A proteomic view of the Plasmodium falciparum life cycle

Abstract

The completion of the Plasmodium falciparum clone 3D7 genome provides a basis on which to conduct comparative proteomics studies of this human pathogen. Here, we applied a high-throughput proteomics approach to identify new potential drug and vaccine targets and to better understand the biology of this complex protozoan parasite. We characterized four stages of the parasite life cycle (sporozoites, merozoites, trophozoites and gametocytes) by multidimensional protein identification technology. Functional profiling of over 2,400 proteins agreed with the physiology of each stage. Unexpectedly, the antigenically variant proteins of var and rif genes, defined as molecules on the surface of infected erythrocytes, were also largely expressed in sporozoites. The detection of chromosomal clusters encoding co-expressed proteins suggested a potential mechanism for controlling gene expression.

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Figure 1: Functional profiles of expressed proteins.
Figure 2: Expression patterns of known stage-specific proteins.
Figure 3: Distribution of expressed proteins by chromosome.

References

  1. 1

    Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002)

  2. 2

    Carlton, J. M. et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii. Nature 419, 512–519 (2002)

  3. 3

    Ben Mamoun, C. et al. Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis. Mol. Microbiol. 39, 26–36 (2001)

  4. 4

    Hayward, R. E. et al. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol. Microbiol. 35, 6–14 (2000)

  5. 5

    Washburn, M. P., Wolters, D. & Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001)

  6. 6

    Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30, 31–34 (2002)

  7. 7

    Pinder, J. C. et al. Actomyosin motor in the merozoite of the malaria parasite, Plasmodium falciparum: implications for red cell invasion. J. Cell Sci. 111, 1831–1839 (1998)

  8. 8

    Holder, A. A. Malaria Vaccine Development: a Multi-immune Response and Multi-stage Perspective (ed. Hoffman, S. L.) 77–104 (ASM Press, Washington, 1996)

  9. 9

    Coppel, R. L. et al. Isolate-specific S-antigen of Plasmodium falciparum contains a repeated sequence of eleven amino acids. Nature 306, 751–756 (1983)

  10. 10

    Taylor, H. M. et al. Plasmodium falciparum homologue of the genes for Plasmodium vivax and Plasmodium yoelii adhesive proteins, which is transcribed but not translated. Infect. Immun. 69, 3635–3645 (2001)

  11. 11

    Kaneko, O. et al. The high molecular mass rhoptry protein, RhopH1, is encoded by members of the clag multigene family in Plasmodium falciparum and Plasmodium yoelii. Mol. Biochem. Parasitol. 118, 223–231 (2001)

  12. 12

    Trenholme, K. R. et al. clag9: A cytoadherence gene in Plasmodium falciparum essential for binding of parasitized erythrocytes to CD36. Proc. Natl Acad. Sci. USA 97, 4029–4033 (2000)

  13. 13

    Klemba, M. & Goldberg, D. E. Biological roles of proteases in parasitic protozoa. Annu. Rev. Biochem. 71, 275–305 (2002)

  14. 14

    Banerjee, R. et al. Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine. Proc. Natl Acad. Sci. USA 99, 990–995 (2002)

  15. 15

    Rosenthal, P. J., Sijwali, P. S., Singh, A. & Shenai, B. R. Cysteine proteases of malaria parasites: targets for chemotherapy. Curr. Pharm. Des. 8, 1659–1672 (2002)

  16. 16

    Eggleson, K. K., Duffin, K. L. & Goldberg, D. E. Identification and characterization of falcilysin, a metallopeptidase involved in hemoglobin catabolism within the malaria parasite Plasmodium falciparum. J. Biol. Chem. 274, 32411–32417 (1999)

  17. 17

    Sinden, R. E., Butcher, G. A., Billker, O. & Fleck, S. L. Regulation of infectivity of Plasmodium to the mosquito vector. Adv. Parasitol. 38, 53–117 (1996)

  18. 18

    Billker, O., Shaw, M. K., Margo, G. & Sinden, R. E. Identification of xanthurenic acid as the putative inducer of malaria development in the mosquito. Nature 392, 289–292 (1998)

  19. 19

    Krungkrai, J., Prapunwattana, P. & Krungkrai, S. R. Ultrastructure and function of mitochondria in gametocytic stage of Plasmodium falciparum. Parasite 7, 19–26 (2000)

  20. 20

    Kappe, S. H. et al. Exploring the transcriptome of the malaria sporozoite stage. Proc. Natl Acad. Sci. USA 98, 9895–9900 (2001)

  21. 21

    Dessens, J. T. et al. CTRP is essential for mosquito infection by malaria ookinetes. EMBO J. 18, 6221–6227 (1999)

  22. 22

    Deitsch, K. W. & Wellems, T. E. Membrane modifications in erythrocytes parasitized by Plasmodium falciparum. Mol. Biochem. Parasitol. 76, 1–10 (1996)

  23. 23

    Kyes, S. A., Rowe, J. A., Kriek, N. & Newbold, C. I. Rifins: a second family of clonally variant proteins expressed on the surface of red cells infected with Plasmodium falciparum. Proc. Natl Acad. Sci. USA 96, 9333–9338 (1999)

  24. 24

    Cohen, B. A., Mitra, R. D., Hughes, J. D. & Church, G. M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genet. 26, 183–186 (2000)

  25. 25

    Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291, 1289–1292 (2001)

  26. 26

    Lercher, M. J., Urrutia, A. O. & Hurst, L. D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet. 31, 180–183 (2002)

  27. 27

    Hernandez-Rivas, R. et al. Expressed var genes are found in Plasmodium falciparum subtelomeric regions. Mol. Cell Biol. 17, 604–611 (1997)

  28. 28

    del Portillo, H. A. et al. A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax. Nature 410, 839–842 (2001)

  29. 29

    Gardner, M. J. et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132 (1998)

  30. 30

    Kanaani, J. & Ginsburg, H. Metabolic interconnection between the human malarial parasite Plasmodium falciparum and its host erythrocyte. J. Biol. Chem. 264, 3194–3199 (1989)

  31. 31

    Dechering, K. J. et al. Isolation and functional characterization of two distinct sexual-stage-specific promoters of the human malaria parasite Plasmodium falciparum. Mol. Cell Biol. 19, 967–978 (1999)

  32. 32

    Lockhart, D. J. & Winzeler, E. A. Genomics, gene expression and DNA arrays. Nature 405, 827–836 (2000)

  33. 33

    Pacheco, N. D., Strome, C. P., Mitchell, F., Bawden, M. P. & Beaudoin, R. L. Rapid, large-scale isolation of Plasmodium berghei sporozoites from infected mosquitoes. J. Parasitol. 65, 414–417 (1979)

  34. 34

    Mellouk, S. et al. Evaluation of an in vitro assay aimed at measuring protective antibodies against sporozoites. Bull. World Health Organ. 68 Suppl., 52–59 (1990)

  35. 35

    Rabilloud, T. et al. Analysis of membrane proteins by two-dimensional electrophoresis: comparison of the proteins extracted from normal or Plasmodium falciparum-infected erythrocyte ghosts. Electrophoresis 20, 3603–3610 (1999)

  36. 36

    Blackman, M. J. Purification of Plasmodium falciparum merozoites for analysis of the processing of merozoite surface protein-1. Methods Cell Biol. 45, 213–220 (1994)

  37. 37

    Haynes, J. D. & Moch, J. K. Automated synchronization of Plasmodium falciparum parasites by culture in a temperature-cycling incubator. Methods Mol. Med. 72, 489–497 (2002)

  38. 38

    Haynes, J. D., Moch, J. K. & Smoot, D. S. Erythrocytic malaria growth or invasion inhibition assays with emphasis on suspension culture GIA. Methods Mol. Med. 72, 535–554 (2002)

  39. 39

    Carter, R., Ranford-Cartwright, L. & Alano, P. The culture and preparation of gametocytes of Plasmodium falciparum for immunochemical, molecular, and mosquito infectivity studies. Methods Mol. Biol. 21, 67–88 (1993)

  40. 40

    Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000)

  41. 41

    Eng, J. K., McCormack, A. L. & Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976–989 (1994)

  42. 42

    Tabb, D. L., McDonald, W. H. & Yates, J. R. DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21–26 (2002)

  43. 43

    Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001)

  44. 44

    Eisenhaber, B., Bork, P. & Eisenhaber, F. Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. Protein Eng. 11, 1155–1161 (1998)

  45. 45

    Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1–6 (1997)

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Acknowledgements

We are grateful to J. Graumann, R. Sadygov, G. Chukkapalli, A. Majumdar and R. Sinkovits for computer programming; C. Deciu for the probability calculations; and C. Delahunty and C. Vieille for critical reading of the manuscript. The authors acknowledge the support of the Office of Naval Research, the US Army Medical Research and Material Command, and the National Institutes of Health (to J.R.Y.). J.D.R. is funded by a Wellcome Trust Prize Studentship. We thank the scientists and funding agencies comprising the international Malaria Genome Project for making sequence data from the genome of P. falciparum clone 3D7 public before publication of the completed sequence. The opinions expressed are those of the authors and do not reflect the official policy of the Department of the Navy, Department of Defense, or the US government.

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Correspondence to John R. Yates.

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Florens, L., Washburn, M., Raine, J. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002). https://doi.org/10.1038/nature01107

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