Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum

Molecular and Biochemical Parasitology

Volumn 153, Issue 1, 2007, Pages 19-30

  Gunasekera, Anusha M ^a   Myrick, Alissa ^a   Militello, Kevin T ^a   Sims, Jennifer S ^a   Dong, Carolyn K ^a   Gierahn, Todd ^a   Le Roch, Karine ^b   Winzeler, Elizabeth ^b   Wirth, Dyann F ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Gene regulation; Oligonucleotide array; Plasmodium falciparum; Regulatory motifs

Indexed keywords

DNA; RNA;

ARTICLE; BIOINFORMATICS; COMPLEX FORMATION; CONTROLLED STUDY; GEL MOBILITY SHIFT ASSAY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCUS; GENE SEQUENCE; GENOME ANALYSIS; LIFE CYCLE; MICROARRAY ANALYSIS; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN RNA BINDING; PROTOZOAL GENETICS; REGULATORY DNA SEQUENCE; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; TRANSIENT TRANSFECTION;

ANIMALS; ANTIMALARIALS; BASE SEQUENCE; CHLOROQUINE; DNA, PROTOZOAN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, PROTOZOAN; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMODIUM FALCIPARUM; PROTEIN SUBUNITS; TRANSFECTION;

EUKARYOTA; PLASMODIUM (APICOMPLEXA); PLASMODIUM FALCIPARUM;

EID: 34047183657     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbiopara.2007.01.011     Document Type: Article

References (57)

1. van Noort V., and Huynen MA. Combinatorial gene regulation in Plasmodium falciparum. Trends Genet 22 (2006) 73-78
2. Florens L., Washburn M.P., Raine J.D., et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419 (2002) 520-526
3. Lasonder E., Ishihama Y., Andersen J.S., et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419 (2002) 537-542
4. Ben Mamoun C., Gluzman I.Y., Hott 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 (2001) 26-36
5. Bozdech Z., Llinas M., Pulliam B.L., Wong E.D., Zhu J., and DeRisi J.L. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1 (2003) E5
6. Hayward R.E., Derisi J.L., Alfadhli S., Kaslow D.C., Brown P.O., and Rathod P.K. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol 35 (2000) 6-14
7. Le Roch K.G., Zhou Y., Blair P.L., et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301 (2003) 1503-1508
8. Duraisingh M.T., Voss T.S., Marty A.J., et al. Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum. Cell 121 (2005) 13-24
9. Freitas-Junior L.H., Hernandez-Rivas R., Ralph S.A., et al. Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites. Cell 121 (2005) 25-36
10. Deitsch K.W., Calderwood M.S., and Wellems T.E. Malaria. Cooperative silencing elements in var genes. Nature 412 (2001) 875-876
11. Deitsch K.W. Gene silencing and antigenic variation in malaria parasites. Sci World J 1 (2001) 650-652
12. Coulson R.M., Hall N., and Ouzounis C.A. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res 14 (2004) 1548-1554
13. Lanzer M., de Bruin D., and Ravetch J.V. A sequence element associated with the Plasmodium falciparum KAHRP gene is the site of developmentally regulated protein-DNA interactions. Nucl Acids Res 20 (1992) 3051-3056
14. Alano P., Silvestrini F., and Roca L. Structure and polymorphism of the upstream region of the pfg27/25 gene, transcriptionally regulated in gametocytogenesis of Plasmodium falciparum. Mol Biochem Parasitol 79 (1996) 207-217
15. Horrocks P., Jackson M., Cheesman S., White J.H., and Kilbey B.J. Stage specific expression of proliferating cell nuclear antigen and DNA polymerase delta from Plasmodium falciparum. Mol Biochem Parasitol 79 (1996) 177-182
16. Scherf A., Hernandez-Rivas R., Buffet P., et al. Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum. EMBO J 17 (1998) 5418-5426
17. Tosh K., Cheesman S., Horrocks P., and Kilbey B. Plasmodium falciparum: stage-related expression of topoisomerase I. Exp Parasitol 91 (1999) 126-132
18. Mbacham W.F., Chow C.S., Daily J., Golightly L.M., and Wirth D.F. Deletion analysis of the 5′ flanking sequence of the Plasmodium gallinaceum sexual stage specific gene pgs28 suggests a bipartite arrangement of cis-control elements. Mol Biochem Parasitol 113 (2001) 183-187
19. Young J.A., Fivelman Q.L., Blair P.L., et al. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol 143 (2005) 67-79
20. Chow C.S., and Wirth D.F. Linker scanning mutagenesis of the Plasmodium gallinaceum sexual stage specific gene pgs28 reveals a novel downstream cis-control element. Mol Biochem Parasitol 129 (2003) 199-208
21. Dechering K.J., Kaan A.M., Mbacham W., et al. Isolation and functional characterization of two distinct sexual-stage-specific promoters of the human malaria parasite Plasmodium falciparum. Mol Cell Biol 19 (1999) 967-978
22. Horrocks P., and Lanzer M. Mutational analysis identifies a five base pair cis-acting sequence essential for GBP130 promoter activity in Plasmodium falciparum. Mol Biochem Parasitol 99 (1999) 77-87
23. Voss T.S., Kaestli M., Vogel D., Bopp S., and Beck H.P. Identification of nuclear proteins that interact differentially with Plasmodium falciparum var gene promoters. Mol Microbiol 48 (2003) 1593-1607
24. Osta M., Gannoun-Zaki L., Bonnefoy S., Roy C., and Vial H.J. A 24 bp cis-acting element essential for the transcriptional activity of Plasmodium falciparum CDP-diacylglycerol synthase gene promoter. Mol Biochem Parasitol 121 (2002) 87-98
25. Porter M.E. Positive and negative effects of deletions and mutations within the 5′ flanking sequences of Plasmodium falciparum DNA polymerase delta. Mol Biochem Parasitol 122 (2002) 9-19
26. Ruvalcaba-Salazar O.K., del Carmen Ramirez-Estudillo M., Montiel-Condado D., Recillas-Targa F., Vargas M., and Hernandez-Rivas R. Recombinant and native Plasmodium falciparum TATA-binding-protein binds to a specific TATA box element in promoter regions. Mol Biochem Parasitol 140 (2005) 183-196
27. Gardner M.J., Hall N., Fung E., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 (2002) 498-511
28. Le Roch K.G., Johnson J.R., Florens L., et al. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res 14 (2004) 2308-2318
29. Cui L., Fan Q., and Li J. The malaria parasite Plasmodium falciparum encodes members of the Puf RNA-binding protein family with conserved RNA binding activity. Nucl Acids Res 30 (2002) 4607-4617
30. Loyevsky M., LaVaute T., Allerson C.R., et al. An IRP-like protein from Plasmodium falciparum binds to a mammalian iron-responsive element. Blood 98 (2001) 2555-2562
31. Loyevsky M., Mompoint F., Yikilmaz E., et al. Expression of a recombinant IRP-like Plasmodium falciparum protein that specifically binds putative plasmodial IREs. Mol Biochem Parasitol 126 (2003) 231-238
32. Paton M.G., Barker G.C., Matsuoka H., et al. Structure and expression of a post-transcriptionally regulated malaria gene encoding a surface protein from the sexual stages of Plasmodium berghei. Mol Biochem Parasitol 59 (1993) 263-275
33. Mair G.R., Braks J.A., Garver L.S., et al. Regulation of sexual development of Plasmodium by translational repression. Science 313 (2006) 667-669
34. Spellman P.T., Sherlock G., Zhang M.Q., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9 (1998) 3273-3297
35. Hall N., Karras M., Raine J.D., et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307 (2005) 82-86
36. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2 (1994) 28-36
37. Bailey T.L., and Elkan C. The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3 (1995) 21-29
38. Bray N., Dubchak I., and Pachter L. AVID: a global alignment program. Genome Res 13 (2003) 97-102
39. Dubchak I., Brudno M., Loots G.G., et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res 10 (2000) 1304-1306
40. Mayor C., Brudno M., Schwartz J.R., et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16 (2000) 1046-1047
41. Militello K.T., and Wirth D.F. A new reporter gene for transient transfection of Plasmodium falciparum. Parasitol Res 89 (2003) 154-157
42. Militello K.T., Dodge M., Bethke L., and Wirth D.F. Identification of regulatory elements in the Plasmodium falciparum genome. Mol Biochem Parasitol 134 (2004) 75-88
43. Agabian N. Trans splicing of nuclear pre-mRNAs. Cell 61 (1990) 1157-1160
44. Lambros C., and Vanderberg J.P. Synchronization of Plasmodium falciparum erythrocytic stages in culture. J Parasitol 65 (1979) 418-420
45. Schuller H.J., Hahn A., Troster F., Schutz A., and Schweizer E. Coordinate genetic control of yeast fatty acid synthase genes FAS1 and FAS2 by an upstream activation site common to genes involved in membrane lipid biosynthesis. EMBO J 11 (1992) 107-114
46. Le Crom S., Devaux F., Marc P., Zhang X., Moye-Rowley W.S., and Jacq C. New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system. Mol Cell Biol 22 (2002) 2642-2649
47. Lagorce A., Hauser N.C., Labourdette D., et al. Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae. J Biol Chem 278 (2003) 20345-20357
48. Lucau-Danila A., Lelandais G., Kozovska Z., et al. Early expression of yeast genes affected by chemical stress. Mol Cell Biol 25 (2005) 1860-1868
49. Murakami A., Ishida S., Thurlow J., Revest J.M., and Dickson C. SOX6 binds CtBP2 to repress transcription from the Fgf-3 promoter. Nucl Acids Res 29 (2001) 3347-3355
50. Sam-Yellowe T.Y., Florens L., Johnson J.R., et al. A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling. Genome Res 14 (2004) 1052-1059
51. Myrick A., Munasinghe A., Patankar S., and Wirth D.F. Mapping of the Plasmodium falciparum multidrug resistance gene 5′-upstream region, and evidence of induction of transcript levels by antimalarial drugs in chloroquine sensitive parasites. Mol Microbiol 49 (2003) 671-683
52. Boorsma A., de Nobel H., ter Riet B., et al. Characterization of the transcriptional response to cell wall stress in Saccharomyces cerevisiae. Yeast 21 (2004) 413-427
53. Gissot M., Briquet S., Refour P., Boschet C., and Vaquero C. PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation. J Mol Biol 346 (2005) 29-42
54. Fan Q., Li J., Kariuki M., and Cui L. Characterization of PfPuf2, member of the Puf family RNA-binding proteins from the malaria parasite Plasmodium falciparum. DNA Cell Biol 23 (2004) 753-760
55. Gannoun-Zaki L., Jost A., Mu J., Deitsch K.W., and Wellems T.E. A silenced Plasmodium falciparum var promoter can be activated in vivo through spontaneous deletion of a silencing element in the intron. Eukaryot Cell 4 (2005) 490-492
56. Martinez-Calvillo S., Yan S., Nguyen D., Fox M., Stuart K., and Myler P.J. Transcription of Leishmania major Friedlin chromosome 1 initiates in both directions within a single region. Mol Cell 11 (2003) 1291-1299
57. Soto M., Quijada L., Larreta R., Iborra S., Alonso C., and Requena J.M. Leishmania infantum possesses a complex family of histone H2A genes: structural characterization and analysis of expression. Parasitology 127 (2003) 95-105