Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

Nature Biotechnology

Volumn 28, Issue 1, 2010, Pages 91-98

  Hu, Guangan ^a   Cabrera, Ana ^b   Kono, Maya ^b   Mok, Sachel ^a   Chaal, Balbir K ^a   Haase, Silvia ^b   Engelberg, Klemens ^b   Cheemadan, Sabna ^a   Spielmann, Tobias ^b   Preiser, Peter R ^a   Gilberger, Tim W ^b   Bozdech, Zbynek ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMALARIAL DRUG; CO-EXPRESSION; CODING GENES; DEVELOPMENT CYCLE; HUMAN MALARIA PARASITE; INTERACTION NETWORKS; PLASMODIUM FALCIPARUM; PREDICTION OF PROTEIN FUNCTION; SEQUENCE HOMOLOGY; SUBCELLULAR LOCALIZATIONS; TRANSCRIPTIONAL PROFILING; YEAST TWO HYBRID;

ASSOCIATION REACTIONS; GENE EXPRESSION; PROTEINS;

MALARIA CONTROL;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DEVELOPMENTAL STAGE; ERYTHROCYTE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENETIC TRANSCRIPTION; GROWTH INHIBITION; MEROZOITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN FUNCTION; SCHIZONT; SEQUENCE HOMOLOGY;

ALGORITHMS; ANIMALS; ANTIMALARIALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MALARIA, FALCIPARUM; MARKOV CHAINS; MEROZOITES; PLASMODIUM FALCIPARUM; PROTOZOAN PROTEINS; TRANSCRIPTION, GENETIC;

PLASMODIUM FALCIPARUM;

EID: 74049111230     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1597     Document Type: Article

References (58)

1. Vitoria, M. et al. The global fght against HIV/AIDS, tuberculosis, and malaria: current status and future perspectives. Am. J. Clin. Pathol. 131, 844-848 (2009).
2. Hay, S.I. et al. A world malaria map: Plasmodium falciparum endemicity in 2007. PLoS Med. 6, e1000048 (2009).
3. Molyneux, D.H. Control of human parasitic diseases: Context and overview. Adv. Parasitol. 61, 1-45 (2006).
4. Nwaka, S. & Hudson, A. Innovative lead discovery strategies for tropical diseases. Nat. Rev. Drug Discov. 5, 941-955 (2006).
5. Gardner, M.J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511 (2002).
6. Balu, B., Shoue, D.A., Fraser, M.J., Jr. & Adams, J.H. High-effciency transformation of Plasmodium falciparum by the lepidopteran transposable element piggyBac. Proc. Natl. Acad. Sci. USA 102, 16391-16396 (2005).
7. Maier, A.G. et al. Exported proteins required for virulence and rigidity of Plasmodium falciparum-infected human erythrocytes. Cell 134, 48-61 (2008).
8. Winzeler, E.A. Applied systems biology and malaria. Nat. Rev. Microbiol. 4, 145-151 (2006).
9. Kato, N. et al. Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility. Nat. Chem. Biol. 4, 347-356 (2008).
10. Date, S.V. & Stoeckert, C.J. Jr. Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res. 16, 542-549 (2006).
11. Wuchty, S. & Ipsaro, J.J. A draft of protein interactions in the malaria parasite P. falciparum. J. Proteome Res. 6, 1461-1470 (2007).
12. Bozdech, Z. et al. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1, E5 (2003).
13. Le Roch, K.G. et al. Discovery of gene function by expression profling of the malaria parasite life cycle. Science 301, 1503-1508 (2003).
14. Hughes, T.R. et al. Functional discovery via a compendium of expression profles. Cell 102, 109-126 (2000).
15. MacCarthy, T., Pomiankowski, A. & Seymour, R. Using large-scale perturbations in gene network reconstruction. BMC Bioinformatics 6, 11 (2005).
16. Ganesan, K. et al. A genetically hard-wired metabolic transcriptome in Plasmodium falciparum fails to mount protective responses to lethal antifolates. PLoS Pathog. 4, e1000214 (2008).
17. Gunasekera, A.M., Myrick, A., Le Roch, K., Winzeler, E. & Wirth, D.F. Plasmodium falciparum: genome wide perturbations in transcript profles among mixed stage cultures after chloroquine treatment. Exp. Parasitol. 117, 87-92 (2007).
18. Oakley, M.S. et al. Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites. Infect. Immun. 75, 2012-2025 (2007).
19. Natalang, O. et al. Dynamic RNA profling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate. BMC Genomics 9, 388 (2008).
20. Tamez, P.A. et al. An erythrocyte vesicle protein exported by the malaria parasite promotes tubovesicular lipid import from the host cell surface. PLoS Pathog. 4, e1000118 (2008).
21. Groth, P., Weiss, B., Pohlenz, H.D. & Leser, U. Mining phenotypes for gene function prediction. BMC Bioinformatics 9, 136 (2008).
22. Kim, W.K., Krumpelman, C. & Marcotte, E.M. Inferring mouse gene functions from genomic-scale data using a combined functional network/classifcation strategy. Genome Biol. 9 Suppl 1, S5 (2008).
23. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004).
24. Lee, H., Deng, M., Sun, F. & Chen, T. An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 7, 269 (2006).
25. LaCount, D.J. et al. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438, 103-107 (2005).
26. Llinas, M., Bozdech, Z., Wong, E.D., Adai, A.T. & DeRisi, J.L. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 34, 1166-1173 (2006).
27. Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum feld isolates. PLoS Pathog. 5, e1000644 (2009).
28. Barabasi, A.L. & Oltvai, Z.N. Network biology: understanding the cell′s functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
29. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
30. Deng, M., Zhang, K., Mehta, S., Chen, T. & Sun, F. Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 10, 947-960 (2003).
31. Cowman, A.F. & Crabb, B.S. Invasion of red blood cells by malaria parasites. Cell 124, 755-766 (2006).
32. Soldati, D., Foth, B.J. & Cowman, A.F. Molecular and functional aspects of parasite invasion. Trends Parasitol. 20, 567-574 (2004).
33. Haase, S. et al. Characterization of a conserved rhoptry-associated leucine zipperlike protein in the malaria parasite Plasmodium falciparum. Infect. Immun. 76, 879-887 (2008).
34. Treeck, M. et al. A conserved region in the EBL proteins is implicated in microneme targeting of the malaria parasite Plasmodium falciparum. J. Biol. Chem. 281, 31995-32003 (2006).
35. Baum, J. et al. A conserved molecular motor drives cell invasion and gliding motility across malaria life cycle stages and other apicomplexan parasites. J. Biol. Chem. 281, 5197-5208 (2006).
36. Baum, J. et al. A malaria parasite formin regulates actin polymerization and localizes to the parasite-erythrocyte moving junction during invasion. Cell Host Microbe 3, 188-198 (2008).
37. Morrissette, N.S. & Sibley, L.D. Disruption of microtubules uncouples budding and nuclear division in Toxoplasma gondii. J. Cell Sci. 115, 1017-1025 (2002).
38. Shock, J.L., Fischer, K.F. & DeRisi, J.L. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol. 8, R134 (2007).
39. De Silva, E.K. et al. Specifc DNA-binding by apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA 105, 8393-8398 (2008).
40. Zhou, Y. et al. Evidence-based annotation of the malaria parasite′s genome using comparative expression profling. PLoS One 3, e1570 (2008).
41. Ginsburg, H. Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends Parasitol. 25, 37-43 (2009).
42. Chattopadhyay, R. et al. PfSPATR, a Plasmodium falciparum protein containing an altered thrombospondin type I repeat domain is expressed at several stages of the parasite life cycle and is the target of inhibitory antibodies. J. Biol. Chem. 278, 25977-25981 (2003).
43. Wickramarachchi, T., Devi, Y.S., Mohmmed, A. & Chauhan, V.S. Identifcation and characterization of a novel Plasmodium falciparum merozoite apical protein involved in erythrocyte binding and invasion. PLoS ONE 3, e1732 (2008).
44. Pearce, J.A., Mills, K., Triglia, T., Cowman, A.F. & Anders, R.F. Characterisation of two novel proteins from the asexual stage of Plasmodium falciparum, H101 and H103. Mol. Biochem. Parasitol. 139, 141-151 (2005).
45. Wickramarachchi, T. et al. A novel Plasmodium falciparum erythrocyte binding protein associated with the merozoite surface, PfDBLMSP. Int. J. Parasitol. 39, 763-773 (2009).
46. Bullen, H.E. et al. A novel family Of apicomplexan glideosome associated proteins With an inner-membrane anchoring role. J. Biol. Chem. 284, 25353-25363 (2009).
47. Rayavara, K. et al. A complex of three related membrane proteins is conserved on malarial merozoites. Mol. Biochem. Parasitol. 167, 135-143 (2009).
48. Arastu-Kapur, S. et al. Identifcation of proteases that regulate erythrocyte rupture by the malaria parasite Plasmodium falciparum. Nat. Chem. Biol. 4, 203-213 (2008).
49. Hu, G., Llinas, M., Li, J., Preiser, P.R. & Bozdech, Z. Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 8, 350 (2007).
50. Huttenhower, C., Hibbs, M., Myers, C. & Troyanskaya, O.G. A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics 22, 2890-2897 (2006).
51. Date, S.V. & Marcotte, E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 21, 1055-1062 (2003).
52. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
53. Wuchty, S. & Ipsaro, J.J. A draft of protein interactions in the malaria parasite P. falciparum. J. Proteome Res. 6, 1461-1470 (2007).
54. Lee, I., Date, S.V., Adai, A.T. & Marcotte, E.M. A probabilistic functional network of yeast genes. Science 306, 1555-1558 (2004).
55. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
56. Deng, M., Zhang, K., Mehta, S., Chen, T. & Sun, F. Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 10, 947-960 (2003).
57. Fidock, D.A. & Wellems, T.E. Transformation with human dihydrofolate reductase renders malaria parasites insensitive to WR99210 but does not affect the intrinsic activity of proguanil. Proc. Natl. Acad. Sci. USA 94, 10931-10936 (1997).
58. Struck, N.S. et al. Re-defning the Golgi complex in Plasmodium falciparum using the novel Golgi marker PfGRASP. J. Cell Sci. 118, 5603-5613 (2005).