Phylogenetic and primary sequence characterization of cathepsin B cysteine proteases from the oxymonad flagellate Monocercomonoides

Journal of Eukaryotic Microbiology

Volumn 55, Issue 1, 2008, Pages 9-17

  Dacks, Joel B ^a,b   Kuru, Teklu ^a   Liapounova, Natalia A ^a   Gedamu, Lashitew ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Cathepsin L; Commensal; Cyst; Evolution; Excavate; Occluding loop; Phylogeny; Protest

Indexed keywords

CATHEPSIN B;

ENZYME ACTIVITY; FLAGELLATE; GENE EXPRESSION; IDENTIFICATION METHOD; PHYLOGENETICS;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; EUKARYOTIC CELL; FLAGELLATE; GENE EXPRESSION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN MOTIF; SEQUENCE ALIGNMENT;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CATHEPSIN B; CONSERVED SEQUENCE; EUKARYOTIC CELLS; GENE EXPRESSION; HUMANS; MASTIGOPHORA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EUKARYOTA; MASTIGOPHORA (FLAGELLATES); MONOCERCOMONOIDES; OXYMONADIDA; PROTISTA;

EID: 38649117560     PISSN: 10665234     EISSN: 15507408     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2007.00296.x     Document Type: Article

References (31)

1. Abascal, F., Zardoya, R. Posada, D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics, 21 : 2104 2105.
2. Adl, S. M., Simpson, A. G., Farmer, M. A., Andersen, R. A., Anderson, O. R., Barta, J. R., Bowser, S. S., Brugerolle, G., Fensome, R. A., Fredericq, S., James, T. Y., Karpov, S., Kugrens, P., Krug, J., Lane, C. E., Lewis, L. A., Lodge, J., Lynn, D. H., Mann, D. G., McCourt, R. M., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S. E., Nerad, T. A., Shearer, C. A., Smirnov, A. V., Spiegel, F. W. Taylor, M. F. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52 : 399 451.
3. Bruchhaus, I., Loftus, B. J., Hall, N. Tannich, E. 2003. The intestinal protozoan parasite Entamoeba histolytica contains 20 cysteine protease genes, of which only a small subset is expressed during in vitro cultivation. Eukaryot. Cell, 2 : 501 509.
4. Carlton, J. M., Hirt, R. P., Silva, J. C., Delcher, A. L., Schatz, M., Zhao, Q., Wortman, J. R., Bidwell, S. L., Alsmark, U. C., Besteiro, S., Sicheritz-Ponten, T., Noel, C. J., Dacks, J. B., Foster, P. G., Simillion, C., Van de Peer, Y., Miranda-Saavedra, D., Barton, G. J., Westrop, G. D., Muller, S., Dessi, D., Fiori, P. L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F. D., Simoes-Barbosa, A., Brown, M. T., Hayes, R. D., Mukherjee, M., Okumura, C. Y., Schneider, R., Smith, A. J., Vanacova, S., Villalvazo, M., Haas, B. J., Pertea, M., Feldblyum, T. V., Utterback, T. R., Shu, C. L., Osoegawa, K., de Jong, P. J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S. B., Logsdon, J. M. Jr., Henze, K., Gupta, A., Wang, C. C., Dunne, R. L., Upcroft, J. A., Upcroft, P., White, O., Salzberg, S. L., Tang, P., Chiu, C. H., Lee, Y. S., Embley, T. M., Coombs, G. H., Mottram, J. C., Tachezy, J., Fraser-Liggett, C. M. Johnson, P. J. 2007. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315 : 207 212.
5. Chan, V. J., Selzer, P. M., McKerrow, J. H. Sakanari, J. A. 1999. Expression and alteration of the S2 subsite of the Leishmania major cathepsin B-like cysteine protease. Biochem. J., 340 : 113 117.
6. Dacks, J. B., Silberman, J. D., Simpson, A. G., Moriya, S., Kudo, T., Ohkuma, M. Redfield, R. J. 2001. Oxymonads are closely related to the excavate taxon Trimastix. Mol. Biol. Evol., 18 : 1034 1044.
7. DuBois, K. N., Abodeely, M., Sajid, M., Engel, J. C. McKerrow, J. H. 2006. Giardia lamblia cysteine proteases. Parasitol. Res., 99 : 313 316.
8. Felsenstein, J. 1993. PHYLIP-phylogeny inference package (version 3.2). Cladistics, 5 : 164 166.
9. Guindon, S. Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52 : 696 704.
10. Hasnain, S., Hirama, T., Huber, C. P., Mason, P. Mort, J. S. 1993. Characterization of cathepsin B specificity by site-directed mutagenesis. Importance of Glu245 in the S2-P2 specificity for arginine and its role in transition state stabilization. J. Biol. Chem., 268 : 235 240.
11. Illy, C., Quraishi, O., Wang, J., Purisima, E., Vernet, T. Mort, J. S. 1997. Role of the occluding loop in cathepsin B activity. J. Biol. Chem., 272 : 1197 1202.
12. Keeling, P. J. Leander, B. S. 2003. Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix. J. Mol. Biol., 326 : 1337 1349.
13. Krupa, J. C., Hasnain, S., Nagler, D. K., Menard, R. Mort, J. S. 2002. S2' substrate specificity and the role of His110 and His111 in the exopeptidase activity of human cathepsin B. Biochem. J., 361 : 613 619.
14. Kulda, J. Nohynková, E. 1978. Flagellates of the human intestine and of intestines of other species. In : Krieier, J. P. (ed.), Parasitic Protozoa. Academic Press, San Diego. II : 104 113.
15. Madern, D. 2002. Molecular evolution within the l-malate and l-lactate dehydrogenase super-family. J. Mol. Evol., 54 : 825 840.
16. Madern, D., Cai, X., Abrahamsen, M. S. Zhu, G. 2004. Evolution of Cryptosporidium parvum lactate dehydrogenase from malate dehydrogenase by a very recent event of gene duplication. Mol. Biol. Evol., 21 : 489 497.
17. Menard, R. Storer, A. C. 1992. Oxyanion hole interactions in serine and cysteine proteases. Biol. Chem. Hoppe Seyler, 373 : 393 400.
18. Menard, R., Plouffe, C., Laflamme, P., Vernet, T., Tessier, D. C., Thomas, D. Y. Storer, A. C. 1995. Modification of the electrostatic environment is tolerated in the oxyanion hole of the cysteine protease papain. Biochemistry, 34 : 464 471.
19. Mottram, J. C., Brooks, D. R. Coombs, G. H. 1998. Roles of cysteine proteinases of trypanosomes and Leishmania in host-parasite interactions. Curr. Opin. Microbiol., 1 : 455 460.
20. Musil, D., Zucic, D., Turk, D., Engh, R. A., Mayr, I., Huber, R., Popovic, T., Turk, V., Towatari, T., Katunuma, N. Bode, W. 1991. The refined 2.15 A X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity. EMBO J., 10 : 2321 2330.
21. Nielsen, H., Engelbrecht, J., Brunak, S. von Heijne, G. 1997. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst., 8 : 581 599.
22. Ronquist, F. Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19 : 1572 1574.
23. Rosenthal, P. J. 2004. Cysteine proteases of malaria parasites. Int. J. Parasitol., 34 : 1489 1499.
24. Sajid, M. McKerrow, J. H. 2002. Cysteine proteases of parasitic organisms. Mol. Biochem. Parasitol., 120 : 1 21.
25. Simpson, A. G. 2003. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int. J. Syst. Evol. Microbiol., 53 : 1759 1777.
26. Slamovits, C. H. Keeling, P. J. 2006. A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol. Biol., 6 : 34.
27. Somanna, A., Mundodi, V. Gedamu, L. 2002. Functional analysis of cathepsin B-like cysteine proteases from Leishmania donovani complex. Evidence for the activation of latent transforming growth factor beta. J. Biol. Chem., 277 : 25305 25312.
28. Strimmer, K. von Haeseler, A. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13 : 964 969.
29. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. Higgins, D. G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25 : 4876 4882.
30. Turk, B., Turk, D. Turk, V. 2000. Lysosomal cysteine proteases: more than scavengers. Biochim. Biophys. Acta, 1477 : 98 111.
31. Villalobo, E., Moch, C., Fryd-Versavel, G., Fleury-Aubusson, A. Morin, L. 2003. Cysteine proteases and cell differentiation: excystment of the ciliated protist Sterkiella histriomuscorum. Eukaryot. Cell, 2 : 1234 1245.