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The Bacterial Scaffoldin: Structure, Function and Potential Applications in the Nanosciences

  • Shi-You Ding
  • Raphael Lamed
  • Edward A. Bayer
  • Michael E. Himmel
Part of the Genetic Engineering: Principles and Methods book series (GEPM, volume 25)

Abstract

Natural protein complexes may provide the best templates for nanometer-scale technology and new biomaterials. The bacterial cellulosome is becoming a well-understood multi-protein complex found in cellulolytic microorganisms. The scaffoldin subunits of the bacterial cellulosome function to organize and position other protein subunits into the complex. The scaffoldins can also serve as an attachment device for harnessing the cellulosome onto the cell surface and/or for its targeting to substrate. Biochemical and molecular biological evidence have identified a receptor/adaptor type of protein domain pair, called “cohesin and dockerin,” which is responsible for cellulosome self-assembly. The recognition between cohesin and dockerin is generally type and/or species specific. More than 80 cohesin and 100 dockerin sequences have been found, mostly from anaerobic bacteria. X-ray crystallography and NMR have been used to determine the three-dimensional structures of representative cohesin and dockerin domains, respectively. The cohesin peptide is about 140 amino acids in length and highly conserved in sequence and domain structure. The dockerin domain comprises about 70 amino acids and contains two 22 amino acid duplicated regions, each of which includes an “F-hand” modification of the EF-hand calcium-binding motif. Biochemical evidence and site-directed mutagenesis have confirmed that the two F-hand motifs are required for function and calcium dependence; at least two amino acids from each motif are critical for cohesin-dockerin recognition. In this report, we review the structure and function of the scaffoldin of the bacterial cellulosome and emphasize a detailed sequence analysis of the cohesin and dockerin domains. We also speculate about potential applications in nanoscience that may be based on cohesin-dockerin recognition.

Key Words

Scaffoldin Cohesin Dockerin Cellulosome 

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References

  1. 1.
    Jones, S. and Thornton, J.M. (1996) Proc. Nat. Acad. Sci. U.S.A. 93, 13–20.CrossRefGoogle Scholar
  2. 2.
    Yeates, O.Y. and Padilla, J.E. (2002) Curr. Opin. Struct. Bio. 12, 464–470.CrossRefGoogle Scholar
  3. 3.
    Lowe, C.R. (2000) Curr. Opin. Struct. Biol. 10, 428–434.PubMedCrossRefGoogle Scholar
  4. 4.
    Coutinho, P.M. and Henrissat, B. (1999) CAZyModO Websitehttp://afmb.cnrs-mrs.fr/--pedro/DB/db.html Google Scholar
  5. 5.
    Coutinho, P.M. and Henrissat, B. (1999) In Genetics, Biochemistry and Ecology of Cellulose Degradation (K. Ohmiya, K. Hayashi, K. Sakka, Y. Kobayashi, S. Karita and T. Kimura, eds.), pp. 15–23. Uni Publishers Co., Tokyo.Google Scholar
  6. 6.
    Bayer, E.A., Kenig, R. and Lamed, R. (1983) J. Bacteriol. 156, 818–827.PubMedGoogle Scholar
  7. 7.
    Bayer, E.A., Setter, E. and Lamed, R. (1985) J. Bacteriol. 163, 552–559.PubMedGoogle Scholar
  8. 8.
    Bayer, E.A. and Lamed, R. (1986) J. Bacteriol. 167, 828–836.PubMedGoogle Scholar
  9. 9.
    Lamed, R., Setter, E. and Bayer, E.A. (1983) J. Bacteriol. 156, 828–836.PubMedGoogle Scholar
  10. 10.
    Lamed, R., Naimark, J., Morgenstern, E. and Bayer, E.A. (1987) J. Microbiol. Methods 7, 233–240.CrossRefGoogle Scholar
  11. 11.
    Lamed, R. and Bayer, E.A. (1988) Adv. Appl. Microbiol. 33, 1–46.CrossRefGoogle Scholar
  12. 12.
    Lamed, R., Setter, E., Kenig, R. and Bayer, E.A. 1983. The Cellulosome a Discrete Cell Surface Organelle ofClostridium thermocellumwhich exhibits separate Antigenic, Cellulose-binding and various Cellulolytic Activities. Biotechnol. Bioeng. Symp. 13, 163–181.Google Scholar
  13. 13.
    Lamed, R., Naimark, J., Morgenstern, E. and Bayer, E.A. (1987) J. Bacteriol. 169, 3792–3800.PubMedGoogle Scholar
  14. 14.
    Mayer, F., Coughlan, M.P., Mori, Y. and Ljungdahl, L.G. (1987) Appl. Environ. Microbiol. 53, 2785–2792.PubMedGoogle Scholar
  15. 15.
    Borneman, W.S., Ljungdahl, L.G., Hartley, R.D. and Akin, D.E. (1993) In Hemicellulose and Hemicellulases (M. P. Coughlan and G. P. Hazlewood, eds.), pp. 85–102. Portland Press, London.Google Scholar
  16. 16.
    Chen, H., Li, L.X., Blum, D.L. and Ljungdahl, L.G. (1998) FEMS Microbiol. Lett. 159, 63–68.PubMedCrossRefGoogle Scholar
  17. 17.
    Gilbert, H.J., Hazlewood, G.P., Laurie, J.I., Orpin, C.G. and Xue, G.P. (1992) Mol. Microbiol. 6, 2065–2072.PubMedCrossRefGoogle Scholar
  18. 18.
    Raghothama, S., Eberhardt, R.Y., Simpson, P., Wigelsworth, D., White, P., Hazlewood, G.P., Nagy, T., Gilbert, H.J. and Williamson, M.P. (2001) Nature Struct. Biol. 8, 775–778.PubMedCrossRefGoogle Scholar
  19. 19.
    Bayer, E.A., Morag, E. and Lamed, R. (1994) Trends Biotechnol. 12, 378–386.CrossRefGoogle Scholar
  20. 20.
    Schwarz, W.H. (2001). Appl. Microbiol. Biotechnol. 56, 634–649.PubMedCrossRefGoogle Scholar
  21. 21.
    Bayer, E.A., Chanzy, H., Lamed, R. and Shoham, Y. (1998) Curr. Opin. Struct. Biol. 8, 548–557.PubMedCrossRefGoogle Scholar
  22. 22.
    Bayer, E.A., Shimon, L.J.W., Lamed, R. and Shoham, Y. (1998) J. Struct. Biol. 124,221–234.PubMedCrossRefGoogle Scholar
  23. 23.
    Bayer, E.A., Shoham, Y. and Lamed, R. (2000) In Glycomicrobiology, (R.J. Doyle, ed.), pp. 387–439. Kluwer Academic/Plenum Publishers, New York.Google Scholar
  24. 24.
    Béguin, P. and Lemaire, M. (1996) Crit. Rev. Biochem. Mol. Biol. 31, 201–236.PubMedCrossRefGoogle Scholar
  25. 25.
    Bélaich, J.-P., Tardif, C., Bélaich, A. and Gaudin, C. (1997) J. Biotechnol. 57, 3–14.PubMedCrossRefGoogle Scholar
  26. 26.
    Coughlan, M.P. and Mayer, F. (1992) In The Prokaryotes (A. Balows, H.G. Triiper, M. Dworkin, W. Harder and K.-H. Schleifer, eds.), 2nd ed, vol. I. pp. 459–516. Springer-Verlag, New York.Google Scholar
  27. 27.
    Doi, R.H. and Tamura, Y. (2001) Chem. Rec. 1, 24–32.PubMedCrossRefGoogle Scholar
  28. 28.
    Doi, R.H., Goldstein, M., Hashida, S., Park, J.S. and Takagi, M. (1994) Crit. Rev. Microbiol. 20, 87–93.PubMedCrossRefGoogle Scholar
  29. 29.
    Felix, C.R. and Ljungdahl L.G. (1993) Annu. Rev. Microbiol. 47, 791–819.PubMedCrossRefGoogle Scholar
  30. 30.
    Shoham, Y., Lamed, R. and Bayer, E.A. (1999) Trends Microbiol. 7(7), 275–281.PubMedCrossRefGoogle Scholar
  31. 31.
    Tamaru, Y., Liu, C.-C., Ichi-ishi, A., Malburg, L. and Doi, R.H. (1999). In Genetics, Biochemistry and Ecology of Cellulose Degradation (K. Ohmiya, K. Hayashi, K. Sakka, Y. Kobayashi, S. Karita and T. Kimura, eds.), pp. 488–494. Uni Publishers Co., Tokyo.Google Scholar
  32. 32.
    Boraston, A.B., McLean, B.W., Kormos, J.M., Alam, M., Gilkes, N.R., Haynes, C.A., Tomme, P., Kilburn, D.G. and Warren, R. A. (1999) In Recent Advances in Carbohydrate Bioengineering (H.J. Gilbert, G.J. Davies, B. Henrissat and B. Svensson, eds.), pp. 202–211. The Royal Society of Chemistry, Cambridge.Google Scholar
  33. 33.
    Chauvaux, S., Matuschek, M. and Béguin, P. (1999) J. Bacteriol. 181, 2455–2458.PubMedGoogle Scholar
  34. 34.
    Linder, M. and Teeri, T.T. (1997) J. Biotechnol. 57, 15–28.CrossRefGoogle Scholar
  35. 35.
    Ding, S.-Y., Bayer, E.A., Steiner, D., Shoham, Y. and Lamed, R. (1999) J. Bacteriol. 181, 6720–6729.PubMedGoogle Scholar
  36. 36.
    Ding, S.-Y., Bayer, E.A., Steiner, D., Shoham, Y. and Lamed, R. (2000) J. Bacteriol. 182, 4915–4925.PubMedCrossRefGoogle Scholar
  37. 37.
    Ding, S.-Y., Rincon, M.T., Lamed, R., Martin, J.C., McCrae, S.I., Aurilia, V., Shoham, Y., Bayer, E.A. and Flint, H.J. (2001) J. Bacteriol. 183, 1945–1953.PubMedCrossRefGoogle Scholar
  38. 38.
    Fujino, T., Béguin, P. and Aubert, J.P. (1993) J. Bacteriol. 175, 1891–1899.PubMedGoogle Scholar
  39. 39.
    Gal, L., Pagès, S., Gaudin, C., Bélaich, A., Reverbel-Leroy, C., Tardif, C. and Bélaich, J.-P. (1997) Appl. Environ. Microbiol. 63, 903–909.PubMedGoogle Scholar
  40. 40.
    Gerngross, U.T., Romaniec, M.P.M., Kobayashi, T., Huskisson, N.S. and Demain, A.L. (1993) Mol. Microbiol. 8, 325–334PubMedCrossRefGoogle Scholar
  41. 41.
    Hilden, L., Eng, L., Johansson, G., Lindqvist, S.E. and Pettersson, G. (2001) Anal. Biochem. 290, 245–250.PubMedCrossRefGoogle Scholar
  42. 42.
    Kakiuchi, M., Isui, A., Suzuki, K., Fujino, T., Fujino, E., Kimura, T., Karita, S., Sakka, K. and Ohmiya, K. (1998) J. Bacteriol. 180, 4303–4308.PubMedGoogle Scholar
  43. 43.
    Karita, S., Sakka, K. and Ohmiya, K. (1997) In Rumen Microbes and Digestive Physiology in Ruminants (R. Onodera, H. Itabashi, K. Ushida, H. Yano and Y. Sasaki, eds.), pp. 47–57, Vol. 14. Japan Sci. Soc. Press, Tokyo/S.Karger, Basel.Google Scholar
  44. 44.
    Leibovitz, E. and Béguin, P. (1996) J. Bacteriol. 178, 3077–3084.PubMedGoogle Scholar
  45. 45.
    Leibovitz, E., Ohayon, H., Gounon, P. and Béguin, P. (1997) J. Bacteriol. 179, 2519–2523.PubMedGoogle Scholar
  46. 46.
    Lemaire, M., Ohayon, H., Gounon, P., Fujino, T. and Béguin, P. (1995) J. Bacteriol. 177, 2451–2459.PubMedGoogle Scholar
  47. 47.
    Lemaire, M., Miras, I., Gounon, P. and Béguin, P. (1998) Microbiology 144, 211–217.PubMedCrossRefGoogle Scholar
  48. 48.
    Nölling, J., Breton, G., Omelchenko, M.V., Makarova, K.S., Zeng, Q., Gibson, R., Lee, H.M., Dubois, J., Qiu, D., Hitti, J., GTC Sequencing Center Production, Finishing, and Bioinformatics Teams, Wolf, Y.I., Tatusov, R.L. Sabathe, F., Doucette-Stamm, L., Soucaille, P., Daly, M.J., Bennett, G.N., Koonin, E.V. and Smith, D.R. (2001) J. Bacteriol. 183, 4823–4838.Google Scholar
  49. 49.
    Rincon, R., Ding, S.-Y., McCrae, S.I., Martin, J.C., Aurilia, V., Lamed R., Shoham, Y., Bayer, E.A. and Flint, H.J. (2003) J. Bacteriol. (in press).Google Scholar
  50. 50.
    Salamitou, S., Lemaire, M., Fujino, T., Ohayon, H., Gounon, P., Béguin, P. and Aubert, J.-P. (1994) J. Bacteriol. 176, 2828–2834.PubMedGoogle Scholar
  51. 51.
    Shoseyov, O., Takagi, M., Goldstein, M.A. and Doi, R.H. (1992) Proc. Nat. Acad. Sci. U. S. A. 89, 3483–3487.CrossRefGoogle Scholar
  52. 52.
    Tamaru, Y., Karita, S., Ibrahim, A., Chan, H. and Doi, R.H. (2000) J. Bacteriol. 182, 5906–5910.PubMedCrossRefGoogle Scholar
  53. 53.
    Sabathe, F., Bélaich, A. and Soucaille, P. (2003) FEMS Microbiol. Lett. (in press).Google Scholar
  54. 54.
    Pagès, S., Bélaich, A., Fierobe, H.-P., Tardif, C., Gaudin, C. and Bélaich, J.-P. (1999) J. Bacteriol. 181, 1801–1810.PubMedGoogle Scholar
  55. 55.
    Shimon, L.J.W., Bayer, E.A., Morag, E., Lamed, R., Yaron, S., Shoham, Y. and Frolow, F. (1997) Structure 5, 381–390.PubMedCrossRefGoogle Scholar
  56. 56.
    Spinelli, S., Fierobe, H.P., Bélaich, A., Bélaich, J.P., Henrissat, B. and Cambillau, C. (2000) J. Mol. Biol. 304, 189–200.PubMedCrossRefGoogle Scholar
  57. 57.
    Tavares, G.A., Béguin, P. and Alzari, P.M. (1997) J. Mol. Biol. 273, 701–713.PubMedCrossRefGoogle Scholar
  58. 58.
    Chauvaux, S., Béguin, P., Aubert, J.-P., Bhat, K.M., Gow, L.A., Wood, T.M. and Bairoch, A. (1990) Biochem. J. 265, 261–265.PubMedGoogle Scholar
  59. 59.
    Yaron, S., Morag, E., Bayer, E.A., Lamed, R. and Shoham, Y. (1995) FEBS Lett. 360, 121–124.PubMedCrossRefGoogle Scholar
  60. 60.
    Lytle, B.L., Volkman, B.F., Westler, W.M., Heckman, M.P. and Wu, J.H. (2001) J. Mol. Biol. 307, 745–753.PubMedCrossRefGoogle Scholar
  61. 61.
    Lytle, B.L., Volkman, B.F., Westler, W.M. and Wu, J.H. (2000) Arch. Biochem. Biophys. 379, 237–244.PubMedCrossRefGoogle Scholar
  62. 62.
    Ohara, H., Noguchi, J., Karita, S., Kimura, T., Sakka, K. and Ohmiya, K. (2000) Biosci. Biotechnol. Biochem. 64, 80–88.Google Scholar
  63. 63.
    Pegden, R.S., Larson, M.A., Grant, R.J. and Morrison, M. (1998) J. Bacteriol. 180, 5921–5927.PubMedGoogle Scholar
  64. 64.
    Mechaly, A., Fierobe, H.-P., Bélaich, A., Bélaich, J.-P., Lamed, R., Shoham, Y. and Bayer, E.A. (2001) J. Biol. Chem. 276, 9883–9888.PubMedCrossRefGoogle Scholar
  65. 65.
    Mechaly, A., Yaron, S., Lamed, R., Fierobe, H.-P., Bélaich, A., Bélaich, J.-P., Shoham, Y. and Bayer, E.A. (2000) Proteins 39, 170–177.PubMedCrossRefGoogle Scholar
  66. 66.
    Pages, S., Bélaich, A., Bélaich, J.-P., Morag, E., Lamed, R., Shoham, Y. and Bayer, E.A. (1997) Proteins 29, 517–527.PubMedCrossRefGoogle Scholar
  67. 67.
    Fierobe, H.-P., Pagès, S., Bélaich, A., Champ, S., Lexa, D. and Bélaich, J.-P. (1999) Biochemistry 38, 12822–12832.CrossRefGoogle Scholar
  68. 68.
    Salamitou, S., Raynaud, O., Lemaire, M., Coughlan, M., Béguin, P. and Aubert, J.-P. (1994) J. Bacteriol. 176, 2822–2827.PubMedGoogle Scholar
  69. 69.
    Tokatlidis, K., Salamitou, S., Béguin, P., Dhurjati, P. and Aubert, J.-P. (1991) FEBS Lett. 291, 185–188.PubMedCrossRefGoogle Scholar
  70. 70.
    Guo P. (2002) Prog. Nucl. Acid Res. Mol. Biol. 72, 415–472.Google Scholar
  71. 71.
    Hess, H. and Vogel, V. (2001) Rev. Mol. Biotechnol. 82, 67–85.CrossRefGoogle Scholar
  72. 72.
    Fierobe, H.-P., Bayer, E.A., Tardif, C., Czjzek, M., Mechaly, A., Bélaich, A., Lamed, R., Shoham, Y. and Bélaich, J.-P. (2002) J. Biol. Chem. 277, 49621–49630.PubMedCrossRefGoogle Scholar
  73. 73.
    Fierobe H.-P., Mechaly, A., Tardif, C., Bélaich, A., Lamed, R., Shoham, Y., Bélaich, J.-P. and Bayer, E.A. (2001) J. Biol. Chem. 276, 21257–21261.PubMedCrossRefGoogle Scholar
  74. 74.
    Woggon, U. (1997) Optical Properties of Semiconductor Quantum Dots. Vol. 136 Springer-Verlag, Berlin-Heidelberg.Google Scholar
  75. 75.
    Gaponenko, S.V. (1998) Optical Properties of Semiconductor Nanocrystals. Cambridge University Press, Cambridge, UK.CrossRefGoogle Scholar
  76. 76.
    Merkle, R. C. (2000) Nanotechnology 11, 89.CrossRefGoogle Scholar
  77. 77.
    Ding, S.-Y., Rumbles, G., Adney, W.S., Jones, M., Nedeljkovic, J., Tucker, M.P., Nozik, A.J. and Himmel, M.E. (2002) 25thDOE OS Photochemistry Program Meeting, Warrenton, VA, June 9–12, 2002Google Scholar
  78. 78.
    Ding, S.-Y., Himmel, M.E., Adney, W.S., Tucker, M.P., Wall, J., Nedeljkovic, J., Micic, O.I., Jones, M., Nozik, A.J. and Rumbles, G. (2003) To be presented at the MRS Symposium H: Bio-Inspired Nanoscale Hybrid Systems, San Francisco, CA, Spring 2003.Google Scholar

Copyright information

© Springer Science+Business Media New York 2003

Authors and Affiliations

  • Shi-You Ding
    • 1
  • Raphael Lamed
    • 2
  • Edward A. Bayer
    • 3
  • Michael E. Himmel
    • 1
  1. 1.National Bioenergy CenterNational Renewable Energy LaboratoryUSA
  2. 2.Department of Molecular Microbiology and BiotechnologyTel Aviv University, Ramat AvivIsrael
  3. 3.Department of Biological Chemistry, RehovotThe Weizmann Institute of ScienceIsrael

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