Current status of the Plasmodium falciparum genome project

Molecular and Biochemical Parasitology

Volumn 79, Issue 1, 1996, Pages 1-12

  Dame, John B ^a   Arnot, David E ^b   Bourke, Peter F ^c   Chakrabarti, Debopam ^d   Christodoulou, Zoe ^e   Coppel, Ross L ^f   Cowman, Alan F ^g   Craig, Alister G ^e   Fischer, Katja ^j   Foster, Jeremy ^e   Goodman, Nathan ^h   Hinterberg, Katherine ^k   Holder, Anthony A ⁱ   Holt, Deborah C ^c   Kemp, David J ^c   Lanzer, Michael ^j   Lim, Amanda ^g   Newbold, Chris I ^e   Ravetch, Jeffery V ^k   Reddy, G Roman ^a   Rubio, Justin ^g   Schuster, Sheldon M ^a   Su, Xin Zhuan ^l   Thompson, Jennifer K ^g   Vital, Ferdinand ^k   Wellems, Thomas E ^l   Werner, Ekkehard B ⁱ   more..

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c MENZIES SCHOOL OF HEALTH RESEARCH   (Australia)

^d UNIVERSITY OF CENTRAL FLORIDA   (United States)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f MONASH UNIVERSITY   (Australia)

^g WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^h WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

ⁱ NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^j UNIVERSITY OF WÜRZBURG   (Germany)

^k MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^l NATIONAL INSTITUTES OF HEALTH   (United States)

more..

Author keywords

cDNA; Expressed sequence tag; Genome project; Malaria; Mapping; Mung bean nuclease; Plasmodium falciparum; Protozoa; Review; Yeast artificial chromosome

Indexed keywords

COMPLEMENTARY DNA; DNA;

DNA DETERMINATION; GENE SEQUENCE; GENOME; MOLECULAR CLONING; MOLECULAR GENETICS; NONHUMAN; PARASITOLOGY; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; REVIEW; YEAST ARTIFICIAL CHROMOSOME;

PHASEOLUS (ANGIOSPERM); PLASMODIUM FALCIPARUM; PROTOZOA; VIGNA RADIATA VAR. RADIATA;

EID: 0030199748     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/0166-6851(96)02641-2     Document Type: Short Survey

References (74)

1. [1] Nussenzweig, R.S. and Long, C.A. (1994) Malaria vaccines: multiple targets. Science 265, 1381-1383.
2. [2] Oaks, S.C., Jr., Mitchell, V.S., Pearson, G.W. and Carpenter, C.C.J.,Eds. (1991) Malaria obstacles and opportunities, National Academy Press, Washington, DC.
3. [3] McKerrow, J.H., McGrath, M.E. and Engel, J.C. (1995) The cysteine protease of Trypanosoma cruzi as a model for antiparasite drug design. Parasitol. Today 11, 279-282.
4. [4] Chakravarti, A., Gibbs, R., Green, E. and Myers, R. (1995) Genome research and Genome Research. Genome Res. 5(1), editorial.
5. [5] Olson, M.V. (1995) A time to sequence. Science 270, 394-396.
6. [6] Gilbert, W. (1991) Towards a paradigm shift in biology. Nature 349, 99.
7. [7] Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.-F., Dougherty, B.A., Merrick, J.M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C.A., Gocayne, J.D., Scott, J.D., Shirley, R., Liu, L.-I., Glodek, A., Kelley, J.M., Weidman, J.F., Phillips, C.A., Spriggs, T., Hedblom, E., Cotton, M.D., Utterback, T.R., Hanna, M.C., Nguyen, D.T., Saudek, D.M., Brandon, R.C., Fine, L.D., Fritchman, J.L., Fuhrman, J.L., Geoghagen, N.S.M., Gnehm, C.L., McDonald, L.A., Small, K.V., Fraser, C.M., Smith, H.O. and Venter, J.C. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
8. [8] Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D., Bult, C.J., Kerlavage, A.R., Sutton, G., Kelley, J.M., Fritchman, J.L., Weidman, J.F., Small, K.V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T.R., Saudek, D.M., Phillips, C.A., Merrick, J.M., Tomb, J.-F., Dougherty, B.A., Bott, K.F., Hu, P.-C., Lucier, T.S., Peterson, S.N., Smith, H.O., Hutchison, C.A.,III and Venter, J.C. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
9. [9] Triglia, T. and Kemp, D.J. (1991) Large fragments of Plasmodium falciparum DNA can be stable when cloned in yeast artificial chromosomes. Mol. Biochem. Parasitol. 44, 207-212.
10. [10] Lehrach, H., Drmanac, R., Hoheisel, J., Larin, Z., Lennon, G., Monaco, A.P., Nizetic, D., Zehetner, G. and Poustka, A. (1990) Hybridization Fingerprinting in Genome Mapping and Sequencing. In: Genome Analysis Volume I: Genetic and Physical Mapping, pp. 39-81, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
11. [11] Maier, E., Hoheisel, J.D., McCarthy, L., Mott, R., Grigoriev, A.V., Monaco, A.P. and Lehrach, H. (1992) Complete coverage of the Schizosaccharomyces pombe genome in yeast artificial chromosomes. Nature Genet. 1, 273-277.
12. [12] McCutchan, T.F., Hansen, J.L., Dame, J.B. and Mullins, J.A. (1984) Mung bean nuclease cleaves Plasmodium genomic DNA at sites before and after genes. Science 225, 625-628.
13. [13] Vernick, K.D., Imberski, R.B. and McCutchan, T.F. (1988) Mung bean nuclease exhibits a generalized gene-excision activity upon purified Plasmodium falciparum genomic DNA. Nucleic Acids Res. 16, 6883-6896.
14. [14] Dame, J.B., Williams, J.L., McCutchan, T.F., Weber, J.L., Wirtz, R.A., Hockmeyer, W.T., Maloy, W.L., Haynes, J.D., Schneider, I., Roberts, D., Sanders, G.S., Reddy, E.P., Diggs, C.L. and Miller, L.H. (1984) Structure of the gene encoding the immunodominant surface antigen on the sporozoite of the human malaria parasite Plasmodium falciparum. Science 225, 593-599.
15. [15] Reddy, G.R., Chakrabarti, D., Schuster, S.M., Ferl, R.J., Almira, E.C. and Dame, J.B. (1993) Gene sequence tags from Plasmodium falciparum genomic DNA fragments prepared by the genease activity of mung bean nuclease. Proc. Natl. Acad. Sci. USA 90, 9867-9871.
16. [16] Chakrabarti, D., Reddy, G.R., Dame, J.B., Almira, E.C., Laipis, P.J., Ferl, R.J., Yang, T.P., Rowe, T.C. and Schuster, S.M. (1994) Analysis of expressed sequence tags from Plasmodium falciparum. Mol. Biochem. Parasitol. 66, 97-104.
17. [17] Triglia, T., Wellems, T.E. and Kemp, D.J. (1992) Towards a high-resolution map of the Plasmodium falciparum genome. Parasitol. Today 8, 225-229.
18. [18] Wilson, R.J.M. and Williamson, D.H. (1996) Extrachromosomal DNA in the Apicomplexa. Microbiol. Rev. (in press).
19. [19] Vaidya, A.B. and Arasu, P. (1987) Tandemly arranged gene clusters of malarial parasites that are highly conserved and transcribed. Mol. Biochem. Parasitol. 22, 249-257.
20. [20] Vaidya, A.B., Akella, R. and Suplick, K. (1989) Sequences similar to genes for two mitochondrial proteins and portions of ribosomal RNA in tandemly arrayed 6-kilobase-pair DNA of a malarial parasite. Mol. Biochem. Parasitol. 35, 97-108.
21. [21] Feagin, J.E., Gardner, M.J., Williamson, D.H. and Wilson, R.J. (1991) The putative mitochondrial genome of Plasmodium falciparum. J. Protozool. 38, 243-245.
22. [22] Suplick, K., Akella, R., Saul, A. and Vaidya, A. (1988) Molecular cloning and partial sequencing of a 5.8 kilobase pair repetitive DNA from Plasmodium falciparum. Mol. Biochem. Parasitol. 30, 289-290.
23. [23] Feagin, J.E., Werner, E., Gardner, M.J., Williamson, D.H. and Wilson, R.J. (1992) Homologies between the contiguous and fragmented rRNAs of the two Plasmodium falciparum extrachromosomal DNAs are limited to core sequences. Nucleic Acids Res. 20, 879-887.
24. [24] Feagin, J.E. (1992) The 6-kb element of Plasmodium falciparum encodes mitochondrial cytochrome genes. Mol. Biochem. Parasitol. 52, 145-148.
25. [25] Feagin, J.E. and Drew, M.E. (1995) Plasmodium falciparum: alterations in organelle transcript abundance during the erythrocytic cycle. Exp. Parasitol. 80, 430-440.
26. [26] Howe, C.J. (1992) Plastid origin of an extrachromosomal DNA molecule from Plasmodium, the causative agent of malaria. J. Theor. Biol. 158, 199-205.
27. [27] Williamson, D.H., Gardner, M.J., Preiser, P., Moore, D.H., Rangachari, K. and Wilson, R.J.M. (1994) The evolutionary origin of the 35 kb circular DNA of Plasmodium falciparum: new evidence supports a possible rhodophyte ancestry. Mol. Gen. Genet. 243, 249-252.
28. [28] Pologe, L.G. and Ravetch, J.V. (1988) Large deletions result from breakage and healing of P. falciparum chromosomes. Cell 55, 869-874.
29. [29] Pologe, L.G. and Ravetch, J.V. (1986) A chromosomal rearrangement in a P. falciparum histidine-rich protein gene is associated with the knobless phenotype. Nature 322, 474-477.
30. [30] Corcoran, L.M., Thompson, J.K., Walliker, D. and Kemp, D.J. (1988) Homologous recombination within subtelomeric repeat sequences generates chromosome size polymorphisms in P. falciparum. Cell 53, 807-813.
31. [31] Hinterberg, K., Mattei, D., Wellems, T.E. and Scherf, A. (1994) Interchromosomal exchange of a large subtelomeric segment in a Plasmodium falciparum cross. EMBO J. 13, 4174-4180.
32. [32] Lanzer, M., Bruin, D.de and Ravetch, J.V. (1993) Transcriptional differences in polymorphic and conserved domains of a complete cloned P. falciparum chromosome. Nature 361, 654-657.
33. [33] Foote, S.J., Thompson, J.K., Cowman, A.F. and Kemp, D.J. (1989) Amplification of multidrug resistance gene in some chloroquine-resistant isolates of P. falciparum. Cell 57, 921-930.
34. [34] Cowman, A.F., Galatis, D. and Thompson, J.K. (1994) Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine. Proc. Natl. Acad. Sci. USA 91, 1143-1147.
35. [35] Foote, S.J. and Kemp, D.J. (1989) Chromosomes of malaria parasites. Trends Genet. 5, 337-342.
36. [36] de-Bruin, D., Lanzer, M. and Ravetch, J.V. (1994) The polymorphic subtelomeric regions of Plasmodium falciparum chromosomes contain arrays of repetitive sequence elements. Proc. Natl. Acad. Sci. USA 91, 619-623.
37. [37] Patarapotikul, J. and Langsley, G. (1988) Chromosome size polymorphism in Plasmodium falciparum can involve deletions of the subtelomeric pPFrep20 sequence. Nucleic Acids Res. 16, 4331-4340.
38. [38] Sinnis, P. and Wellems, T.E. (1988) Long-range restriction maps of Plasmodium falciparum Chromosomes: crossingover and size variation among geographically distant isolates. Genomics 3, 287-295.
39. [39] Kemp, D.J., Cowman, A.F. and Walliker, D. (1990) Genetic diversity in Plasmodium falciparum. Adv. Parasitol. 29, 75-149.
40. [40] Walliker, D., Quakyi, I.A., Wellems, T.E., McCutchan, T.F., Szarfman, A., London, W.T., Corcoran, L.M., Burkot, T.R. and Carter, R. (1987) Genetic analysis of the human malaria parasite Plasmodium falciparum. Science 236, 1661-1666.
41. [41] Wellems, T.E., Walliker, D., Smith, C.L., do-Rosario, V.E., Maloy, W.L., Howard, R.J., Carter, R. and McCutchan, T.F. (1987) A histidine-rich protein gene marks a linkage group favored strongly in a genetic cross of Plasmodium falciparum. Cell 49, 633-642.
42. [42] Shirley, M.W., Biggs, B.A., Forsyth, K.P., Brown, H.J., Thompson, J.K., Brown, G.V. and Kemp, D.J. (1990) Chromosome 9 from independent clones and isolates of Plasmodium falciparum undergoes subtelomeric deletions with similar breakpoints in vitro. Mol. Biochem. Parasitol. 40, 137-145.
43. [43] Walker-Jonah, A., Dolan, S.A., Gwadz, R.W., Panton, L.J. and Wellems, T.E. (1992) An RFLP map of the Plasmodium falciparum genome, recombination rates and favored linkage groups in a genetic cross. Mol. Biochem. Parasitol. 51, 313-320.
44. [44] Rubio, J.P., Triglia, T., Kemp, D.J., de-Bruin, D., Ravetch, J.V. and Cowman, A.F. (1995) A YAC contig map of Plasmodium falciparum chromosome 4: characterization of a DNA amplification between two recently separated isolates. Genomics 26, 192-198.
45. [45] Wellems, T.E. (1991) Molecular genetics of drug resistance in Plasmodium falciparum malaria. Parasitol. Today 7, 110-112.
46. [46] Wellems, T.E., Walker-Jonah, A. and Panton, L.J. (1991) Genetic mapping of the chloroquine-resistance locus on Plasmodium falciparum chromosome 7. Proc. Natl. Acad. Sci. USA 88, 3382-3386.
47. [47] Chaiyaroj, S.C., Thompson, J.K., Coppel, R.L. and Brown, G.V. (1994) Gametocytogenesis occurs in Plasmodium falciparum isolates carrying a chromosome 9 deletion. Mol. Biochem. Parasitol. 63, 163-165.
48. [48] Barnes, D.A., Thompson, J., Triglia, T., Day, K. and Kemp, D.J. (1994) Mapping the genetic locus implicated in cytoadherence of Plasmodium falciparum to melanoma cells. Mol. Biochem. Parasitol. 66, 21-29.
49. [49] Janse, C.J., Carlton, J.M., Walliker, D. and Waters, A.P. (1994) Conserved location of genes on polymorphic chromosomes of four species of malaria parasites. Mol. Biochem. Parasitol. 68, 285-296.
50. [50] de Bruin, D., Lanzer, M. and Ravetch, J.V. (1992) Characterization of yeast artificial chromosomes from Plasmodium falciparum: construction of a stable, representative library and cloning of telomeric DNA fragments. Genomics 14, 332-339.
51. [51] Goman, M., Langsley, G., Hyde, J.E., Yanofsky, N.K., Zolg, J.W. and Scaife, J.G. (1982) The establishment of genomic DNA libraries for the human malaria parasite Plasmodium falciparum and identification of individual clones by hybridisation. Mol. Biochem. Parasitol. 5, 391-400.
52. [52] Foster, J. and Thompson, J. (1995) The Plasmodium falciparum genome project: a resource for researchers. Parasitol. Today 11, 1-4.
53. [53] Adams, M.D., Kelley. J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R. and Venter, J.C. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-1656.
54. [54] Saul, A. and Battistutta, D. (1988) Codon usage in Plasmodium falciparum. Mol. Biochem. Parasitol. 27, 35-42.
55. [55] Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
56. [56] Adams, M.D., Dubnick, M., Kerlavage, A.R., Moreno, R., Kelley, J.M., Utterback, T.R., Nagle, J.W., Fields, C. and Venter, C.J. (1992) Sequence identification of 2375 human brain genes. Nature 335, 632-634.
57. [57] Waterston, R., Martin, C., Craxton, M., Huynh, C., Coulson, A., Hillier, L., Durbin, R., Green, P., Shownkeen, R., Halloran, N., Metzstein, M., Hawkins, T., Wilson, R., Berks, M., Du, Z., Thomas, K., Thierry-Mieg, J. and Sulston, J. (1992) A survey of expressed genes in Caenorhabditis elegans. Nature Genet. 1, 114-123.
58. [58] McCombie, W.R., Adams, M.D., Kelley, J.M., FitzGerald, M.G., Utterback, T.R., Khan, M., Dubnick, M., Kerlavage, A.R., Venter, J.C. and Fields, C. (1992) Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genet. 1, 124-131.
59. [59] El-Sayed, N.M.A., Alarcon, C.M., Beck, J.C., Sheffield, V.C. and Donelson, J.E. (1995) cDNA expressed sequence tags of Trypanosoma brucei rhodesiense provide new insights into the biology of the parasite. Mol. Biochem. Parasitol. 73, 75-90.
60. [60] Reddy, G.R. (1995) Determining the Sequence of Parasite DNA. Parasitol. Today 11, 37-42.
61. [61] Clarke, L. and Carbon, J. (1976) A colony bank containing synthetic Co1 E1 hybrid plasmids representative of the entire E. coli genome. Cell 9, 91-99.
62. [62] Triglia, T., Foote, S.J., Kemp, D.J. and Cowman, A.F. (1991) Amplification of the multidrug resistance gene pfmdr1 in Plasmodium falciparum has arisen as multiple independent events. Mol. Cell Biol. 11, 5244-5250.
63. [63] Chakrabarti, D., Schuster, S.M. and Chakrabarti, R. (1993) Cloning and characterization of subunit genes of ribonucleotide reductase, a cell-cycle-regulated enzyme, from Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 90, 12020-12024.
64. [64] Dame, J.B., Reddy, G.R., Yowell, C.A., Dunn, B.M., Kay, J. and Berry, C. (1994) Sequence, expression and modeled structure of an aspartic proteinase from the human malaria parasite Plasmodium falciparum. Mol. Biochem. Parasitol. 64, 177-190.
65. [65] Hill, J., Tyas, L., Phylip, L.H., Kay, J., Dunn, B.M. and Berry, C. (1994) High level expression and characterisation of plasmepsin II, an aspartic proteinase from Plasmodium falciparum. FEBS Lett. 352, 155-158.
66. [66] Dontfraid, F.F. and Chakrabarti, D. (1994) Cloning and expression of a cDNA encoding the homolog of ran/TC4 GTP binding protein from Plasmodium falciparum. Biochem. Biophys. Res. Commun. 201, 423-429.
67. [67] Reddy, G.R. (1995) Cloning and characterization of a Plasmodium falciparum cyclophilin gene that is stage-specifically expressed. Mol. Biochem. Parasitol. 73, 111-121.
68. [68] Wu, Y., Sifri, C.D., Lei, H.H., Su, X.Z. and Wellems, T.E. (1995) Transfection of Plasmodium falciparum within human red blood cells. Proc. Natl. Acad. Sci. USA 92, 973-977.
69. [69] Wu, Y., Kirkman, L.A. and Wellems, T.E. (1995) Transformation of Plasmodium falciparum malaria parasites by homologous integration of plasmids that confer resistance to pyrimethamine. Proc. Natl. Acad. Sci. USA 93, 1130-1134.
70. [70] Su, X.Z. and Wellems, T.E. (1996) Toward a high resolution Plasmodium falciparum linkage map: polymorphic markers from hundreds of simple sequence repeats. Genomics 33: 430-444.
71. [71] Wellems, T.E., Panton, L.J., Gluzman, I.Y., do-Rosario, V.E., Gwadz, R.W., Walker-Jonah, A. and Krogstad, D.J. (1990) Chloroquine resistance not linked to mdr-like genes in a Plasmodium falciparum cross [see comments]. Nature 345, 253-255.
72. [72] Gavaghan, H. (1994) Tunisian institute to tackle secrets of malaria genome. Nature 371, 732.
73. [73] Pollack, Y., Katzen, A.L., Spira, D.T. and Golenser, J. (1982) The genome of Plasmodium falciparum I. DNA base composition. Nucleic Acids Res. 10, 539-546.
74. [74] Su, X.Z., Heatwole, V.M., Wertheimer, S.P., Guinet, F., Herrfeldt, J.A., Peterson, D.S., Ravetch, J.A. and Wellems, T.E. (1995) The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes [see comments]. Cell 82, 89-100.