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The annotation of full zinc proteomes

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Abstract

We obtained an extended functional annotation of zinc proteins using a combination of bioinformatic methods. This work was performed using a number of available predicted zinc proteomes of various representative organisms, leading to the almost complete annotation of, among others, the predicted human zinc proteome. The computational tools exploited included sequence-based and, when possible, structure-based functional predictions. We assigned a hypothetical function to 74% of the 1,472 sequences analyzed that lacked annotation in the starting dataset. We also added new functional categories, not described in the reference dataset, such as ubiquitin binding and DNA replication. As a general conclusion, we can state that the quality of each functional prediction parallels the amount of information for the sequence analyzed: the larger the amount of information, the more detailed and reliable is the proposed functional prediction. Among the findings, we have propose a zinc binding site for archaeal zinc-importing proteins. Furthermore, we propose two groups of transcriptional regulators that are involved in fatty acid metabolism.

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References

  1. Andreini C, Banci L, Bertini I, Rosato A (2006) J Proteome Res 5:3173–3178

    Article  CAS  PubMed  Google Scholar 

  2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Nat Genet 25:25–29

    Article  CAS  PubMed  Google Scholar 

  3. Dobson PD, Cai YD, Stapley BJ, Doig AJ (2004) Curr Med Chem 11:2135–2142

    CAS  PubMed  Google Scholar 

  4. Baker EN, Arcus VL, Lott JS (2003) Appl Bioinformatics 2:S3–10

    CAS  PubMed  Google Scholar 

  5. Lee D, Redfern O, Orengo C (2007) Nat Rev Mol Cell Biol 8:995–1005

    Article  CAS  PubMed  Google Scholar 

  6. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) Nucleic Acids Res 32(Database issue):D138–D141

    Google Scholar 

  7. Sonnhammer EL, Eddy SR, Durbin R (1997) Proteins 28:405–420

    Article  CAS  PubMed  Google Scholar 

  8. Andreini C, Bertini I, Rosato A (2009) Acc Chem Res 42:1471–1479

    Article  CAS  PubMed  Google Scholar 

  9. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235–242

    Article  CAS  PubMed  Google Scholar 

  10. Eddy SR (1998) Bioinformatics 14:755–763

    Article  CAS  PubMed  Google Scholar 

  11. Andreini C, Bertini I, Rosato A (2004) Bioinformatics 20:1373–1380

    Article  CAS  PubMed  Google Scholar 

  12. Andreini C, Banci L, Bertini I, Rosato A (2006) J Proteome Res 5:196–201

    Article  CAS  PubMed  Google Scholar 

  13. Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, Piquet ME (2002) Nucleic Acids Res 30:379–382

    Article  CAS  PubMed  Google Scholar 

  14. Coggill P, Finn RD, Bateman A (2008) Curr Protoc Bioinformatics 23:2.5.1–2.5.17

  15. Zhang Y, Gladyshev VN (2009) Chem Rev 109:4828–4861

    Article  CAS  PubMed  Google Scholar 

  16. Tatusov RL, Koonin EV, Lipman DJ (1997) Science 278:631–637

    Article  CAS  PubMed  Google Scholar 

  17. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova RD, Koonin EV (2001) Nucleic Acids Res 29:22–28

    Article  CAS  PubMed  Google Scholar 

  18. Chen Y, Yu P, Luo J, Jiang Y (2003) Mamm Genome 14:859–865

    Article  CAS  PubMed  Google Scholar 

  19. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) J Mol Biol 305:567–580

    Article  CAS  PubMed  Google Scholar 

  20. Moller S, Croning MD, Apweiler R (2001) Bioinformatics 17:646–653

    Article  CAS  PubMed  Google Scholar 

  21. Sonnhammer EL, von Heijne G, Krogh A (1998) Proc Int Conf Intell Syst Mol Biol 6:175–182

    CAS  PubMed  Google Scholar 

  22. Sprenger J, Fink JL, Teasdale RD (2006) BMC Bioinformatics 7(Suppl 5):S3

    Google Scholar 

  23. Liu J, Kang S, Tang C, Ellis LB, Li T (2007) Nucleic Acids Res 35:e96

    Article  PubMed  Google Scholar 

  24. Snel B, Lehmann G, Bork P, Huynen MA (2000) Nucleic Acids Res 28:3442–3444

    Article  CAS  PubMed  Google Scholar 

  25. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) Nucleic Acids Res 31:258–261

    Article  Google Scholar 

  26. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P (2007) Nucleic Acids Res 35:D358–D362

    Article  Google Scholar 

  27. van Bakel H, Huynen M, Wijmenga C (2004) Bioinformatics 20:2644–2655

    Article  PubMed  Google Scholar 

  28. Galperin MY, Koonin EV (2000) Nat Biotechnol 18:609–613

    Article  CAS  PubMed  Google Scholar 

  29. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2007) Curr Protoc Protein Sci 50:2.9.1–2.9.31

  30. Sali A, Potterton L, Yuan F, Van Vlijmen H, Karplus M (1995) Proteins Struct Funct Genet 23:318–326

    Article  CAS  PubMed  Google Scholar 

  31. Eswar N, Eramian D, Webb B, Shen MY, Sali A (2008) Methods Mol Biol 426:145–159

    Article  CAS  PubMed  Google Scholar 

  32. Laskowski RA, Watson JD, Thornton JM (2005) Nucleic Acids Res 33:W89–W93

    Article  CAS  PubMed  Google Scholar 

  33. de Vries SJ, van Dijk AD, Bonvin AM (2006) Proteins 63:479–489

    Article  PubMed  Google Scholar 

  34. Neuvirth H, Raz R, Schreiber G (2004) J Mol Biol 338:181–199

    Article  CAS  PubMed  Google Scholar 

  35. Consortium The Uniprot (2007) Nucleic Acids Res 35:D193–D197

    Article  Google Scholar 

  36. Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R (2004) Bioinformatics 20:3236–3237

    Article  CAS  PubMed  Google Scholar 

  37. Bennett-Lovsey RM, Herbert AD, Sternberg MJ, Kelley LA (2008) Proteins 70:611–625

    Article  CAS  PubMed  Google Scholar 

  38. Kelley LA, Sternberg MJ (2009) Nat Protoc 4:363–371

    Article  CAS  PubMed  Google Scholar 

  39. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Annu Rev Biophys Biomol Struct 29:291–325

    Article  CAS  PubMed  Google Scholar 

  40. Brent MR, Guigo R (2004) Curr Opin Struct Biol 14:264–272

    Article  CAS  PubMed  Google Scholar 

  41. Grotz N, Fox T, Connolly E, Park W, Guerinot ML, Eide D (1998) Proc Natl Acad Sci USA 95:7220–7224

    Article  CAS  PubMed  Google Scholar 

  42. Eide DJ (2006) Biochim Biophys Acta 1763:711–722

    Article  CAS  PubMed  Google Scholar 

  43. Gaither LA, Eide DJ (2001) Biometals 14:251–270

    Article  CAS  PubMed  Google Scholar 

  44. Dutzler R, Campbell EB, Cadene M, Chait BT, MacKinnon R (2002) Nature 415:287–294

    Article  CAS  PubMed  Google Scholar 

  45. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) Nucleic Acids Res 34:W116–W118

    Article  CAS  PubMed  Google Scholar 

  46. Ramelot TA, Cort JR, Yee AA, Semesi A, Edwards AM, Arrowsmith CH, Kennedy MA (2002) Proteins 49:289–293

    Article  CAS  PubMed  Google Scholar 

  47. Godzik A, Jambon M, Friedberg I (2007) Cell Mol Life Sci 64:2505–2511

    Article  CAS  PubMed  Google Scholar 

  48. Baker D, Sali A (2001) Science 294:93–96

    Article  CAS  PubMed  Google Scholar 

  49. Pandit SB, Bhadra R, Gowri VS, Balaji S, Anand B, Srinivasan N (2004) BMC Bioinformatics 5:28

    Article  PubMed  Google Scholar 

  50. Madera M (2008) Bioinformatics 24:2630–2631

    Article  CAS  PubMed  Google Scholar 

  51. Serres MH, Riley M (2004) OMICS 8:306–321

    Article  CAS  PubMed  Google Scholar 

Download references

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Authors and Affiliations

  1. Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy

    Ivano Bertini, Leonardo Decaria & Antonio Rosato

  2. Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy

    Ivano Bertini & Antonio Rosato

Authors
  1. Ivano Bertini
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  2. Leonardo Decaria
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  3. Antonio Rosato
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Correspondence to Ivano Bertini.

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Bertini, I., Decaria, L. & Rosato, A. The annotation of full zinc proteomes. J Biol Inorg Chem 15, 1071–1078 (2010). https://doi.org/10.1007/s00775-010-0666-6

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  • DOI: https://doi.org/10.1007/s00775-010-0666-6

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