- Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite


Aravind, L., Dixit, V.M., and Koonin, E.V. 1999. The domains of death: Evolution of the apoptosis machinery. Trends Biochem. Sci. 24: 47-53.[CrossRef][Medline] Arthur, J.S., Gauthier, S., and Elce, J.S. 1995. Active site residues in m-calpain: Identification by site-directed mutagenesis. FEBS Lett. 368: 397-400.[CrossRef][Medline] Banerjee, R., Liu, J., Beatty, W., Pelosof, L., Klemba, M., and Goldberg, D.E. 2002. Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine. Proc. Natl. Acad. Sci. 99: 990-995.[Abstract/Free Full Text] Barale, J.C., Blisnick, T., Fujioka, H., Alzari, P.M., Aikawa, M., Braun-Breton, C., and Langsley, G. 1999. Plasmodium falciparum subtilisin-like protease 2, a merozoite candidate for the merozoite surface protein 1–42 maturase. Proc. Natl. Acad. Sci. 96: 6445-6450.[Abstract/Free Full Text] Ben Mamoun, C., Gluzman, I.Y., Hott, C., MacMillan, S.K., Amarakone, A.S., Anderson, D.L., Carlton, J.M., Dame, J.B., Chakrabarti, D., Martin, R.K., et al. 2001. Coordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis. Mol. Microbiol. 39: 26-36.[CrossRef][Medline] Bernstein, N.K., Cherney, M.M., Loetscher, H., Ridley, R.G., and James, M.N. 1999. Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from Plasmodium falciparum. Nat. Struct. Biol. 6: 32-37.[CrossRef][Medline] Blackman, M.J. 2000. Proteases involved in erythrocyte invasion by the malaria parasite: Function and potential as chemotherapeutic targets. Curr. Drug Targets 1: 59-83.[CrossRef][Medline] Blackman, M.J., Fujioka, H., Stafford, W.H., Sajid, M., Clough, B., Fleck, S.L., Aikawa, M., Grainger, M., and Hackett, F. 1998. A subtilisin-like protein in secretory organelles of Plasmodium falciparum merozoites. J. Biol. Chem. 273: 23398-23409.[Abstract/Free Full Text] Braun-Breton, C., Rosenberry, T.L., and da Silva, L.P. 1988. Induction of the proteolytic activity of a membrane protein in Plasmodium falciparum by phosphatidyl inositol-specific phospholipase C. Nature 332: 457-459.[CrossRef][Medline] Coombs, G.H., Goldberg, D.E., Klemba, M., Berry, C., Kay, J., and Mottram, J.C. 2001. Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends Parasitol. 17: 532-537.[CrossRef][Medline] Craik, C.S., Rutter, W.J., and Fletterick, R. 1983. Splice junctions: Association with variation in protein structure. Science 220: 1125-1129.[Abstract/Free Full Text] Curley, G.P., O'Donovan, S.M., McNally, J., Mullally, M., O'Hara, H., Troy, A., O'Callaghan, S.A., and Dalton, J.P. 1994. Aminopeptidases from Plasmodium falciparum, Plasmodium chabaudi chabaudi and Plasmodium berghei. J. Eukaryot. Microbiol. 41: 119-123.[Medline] David, P.H., Hadley, T.J., Aikawa, M., and Miller, L.H. 1984. Processing of a major parasite surface glycoprotein during the ultimate stages of differentiation in Plasmodium knowlesi. Mol. Biochem. Parasitol. 11: 267-282.[CrossRef][Medline] Delplace, P., Bhatia, A., Cagnard, M., Camus, D., Colombet, G., Debrabant, A., Dubremetz, J.F., Dubreuil, N., Prensier, G., Fortier, B., et al. 1988. Protein p126: A parasitophorous vacuole antigen associated with the release of Plasmodium falciparum merozoites. Biol. Cell 64: 215-221.[CrossRef][Medline] Denison, S.H., Orejas, M., and Arst, H.N., Jr. 1995. Signaling of ambient pH in Aspergillus involves a cysteine protease. J. Biol. Chem. 270: 28519-28522.[Abstract/Free Full Text] Doerig, C., Meijer, L., and Mottram, J.C. 2002. Protein kinases as drug targets in parasitic protozoa. Trends Parasitol. 18: 366-371.[CrossRef][Medline] Dua, M., Raphael, P., Sijwali, P.S., Rosenthal, P.J., and Hanspal, M. 2001. Recombinant falcipain-2 cleaves erythrocyte membrane ankyrin and protein 4.1. Mol. Biochem. Parasitol. 116: 95-99.[CrossRef][Medline] Eggleson, K.K., Duffin, K.L., and Goldberg, D.E. 1999. Identification and characterization of falcilysin, a metallopeptidase involved in hemoglobin catabolism within the malaria parasite Plasmodium falciparum. J. Biol. Chem. 274: 32411-32417.[Abstract/Free Full Text] Fast, N.M., Kissinger, J.C., Roos, D.S., and Keeling, P.J. 2001. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 18: 418-426.[Abstract/Free Full Text] Florens, L., Washburn, M.P., Raine, J.D., Anthony, R.M., Grainger, M., Haynes, J.D., Moch, J.K., Muster, N., Sacci, J.B., Tabb, D.L., et al. 2002. A proteomic view of the Plasmodium falciparum life cycle. Nature 419: 520-526.[CrossRef][Medline] Florent, I., Derhy, Z., Allary, M., Monsigny, M., Mayer, R., and Schrevel, J. 1998. A Plasmodium falciparum aminopeptidase gene belonging to the M1 family of zinc-metallopeptidases is expressed in erythrocytic stages. Mol. Biochem. Parasitol. 97: 149-160.[CrossRef][Medline] Franz, T., Vingron, M., Boehm, T., and Dear, T.N. 1999. Capn7: A highly divergent vertebrate calpain with a novel C-terminal domain. Mamm. Genome. 10: 318-321.[CrossRef][Medline] Friedman, R. and Hughes, A.L. 2001. Pattern and timing of gene duplication in animal genomes. Genome Res. 11: 1842-1847.[Abstract/Free Full Text] Gantt, S.M., Myung, J.M., Briones, M.R., Li, W.D., Corey, E.J., Omura, S., Nussenzweig, V., and Sinnis, P. 1998. Proteasome inhibitors block development of Plasmodium spp. Antimicrob. Agents Chemother. 42: 2731-2738.[Abstract/Free Full Text] Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., et al. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 41: 498-511. Glading, A., Lauffenburger, D.A., and Wells, A. 2002. Cutting to the chase: Calpain proteases in cell motility. Trends Cell Biol. 12: 46-54.[CrossRef][Medline] Gu, X., Wang, Y., and Gu, J. 2002. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet. 31: 205-209.[CrossRef][Medline] Hackett, F., Sajid, M., Withers-Martinez, C., Grainger, M., and Blackman, M.J. 1999. PfSUB-2: A second subtilisin-like protein in Plasmodium falciparum merozoites. Mol. Biochem. Parasitol. 103: 183-195.[CrossRef][Medline] Hayward, R.E., Derisi, J.L., Alfadhli, S., Kaslow, D.C., Brown, P.O., and Rathod, P.K. 2000. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol. Microbiol. 35: 6-14.[CrossRef][Medline] Jean, L., Long, M., Young, J., Pery, P., and Tomley, F. 2001. Aspartyl proteinase genes from apicomplexan parasites: Evidence for evolution of the gene structure. Trends Parasitol. 17: 491-498.[CrossRef][Medline] Kissinger, J.C., Brunk, B.P., Crabtree, J., Fraunholz, M.J., Gajria, B., Milgram, A.J., Pearson, D.S., Schug, J., Bahl, A., Diskin, S.J., et al. 2002. The Plasmodium genome database. Nature 419: 490-492.[CrossRef][Medline] Li, J., Matsuoka, H., Mitamura, T., and Horii, T. 2002. Characterization of proteases involved in the processing of Plasmodium falciparum serine repeat antigen (SERA). Mol. Biochem. Parasitol. 120: 177-186.[CrossRef][Medline] Li, W-H. 1983. Evolution of duplicate genes and pseudogenes. In Evolution of genes and proteins (eds. M. Nei & R.K. Keohn), pp. 14–37. RK Sinauer Associates, Sunderland, MA. Madeo, F., Herker, E., Maldener, C., Wissing, S., Lachelt, S., Herlan, M., Fehr, M., Lauber, K., Sigrist, S.J., Wesselborg, S., et al. 2002. A caspase-related protease regulates apoptosis in yeast. Mol. Cell. 9: 911-917.[CrossRef][Medline] McKerrow, J.H., Sun, E., Rosenthal, P.J., and Bouvier, J. 1993. The proteases and pathogenicity of parasitic protozoa. Annu. Rev. Microbiol. 47: 821-853.[CrossRef][Medline] McLysaght, A., Hokamp, K., and Wolfe, K.H. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31: 200-204.[CrossRef][Medline] Miller, S.K., Good, R., Drew, D.R., Delorenzi, M., Sanders, P.R., Hodder, A.N., Speed, T.P., Cowman, A.F., De Koning-Ward, T.F., and Crabb, B.S. 2002. A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycle. J. Biol. Chem. 277: 47524-47532.[Abstract/Free Full Text] Mu, J., Duan, J., Makova, K.D., Joy, D.A., Huynh, C.Q., Branch, O.H., Li, W.H., and Su, X.Z. 2002. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature 418: 323-326.[CrossRef][Medline] Narum, D.L. and Thomas, A.W. 1994. Differential localization of full-length and processed forms of PF83/AMA-1 an apical membrane antigen of Plasmodium falciparum merozoites. Mol. Biochem. Parasitol. 67: 59-68.[CrossRef][Medline] Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217.[CrossRef][Medline] Ohno, S., 1970. Evolution by gene duplication. Springer-Verlag, Berlin. Olaya, P. and Wasserman, M. 1991. Effect of calpain inhibitors on the invasion of human erythrocytes by the parasite Plasmodium falciparum. Biochim. Biophys. Acta. 1096: 217-221.[Medline] Paetzel, M., Dalbey, R.E., and Strynadka, N.C. 2000. The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target. Pharmacol. Ther. 87: 27-49.[CrossRef][Medline] Rawlings, N.D. and Barrett, A.J. 1993. Evolutionary families of peptidases. Biochem. J. 290: 205-218.[Medline] Rich, S.M., Licht, M.C., Hudson, R.R., and Ayala, F.J. 1998. Malaria's Eve: Evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. 95: 4425-4430.[Abstract/Free Full Text] Rosenthal, P.J. 1998. Proteases of malaria parasites: New targets for chemotherapy. Emerg. Infect. Dis. 4: 49-57.[Medline] Rosenthal, P.J. 2002. Hydrolysis of erythrocyte proteins by proteases of malaria parasites. Curr. Opin. Hematol. 9: 140-145.[CrossRef][Medline] Rosenthal, P.J., Kim, K., McKerrow, J.H., and Leech, J.H. 1987. Identification of three stage-specific proteinases of Plasmodium falciparum. J. Exp. Med. 166: 816-821.[Abstract/Free Full Text] Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.[Abstract] Salmon, B.L., Oksman, A., and Goldberg, D.E. 2001. Malaria parasite exit from the host erythrocyte: A two-step process requiring extraerythrocytic proteolysis. Proc. Natl. Acad. Sci. 98: 271-276.[Abstract/Free Full Text] Shenai, B.R., Sijwali, P.S., Singh, A., and Rosenthal, P.J. 2000. Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparum. J. Biol. Chem. 275: 29000-29010.[Abstract/Free Full Text] Silva, A.M., Lee, A.Y., Gulnik, S.V., Maier, P., Collins, J., Bhat, T.N., Collins, P.J., Cachau, R.E., Luker, K.E., Gluzman, I.Y., et al. 1996. Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum. Proc. Natl. Acad. Sci. 93: 10034-10039.[Abstract/Free Full Text] Sorimachi, H., Ishiura, S., and Suzuki, K. 1997. Structure and physiological function of calpains. Biochem. J. 328: 721-732.[Medline] Southan, C. 2001. A genomic perspective on human proteases. FEBS Lett. 498: 214-218.[CrossRef][Medline] Thornberry, N.A. and Lazbnik, L. 1998. Caspases: Enemies within. Science 281: 1312-1316.[Abstract/Free Full Text] Trager, W. and Jensen, J.B. 1976. Human malaria parasites in continuous culture. Science. 193: 673-675.[Abstract/Free Full Text] Triglia, T., Thompson, J.K., and Cowman, A.F. 2001. An EBA175 homolog which is transcribed but not translated in erythrocytic stages of Plasmodium falciparum. Mol. Biochem. Parasitol. 116: 55-63.[CrossRef][Medline] Tyas, L., Gluzman, I., Moon, R.P., Rupp, K., Westling, J., Ridley, R.G., Kay, J., Goldberg, D.E., and Berry, C. 1999. Naturally-occurring and recombinant forms of the aspartic proteinases plasmepsins I and II from the human malaria parasite Plasmodium falciparum. FEBS Lett. 454: 210-214.[CrossRef][Medline] Uren, A.G., O'Rourke, K., Aravind, L.A., Pisabarro, M.T., Seshagiri, S., Koonin, E.V., and Dixit, V.M. 2000. Identification of paracaspases and metacaspases: Two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma. Mol. Cell 6: 961-967.[Medline] Verma, R., Aravind, L., Oania, R., McDonald, W.H., Yates, J.R., III, Koonin, E.V., and Deshaies, R.J. 2002. Role of Rpn11 Metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298: 611-615.[Abstract/Free Full Text] Verra, F. and Hughes, A.L. 1999. Natural selection on apical membrane antigen-1 of Plasmodium falciparum. Parassitologi. 41: 93-95. Volkman, S.K., Barry, A.E., Lyons, E.J., Nielsen, K.M., Thomas, S.M., Choi, M., Thakore, S.S., Day, K.P., Wirth, D.F., and Hartl, D.L. 2001. Recent origin of Plasmodium falciparum from a single progenitor. Science 293: 482-484.[Abstract/Free Full Text] Wang, Y. and Gu, X. 2001. Functional divergence in caspase gene family and altered functional constraints: Statistical analysis and prediction. Genetics 158: 1311-1320.[Abstract/Free Full Text] Wilson, R.J., Denny, P.W., Preiser, P.R., Rangachari, K., Roberts, K., Roy, A., Whyte, A., Strath, M., Moore, D.J., Moore, P.W., et al. 1996. Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J. Mol. Biol. 261: 155-172.[CrossRef][Medline] Wootton, J.C., Feng, X., Ferdig, M.T., Cooper, R.A., Mu, J., Baruch, D.I., Magill, A.J., and Su, X.Z. 2002. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418: 320-323.[CrossRef][Medline] Yoshizawa, T., Sorimachi, H., Tomioka, S., Ishiura, S., and Suzuki, K. 1995. A catalytic subunit of calpain possesses full proteolytic activity. FEBS Lett. 358: 101-103.[CrossRef][Medline] Zuegge, J., Ralph, S., Schmuker, M., McFadden, G.I., and Schneider, G. 2001. Deciphering apicoplast targeting signals—feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. Gene 280: 19-26

rating: 4.29 from 7 votes | updated on: 28 Apr 2007 | views: 13988 |

Rate article:

excellent! bad…