Cell Biochemistry and Biophysics

, Volume 53, Issue 2, pp 101–114 | Cite as

In Silico Construction of a Protein Interaction Landscape for Nucleotide Excision Repair

  • Nancy Tran
  • Ping-Ping Qu
  • Dennis A. Simpson
  • Laura Lindsey-Boltz
  • Xiaojun Guan
  • Charles P. Schmitt
  • Joseph G. Ibrahim
  • William K. KaufmannEmail author
Original Paper


To obtain a systems-level perspective on the topological and functional relationships among proteins contributing to nucleotide excision repair (NER) in Saccharomyces cerevisiae, we built two models to analyze protein–protein physical interactions. A recursive computational model based on set theory systematically computed overlaps among protein interaction neighborhoods. A statistical model scored computation results to detect significant overlaps which exposed protein modules and hubs concurrently. We used these protein entities to guide the construction of a multi-resolution landscape which showed relationships among NER, transcription, DNA replication, chromatin remodeling, and cell cycle regulation. Literature curation was used to support the biological significance of identified modules and hubs. The NER landscape revealed a hierarchical topology and a recurrent pattern of kernel modules coupling a variety of proteins in structures that provide diverse functions. Our analysis offers a computational framework that can be applied to construct landscapes for other biological processes.


DNA repair Excision Network Computation 



We thank Keziban Űnsal-Kaçmaz and Marila Cordeiro-Stone for helpful discussions and ideas and Dan Reed for initial support of this work. Nancy Tran was supported by the Leon and Bertha Goldberg Fellowship. Funding was also provided by PHS grants (ES014635, ES011391, ES010126, CA081343, GM070335, CA074015) and NSF grants to the National Center for Supercomputing Applications (CA SCI-0525308 and CSA SCI-0438712).

Supplementary material

12013_2009_9042_MOESM1_ESM.pdf (127 kb)
(PDF 127 kb)
12013_2009_9042_MOESM2_ESM.pdf (104 kb)
(PDF 104 kb)
12013_2009_9042_MOESM3_ESM.pdf (91 kb)
(PDF 91 kb)


  1. 1.
    Kolodner, R. D., Putnam, C. D., & Myung, K. (2002). Maintenance of genome stability in Saccharomyces cerevisiae. Science, 297, 552–557.PubMedCrossRefGoogle Scholar
  2. 2.
    Friedberg, E. C., et al. (2006). DNA repair and mutagenesis (2nd ed.). Washington, DC: ASM Press.Google Scholar
  3. 3.
    Ataian, Y., & Krebs, J. E. (2006). Five repair pathways in one context: Chromatin modification during DNA repair. Biochemistry and Cell Biology, 84, 490–504.PubMedCrossRefGoogle Scholar
  4. 4.
    Kraemer, K. H., Lee, M. M., & Scotto, J. (1984). DNA repair protects against cutaneous and internal neoplasia: Evidence from xeroderma pigmentosum. Carcinogenesis, 5, 511–514.PubMedCrossRefGoogle Scholar
  5. 5.
    Sancar, A., Lindsey-Boltz, L. A., Unsal-Kacmaz, K., & Linn, S. (2004). Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annual Review of Biochemistry, 73, 39–85.PubMedCrossRefGoogle Scholar
  6. 6.
    Hong, E. L., et al. (2007). Saccharomyces genome database., .
  7. 7.
    Wood, R. D., Mitchell, M., & Lindahl, T. (2005). Human DNA repair genes. Mutation Research, 577, 275–283.PubMedGoogle Scholar
  8. 8.
    Altschul, S. F., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.PubMedCrossRefGoogle Scholar
  9. 9.
    Begley, T. J., Rosenbach, A. S., Ideker, T., & Samson, L. D. (2002). Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Molecular Cancer Research, 1, 103–112.PubMedGoogle Scholar
  10. 10.
    Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabasi, A. L. (2002). Hierarchical organization of modularity in metabolic networks. Science, 297, 1551–1555.PubMedCrossRefGoogle Scholar
  11. 11.
    Pawson, T., & Nash, P. (2000). Protein-protein interactions define specificity in signal transduction. Genes & Development, 14, 1027–1047.Google Scholar
  12. 12.
    Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate—a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B, 57, 289–300.Google Scholar
  13. 13.
    McLachlan, G. J., Do, K. -A., & Ambroise, C. (2004). Analyzing microarray gene expression data. Hoboken, NJ: Wiley-Interscience.Google Scholar
  14. 14.
    Spirin, V., & Mirny, L. A. (2003). Protein complexes and functional modules in molecular networks. PNAS, 100, 12123–12128.PubMedCrossRefGoogle Scholar
  15. 15.
    Stepanov, A., & Lee, M. (1995). The standard template library. HPLabs Technical Report 95.Google Scholar
  16. 16.
    Shannon, P., et al. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.PubMedCrossRefGoogle Scholar
  17. 17.
    Chen, L., & Madura, K. (2002). Rad23 promotes the targeting of proteolytic substrates to the proteasome. Molecular and Cellular Biology, 22, 4902–4913.PubMedCrossRefGoogle Scholar
  18. 18.
    Ng, J. M., et al. (2003). A novel regulation mechanism of DNA repair by damage-induced and RAD23-dependent stabilization of xeroderma pigmentosum group C protein. Genes & Development, 17, 1630–1645.CrossRefGoogle Scholar
  19. 19.
    Ramsey, K. L., et al. (2004). The NEF4 complex regulates Rad4 levels and utilizes Snf2/Swi2-related ATPase activity for nucleotide excision repair. Molecular and Cellular Biology, 24, 6362–6378.PubMedCrossRefGoogle Scholar
  20. 20.
    Ribar, B., Prakash, L., & Prakash, S. (2006). Requirement of ELC1 for RNA polymerase II polyubiquitylation and degradation in response to DNA damage in Saccharomyces cerevisiae. Molecular and Cellular Biology, 26, 3999–4005.PubMedCrossRefGoogle Scholar
  21. 21.
    Yu, S., Owen-Hughes, T., Friedberg, E. C., Waters, R., & Reed, S. H. (2004). The yeast Rad7/Rad16/Abf1 complex generates superhelical torsion in DNA that is required for nucleotide excision repair. DNA Repair, 3, 277–287.PubMedCrossRefGoogle Scholar
  22. 22.
    Venditti, P., Costanzo, G., Negri, R., & Camilloni, G. (1994). ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochimica et Biophysica Acta, 1219, 677–689.PubMedGoogle Scholar
  23. 23.
    Keogh, M. C., Cho, E. J., Podolny, V., & Buratowski, S. (2002). Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation. Molecular and Cellular Biology, 22, 1288–1297.PubMedCrossRefGoogle Scholar
  24. 24.
    Feaver, W. J., et al. (1993). Dual roles of a multiprotein complex from S cerevisiae in transcription and DNA repair. Cell, 75, 1379–1387.PubMedCrossRefGoogle Scholar
  25. 25.
    Lauder, S., et al. (1996). Dual requirement for the yeast MMS19 gene in DNA repair and RNA polymerase II transcription. Molecular and Cellular Biology, 16, 6783–6793.PubMedGoogle Scholar
  26. 26.
    Svejstrup, J. Q. (2002). Mechanisms of transcription-coupled DNA repair. Nature Reviews. Molecular Cell Biology, 3, 21–29.PubMedCrossRefGoogle Scholar
  27. 27.
    Kunkel, T. A., & Erie, D. A. (2005). DNA mismatch repair. Annual Review of Biochemistry, 74, 681–710.PubMedCrossRefGoogle Scholar
  28. 28.
    Guzder, S. N., Sommers, C. H., Prakash, L., & Prakash, S. (2006). Complex formation with damage recognition protein Rad14 is essential for Saccharomyces cerevisiae Rad1-Rad10 nuclease to perform its function in nucleotide excision repair in vivo. Mol Cell Biol, 26, 1135–1141.PubMedCrossRefGoogle Scholar
  29. 29.
    Budd, M. E., & Campbell, J. L. (2000). The pattern of sensitivity of yeast DNA2 mutants to DNA damaging agents suggests a role in DSB and postreplication repair pathways. Mutation Research, 459, 173–186.PubMedCrossRefGoogle Scholar
  30. 30.
    Eissenberg, J. C., Ayyagari, R., Gomes, X. V., & Burgers, P. M. (1997). Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase delta and DNA polymerase epsilon. Molecular and Cellular Biology, 17, 6367–6378.PubMedGoogle Scholar
  31. 31.
    Shivji, M. K., Podust, V. N., Hubscher, U., & Wood, R. D. (1995). Nucleotide excision repair DNA synthesis by DNA polymerase epsilon in the presence of PCNA, RFC, and RPA. Biochemistry, 34, 5011–5017.PubMedCrossRefGoogle Scholar
  32. 32.
    Pfander, B., Moldovan, G. L., Sacher, M., Hoege, C., & Jentsch, S. (2005). SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature, 436, 428–433.PubMedGoogle Scholar
  33. 33.
    Li, X., Li, J., Harrington, J., Lieber, M. R., & Burgers, P. M. (1995). Lagging strand DNA synthesis at the eukaryotic replication fork involves binding and stimulation of FEN–1 by proliferating cell nuclear antigen. The Journal of Biological Chemistry, 270, 22109–22112.PubMedCrossRefGoogle Scholar
  34. 34.
    Majka, J., & Burgers, P. M. (2004). The PCNA-RFC families of DNA clamps and clamp loaders. Progress in Nucleic Acid Research and Molecular Biology, 78, 227–260.PubMedCrossRefGoogle Scholar
  35. 35.
    Bellaoui, M., et al. (2003). Elg1 forms an alternative RFC complex important for DNA replication and genome integrity. The EMBO Journal, 22, 4304–4313.PubMedCrossRefGoogle Scholar
  36. 36.
    Franco, A. A., Lam, W. M., Burgers, P. M., & Kaufman, P. D. (2005). Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes & Development, 19, 1365–1375.CrossRefGoogle Scholar
  37. 37.
    Sprouse, R. O., Brenowitz, M., & Auble, D. T. (2006). Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA. The EMBO Journal, 25, 1492–1504.PubMedCrossRefGoogle Scholar
  38. 38.
    Hsu, J. M., Huang, J., Meluh, P. B., & Laurent, B. C. (2003). The yeast RSC chromatin-remodeling complex is required for kinetochore function in chromosome segregation. Molecular and Cellular Biology, 23, 3202–3215.PubMedCrossRefGoogle Scholar
  39. 39.
    Tyler, J. K., et al. (1999). The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature, 402, 555–560.PubMedCrossRefGoogle Scholar
  40. 40.
    Espinoza, F. H., et al. (1998). Cak1 is required for Kin28 phosphorylation and activation in vivo. Molecular and Cellular Biology, 18, 6365–6373.PubMedGoogle Scholar
  41. 41.
    Tijsterman, M., Tasseron-de Jong, J. G., Verhage, R. A., & Brouwer, J. (1998). Defective Kin28, a subunit of yeast TFIIH, impairs transcription-coupled but not global genome nucleotide excision repair. Mutation Research, 409, 181–188.PubMedCrossRefGoogle Scholar
  42. 42.
    Cheeseman, I. M., et al. (2002). Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell, 111, 163–172.PubMedCrossRefGoogle Scholar
  43. 43.
    Bauer, F., Urdaci, M., Aigle, M., & Crouzet, M. (1993). Alteration of a yeast SH3 protein leads to conditional viability with defects in cytoskeletal and budding patterns. Molecular and Cellular Biology, 13, 5070–5084.PubMedGoogle Scholar
  44. 44.
    Nath, N., McCartney, R. R., & Schmidt, M. C. (2003). Yeast Pak1 kinase associates with and activates Snf1. Molecular and Cellular Biology, 23, 3909–3917.PubMedCrossRefGoogle Scholar
  45. 45.
    Hyman, L. E., et al. (2002). Binding to Elongin C inhibits degradation of interacting proteins in yeast. The Journal of Biological Chemistry, 277, 15586–15591.PubMedCrossRefGoogle Scholar
  46. 46.
    Zachariae, W., & Nasmyth, K. (1999). Whose end is destruction: Cell division and the anaphase-promoting complex. Genes & Development, 13, 2039–2058.CrossRefGoogle Scholar
  47. 47.
    Yip, A. M., & Horvath, S. (2006) The generalized topological overlap matrix for detecting modules in gene networks. In Biocomp, Las Vegas, NV, USA (pp. 451–457).Google Scholar
  48. 48.
    Li, A., & Horvath, S. (2006). The multi-node topological overlap measure for gene neighborhoods analysis. In Biocomp, Las Vegas, NV, USA (pp. 445–450).Google Scholar
  49. 49.
    Iyer, L. M., Babu, M. M., & Aravind, L. (2006). The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA. Cell Cycle, 5, 775–782.PubMedGoogle Scholar
  50. 50.
    Nakatsu, Y., et al. (2000). XAB2, a novel tetratricopeptide repeat protein involved in transcription-coupled DNA repair and transcription. The Journal of Biological Chemistry, 275, 34931–34937.PubMedCrossRefGoogle Scholar
  51. 51.
    Nouspikel, T., & Hanawalt, P. C. (2006). Impaired nucleotide excision repair upon macrophage differentiation is corrected by E1 ubiquitin-activating enzyme. Proceedings of the National Academy of Sciences of the United States of America, 103, 16188–16193.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2009

Authors and Affiliations

  • Nancy Tran
    • 1
  • Ping-Ping Qu
    • 2
  • Dennis A. Simpson
    • 1
  • Laura Lindsey-Boltz
    • 3
  • Xiaojun Guan
    • 4
  • Charles P. Schmitt
    • 4
  • Joseph G. Ibrahim
    • 2
    • 5
    • 6
  • William K. Kaufmann
    • 1
    • 5
    • 6
    Email author
  1. 1.Department of Pathology and Laboratory MedicineUniversity of North Carolina at Chapel HillChapel HillUSA
  2. 2.Department of BiostatisticsUniversity of North Carolina at Chapel HillChapel HillUSA
  3. 3.Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillUSA
  4. 4.Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillUSA
  5. 5.Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillUSA
  6. 6.Center for Environmental Health and SusceptibilityUniversity of North Carolina at Chapel HillChapel HillUSA

Personalised recommendations