorylation levels are decreased with siRNAs targeting members of conserved modules. (j–l) Novel modules not conserved with yeast.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2967489&req=5

Figure 3: Functional modules in the core network. (a) Bird’s eye view of the core MAPK Y2H network. (b–g) High confidence conserved functional modules. Red edges correspond to core MAPK Y2H interactions which were conserved with yeast. Grey edges indicate core interactions not conserved with yeast. Thickness of the edge increases with the number of observations. (h) AP-1 luciferase activation assay for various siRNAs targeting members of conserved modules. (i) p38 phosphorylation levels are decreased with siRNAs targeting members of conserved modules. (j–l) Novel modules not conserved with yeast.
Mentions: To shed further light on the structure and function of the Core MAPK Network (Fig. 3a), we analyzed this network to extract conserved and/or species-specific modules (Methods). To form these modules, we first combined the Core MAPK Network with the Positive Reference Set to capture novel as well as literature-curated MAPK interactions. Network “modules” were identified as all complete interacting triplets of proteins (i.e., triangles) for which at least two interactions were from the Core MAPK Network. Triangles and other dense regions of interactions have been shown to be indicative of protein complexes, signaling pathways, and other functionally cohesive groups of proteins21. In total, 134 triplets were found covering 195 core MAPK Y2H interactions (Supplementary Table 5). We next identified a subset of 19 “Conserved modules”, which were modules for which at least two of the interactions were conserved with yeast. We found that such modules fell into six connected components, highlighting potential conserved mechanisms of signaling and regulation (Fig. 3b–g).

Bottom Line: Multiple lines of evidence including conservation with yeast supported a core network of 641 interactions.Using small interfering RNA knockdowns, we observed that approximately one-third of MAPK-interacting proteins modulated MAPK-mediated signaling.We uncovered the Na-H exchanger NHE1 as a potential MAPK scaffold, found links between HSP90 chaperones and MAPK pathways and identified MUC12 as the human analog to the yeast signaling mucin Msb2.

View Article: PubMed Central - PubMed

Affiliation: Departments of Medicine and Bioengineering, University of California at San Diego, La Jolla, California, USA.

ABSTRACT
Mitogen-activated protein kinase (MAPK) pathways form the backbone of signal transduction in the mammalian cell. Here we applied a systematic experimental and computational approach to map 2,269 interactions between human MAPK-related proteins and other cellular machinery and to assemble these data into functional modules. Multiple lines of evidence including conservation with yeast supported a core network of 641 interactions. Using small interfering RNA knockdowns, we observed that approximately one-third of MAPK-interacting proteins modulated MAPK-mediated signaling. We uncovered the Na-H exchanger NHE1 as a potential MAPK scaffold, found links between HSP90 chaperones and MAPK pathways and identified MUC12 as the human analog to the yeast signaling mucin Msb2. This study makes available a large resource of MAPK interactions and clone libraries, and it illustrates a methodology for probing signaling networks based on functional refinement of experimentally derived protein-interaction maps.

Show MeSH