Multi-character population study of the vir subtelomeric multigene superfamily of Plasmodium vivax, a major human malaria parasite

Molecular and Biochemical Parasitology

Volumn 149, Issue 1, 2006, Pages 10-16

  Merino, Emilio F ^a   Fernandez Becerra, Carmen ^a   Durham, Alan M ^a   Ferreira, João E ^a   Tumilasci, Vanessa F ^a   d'Arc Neves, Joana ^b   da Silva Nunes, Monica ^a   Ferreira, Marcelo U ^a   Wickramarachchi, Thilan ^c   Udagama Randeniya, Preethi ^c   Handunnetti, Shiroma M ^c   del Portillo, Hernando A ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b Instituto de Pesquisa em Patologias Tropicais   (Brazil)

^c UNIVERSITY OF COLOMBO   (Sri Lanka)

Author keywords

Malaria; Multi character in silico analysis; Plasmodium vivax; Variant genes; vir subtelomeric multigene family

Indexed keywords

GENE PRODUCT; PROTEIN VIR; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; BRAZIL; CELL MEMBRANE; CELL TRANSPORT; CELLULAR DISTRIBUTION; CLADISTICS; CLINICAL ARTICLE; CONTROLLED STUDY; ENDEMIC DISEASE; ERYTHROCYTE; GENE FUNCTION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; HUMAN; MALARIA; MICROBIAL POPULATION DYNAMICS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; SIGNAL TRANSDUCTION; SRI LANKA; TELOMERE; UNINDEXED SEQUENCE;

AMINO ACID MOTIFS; ANIMALS; BRAZIL; GENES, PROTOZOAN; GENOME, PROTOZOAN; HUMANS; MALARIA, VIVAX; MULTIGENE FAMILY; PLASMODIUM VIVAX; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SRI LANKA; TELOMERE;

PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; VIR;

EID: 33745841923     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbiopara.2006.04.002     Document Type: Article

References (35)

1. Mendis K., Sina B.J., Marchesini P., and Carter R. The neglected burden of Plasmodium vivax malaria. Am J Trop Med Hyg 64 (2001) 97-106
2. Scherf A., Figueiredo L.M., and Freitas-Junior L.H. Chromosome structure and dynamics of Plasmodium subtelomeres. In: Waters A.P., and Janse C.J. (Eds). Malaria parasites: genomes and molecular biology vol. 1 (2004), Caister Academic Press 187-204
3. Su X.Z., Heatwole V.M., Wertheimer S.P., Guinet F., Herrfeldt J.A., Peterson D.S., et al. The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82 (1995) 89-100
4. Weber J.L. Interspersed repetitive DNA from Plasmodium falciparum. Mol Biochem Parasitol 29 (1988) 117-124
5. Cheng Q., Cloonan N., Fischer K., Thompson J., Waine G., Lanzer M., et al. stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens. Mol Biochem Parasitol 97 (1998) 161-176
6. Holt D.C., Gardiner D.L., Thomas E.A., Mayo M., Bourke P.F., Sutherland C.J., et al. The cytoadherence linked asexual gene family of Plasmodium falciparum: are there roles other than cytoadherence?. Int J Parasitol 29 (1999) 939-944
7. Carey B., Bonnefoy S., Guillotte M., Le Scanf C., Grellier P., Schrevel J., et al. A large multigene family expressed during the erythrocytic schizogony of Plasmodium falciparum. Mol Biochem Parasitol 68 (1994) 221-233
8. Sam-Yellowe T.Y., Florens L., Johnson J.R., Wang T., Drazba J.A., Le Roch K.G., et al. A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling. Genome Res 14 (2004) 1052-1059
9. Winter G., Kawai S., Haeggstrom M., Kaneko O., von Euler A., Kawazu S., et al. SURFIN is a polymorphic antigen expressed on Plasmodium falciparum merozoites and infected erythrocytes. J Exp Med 201 (2005) 1853-1863
10. del Portillo H.A., Fernandez-Becerra C., Bowman S., Oliver K., Preuss M., Sanchez C.P., et al. A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax. Nature 410 (2001) 839-842
11. Janssen C.S., Barrett M.P., Turner C.M., and Phillips R.S. A large gene family for putative variant antigens shared by human and rodent malaria parasites. Proc R Soc Lond B Biol Sci 269 (2002) 431-436
12. Hall N., Karras M., Raine J.D., Carlton J.M., Kooij T.W., Berriman M., et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307 (2005) 82-86
13. Janssen C.S., Phillips R.S., Turner C.M., and Barrett M.P. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucleic Acids Res 32 (2004) 5712-5720
14. Kirchgatter K., Mosbach R., and del Portillo H.A. Plasmodium falciparum: DBL-1 var sequence analysis in field isolates from central Brazil. Exp Parasitol 95 (2000) 154-157
15. Fowler E.V., Peters J.M., Gatton M.L., Chen N., and Cheng Q. Genetic diversity of the DBLalpha region in Plasmodium falciparum var genes among Asia-Pacific isolates. Mol Biochem Parasitol 120 (2002) 117-126
16. Fernandez-Becerra C., Pein O., de Oliveira T.R., Yamamoto M.M., Cassola A.C., Rocha C., et al. Variant proteins of Plasmodium vivax are not clonally expressed in natural infections. Mol Microbiol 58 (2005) 648-658
17. Durham A.M., Kashiwabara A.Y., Matsunaga F.T., Ahagon P.H., Rainone F., Varuzza L., et al. EGene: a configurable pipeline generation system for automated sequence analysis. Bioinformatics 21 (2005) 2812-2813
18. Ewing B., Hillier L., Wendl M.C., and Green P. Base-calling of automated sequencer traces using phred I. Accuracy assessment. Genome Res 8 (1998) 175-185
19. Rice P., Longden I., and Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 16 (2000) 276-277
20. Morgenstern B., Freeh K., Dress A., and Werner T. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14 (1998) 290-294
21. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
22. Cuff J.A., and Barton G.J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40 (2000) 502-511
23. King R.D., Saqi M., Sayle R., and Sternberg M.J. DSC: public domain protein secondary structure predication. Comput Appl Biosci 13 (1997) 473-474
24. 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
25. Bailey T.L., and Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14 (1998) 48-54
26. Eddy S.R. Profile hidden Markov models. Bioinformatics 14 (1998) 755-763
27. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17 (2000) 540-552
28. Marti M., Good R.T., Rug M., Knuepfer E., and Cowman A.F. Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306 (2004) 1930-1933
29. Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 (2002) 498-511
30. Carlton J.M., Angiuoli S.V., Suh B.B., Kooij T.W., Pertea M., Silva J.C., et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419 (2002) 512-519
31. Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H., Bartholomeu D.C., et al. The genome of the African trypanosome Trypanosoma brucei. Science 309 (2005) 416-422
32. El-Sayed N.M., Myler P.J., Blandin G., Berriman M., Crabtree J., Aggarwal G., et al. Comparative genomics of trypanosomatid parasitic protozoa. Science 309 (2005) 404-409
33. El-Sayed N.M., Myler P.J., Bartholomeu D.C., Nilsson D., Aggarwal G., Tran A.N., et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309 (2005) 409-415
34. del Portillo H.A., Lanzer M., Rodriguez-Malaga S., Zavala F., and Fernandez-Becerra C. Variant genes and the spleen in Plasmodium vivax malaria. Int J Parasitol 34 (2004) 1547-1554
35. Suwanarusk R., Cooke B.M., Dondorp A.M., Silamut K., Sattabongkot J., White N.J., et al. The deformability of red blood cells parasitized by Plasmodium falciparum and P. vivax. J Infect Dis 189 (2004) 190-194