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Background  The  SICAvar  gene family, expressed at the surface of infected erythrocytes, is critical for antigenic variation in  Plasmodium knowlesi . When this family was discovered, a prototypic  SICAvar  gene was characterized and defined by a 10-exon structure. The predicted 205-kDa protein lacked a convincing signal peptide, but included a series of variable cysteine-rich modules, a transmembrane domain encoded by the penultimate exon, and a cytoplasmic domain encoded by the final highly conserved exon. The  205 SICAvar  gene and its family with up to 108 possible family members, was identified prior to the sequencing of the  P. knowlesi  genome. However, in the published  P. knowlesi  database this gene remains disjointed in five fragments. This study addresses a number of structural and functional questions that are critical for understanding  SICAvar  gene expression.    Methods  Database mining, bioinformatics, and traditional genomic and post-genomic experimental methods including proteomic technologies are used here to confirm the genomic context and expressed structure of the prototype  205 SICAvar  gene.  Results  This study reveals that the  205 SICAvar  gene reported previously to have a 10-exon expressed gene structure has, in fact, 12 exons, with an unusually large and repeat-laden intron separating two newly defined upstream exons and the  bona fide  5'UTR from the remainder of the gene sequence. The initial exon encodes a PEXEL motif, which may function to localize the SICA protein in the infected erythrocyte membrane. This newly defined start of the 205  SICAvar  sequence is positioned on chromosome 5, over 340 kb upstream from the rest of the telomerically positioned  SICAvar  gene sequence in the published genome assembly. This study, however, verifies the continuity of these sequences, a 9.5 kb transcript, and provides evidence that the 205  SICAvar  gene is located centrally on chromosome 5.    Conclusion  The prototype  205 SICAvar  gene has been redefined to have a 12-exon structure. These data are important because they 1) address questions raised in the  P. knowlesi  genome database regarding  SICAvar  gene fragments, numbers and structures, 2) show that this prototype gene encodes a PEXEL motif, 3) emphasize the need for further refinement of the  P. knowlesi  genome data, and 4) retrospectively, provide evidence for recombination within centrally located  SICAvar  sequences.

Redefining the expressed prototype SICAvar gene involved in Plasmodium knowlesi antigenic variation