Evolutionary Conservation of Domain-domain Interactions

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2006 Dec 23

PMID 17184549

Citations 41

Authors

Zohar Itzhaki

Eyal Akiva

Yael Altuvia

Hanah Margalit

Affiliations

Soon will be listed here.

Abstract

Background: Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.

Results: Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved.

Conclusion: Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.

Citing Articles

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References

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B . STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003; 31(1):258-61. PMC: 165481. DOI: 10.1093/nar/gkg034. View

Deng M, Mehta S, Sun F, Chen T . Inferring domain-domain interactions from protein-protein interactions. Genome Res. 2002; 12(10):1540-8. PMC: 187530. DOI: 10.1101/gr.153002. View

Ng S, Zhang Z, Tan S . Integrative approach for computationally inferring protein domain interactions. Bioinformatics. 2003; 19(8):923-9. DOI: 10.1093/bioinformatics/btg118. View

Kelley B, Sharan R, Karp R, Sittler T, Root D, Stockwell B . Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A. 2003; 100(20):11394-9. PMC: 208768. DOI: 10.1073/pnas.1534710100. View

Stuart J, Segal E, Koller D, Kim S . A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003; 302(5643):249-55. DOI: 10.1126/science.1087447. View

Gomez S, Noble W, Rzhetsky A . Learning to predict protein-protein interactions from protein sequences. Bioinformatics. 2003; 19(15):1875-81. DOI: 10.1093/bioinformatics/btg352. View

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

Mewes H, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G . MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2003; 32(Database issue):D41-4. PMC: 308826. DOI: 10.1093/nar/gkh092. View

Salwinski L, Miller C, Smith A, Pettit F, Bowie J, Eisenberg D . The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2003; 32(Database issue):D449-51. PMC: 308820. DOI: 10.1093/nar/gkh086. View

10.

Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S . IntAct: an open source molecular interaction database. Nucleic Acids Res. 2003; 32(Database issue):D452-5. PMC: 308786. DOI: 10.1093/nar/gkh052. View

11.

Liu J, Rost B . CHOP proteins into structural domain-like fragments. Proteins. 2004; 55(3):678-88. DOI: 10.1002/prot.20095. View

12.

Yu H, Luscombe N, Lu H, Zhu X, Xia Y, Han J . Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004; 14(6):1107-18. PMC: 419789. DOI: 10.1101/gr.1774904. View

13.

Marianayagam N, Sunde M, Matthews J . The power of two: protein dimerization in biology. Trends Biochem Sci. 2004; 29(11):618-25. DOI: 10.1016/j.tibs.2004.09.006. View

14.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

15.

Tatusov R, Koonin E, Lipman D . A genomic perspective on protein families. Science. 1997; 278(5338):631-7. DOI: 10.1126/science.278.5338.631. View

16.

Marcotte E, Pellegrini M, Ng H, Rice D, Yeates T, Eisenberg D . Detecting protein function and protein-protein interactions from genome sequences. Science. 1999; 285(5428):751-3. DOI: 10.1126/science.285.5428.751. View

17.

Han D, Kim H, Jang W, Lee S, Suh J . PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res. 2004; 32(21):6312-20. PMC: 535680. DOI: 10.1093/nar/gkh972. View

18.

Dueber J, Yeh B, Bhattacharyya R, Lim W . Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol. 2004; 14(6):690-9. DOI: 10.1016/j.sbi.2004.10.004. View

19.

Mulder N, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro, progress and status in 2005. Nucleic Acids Res. 2004; 33(Database issue):D201-5. PMC: 540060. DOI: 10.1093/nar/gki106. View

20.

Littler S, Hubbard S . Conservation of orientation and sequence in protein domain--domain interactions. J Mol Biol. 2005; 345(5):1265-79. DOI: 10.1016/j.jmb.2004.11.011. View