Using Hidden Markov Models to Discover New Protein Transport Machines

  • Vladimir A. Likic
  • Pavel Dolezal
  • Nermin Celik
  • Michael Dagley
  • Trevor Lithgow
Part of the Methods in Molecular Biology book series (MIMB, volume 619)


Protein import and export pathways are driven by protein translocases, often comprised of multiple subunits, and usually conserved across a range of organisms. Protein import into mitochondria is fundamental to eukaryotic organisms and is initiated when substrate proteins are translocated across the mitochondrial outer membrane by the TOM complex. The essential subunit of this complex is a protein called Tom40, which is probably a β-barrel in structure and serves as the translocation pore. We describe a hidden Markov model search designed to find the Tom40 sequence in the amoeba Entamoeba histolytica. This organism has a highly reduced “mitosome”, an organelle whose relationship to mitochondria has been the subject of controversy. The Tom40 sequence could not be found with BLAST-based searches, but a hidden Markov model search identified a likely candidate to form the protein import pore in the outer mitosomal membrane in E. histolytica.

Key words

Hidden Markov models sequence database search protein translocases mitochondria TOM complexes Tom40 


  1. 1.
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J Mol Biol 215, 403–410.PubMedGoogle Scholar
  2. 2.
    Kulikova, T., Akhtar, R., Aldebert, P., Althorpe, N., Andersson, M., Baldwin, A., Bates, K., Bhattacharyya, S., Bower, L., Browne, P., Castro, M., Cochrane, G., Duggan, K., Eberhardt, R., Faruque, N., Hoad, G., Kanz, C., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Lorenc, D., McWilliam, H., Mukherjee, G., Nardone, F., Pastor, M. P., Plaister, S., Sobhany, S., Stoehr, P., Vaughan, R., Wu, D., Zhu, W., and Apweiler, R. (2007) EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res 35, D16–20.CrossRefGoogle Scholar
  3. 3.
    Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O’Donovan, C., Redaschi, N., and Suzek, B. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34, D187–191.CrossRefGoogle Scholar
  4. 4.
    Needleman, S. B., and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48, 443–453.CrossRefPubMedGoogle Scholar
  5. 5.
    Smith, T. F., and Waterman, M. S. (1981) Identification of common molecular subsequences. J Mol Biol 147, 195–197.CrossRefPubMedGoogle Scholar
  6. 6.
    Vestweber, D., Brunner, J., Baker, A., and Schatz, G. (1989) A 42 K outer-membrane protein is a component of the yeast mitochondrial protein import site. Nature 341, 205–209.CrossRefPubMedGoogle Scholar
  7. 7.
    Model, K., Prinz, T., Ruiz, T., Radermacher, M., Krimmer, T., Kuhlbrandt, W., Pfanner, N., and Meisinger, C. (2002) Protein translocase of the outer mitochondrial membrane: role of import receptors in the structural organization of the TOM complex. J Mol Biol 316, 657–666.CrossRefPubMedGoogle Scholar
  8. 8.
    Kiebler, M., Pfaller, R., Sollner, T., Griffiths, G., Horstmann, H., Pfanner, N., and Neupert, W. (1990) Identification of a mitochondrial receptor complex required for recognition and membrane insertion of precursor proteins. Nature 348, 610–616.CrossRefPubMedGoogle Scholar
  9. 9.
    Gabriel, K., Buchanan, S. K., and Lithgow, T. (2001) The alpha and the beta: protein translocation across mitochondrial and plastid outer membranes. Trends Biochem Sci 26, 36–40.CrossRefPubMedGoogle Scholar
  10. 10.
    Hill, K., Model, K., Ryan, M. T., Dietmeier, K., Martin, F., Wagner, R., and Pfanner, N. (1998) Tom40 forms the hydrophilic channel of the mitochondrial import pore for preproteins. Nature 395, 516–521.CrossRefPubMedGoogle Scholar
  11. 11.
    Dolezal, P., Likic, V., Tachezy, J., and Lithgow, T. (2006) Evolution of the molecular machines for protein import into mitochondria. Science 313, 314–318.CrossRefPubMedGoogle Scholar
  12. 12.
    Tovar, J., Fischer, A., and Clark, C. G. (1999) The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol Microbiol 32, 1013–1021.CrossRefPubMedGoogle Scholar
  13. 13.
    Mai, Z., Ghosh, S., Frisardi, M., Rosenthal, B., Rogers, R., and Samuelson, J. (1999) Hsp60 is targeted to a cryptic mitochondrion-derived organelle (“crypton”) in the microaerophilic protozoan parasite Entamoeba histolytica. Mol Cell Biol 19, 2198–2205.PubMedGoogle Scholar
  14. 14.
    Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 84, 4355–4358.CrossRefPubMedGoogle Scholar
  15. 15.
    Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–763.CrossRefPubMedGoogle Scholar
  16. 16.
    Dolezal, P., Dagley, M., Kono, M., Wolynec, P., Likic, V., Foo, J.H., Sedinova, M. Tachezy, J., Bachmann, A., Bruchhaus, I., and Lithgow, T. (under revision) The essentials of protein import in the degenerate mitochondrion of Entamoeba histolytica. PLoS Pathogens (under revision).Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Vladimir A. Likic
    • 1
  • Pavel Dolezal
    • 2
  • Nermin Celik
    • 3
  • Michael Dagley
    • 3
  • Trevor Lithgow
    • 3
  1. 1.Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleAustralia
  2. 2.Department of Parasitology, Faculty of ScienceCharles UniversityPragueCzech Republic
  3. 3.Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia

Personalised recommendations