Expression profiling of the schizont and trophozoite stages of Plasmodium falciparumwith a long-oligonucleotide microarray

Genome Biology

Volumn 4, Issue 2, 2003, Pages

  Bozdech, Zbynek ^a   Zhu, Jingchun ^a   Joachimiak, Marcin P ^b   Cohen, Fred E ^b   Pulliam, Brian ^a   DeRisi, Joseph L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Additional Data File; Apical Membrane Antigen; Malaria; Microarray Hybridization; Plastid Genome

Indexed keywords

PROTOZOAL RNA;

ANIMAL; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; NORTHERN BLOTTING; PLASMODIUM FALCIPARUM;

ANIMALS; BLOTTING, NORTHERN; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMODIUM FALCIPARUM; RNA, PROTOZOAN;

EID: 1342303735     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-4-2-r9     Document Type: Article

References (56)

1. Sachs J, Malaney P: The economic and social burden of malaria. Nature. 2002, 415: 680-685. 10.1038/415680a. DOI: 10.1038/415680a
2. Ridley RG: Medical need, scientific opportunity and the drive for antimalarial drugs. Nature. 2002, 415: 686-693. 10.1038/415686a. DOI: 10.1038/415686a
3. Richie TL, Saul A: Progress and challenges for malaria vaccines. Nature. 2002, 415: 694-701. 10.1038/415694a. DOI: 10.1038/415694a
4. Gardner MJ, Hall N, Fung E, White O, Berrlman M, Hyman R, Carlton JM, Pain A, Nelson K, Bowman S, et al: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002, 419: 498-511. 10.1038/nature01097. DOI: 10.1038/nature01097
5. PlasmoDB: The Plasmodium Genome Resource. [http://plasmodb.org]
6. Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, et al: PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Res. 2002, 30: 87-90. 10.1093/nar/30.1.87. DOI: 10.1093/nar/30.1.87
7. Deitsch K, Driskill C, Wellems T: Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes. Nucleic Acids Res. 2001, 29: 850-853. 10.1093/nar/29.3.850. DOI: 10.1093/nar/29.3.850
8. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996, 14: 457-460. DOI: 10.1038/ng1296-457
9. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997, 278: 680-686. 10.1126/science.278.5338.680. DOI: 10.1126/science.278.5338.680
10. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 2001, 98: 10869-10874. 10.1073/pnas.191367098. DOI: 10.1073/pnas.191367098
11. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al: Functional discovery via a compendium of expression profiles. Cell. 2000, 102: 109-126. DOI: 10.1016/S0092-8674(00)00015-5
12. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, et al: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998, 4: 1293-1301. 10.1038/3282. DOI: 10.1038/3282
13. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998, 9: 3273-3297. DOI: 10.1091/mbc.9.12.3273
14. de Avalos SV, Blader IJ, Fisher M, Boothroyd JC, Burleigh BA: Immediate/early response to Trypanosoma cruzi infection involves minimal modulation of host cell transcription. J Biol Chem. 2002, 277: 639-644. 10.1074/jbc.M109037200. DOI: 10.1074/jbc.M109037200
15. Ben Mamoun C, Gluzman IY, Hott C, MacMillan SK, Amarakone AS, Anderson DL, Carlton JM, Dame JB, Chakrabarti D, Martin RK, 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. 2001, 39: 26-36. 10.1046/j.1365-2958.2001.02222.x. DOI: 10.1046/j.1365-2958.2001.02222.x
16. Hayward RE: Plasmodium falciparum phosphoenolpyruvate carboxykinase is developmentally regulated in gametocytes. Mol Biochem Parasitol. 2000, 107: 227-240. 10.1016/S0166-6851(00)00191-2. DOI: 10.1016/S0166-6851(00)00191-2
17. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK: Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol. 2000, 35: 6-14. 10.1046/j.1365-2958.2000.01730.x. DOI: 10.1046/j.1365-2958.2000.01730.x
18. The Sanger Centre Plasmodium falciparum Genome Project. [http://www.sanger.ac.uk/Projects/P_falciparum]
19. Stanford Genome Technology Center Malaria Genome Project. [http://sequence-www.stanford.edu/group/malaria/index.html]
20. TIGR Plasmodium falciparum Genome Database (PFDB). [http://www.tigr.org/tdb/edb2/pfa1/htmls]
21. Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, et al: Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science. 1998, 282: 1126-1132. 10.1126/science.282.5391.1126. DOI: 10.1126/science.282.5391.1126
22. Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H: Interpolated Markov models for eukaryotic gene finding. Genomics. 1999, 59: 24-31. 10.1006/geno.1999.5854. DOI: 10.1006/geno.1999.5854
23. Joseph DeRisi lab: web supplement. [http://derisilab.ucsf.edu/falciparum]
24. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol. 1981, 147: 195-197. DOI: 10.1016/0022-2836(81)90087-5
25. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, et al: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001, 19: 342-347. 10.1038/86730. DOI: 10.1038/86730
26. ArrayOligoSelector. [http://arrayoligosel.sourceforge.net]
27. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, et al: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996, 14: 1675-1680. DOI: 10.1038/nbt1296-1675
28. Rouillard J-M, Herbert CJ, Zuker M: OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics. 2002, 18: 486-487. 10.1093/bioinformatics/18.3.486. DOI: 10.1093/bioinformatics/18.3.486
29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. DOI: 10.1016/S0022-2836(05)80360-2
30. Jaeger J, Turner DH, Zuker M: Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA. 1989, 86: 7706-7710. DOI: 10.1073/pnas.86.20.7706
31. Allawi HT, SantaLucia J: Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry. 1998, 37: 2170-2179. 10.1021/bi9724873. DOI: 10.1021/bi9724873
32. Lyngso RB, Zuker M, Pedersen CN: Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics. 1999, 15: 440-445. 10.1093/bioinformatics/15.6.440. DOI: 10.1093/bioinformatics/15.6.440
33. Peritz AE, Kierzek R, Sugimoto N, Turner DH: Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. Biochemistry. 1991, 30: 6428-6436. DOI: 10.1021/bi00240a013
34. Peyret N, Seneviratne PA, Allawi HT, Santa Lucia J: Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry. 1999, 38: 3468-3477. 10.1021/bi9825091. DOI: 10.1021/bi9825091
35. Sugimoto N, Nakano S, Yoneyama M, Honda K: Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 1996, 24: 4501-4505. 10.1093/nar/24.22.4501. DOI: 10.1093/nar/24.22.4501
36. Ziv J, Lempel A: A universal algorithm for sequential data compression. IEEE Trans Inf Theory. 1977, 23: 337-343. DOI: 10.1109/TIT.1977.1055714
37. Kumar VP, Datta S: Use of variability in the stage-specific transcription levels of Plasmodium falciparum in the selection of target genes. Parasitol Int. 2001, 50: 165-173. 10.1016/S1383-5769(01)00075-7. DOI: 10.1016/S1383-5769(01)00075-7
38. Certa U, Ghersa P, Dobeli H, Matile H, Kocher HP, Shrivastava IK, Shaw AR, Perrin LH: Aldolase activity of a Plasmodium falciparum protein with protective properties. Science. 1988, 240: 1036-1038. DOI: 10.1126/science.3285469
39. Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K, Feltwell T, et al: The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature. 1999, 400: 532-538. 10.1038/22964. DOI: 10.1038/22964
40. Vinkenoog R, Speranca MA, van Breemen O, Ramesar J, Williamson DH, Ross-MacDonald PB, Thomas AW, Janse CJ, del Portillo HA, Waters AP: Malaria parasites contain two identical copies of an elongation factor 1 alpha gene. Mol Biochem Parasitol. 1998, 94: 1-12. 10.1016/S0166-6851(98)00035-8. DOI: 10.1016/S0166-6851(98)00035-8
41. Song P, Malhotra P, Tuteja N, Chauhan VS: RNA helicase-related genes of Plasmodium falciparum and Plasmodium cynomolgi. Biochem Biophys Res Commun. 1999, 255: 312-316. 10.1006/bbrc.1999.0204. DOI: 10.1006/bbrc.1999.0204
42. Watanabe J: Cloning and characterization of heat shock protein DnaJ homologues from Plasmodium falciparum and comparison with ring infected erythrocyte surface antigen. Mol Biochem Parasitol. 1997, 88: 253-258. 10.1016/S0166-6851(97)00073-X. DOI: 10.1016/S0166-6851(97)00073-X
43. Joachimiak MP, Chang C, Rosenthal PJ, Cohen FE: The impact of whole genome sequence data on drug discovery - a malaria case study. Mol Med. 2001, 7: 698-710.
44. Coombs GH, Goldberg DE, Klemba M, Berry C, Kay J, Mottram JC: Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends Parasitol. 2001, 17: 532-537. 10.1016/S1471-4922(01)02037-2. DOI: 10.1016/S1471-4922(01)02037-2
45. Pinder J, Fowler R, Bannister L, Dluzewski A, Mitchell GH: Motile systems in malaria merozoites: how is the red blood cell invaded?. Parasitol Today. 2000, 16: 240-245. 10.1016/S0169-4758(00)01664-1. DOI: 10.1016/S0169-4758(00)01664-1
46. McColl DJ, Silva A, Foley M, Kun JF, Favaloro JM, Thompson JK, Marshall VM, Coppel RL, Kemp DJ, Anders RF: Molecular variation in a novel polymorphic antigen associated with Plasmodium falciparum merozoites. Mol Biochem Parasitol. 1994, 68: 53-67. 10.1016/0166-6851(94)00149-9. DOI: 10.1016/0166-6851(94)00149-9
47. de Stricker K, Vuust J, Jepsen S, Oeuvray C, Theisen M: Conservation and heterogeneity of the glutamate-rich protein (GLURP) among field isolates and laboratory lines of Plasmodium falciparum. Mol Biochem Parasitol. 2000, 111: 123-130. 10.1016/S0166-6851(00)00304-2. DOI: 10.1016/S0166-6851(00)00304-2
48. Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF: Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of antisense transcripts in the malarial parasite. Mol Biol Cell. 2001, 12: 3114-3125. DOI: 10.1091/mbc.12.10.3114
49. van Lin LH, Pace T, Janse CJ, Birago C, Ramesar J, Picci L, Ponzi M, Waters AP: Interspecies conservation of gene order and intron-exon structure in a genomic locus of high gene density and complexity in Plasmodium. Nucleic Acids Res. 2001, 29: 2059-2068. 10.1093/nar/29.10.2059. DOI: 10.1093/nar/29.10.2059
50. Van Dooren GG, Su V, DiOmbrain MC, McFadden GI: Processing of an apicoplast leader sequence in Plasmodium falciparum, and the identification of a putative leader cleavage enzyme. J Biol Chem. 2002, 277: 23612-23619. 10.1074/jbc.M201748200. DOI: 10.1074/jbc.M201748200
51. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001, 409: 533-538. 10.1038/35054095. DOI: 10.1038/35054095
52. Horrocks P, Dechering K, Lanzer M: Control of gene expression in Plasmodium falciparum. Mol Biochem Parasitol. 1998, 95: 171-181. 10.1016/S0166-6851(98)00110-8. DOI: 10.1016/S0166-6851(98)00110-8
53. Eisen MB, Brown PO: DNA arrays for analysis of gene expression. Methods Enzymol. 1999, 303: 179-205. DOI: 10.1016/S0076-6879(99)03014-1
54. Trager W, Jensen JB: Human malaria parasites in continuous culture. Science. 1976, 193: 673-675. DOI: 10.1126/science.781840
55. Microarrays: source for microarray protocols and software. [http://derisilab.ucsf.edu/microarray/index.html]
56. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning, a Laboratory Manual. 1989, Cold Spring Harbor, NY: Cold Spring Harbor Press