Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Malaria research in the post-genomic era

Abstract

For many pathogens the availability of genome sequence, permitting genome-dependent methods of research, can partially substitute for powerful forward genetic methods (genome-independent) that have advanced model organism research for decades. In 2002 the genome sequence of Plasmodium falciparum, the parasite causing the most severe type of human malaria, was completed, eliminating many of the barriers to performing state-of-the-art molecular biological research on malaria parasites. Although new, licensed therapies may not yet have resulted from genome-dependent experiments, they have produced a wealth of new observations about the basic biology of malaria parasites, and it is likely that these will eventually lead to new therapeutic approaches. This review will focus on the basic research discoveries that have depended, in part, on the availability of the Plasmodium genome sequences.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Diagram of the malaria parasite’s life cycle.
Figure 2: Export pathways shared by eukaryotic pathogens.

Similar content being viewed by others

References

  1. Sachs, J. & Malaney, P. The economic and social burden of malaria. Nature 415, 680–685 (2002)

    Article  CAS  Google Scholar 

  2. Snow, R. W., Guerra, C. A., Noor, A. M., Myint, H. Y. & Hay, S. I. The global distribution of clinical episodes of Plasmodium falciparum malaria. Nature 434, 214–217 (2005)

    Article  ADS  CAS  Google Scholar 

  3. Okiro, E. A. et al. The decline in paediatric malaria admissions on the coast of Kenya. Malar. J. 6 151 10.1186/1475-2875-6-151 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  4. Boivin, M. J. et al. Cognitive impairment after cerebral malaria in children: a prospective study. Pediatrics 119, e360–e366 (2007)

    Article  Google Scholar 

  5. Tjitra, E. et al. Multidrug-resistant Plasmodium vivax associated with severe and fatal malaria: a prospective study in Papua, Indonesia. PLoS Med. 5, e128 (2008)

    Article  Google Scholar 

  6. Baird, J. K. Effectiveness of antimalarial drugs. N. Engl. J. Med. 352, 1565–1577 (2005)

    Article  CAS  Google Scholar 

  7. Vennerstrom, J. L. et al. Identification of an antimalarial synthetic trioxolane drug development candidate. Nature 430, 900–904 (2004)

    Article  ADS  CAS  Google Scholar 

  8. Ro, D. K. et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940–943 (2006)

    Article  ADS  CAS  Google Scholar 

  9. Afonso, A. et al. Malaria parasites can develop stable resistance to artemisinin but lack mutations in candidate genes atp6 (encoding the sarcoplasmic and endoplasmic reticulum Ca2+ ATPase), tctp, mdr1, and cg10 . Antimicrob. Agents Chemother. 50, 480–489 (2006)

    Article  CAS  Google Scholar 

  10. Wongsrichanalai, C. & Meshnick, S. R. Declining artesunate-mefloquine efficacy against falciparum malaria on the Cambodia-Thailand border. Emerg. Infect. Dis. 14, 716–719 (2008)

    Article  Google Scholar 

  11. Aponte, J. J. et al. Safety of the RTS,S/AS02D candidate malaria vaccine in infants living in a highly endemic area of Mozambique: a double blind randomised controlled phase I/IIb trial. Lancet 370, 1543–1551 (2007)

    Article  CAS  Google Scholar 

  12. Todryk, S. M. & Hill, A. V. S. Malaria vaccines: the stage we are at. Nature Rev. Microbiol. 5, 487–489 (2007)

    Article  CAS  Google Scholar 

  13. Epstein, J. E. et al. Safety and clinical outcome of experimental challenge of human volunteers with Plasmodium falciparum-infected mosquitoes: an update. J. Infect. Dis. 196, 145–154 (2007)

    Article  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  16. Hall, N. et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307, 82–86 (2005)

    Article  ADS  CAS  Google Scholar 

  17. Carlton, J. M. et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax . Nature 10.1038/nature07327 (this issue)

  18. Pain, A. et al. The genome of the simian and human malaria parasite Plasmodium knowlesi . Nature 10.1038/nature07306 (this issue)

  19. Holt, R. A. et al. The genome sequence of the malaria mosquito Anopheles gambiae . Science 298, 129–149 (2002)

    Article  ADS  CAS  Google Scholar 

  20. Jomaa, H. et al. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science 285, 1573–1576 (1999)

    Article  CAS  Google Scholar 

  21. Daily, J. P. et al. Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature 450, 1091–1095 (2007)

    Article  ADS  CAS  Google Scholar 

  22. Tarun, A. S. et al. A combined transcriptome and proteome survey of malaria parasite liver stages. Proc. Natl Acad. Sci. USA 105, 305–310 (2008)

    Article  ADS  CAS  Google Scholar 

  23. Zhou, Y. et al. Evidence-based annotation of the malaria parasite’s genome using comparative expression profiling. PLoS ONE 3, e1570 (2008)

    Article  ADS  Google Scholar 

  24. Le Roch, K. G. et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301, 1503–1508 (2003)

    Article  ADS  CAS  Google Scholar 

  25. Bozdech, Z. et al. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum . PLoS Biol. 1, E5 (2003)

    Article  Google Scholar 

  26. LaCount, D. J. et al. A protein interaction network of the malaria parasite Plasmodium falciparum . Nature 438, 103–107 (2005)

    Article  ADS  CAS  Google Scholar 

  27. Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002)

    Article  ADS  CAS  Google Scholar 

  28. Lasonder, E. et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419, 537–542 (2002)

    Article  ADS  CAS  Google Scholar 

  29. Khan, S. M. et al. Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell 121, 675–687 (2005)

    Article  CAS  Google Scholar 

  30. Balu, B., Shoue, D. A., Fraser, M. J. & Adams, J. H. High-efficiency transformation of Plasmodium falciparum by the lepidopteran transposable element piggyBac. Proc. Natl Acad. Sci. USA 102, 16391–16396 (2005)

    Article  ADS  CAS  Google Scholar 

  31. Nkrumah, L. J. et al. Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase. Nature Methods 3, 615–621 (2006)

    Article  CAS  Google Scholar 

  32. Vedadi, M. et al. Genome-scale protein expression and structural biology of Plasmodium falciparum and related apicomplexan organisms. Mol. Biochem. Parasitol. 151, 100–110 (2007)

    Article  CAS  Google Scholar 

  33. Mehlin, C. et al. Heterologous expression of proteins from Plasmodium falciparum: results from 1000 genes. Mol. Biochem. Parasitol. 148, 144–160 (2006)

    Article  CAS  Google Scholar 

  34. Billker, O. et al. Calcium and a calcium-dependent protein kinase regulate gamete formation and mosquito transmission in a malaria parasite. Cell 117, 503–514 (2004)

    Article  CAS  Google Scholar 

  35. Le Roch, K. G. et al. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 14, 2308–2318 (2004)

    Article  CAS  Google Scholar 

  36. Mair, G. R. et al. Regulation of sexual development of Plasmodium by translational repression. Science 313, 667–669 (2006)

    Article  ADS  CAS  Google Scholar 

  37. Siau, A. et al. Temperature shift and host cell contact up-regulate sporozoite expression of Plasmodium falciparum genes involved in hepatocyte infection. PLoS Pathog. 4, e1000121 (2008)

    Article  Google Scholar 

  38. Mourier, T. et al. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum . Genome Res. 18, 281–292 (2008)

    Article  CAS  Google Scholar 

  39. Saul, A. Mosquito stage, transmission blocking vaccines for malaria. Curr. Opin. Infect. Dis. 20, 476–481 (2007)

    Article  Google Scholar 

  40. Waterhouse, R. M. et al. Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes. Science 316, 1738–1743 (2007)

    Article  ADS  CAS  Google Scholar 

  41. Blandin, S. et al. Complement-like protein TEP1 is a determinant of vectorial capacity in the malaria vector Anopheles gambiae . Cell 116, 661–670 (2004)

    Article  CAS  Google Scholar 

  42. Alphey, L. et al. Malaria control with genetically manipulated insect vectors. Science 298, 119–121 (2002)

    Article  ADS  CAS  Google Scholar 

  43. Kyes, S. A., Kraemer, S. M. & Smith, J. D. Antigenic variation in Plasmodium falciparum: gene organization and regulation of the var multigene family. Eukaryot. Cell 6, 1511–1520 (2007)

    Article  CAS  Google Scholar 

  44. Duraisingh, M. T. et al. Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum . Cell 121, 13–24 (2005)

    Article  CAS  Google Scholar 

  45. Voss, T. S. et al. A var gene promoter controls allelic exclusion of virulence genes in Plasmodium falciparum malaria. Nature 439, 1004–1008 (2006)

    Article  ADS  CAS  Google Scholar 

  46. Dzikowski, R., Frank, M. & Deitsch, K. Mutually exclusive expression of virulence genes by malaria parasites is regulated independently of antigen production. PLoS Pathog. 2, e22 (2006)

    Article  Google Scholar 

  47. Stubbs, J. et al. Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes. Science 309, 1384–1387 (2005). This paper demonstrates how malaria parasites can switch transcription between different members of multigene families potentially under selection pressure, contributing to their ability to evade host immune response.

    Article  ADS  CAS  Google Scholar 

  48. Cortes, A. et al. Epigenetic silencing of Plasmodium falciparum genes linked to erythrocyte invasion. PLoS Pathog. 3, e107 (2007)

    Article  Google Scholar 

  49. Doolan, D. L. et al. Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc. Natl Acad. Sci. USA 100, 9952–9957 (2003). This study shows that vaccine candidates potentially superior to historical vaccine candidates may be discovered by mining proteomic and transcriptional data.

    Article  ADS  CAS  Google Scholar 

  50. Kariu, T., Ishino, T., Yano, K., Chinzei, Y. & Yuda, M. CelTOS, a novel malarial protein that mediates transmission to mosquito and vertebrate hosts. Mol. Microbiol. 59, 1369–1379 (2006)

    Article  CAS  Google Scholar 

  51. Moran, M. et al. The Malaria Product Pipeline: Planning for the Future (The George Institute for International Health, 2007)

    Google Scholar 

  52. Matuschewski, K. et al. Infectivity-associated changes in the transcriptional repertoire of the malaria parasite sporozoite stage. J. Biol. Chem. 277, 41948–41953 (2002)

    Article  CAS  Google Scholar 

  53. Mueller, A. K. et al. Plasmodium liver stage developmental arrest by depletion of a protein at the parasite-host interface. Proc. Natl Acad. Sci. USA 102, 3022–3027 (2005)

    Article  ADS  CAS  Google Scholar 

  54. Mueller, A. K., Labaied, M., Kappe, S. H. & Matuschewski, K. Genetically modified Plasmodium parasites as a protective experimental malaria vaccine. Nature 433, 164–167 (2005). This work demonstrates how genes identified by transcriptional profiling (using cDNA sequencing) can lead to innovative vaccination strategies for malaria.

    Article  ADS  CAS  Google Scholar 

  55. van Dijk, M. R. et al. Genetically attenuated, P36p-deficient malarial sporozoites induce protective immunity and apoptosis of infected liver cells. Proc. Natl Acad. Sci. USA 102, 12194–12199 (2005)

    Article  ADS  CAS  Google Scholar 

  56. Sidhu, A. B., Verdier-Pinard, D. & Fidock, D. A. Chloroquine resistance in Plasmodium falciparum malaria parasites conferred by pfcrt mutations. Science 298, 210–213 (2002)

    Article  ADS  CAS  Google Scholar 

  57. Wootton, J. C. et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum . Nature 418, 320–323 (2002). This work demonstrates that loci involved in drug resistance can be mapped using parasite population studies, setting the stage for more extensive analyses of parasite phenotypes.

    Article  ADS  CAS  Google Scholar 

  58. Roper, C. et al. Intercontinental spread of pyrimethamine-resistant malaria. Science 305, 1124 (2004)

    Article  CAS  Google Scholar 

  59. Jeffares, D. C. et al. Genome variation and evolution of the malaria parasite Plasmodium falciparum . Nature Genet. 39, 120–125 (2007)

    Article  CAS  Google Scholar 

  60. Volkman, S. K. et al. A genome-wide map of diversity in Plasmodium falciparum . Nature Genet. 39, 113–119 (2007)

    Article  CAS  Google Scholar 

  61. Mu, J. et al. Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nature Genet. 39, 126–130 (2007)

    Article  CAS  Google Scholar 

  62. Kidgell, C. et al. A systematic map of genetic variation in Plasmodium falciparum . PLoS Pathog. 2, e57 (2006). This is the first genome-wide study of diversity, which also reveals that copy number variations are widespread in malaria parasites.

    Article  Google Scholar 

  63. Carret, C. K. et al. Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Mol. Biochem. Parasitol. 144, 177–186 (2005)

    Article  CAS  Google Scholar 

  64. Joy, D. A. et al. Early origin and recent expansion of Plasmodium falciparum . Science 300, 318–321 (2003)

    Article  ADS  CAS  Google Scholar 

  65. Volkman, S. K. et al. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum . Science 298, 216–218 (2002)

    Article  ADS  CAS  Google Scholar 

  66. Polley, S. D. et al. Plasmodium falciparum merozoite surface protein 3 is a target of allele-specific immunity and alleles are maintained by natural selection. J. Infect. Dis. 195, 279–287 (2007)

    Article  CAS  Google Scholar 

  67. Hiller, N. L. et al. A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science 306, 1934–1937 (2004)

    Article  ADS  CAS  Google Scholar 

  68. Marti, M., Good, R. T., Rug, M., Knuepfer, E. & Cowman, A. F. Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306, 1930–1933 (2004)

    Article  ADS  CAS  Google Scholar 

  69. Bhattacharjee, S. et al. The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathog. 2, e50 (2006). This is the first evidence that eukaryotic microbes share similar host trafficking signals.

    Article  Google Scholar 

  70. Tian, M., Huitema, E., Da Cunha, L., Torto-Alalibo, T. & Kamoun, S. A. Kazal-like extracellular serine protease inhibitor from Phytophthora infestans targets the tomato pathogenesis-related protease P69B. J. Biol. Chem. 279, 26370–26377 (2004)

    Article  CAS  Google Scholar 

  71. Armstrong, M. R. et al. An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc. Natl Acad. Sci. USA 102, 7766–7771 (2005)

    Article  ADS  CAS  Google Scholar 

  72. Sargeant, T. J. et al. Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol. 7, R12 (2006)

    Article  Google Scholar 

  73. Singh, A. P. et al. Plasmodium circumsporozoite protein promotes the development of the liver stages of the parasite. Cell 131, 492–504 (2007). This paper shows that the abundant surface protein CSP is exported to the host cytoplasm where it may have an immunomodulatory role.

    Article  CAS  Google Scholar 

  74. Kumar, K. A. et al. The circumsporozoite protein is an immunodominant protective antigen in irradiated sporozoites. Nature 444, 937–940 (2006)

    Article  ADS  CAS  Google Scholar 

  75. Menard, R. et al. Circumsporozoite protein is required for development of malaria sporozoites in mosquitoes. Nature 385, 336–340 (1997)

    Article  ADS  CAS  Google Scholar 

  76. Sturm, A. et al. Manipulation of host hepatocytes by the malaria parasite for delivery into liver sinusoids. Science 313, 1287–1290 (2006). This work describes how hepatocyte-derived merosomes signal to the host to both ensure migration of the parasite into the bloodstream and to protect themselves from host immunity.

    Article  ADS  CAS  Google Scholar 

  77. Taylor, S. et al. A secreted serine-threonine kinase determines virulence in the eukaryotic pathogen Toxoplasma gondii . Science 314, 1776–1780 (2006)

    Article  ADS  CAS  Google Scholar 

  78. Saeij, J. P. et al. Toxoplasma co-opts host gene expression by injection of a polymorphic kinase homologue. Nature 445, 324–327 (2007)

    Article  ADS  CAS  Google Scholar 

  79. Baniecki, M. L., Wirth, D. F. & Clardy, J. High-throughput Plasmodium falciparum growth assay for malaria drug discovery. Antimicrob. Agents Chemother. 51, 716–723 (2007)

    Article  CAS  Google Scholar 

  80. Chong, C. R., Chen, X., Shi, L., Liu, J. O. & Sullivan, D. J. A clinical drug library screen identifies astemizole as an antimalarial agent. Nature Chem. Biol. 2, 415–416 (2006)

    Article  CAS  Google Scholar 

  81. Plouffe, D. et al. In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen. Proc. Natl Acad. Sci. USA 105, 9059–9064 (2008)

    Article  ADS  CAS  Google Scholar 

  82. Whisson, S. C. et al. A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450, 115–118 (2007)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

E. A.W. is grateful for support from the Keck Foundation, the Wellcome Trust, Novartis and NIH RO1 AI059742.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Elizabeth Ann Winzeler.

Ethics declarations

Competing interests

E. A.W. receives support from Novartis, a manufacturer of artemisinin-based drugs.

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Winzeler, E. Malaria research in the post-genomic era. Nature 455, 751–756 (2008). https://doi.org/10.1038/nature07361

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07361

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing