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Loops and repeats in proteins as footprints of molecular evolution

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Abstract

This review is devoted to substantiation of new characteristics for classification of living organisms. The novel view of a role of flexible regions in protein functioning and evolution is suggested. It is based on the newly revealed correlation between the number of loops in elongation factors and the complexity of organisms. This correlation allowed us to formulate a hypothesis of evolution of this protein family. In addition, the study of the ribosomal protein S1 family made it possible to consider the number of structural domains as a reliable indicator of a microorganism’s affiliation with a particular division and to judge about “direction” of their evolution. The findings allow us to consider the loops and repeats in these proteins as unique imprints of molecular evolution.

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Abbreviations

EF-1:

elongation factor 1 (EF-1 in this work is interpreted as elongation factor EF-Tu and EF-Ts for eubacteria, aEF-1 for archaea, and EEF-1 for eukaryotes)

EF-2:

elongation factor 2 (EF-2 in this work is interpreted as elongation factor EF-G for eubacteria, aEF-2 for archaea, and EEF-2 for eukaryotes)

G-family:

the GTP-binding protein family (GTP)

PNPase:

polynucleotide phosphorylase

References

  1. Lemieux, U., and Spohr, U. (1994) Adv. Carbohydrate Chem. Biochem., 50, 1–20.

    Article  CAS  Google Scholar 

  2. Karush, F. (1950) J. Am. Chem. Soc., 72, 2705–2713.

    Article  CAS  Google Scholar 

  3. Blake, C., Koenig, D., Mair, G., North, A., Phillips, D., and Sarma, V. (1965) Nature, 206, 757–761.

    Article  PubMed  CAS  Google Scholar 

  4. McDonald, R., Steitz, T., and Engelman, D. (1979) Biochemistry, 18, 338–342.

    Article  PubMed  CAS  Google Scholar 

  5. Kjeldgaard, M., Nissen, P., Thirup, S., and Nyborg, J. (1993) Structure, 1, 35–50.

    Article  PubMed  CAS  Google Scholar 

  6. Dobson, C. (1999) Trends Biochem. Sci., 24, 329–332.

    Article  PubMed  CAS  Google Scholar 

  7. Pedersen, J., Andersen, C., and Otzen, D. (2010) FEBS J., 277, 4591–4601.

    Article  PubMed  CAS  Google Scholar 

  8. Uversky, A., Gillspie, J., and Fink, A. (2000) Proteins, 41, 415–427.

    Article  PubMed  CAS  Google Scholar 

  9. Serdyuk, I. N. (2007) Mol. Biol. (Moscow), 42, 287–313.

    Google Scholar 

  10. Murzin, A. (1993) The EMBO J., 12, 861–867.

    CAS  Google Scholar 

  11. Mosavi, L., Cammett, T., Desrosiers, D., and Peng, Z. (2004) Protein Sci., 13, 1435–1448.

    Article  PubMed  CAS  Google Scholar 

  12. Betz, S. (1993) Protein Sci., 2, 1551–1558.

    Article  PubMed  CAS  Google Scholar 

  13. Fraser, R., MacRae, T., and Suzuki, E. (1979) J. Mol. Biol., 129, 463–448.

    Article  PubMed  CAS  Google Scholar 

  14. Daley, D. (2008) Curr. Opin. Struct. Biol., 18, 420–424.

    Article  PubMed  CAS  Google Scholar 

  15. Timasheff, S., and Gorbunoff, M. (1967) Annu. Rev. Biochem., 36, 13–54.

    Article  PubMed  CAS  Google Scholar 

  16. Dunker, A., and Lawson, J. (2001) J. Mol. Graphics Model., 19, 26–59.

    Article  CAS  Google Scholar 

  17. Dunker, A., Brown, C., and Lawson, J. (2002) Biochemistry, 41, 6573–6582.

    Article  PubMed  CAS  Google Scholar 

  18. Ptitsyn, O. (1995) Adv. Protein Chem., 47, 183–229.

    Google Scholar 

  19. Receveur-Brechot, V., Bourish, J., and Uversky, V. (2006) Proteins, 62, 24–45.

    Article  PubMed  CAS  Google Scholar 

  20. Jeffry, C. (1999) TIBS, 24, 8–11.

    Google Scholar 

  21. Budkevich, T., Timchenko, A., and Tiktopulo, E. (2002) Biochemistry, 41, 15342–15349.

    Article  PubMed  CAS  Google Scholar 

  22. Deryusheva, E. I., Galzitskaya, O. V., and Serdyuk, I. N. (2008) Mol. Biol. (Moscow), 42, 1067–1078.

    Article  Google Scholar 

  23. Deryusheva, E. I., Levin, D. M., and Serdyuk, I. N. (2009) Izv. TulGU. Estestv. Nauki, 3, 229–237.

    Google Scholar 

  24. Evarsson, A., Brazhnikov, E., and Garber, M. (1994) The EMBO J., 13, 3669–3677.

    Google Scholar 

  25. McGinness, K., and Sauer, R. (2004) PNAS, 101, 13454–13459.

    Article  PubMed  CAS  Google Scholar 

  26. Dahlberg, A., and Dahlberg, J. (1975) Proc. Natl. Acad. Sci. USA, 72, 2940–2944.

    Article  PubMed  CAS  Google Scholar 

  27. Blumenthal, T., Young, R., and Brown, S. (1976) J. Biol. Chem., 251, 2740–2743.

    PubMed  CAS  Google Scholar 

  28. Regnier, P., Grunberg-Manago, M., and Portier, C. (1987) J. Biol. Chem., 262, 63–68.

    PubMed  CAS  Google Scholar 

  29. Subramanian, A. (1983) Prog. Nucleic Acid Res. Mol. Biol., 28, 101–142.

    Article  PubMed  CAS  Google Scholar 

  30. Deryusheva, E. I., Machulin, A. V., Selivanova, O. M., and Serdyuk, I. N. (2010) Mol. Biol. (Moscow), 44, 728–734.

    Article  Google Scholar 

  31. Bycroft, M., Hubbard, T., Proctor, M., Freud, S., and Murzin, G. (1997) Cell, 24, 235–242.

    Article  Google Scholar 

  32. Kim, D., Chivian, D., and Baker, D. (2004) Nucleic Acids Res., 32, W526–W531.

    Article  PubMed  CAS  Google Scholar 

  33. Frank, J. (2001) Proc. Natl. Acad. Sci. USA, 98, 11991–11996.

    Article  PubMed  Google Scholar 

  34. Fink, A. (2005) Curr. Opin. Struct. Biol., 15, 35–41.

    Article  PubMed  CAS  Google Scholar 

  35. Dyson, H., and Wright, P. (2005) Nat. Rev. Mol. Cell Biol., 6, 197–208.

    Article  PubMed  CAS  Google Scholar 

  36. Tompa, P. (2002) Trends Biochem. Sci., 27, 527–533.

    Article  PubMed  CAS  Google Scholar 

  37. Romero, P., Obradovic, Z., Li, X., Garner, E., Brown, C., and Dunker, A. (2001) Proteins, 42, 38–48.

    Article  PubMed  CAS  Google Scholar 

  38. Yang, Z., Thomson, R., McNeil, P., and Esnouf, R. (2005) Bioinformatics, 21, 3369–3376.

    Article  PubMed  CAS  Google Scholar 

  39. Linding, R., Jensen, L., Diella, F., Bork, P., Gibson, T., and Russell, R. (2003) Structure, 11, 1453–1459.

    Article  PubMed  CAS  Google Scholar 

  40. Coeytaux, K., and Poupon, A. (2005) Bioinformatics, 21, 1891–1900.

    Article  PubMed  CAS  Google Scholar 

  41. Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. (2005) Bioinformatics, 21, 3433–3434.

    Article  PubMed  CAS  Google Scholar 

  42. Linding, R., Russell, R., Neduva, V., and Gibson, T. (2003) Nucleic Acids Res., 31, 3701–3708.

    Article  PubMed  CAS  Google Scholar 

  43. Prilusky, J., Felder, C., Zeev-Ben-Mordehai, T., Rydberg, E., Man, O., Beckmann, J., Silman, I., and Sussman, J. (2005) Bioinformatics, 21, 3435–3438.

    Article  PubMed  CAS  Google Scholar 

  44. Galzitskaya, O. V., Garbuzinsky, S. A., and Lobanov, M. Yu. (2006) Mol. Biol. (Moscow), 40, 341–348.

    Google Scholar 

  45. Galzitskaya, O., Garbuzynskiy, S., and Lobanov, M. (2006) Bioinformatics, 22, 2948–2949.

    Article  PubMed  CAS  Google Scholar 

  46. Andersen, G., Pedersen, L., and Valente, L. (2000) Mol. Cell, 6, 1261–1266.

    Article  PubMed  CAS  Google Scholar 

  47. Steenkamp, E., Wright, J., and Baldauf, S. (2005) Mol. Biol. Evol., 23, 93–106.

    Article  PubMed  Google Scholar 

  48. Galzitskaya, O., Deryusheva, E., and Serdyuk, I. (2008) J. Comput. Sci. Syst. Biol., 1, 73–80.

    Article  CAS  Google Scholar 

  49. Kjeldgard, M., Nissen, P., Thirup, S., and Nyborg, J. (1993) Structure, 1, 35–50.

    Article  Google Scholar 

  50. Kjeldgard, M., and Nyborg, J. (1992) J. Mol. Biol., 223, 721–742.

    Article  Google Scholar 

  51. Schultz, J., Milpetz, F., Bork, P., and Ponting, C. (1998) Proc. Natl. Acad. Sci. USA, 95, 5857–5864.

    Article  PubMed  CAS  Google Scholar 

  52. Sonnhammer, E., Eddy, S., Birney, E., Bateman, A., and Durbin, R. (1998) Nucleic Acids Res., 26, 320–322.

    Article  PubMed  CAS  Google Scholar 

  53. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B., Castro, E., Lachaize1, C., Langendijk-Genevaux, P., and Sigrist, C. (2008) Nucleic Acids Res., 36, 245–249.

    Article  Google Scholar 

  54. Bairoch, A., and Apweiler, R. (2000) Nucleic Acids Res., 28, 45–48.

    Article  PubMed  CAS  Google Scholar 

  55. Bryson, K., McGuffin, L., Marsden, R., Ward, J., Sodhi, J., and Jones, D. (2005) Nucleic Acids Res., 33, 36–38.

    Article  Google Scholar 

  56. Guttel, R., Larsen, N., and Woese, C. (1994) Microbiol. Rev., 58, 10–26.

    Google Scholar 

  57. Doolittle, W. (1999) Science, 284, 2124–2128.

    Article  PubMed  CAS  Google Scholar 

  58. Lartigue, C., Glass, J., Alperovich, N., Pieper, R., Parmar, P., Hutchison, C., Smith, H., and Venter, J. (2007) Science, 317, 632–638.

    Article  PubMed  CAS  Google Scholar 

  59. Dagan, T., Artzy-Randrup, Y., and Martin, W. (2008) Proc. Natl. Acad. Sci. USA, 105, 10039–10044.

    Article  PubMed  CAS  Google Scholar 

  60. Bhugra, B. (1992) Mol. Microbiol., 6, 1149–1154.

    Article  PubMed  CAS  Google Scholar 

  61. Neimark, H. C. (1979) Phylogenetic Relations between Mycoplasmas and Other Prokaryotes. The Mycoplasmas (Barile, M. F., and Razin, S., eds.) New York, Vol. 1, pp. 43–61.

  62. Borkhsenius, S. N. (2000) Mycoplasms. Molecular and Cell Biology, Interaction with Mammalian Immune System, Pathogenicity, Diagnostics [in Russian], Nauka, Moscow.

    Google Scholar 

  63. Blanchard, A. (1990) Mol. Microbiol., 4, 669–676.

    Article  PubMed  CAS  Google Scholar 

  64. Amblar, M., Barbas, A., Gomez-Puertas, P., and Arraiano, C. (2007) RNA, 13, 317–327.

    Article  PubMed  CAS  Google Scholar 

  65. Boni, I., Artamonova, V., and Dreyfus, M. (2000) J. Bacteriol., 182, 5872–5879.

    Article  PubMed  CAS  Google Scholar 

  66. De Boer, P., Vos, H., Faber, A., Vos, J., and Raue, H. (2006) RNA, 12, 263–271.

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Tula State University, 300012, Tula, Russia

    E. I. Deryusheva

  2. Institute of Protein Research, 142290, Pushchino, Moscow Region, Russia

    O. M. Selivanova & I. N. Serdyuk

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  1. E. I. Deryusheva
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  2. O. M. Selivanova
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  3. I. N. Serdyuk
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Correspondence to E. I. Deryusheva.

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Original Russian Text © E. I. Deryusheva, O. M. Selivanova, I. N. Serdyuk, 2012, published in Uspekhi Biologicheskoi Khimii, 2012, Vol. 52, pp. 177–202.

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Deryusheva, E.I., Selivanova, O.M. & Serdyuk, I.N. Loops and repeats in proteins as footprints of molecular evolution. Biochemistry Moscow 77, 1487–1499 (2012). https://doi.org/10.1134/S000629791213007X

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  • DOI: https://doi.org/10.1134/S000629791213007X

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