A SICAvar switching event in Plasmodium knowlesi is associated with the DNA rearrangement of conserved 3' non-coding sequences.

Plasmodium knowlesi variant antigens are expressed at the surface of infected erythrocytes and are encoded by the Schizont Infected Cell Agglutination variant antigen (SICAvar) multigene family. The 3' region of the SICAvar gene locus encoding the 205 kDa variant antigen expressed in the Pk1(B+)1+ parasites was found to be altered compared to the Pk1(A+) parental clone. Here we report that this alteration is the result of a DNA rearrangement and that the original and altered 205 SICAvar alleles appear to encode bona fide variant antigens. Importantly, 205A and 205B SICAvar RNA sequences are detectable in similar apparent quantities as determined by quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) amplification experiments. However, expression of the 205 kDa SICA protein at the surface of the infected erythrocyte is not characteristic of the Pk1(A+) parasites and the 205 SICAvar transcript has not been detected in Pk1(A+) parasites by northern blot analysis. Furthermore, we report that many distinct SICAvar transcripts were detected in P. knowlesi Pk1(B+)1+ cDNA library hybridization screens. Of special interest, in light of these data, distinctive differences at the 3' end of the 205A and 205B alleles are observed, which may be of functional importance. An analysis of the 3' untranslated region (UTR) of SICAvar genes in more than 100 sequences revealed a surprising common sequence pattern characterized by blocks of imperfect, GT-rich, heptad repeated motifs (Block I), followed by A and T rich homopolymers (Block II) and in a large number of genes, GC-rich segments (Block III). We show that this region undergoes extensive recombination and that the preferential stability of the 205 SICAvar transcript in Pk1(B+)1+ parasites may be associated with the presence of its specific Block III sequences. We speculate that the conserved yet polymorphic SICAvar 3'UTR sequences, and comparable regions in P. falciparum var genes, function in the stage-specific and developmentally regulated post-transcriptional gene silencing (PTGS) of variant antigen transcripts.