This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

Protein Interaction Networks

To determine the proteins with which GRM7 interacts, GRM7 and its homologs were queried on the STRING, Osprey Version 1,0.1, and MINT databases (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Breitkreutz, et al., 2003; Snel, et al., 2000). The STRING database returned the largest number of interactions, giving ten predicted functional partners for human GRM7, nine predicted functional partners for mouse Grm7, nine predicted functional partners for rat Grm7, and one predicted functional partner for chicken GRM7 (Figures 1, 3, 4, 6) (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). Osprey Version 1,0.1 returned three functional partners for human GRM7, all of which were also found by the STRING database, as well as one functional partner for fruit fly mGluRA (Figures 2 and 8) (Breitkreutz, et al., 2003). The MINT database was less useful, as it did not find any functional partners for human GRM7, and those found for rat Grm7 and fruit fly mGluRA were also found by the STRING and Osprey Version 1,0.1 databases (Figures 5 and 7) (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Breitkreutz, et al., 2003; Snel, et al., 2000). Other databases in which GRM7 and its homologs were queried, including KEGG, PANTHER, and BioCarta, did not return any interaction networks or pathways for GRM7 or its homologs.

Human GRM7

The protein interaction networks for human GRM7 show that the protein interacts with regulatory proteins, other glutamate receptors, an actin-binding protein, and the signal transducer GNAQ (Figures 1 and 2) (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; Breitkreutz, et al., 2003; von Mering, et al., 2003; Snel, et al., 2000). The large number of regulatory proteins that GRM7 is predicted to interact with, including Calmodulin 3 (CAM3), Protein kinase C alpha type (PKCA or PRKCA), Protein kinase C alpha type binding protein 1 (PICK1 or PRKCABP), Macrophage myristoylated alanine-rich C kinase substrate (MARCKSL1), homer protein homolog 1 (Syn47), and homer protein homolog 2 (Vesl-2), suggest that this protein is highly regulated at the post-translational level (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; Breitkreutz, et al., 2003; von Mering, et al., 2003; Snel, et al., 2000). Given that GRM7 is one of the major regulators of glutamate transmission in the central nervous system, this finding is not surprising (Okamoto, et al., 1994). Another interesting, although somewhat expected, functional partner of the human GRM7 protein, found by both the STRING and Osprey Version 1,0.1 databases, was the guanine nucleotide binding protein (G protein), q polypeptide (GNAQ) (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; Breitkreutz, et al., 2003; von Mering, et al., 2003; Snel, et al., 2000). This protein, which is a part of G-protein coupled receptor protein signaling and activates phosopholipase C, is likely to be one of the proteins directly downstream of GRM7 in the glutamate signaling pathway (Breitkreutz, et al., 2003). In addition to its interaction with the regulatory proteins and GNAQ, GRM7 also interacts with two glutamate receptors, including Glutamate receptor subunit epsilon-1 (GRIN2A) and Glutamate receptor, ionotropic kainate 5 (KA2) (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). The interaction of GRM7 with GRIN2A and KA2 suggests that GRM7 does not act alone, but rather in cooperation with other glutamate receptors to send and receive glutamate signals (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). The last functional partner found for human GRM7, the actin-binding protein, Filamin-A (FLNA), suggests that GRM7 is likely to be tethered in some way to the cytoskeleton, perhaps for support (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000).


Figure 1. Human GRM7 protein interaction network as determined by the STRING database. The STRING 8.0 database returned the predicted protein interaction network, as shown above, for human GRM7. The nodes of the network (the marbles in the figure) represent the proteins, while the edges of the network (the lines between the marbles) represent the predicted functional associations between the proteins. The color of each of the edges represents the type of evidence that exists for that interaction: a red line indicates the presence of fusion evidence, a green line indicates neighborhood evidence, a blue line indicates co-occurrence evidence, a magenta/purple line indicates experimental evidence, a yellow line indicates text-mining evidence, a light blue line indicates database evidence, and a black line indicates co-expression evidence. The table below the interaction network lists the proteins found to interact with GRM7 in the first column, with details of the proteins' full names and sizes in the second column. The third through tenth columns indicate what type of evidence exists for the interaction of each of the proteins with GRM7. Lastly, the fourth column gives the confidence score, as determined by the evidence, for the interaction of each protein with GRM7: 0 indicates no confidence, while 1 indicates complete confidence. (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000).


Figure 2. Human GRM7 protein interaction network as determined by Osprey. Osprey Version 1,0.1 returned the protein interaction network, as shown above, for human GRM7. The nodes of the network (the circles in the figure) represent the proteins, while the edges of the network (the arrows between the circles) represent the predicted functional associations between the proteins. The color of each of the proteins indicates its function, while the colors of the edges connecting the proteins indicate the type of evidence supporting the association between the proteins. GRM7 and GNAQ (guanine nucleotide binding protein (G protein), q polypeptide) are light blue because they are involved in signal transduction; PRKCA (protein kinase C, alpha) is brown because it is involved in protein amino acid phosphorylation; and PRKCABP (protein kinase C, alpha binding protein) is purple because it is involved in cell organization and biogenesis. The edge between GRM7 and GNAQ is brown because reconstituted complex evidence supports the interaction of GRM7 with GNAQ , while the edge between GRM7 and PRCKA is gray because affinity capture western evidence supports the interaction of GRM7 with PRKCA. The edge between GRM7 and PRKCABP is a combination of purple, brown, gray, and green because two-hybrid, reconstituted complex, affinity capture western, and biochemical activity evidence, respectively, support the interaction of GRM7 with PRKCABP (protein kinase C, alpha binding protein). (Breitkreutz, et al., 2003).

GRM7 Homologs

The protein interaction networks found for the homologs of GRM7, in general, show many of the same interactions as the human protein networks (Figures 3-8) (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Breitkreutz, et al., 2003; Snel, et al., 2000). In particular, the rat Grm7 network returned by the STRING database is nearly identical to that of the human GRM7 interaction networks (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). While the rat Grm7 network retrieved from the MINT database includes two novel interactions, which are not found for human GRM7, these interactions are between proteins of different species and likely do not represent native interactions for Grm7 (Ceol, et al., 2006). The mouse Grm7 network returned by the STRING database, like the rat Grm7 network, is also very similar to that of the human network, although it contains a number of proteins about which little is known (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). Based on the rat and human GRM7 networks, these unknown proteins are likely to function as protein regulators, or perhaps, other glutamate signal transmitters (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000). The chicken and fruit fly networks were quite a bit more sparse than either the rat or mouse protein homolog interaction networks; both showed only one interaction (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Breitkreutz, et al., 2003; Snel, et al., 2000). However, while the function partner of fruit fly mGluRA was not characterized, the functional partner found for chicken GRM7 was one of the same regulatory proteins found for all the mammalian GRM7 homologs: PICK1 (Jensen, et al., 2009; von Mering, et al., 2007; Ceol, et al., 2006; von Mering, et al., 2005; von Mering, et al., 2003; Breitkreutz, et al., 2003; Snel, et al., 2000). Although our knowledge of the protein network for human GRM7 is currently greater than our knowledge of the protein networks for any of its homologs, understanding the how the homologs of human GRM7 function in the cell, including what interaction partners those homologs have, will likely be an important part of better characterizing this protein in the future, especially in light of the fact that GRM7 is primarily expressed in the brain, which can be a difficult tissue to study in humans (Makoff, et al., 1996).

Mouse Grm7

Figure 3. Mouse Grm7 protein interaction network as determined by the STRING database. The STRING 8.0 database returned the predicted protein interaction network, as shown above, for mouse (Mus musculus) Grm7. The nodes of the network (the marbles in the figure) represent the proteins, while the edges of the network (the lines between the marbles) represent the predicted functional associations between the proteins. The color of each of the edges represents the type of evidence that exists for that interaction: a red line indicates the presence of fusion evidence, a green line indicates neighborhood evidence, a blue line indicates co-occurrence evidence, a magenta/purple line indicates experimental evidence, a yellow line indicates text-mining evidence, a light blue line indicates database evidence, and a black line indicates co-expression evidence. The table below the interaction network lists the proteins found to interact with Grm7 in the first column, with details of the proteins' full names and sizes in the second column. The third through tenth columns indicate what type of evidence exists for the interaction of each of the proteins with Grm7. Lastly, the fourth column gives the confidence score, as determined by the evidence, for the interaction of each protein with Grm7: 0 indicates no confidence, while 1 indicates complete confidence. (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000).

Rat Grm7

Figure 4. Rat Grm7 protein interaction network as determined by the STRING database. The STRING 8.0 database returned the predicted protein interaction network, as shown above, for rat (Rattus norvegicus) Grm7. The nodes of the network (the marbles in the figure) represent the proteins, while the edges of the network (the lines between the marbles) represent the predicted functional associations between the proteins. The color of each of the edges represents the type of evidence that exists for that interaction: a red line indicates the presence of fusion evidence, a green line indicates neighborhood evidence, a blue line indicates co-occurrence evidence, a magenta/purple line indicates experimental evidence, a yellow line indicates text-mining evidence, a light blue line indicates database evidence, and a black line indicates co-expression evidence. The table below the interaction network lists the proteins found to interact with Grm7 in the first column, with details of the proteins' full names and sizes in the second column. The third through tenth columns indicate what type of evidence exists for the interaction of each of the proteins with Grm7. Lastly, the fourth column gives the confidence score, as determined by the evidence, for the interaction of each protein with Grm7: 0 indicates no confidence, while 1 indicates complete confidence. (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000).

Figure 5. Rat Grm7 protein interaction network as determined by the MINT database. The MINT database returned the protein interaction network, as shown above, for rat (Rattus norvegicus) Grm7. The nodes of the network (the orange circles) represent the proteins, while the edges of the network (the lines between the orange circles) represent the predicted functional associations between the proteins. The numbers in yellow circles on each of the edges gives the number of pieces of evidence for each interaction. The plus and minus signs on the nodes simply indicate whether or not that protein's interaction network is expanded ("+" indicates it is not, while "-" indicates it is). Grm7 is shown to interact with PRKCA-binding protein (Pick1), Glutamate receptor-interacting protein 1 (Grip1), Protein kinase C alpha type (Prkca), and Syntenin-1 (Sdcbp). It is also shown to interact with two non-rat proteins, including human Ran-binding protein 9 (RANBP9) and cow q8wmq6_bovin. These interactions obviously do not occur in nature; they were found in a two-hybrid experiment. (Ceol, et al., 2006).

Chicken GRM7

Figure 6. Chicken GRM7 protein interaction network as determined by the STRING database. The STRING 8.0 database returned the predicted protein interaction network, as shown above, for chicken (Gallus gallus) GRM7. The nodes of the network (the marbles in the figure) represent the proteins, while the edges of the network (the lines between the marbles) represent the predicted functional associations between the proteins. The color of each of the edges represents the type of evidence that exists for that interaction: a red line indicates the presence of fusion evidence, a green line indicates neighborhood evidence, a blue line indicates co-occurrence evidence, a magenta/purple line indicates experimental evidence, a yellow line indicates text-mining evidence, a light blue line indicates database evidence, and a black line indicates co-expression evidence. The table below the interaction network lists the proteins found to interact with GRM7 in the first column, with details of the proteins' full names and sizes in the second column. The third through tenth columns indicate what type of evidence exists for the interaction of each of the proteins with GRM7. Lastly, the fourth column gives the confidence score, as determined by the evidence, for the interaction of each protein with GRM7: 0 indicates no confidence, while 1 indicates complete confidence. (Jensen, et al., 2009; von Mering, et al., 2007; von Mering, et al., 2005; von Mering, et al., 2003; Snel, et al., 2000).

Fruit Fly mGluRA

Figure 7. Fruit fly mGluRA protein interaction network as determined by the MINT database. The MINT database returned the protein interaction network, as shown above, for fruit fly (Drosophila melanogaster) mGluRA. The nodes of the network (the pink circles) represent the proteins, while the edges of the network (the lines between the circles) represent the predicted functional associations between the proteins. The numbers in yellow circles on each of the edges gives the number of pieces of evidence for each interaction. The plus and minus signs on the nodes simply indicate whether or not that protein's interaction network is expanded ("+" indicates it is not, while "-" indicates it is). mGluRA is shown to interact with Dmel_CG9170 on the basis of one piece of evidence from a two-hybrid pooling experiment. (Ceol, et al., 2006).

Figure 8. Fruit fly mGluRA protein interaction network as determined by Osprey. Osprey Version 1,0.1 returned the protein interaction network, as shown above, for fruit fly (Drosophila melanogaster) mGluRA. The nodes of the network (the circles in the figure) represent the proteins, while the edges of the network (the arrows between the circles) represent the predicted functional associations between the proteins. The color of each of the proteins indicates its function, while the colors of the edges connecting the proteins indicate the type of evidence supporting the association between the proteins. mGluRA is light blue because it is involved in signal transduction, while Dmel_CG9170 is dark gray because its function is unknown. The edge between mGluRA and Dmel_CG9170 is purple because two-hybrid evidence supports their interaction. (Breitkreutz, et al., 2003).

References

 

Breitkreutz, B.J., Stark, C., Tyers, M. (2003). Osprey: A Network Visualization System. Genome Biology, 4(3):R22. doi:10.1186/gb-2003-4-3-r22.

Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G., Chatr-aryamontri, A. (2006). MINT: the Molecular INTeraction database. Nucleic Acids Research, 35(Database issue):D572. doi: 10.1093/nar/gkl950.

Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., von Mering, C. (2009). STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37(Database issue):D412. doi:10.1093/nar/gkn760.

Makoff, A.; Pilling, C.; Harrington, K.; Emson, P. (1996, August). Human metabotropic glutamate receptor type 7: molecular cloning and mRNA distribution in the CNS. [Abstract]. Brain research. Molecular brain research 40(1), 165. Retrieved on February 2, 2009, from http://www.ncbi.nlm.nih.gov/pubmed/8840028?dopt=Abstract

Okamoto, N., Hori, S., Akazawa, C., Hayashi, Y., Shigemoto, R., Mizuno, M., and Nakanishi, S. (1994, January 14). Molecular characterization of a new metabotropic glutamate receptor mGluR7 coupled to inhibatory cyclic AMP signal transduction. [Abstract]. The Journal of Biological Chemistry, 269(2), 1231. Retrieved February 2, 2009, from http://www.ncbi.nlm.nih.gov/pubmed/8288585?dopt=Abstract

Snel, B., Lehmann, G., Bork, P., Huynen, M.A. (2000). STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research, 28(18):3442. doi:10.1093/nar/28.18.3442.

von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., Snel, B. (2003). STRING: a database of predicted functional associations between proteins. Nucleic Acids Research, 31(1):258. doi:10.1093/nar/gkg034.

von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B., Bork, P. (2007). STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35(Database issue):D358. doi:10.1093/nar/gkl825.

von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A., Bork, P. (2005). STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research 2005 33(Database Issue):D433-D437; doi:10.1093/nar/gki005


Jennifer Wagner
wagner4@wisc.edu
Updated May 14, 2009
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