VarDB: A database of antigenic variant sequences-Current status and future prospects

Acta Tropica

Volumn 114, Issue 3, 2010, Pages 144-151

  Diez, Diego ^a   Hayes, Nelson ^a   Joannin, Nicolas ^b,c   Normark, Johan ^b,c   Kanehisa, Minoru ^a   Wahlgren, Mats ^b,c   Wheelock, Craig E ^a,b   Goto, Susumu ^a  

^a KYOTO UNIVERSITY   (Japan)

^b KAROLINSKA INSTITUTE   (Sweden)

^c SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

Author keywords

Antigenic variation; Database; Hyper variable sequence; Malaria; Plasmodium; VarDB

Indexed keywords

ANTIGEN; COMPARATIVE STUDY; DATABASE; FUTURE PROSPECT; MALARIA; PARASITE; PROTOZOAN;

AMINO ACID SEQUENCE; ANTIGENIC VARIATION; GENE SEQUENCE; HUMAN; IMMUNE SYSTEM; INFORMATION PROCESSING; INTERNET; MALARIA FALCIPARUM; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; REVIEW; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY;

ANIMALS; ANTIGENIC VARIATION; ANTIGENS, PROTOZOAN; COMMUNICABLE DISEASES; DATABASES, GENETIC; HUMANS; MULTIGENE FAMILY; PLASMODIUM FALCIPARUM; PROTOZOAN PROTEINS;

PLASMODIUM FALCIPARUM;

EID: 77950063753     PISSN: 0001706X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.actatropica.2009.06.006     Document Type: Review

References (36)

1. Allred D.R., Barbet A.F., Barry J.D., Deitsch K.W. varDB: common ground for a shifting landscape. Trends Parasitol. 2009, 25:249-252.
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Andersen P., Nielsen M.A., Resende M., Rask T.S., Dahlback M., Theander T., Lund O., Salanti A. Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA. PLoS Pathog. 2008, 4:e42.
4. Baratin M., Roetynck S., Pouvelle B., Lemmers C., Viebig N.K., Johansson S., Bierling P., Scherf A., Gysin J., Vivier E., Ugolini S. Dissection of the role of PfEMP1 and ICAM-1 in the sensing of Plasmodium falciparum-infected erythrocytes by natural killer cells. PLoS One 2007, 2:e228.
5. Barry J.D., Ginger M.L., Burton P., McCulloch R. Why are parasite contingency genes often associated with telomeres?. Int. J. Parasitol. 2003, 33:29-45.
6. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2009, 37:D26-D31.
7. Bertonati C., Tramontano A. A model of the complex between the PfEMP1 malaria protein and the human ICAM-1 receptor. Proteins 2007, 69:215-222.
8. Birney E., Clamp M., Durbin R. GeneWise and genomewise. Genome Res. 2004, 14:988-995.
9. Bockhorst J., Lu F., Janes J.H., Keebler J., Gamain B., Awadalla P., Su X.Z., Samudrala R., Jojic N., Smith J.D. Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Mol. Biochem. Parasitol. 2007, 155:103-112.
10. Bull P.C., Buckee C.O., Kyes S., Kortok M.M., Thathy V., Guyah B., Stoute J.A., Newbold C.I., Marsh K. Plasmodium falciparum antigenic variation. Mapping mosaic var gene sequences onto a network of shared, highly polymorphic sequence blocks. Mol. Microbiol. 2008, 68:1519-1534.
11. Cannon J.P., Haire R.N., Rast J.P., Litman G.W. The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms. Immunol. Rev. 2004, 200:12-22.
12. Carlton J.M., Adams J.H., Silva J.C., Bidwell S.L., Lorenzi H., Caler E., Crabtree J., Angiuoli S.V., Merino E.F., Amedeo P., Cheng Q., Coulson R.M., Crabb B.S., Del Portillo H.A., Essien K., Feldblyum T.V., Fernandez-Becerra C., Gilson P.R., Gueye A.H., Guo X., Kang'a S., Kooij T.W., Korsinczky M., Meyer E.V., Nene V., Paulsen I., White O., Ralph S.A., Ren Q., Sargeant T.J., Salzberg S.L., Stoeckert C.J., Sullivan S.A., Yamamoto M.M., Hoffman S.L., Wortman J.R., Gardner M.J., Galinski M.R., Barnwell J.W., Fraser-Liggett C.M. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 2008, 455:757-763.
13. Carlton J.M., Angiuoli S.V., Suh B.B., Kooij T.W., Pertea M., Silva J.C., Ermolaeva M.D., Allen J.E., Selengut J.D., Koo H.L., Peterson J.D., Pop M., Kosack D.S., Shumway M.F., Bidwell S.L., Shallom S.J., van Aken S.E., Riedmuller S.B., Feldblyum T.V., Cho J.K., Quackenbush J., Sedegah M., Shoaibi A., Cummings L.M., Florens L., Yates J.R., Raine J.D., Sinden R.E., Harris M.A., Cunningham D.A., Preiser P.R., Bergman L.W., Vaidya A.B., van Lin L.H., Janse C.J., Waters A.P., Smith H.O., White O.R., Salzberg S.L., Venter J.C., Fraser C.M., Hoffman S.L., Gardner M.J., Carucci D.J. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 2002, 419:512-519.
14. Clamp M., Cuff J., Searle S.M., Barton G.J. The Jalview Java alignment editor. Bioinformatics 2004, 20:426-427.
15. Cunningham D.A., Jarra W., Koernig S., Fonager J., Fernandez-Reyes D., Blythe J.E., Waller C., Preiser P.R., Langhorne J. Host immunity modulates transcriptional changes in a multigene family (yir) of rodent malaria. Mol. Microbiol. 2005, 58:636-647.
16. Dzikowski R., Deitsch K.W. Active transcription is required for maintenance of epigenetic memory in the malaria parasite Plasmodium falciparum. J. Mol. Biol. 2008, 382:288-297.
17. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
18. Fischer K., Chavchich M., Huestis R., Wilson D.W., Kemp D.J., Saul A. Ten families of variant genes encoded in subtelomeric regions of multiple chromosomes of Plasmodium chabaudi, a malaria species that undergoes antigenic variation in the laboratory mouse. Mol. Microbiol. 2003, 48:1209-1223.
19. Fonager J., Cunningham D., Jarra W., Koernig S., Henneman A.A., Langhorne J., Preiser P. Transcription and alternative splicing in the yir multigene family of the malaria parasite Plasmodium y. yoelii: identification of motifs suggesting epigenetic and post-transcriptional control of RNA expression. Mol. Biochem. Parasitol. 2007, 156:1-11.
20. Frank M., Kirkman L., Costantini D., Sanyal S., Lavazec C., Templeton T.J., Deitsch K.W. Frequent recombination events generate diversity within the multi-copy variant antigen gene families of Plasmodium falciparum. Int. J. Parasitol. 2008, 38:1099-1109.
21. Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W., Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T., James K., Eisen J.A., Rutherford K., Salzberg S.L., Craig A., Kyes S., Chan M.S., Nene V., Shallom S.J., Suh B., Peterson J., Angiuoli S., Pertea M., Allen J., Selengut J., Haft D., Mather M.W., Vaidya A.B., Martin D.M., Fairlamb A.H., Fraunholz M.J., Roos D.S., Ralph S.A., McFadden G.I., Cummings L.M., Subramanian G.M., Mungall C., Venter J.C., Carucci D.J., Hoffman S.L., Newbold C., Davis R.W., Fraser C.M., Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511.
22. Hayes C.N., Diez D., Joannin N., Honda W., Kanehisa M., Wahlgren M., Wheelock C.E., Goto S. varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 2008, 24:2564-2565.
23. Janssen C.S., Phillips R.S., Turner C.M., Barrett M.P. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucleic Acids Res. 2004, 32:5712-5720.
24. Joannin N., Abhiman S., Sonnhammer E.L., Wahlgren M. Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family. BMC Genom. 2008, 9:19.
25. Katoh K., Kuma K., Toh H., Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33:511-518.
26. Klein M.M., Gittis A.G., Su H.P., Makobongo M.O., Moore J.M., Singh S., Miller L.H., Garboczi D.N. The cysteine-rich interdomain region from the highly variable Plasmodium falciparum erythrocyte membrane protein-1 exhibits a conserved structure. PLoS Pathog. 2008, 4:e1000147.
27. Korir C.C., Galinski M.R. Proteomic studies of Plasmodium knowlesi SICA variant antigens demonstrate their relationship with P. falciparum EMP1. Infect. Genet. Evol. 2006, 6:75-79.
28. Normark J., Nilsson D., Ribacke U., Winter G., Moll K., Wheelock C.E., Bayarugaba J., Kironde F., Egwang T.G., Chen Q., Andersson B., Wahlgren M. PfEMP1-DBL1alpha amino acid motifs in severe disease states of Plasmodium falciparum malaria. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:15835-15840.
29. Oliveira T.R., Fernandez-Becerra C., Jimenez M.C., Del Portillo H.A., Soares I.S. Evaluation of the acquired immune responses to Plasmodium vivax VIR variant antigens in individuals living in malaria-endemic areas of Brazil. Malar. J. 2006, 5:83.
30. Pain A., Bohme U., Berry A.E., Mungall K., Finn R.D., Jackson A.P., Mourier T., Mistry J., Pasini E.M., Aslett M.A., Balasubrammaniam S., Borgwardt K., Brooks K., Carret C., Carver T.J., Cherevach I., Chillingworth T., Clark T.G., Galinski M.R., Hall N., Harper D., Harris D., Hauser H., Ivens A., Janssen C.S., Keane T., Larke N., Lapp S., Marti M., Moule S., Meyer I.M., Ormond D., Peters N., Sanders M., Sanders S., Sargeant T.J., Simmonds M., Smith F., Squares R., Thurston S., Tivey A.R., Walker D., White B., Zuiderwijk E., Churcher C., Quail M.A., Cowman A.F., Turner C.M., Rajandream M.A., Kocken C.H., Thomas A.W., Newbold C.I., Barrell B.G., Berriman M. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature 2008, 455:799-803.
31. Pettersson F., Vogt A.M., Jonsson C., Mok B.W., Shamaei-Tousi A., Bergstrom S., Chen Q., Wahlgren M. Whole-body imaging of sequestration of Plasmodium falciparum in the rat. Infect. Immun. 2005, 73:7736-7746.
32. Ralph S.A., Bischoff E., Mattei D., Sismeiro O., Dillies M.A., Guigon G., Coppee J.Y., David P.H., Scherf A. Transcriptome analysis of antigenic variation in Plasmodium falciparum-var silencing is not dependent on antisense RNA. Genome Biol. 2005, 6:R93.
33. Rasti N., Wahlgren M., Chen Q. Molecular aspects of malaria pathogenesis. FEMS Immunol. Med. Microbiol. 2004, 41:9-26.
34. Springer A.L., Smith L.M., Mackay D.Q., Nelson S.O., Smith J.D. Functional interdependence of the DBLbeta domain and c2 region for binding of the Plasmodium falciparum variant antigen to ICAM-1. Mol. Biochem. Parasitol. 2004, 137:55-64.
35. Tham W.H., Payne P.D., Brown G.V., Rogerson S.J. Identification of basic transcriptional elements required for rif gene transcription. Int. J. Parasitol. 2007, 37:605-615.
36. Vigan-Womas I., Guillotte M., Le Scanf C., Igonet S., Petres S., Juillerat A., Badaut C., Nato F., Schneider A., Lavergne A., Contamin H., Tall A., Baril L., Bentley G.A., Mercereau-Puijalon O. An in vivo and in vitro model of Plasmodium falciparum rosetting and autoagglutination mediated by varO, a group A var gene encoding a frequent serotype. Infect. Immun. 2008, 76:5565-5580.