Phylogeny and evolution of the SERA multigene family in the genus Plasmodium

Journal of Molecular Evolution

Volumn 65, Issue 1, 2007, Pages 82-91

  Arisue, Nobuko ^a   Hirai, Makoto ^b   Arai, Meiji ^b,c   Matsuoka, Hiroyuki ^b   Horii, Toshihiro ^a  

^a OSAKA UNIVERSITY   (Japan)

^b JICHI MEDICAL UNIVERSITY   (Japan)

^c UNIVERSITY OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH   (Japan)

Author keywords

Multigene family; Plasmodium; Serine repeat antigen; Synteny

Indexed keywords

PROTOZOAL PROTEIN; SERINE REPEAT ANTIGEN; SERINE REPEAT ANTIGEN 1; SERINE REPEAT ANTIGEN 5; SERINE REPEAT ANTIGEN 6; SERINE REPEAT ANTIGEN 7; SERINE REPEAT ANTIGEN 8; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; DATA BASE; FEMALE; GENE CLUSTER; GENE DUPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMODIUM; PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM FALCIPARUM; PLASMODIUM GALLINACEUM; PLASMODIUM KNOWLESI; PLASMODIUM REICHENOWI; PLASMODIUM VIVAX; PLASMODIUM YOELII; POLYMERASE CHAIN REACTION; PROTOZOAL GENETICS; PSEUDOGENE;

ANIMALS; ANTIGENS, PROTOZOAN; EVOLUTION, MOLECULAR; FEMALE; MICE; MICE, INBRED BALB C; MULTIGENE FAMILY; PHYLOGENY; PLASMODIUM;

PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM FALCIPARUM; PLASMODIUM GALLINACEUM; PLASMODIUM KNOWLESI; PLASMODIUM REICHENOWI; PLASMODIUM VIVAX; PLASMODIUM YOELII;

EID: 34547667334     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-006-0253-1     Document Type: Article

References (42)

1. Aly AS, Matuschewski K (2005) A malarial cysteine protease is necessary for Plasmodium sporozoite egress from oocysts. J Exp Med 202:225-230
2. Aoki S, Li J, Itagaki S, Okech BA, Egwang TG, Matsuoka H, Palacpac NM, Mitamura T, Horii T (2002) Serine repeat antigen (SERA5) is predominantly expressed among the SERA multigene family of Plasmodium falciparum, and the acquired antibody titers correlate with serum inhibition of the parasite growth. J Biol Chem 277:47533-47540
3. Baca AM, Hol WG (2000) Overcoming codon bias: a method for high-level overexpression of Plasmodium and other AT-rich parasite genes in Escherichia coli. Int J Parasitol 30:113-118
4. Bourgon R, Delorenzi M, Sargeant T, Hodder AN, Crabb BS, Speed TP (2004) The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees. Mol Biol Evol 21:2161-2171
5. Bzik DJ, Li WB, Horii T, Inselburg J (1988) Amino acid sequence of the serine-repeat antigen (SERA) of Plasmodium falciparum determined from cloned cDNA. Mol Biochem Parasitol 30:279-288
6. Carlton JM, Angiuoli SV, Suh BB, et al. (2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419:512-519
7. Delplace P, Fortier B, Tronchin G, Dubremetz JF, Vernes A (1987) Localization, biosynthesis, processing and isolation of a major 126 kDa antigen of the parasitophorous vacuole of Plasmodium falciparum. Mol Biochem Parasitol 23:193-201
8. Escalante AA, Ayala FJ (1995) Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. Proc Natl Acad Sci USA 92:5793-5797
9. Felsenstein J (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266:418-427
10. Felsenstein J, Churchill GA (1996) A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol 13:93-104
11. Florens L, Washburn MP, Raine JD, et al. (2002) A proteomic view of the Plasmodium falciparum life cycle. Nature 419:520-526
12. Fox BA, Bzik DJ (1994) Analysis of stage-specific transcripts of the Plasmodium falciparum serine repeat antigen (SERA) gene and transcription from the SERA locus. Mol Biochem Parasitol 68:133-144
13. Fox BA, Pang XL, Suzue K, Horii T, Bzik DJ (1997) Plasmodium falciparum: an epitope within a highly conserved region of the 47-kDa amino-terminal domain of the serine repeat antigen is a target of parasite-inhibitory antibodies. Exp Parasitol 85:121-134
14. Gardner MJ, Tettelin H, Carucci DJ, et al. (1998) Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282:1126-1132
15. Gardner MJ, Hall N, Fung E, et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498-511
16. Gor DO, Li AC, Rosenthal PJ (1998) Protective immune responses against protease-like antigens of the murine malaria parasite Plasmodium vinckei. Vaccine 16:1193-1202
17. Hall N, Karras M, Raine JD, et al. (2005) A comprehensive survey of the Plasmodium life cycle by genomic, transcriptonic, and proteomic analyses. Science 307:82-86
18. Hashimoto T, Nakamura Y, Nakamura F, Shirakura T, Adachi J, Goto N, Okamoto K, Hasegawa M (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol Biol Evol 11:65-71
19. Hirai M, Wang J, Yoshida S, Ishii A, Matsuoka H (2001) Characterization and identification of exflagellation-inducing factor in the salivary gland of Anopheles stephensi (Diptera: Culicidae). Biochem Biophys Res Commun 287:859-864
20. Hodder AN, Drew DR, Epa VC, Delorenzi M, Bourgon R, Miller SK, Moritz RL, Frecklington DF, Simpson RJ, Speed TP, Pike RN, Crabb BS (2003) Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5. J Biol Chem 278:48169-48177
21. Huff CG (1969) Exoerythrocytic stages of avian and reptilian malarial parasites. Exp Parasitol 24:383-421
22. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
23. Kiefer MC, Crawford KA, Boley LJ, Landsberg KE, Gibson HL, Kaslow DC, Barr PJ (1996) Identification and cloning of a locus of serine repeat antigen (sera)-related genes from Plasmodium vivax. Mol Biochem Parasitol 78:55-65
24. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179
25. Kooij TW, Carlton JM, Bidwell SL, Hall N, Ramesar J, Janse CJ, Waters AP (2005) A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes. PLoS Pathog 1:e44
26. Lake JA. (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc Natl Acad Sci USA 91:1455-1459
27. Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De La Vega P, Holder AA, Batalov S, Carucci DJ, Winzeler EA (2003) Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301:1503-1508
28. Li J, Matsuoka H, Mitamura T, Horii T (2002) Characterization of proteases involved in the processing of Plasmodium falciparum serine repeat antigen (SERA). Mol Biochem Parasitol 120:177-186
29. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence. Mol Biol Evol 11:605-612
30. Miller SK, Good RT, Drew DR, Delorenzi M, Sanders PR, Hodder AN, Speed TP, Cowman AF, de Koning-Ward TF, Crabb BS (2002) A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycle. J Biol Chem 277:47524-47532
31. Okech BA, Nalunkuma A, Okello D, Pang XL, Suzue K, Li J, Horii T, Egwang TG (2001) Natural human immunoglobulin G subclass responses to Plasmodium falciparum serine repeat antigen in Uganda. Am J Trop Med Hyg 65:912-917
32. Okech B, Mujuzi G, Ogawal A, Shirai H, Horii T, Egwang TG (2006) High titers of IgG antibodies against Plasmodium falciparum serine repeat antigen 5 (SERA5) are associated with protection against severe malaria in Ugandan children. Am J Trop Med Hyg 74:191-197
33. Palacpac NM, Leung BW, Arisue N, Tanabe K, Sattabongkot J, Tsuboi T, Torii M, Udomsangpetch R, Horii T (2006) Plasmodium vivax serine repeat antigen (SERA) multigene family exhibits similar expression patterns in independent infections. Mol Biochem Parasitol 150:353-358
34. Pang XL, Mitamura T, Horii T (1999) Antibodies reactive with the N-terminal domain of Plasmodium falciparum serine repeat antigen inhibit cell proliferation by agglutinating merozoites and schizonts. Infect Immun 67:1821-1827
35. Perkins SL, Schall JJ (2002) A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J Parasitol 88:972-978
36. Peterson DS (2001) Plasmodium gallinaceum: cloning and characterization of dihydrofolate reductase/thymidylate synthase. Exp Parasitol 99:111-114
37. Qari SH, Shi YP, Pieniazek NJ, Collins WE, Lal AA (1996) Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: monophyletic nature of the human malaria parasite, Plasmodium falciparum. Mol Phylogenet Evol 6:157-165
38. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504
39. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247
40. Shimodaira H (2002) An approximately unbiased test of phylogenic tree selection. Syst Biol 51:492-508
41. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
42. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556