In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum

Abstract

The Plasmodium falciparum genome being AT-rich, the presence of GC-rich regions suggests functional significance. Evolution imposes selection pressure to retain functionally important coding and regulatory elements. Hence searching for evolutionarily conserved GC-rich, intergenic regions in an AT-rich genome will help in discovering new coding regions and regulatory elements. We have used elevated GC content in intergenic regions coupled with sequence conservation against P. reichenowi, which is evolutionarily closely related to P. falciparum to identify potential sequences of functional importance. Interestingly, ~30% of the GC-rich, conserved sequences were associated with antigenic proteins encoded by var and rifin genes. The majority of sequences identified in the 5' UTR of var genes are represented by short expressed sequence tags (ESTs) in cDNA libraries signifying that they are transcribed in the parasite. Additionally, 19 sequences were located in the 3' UTR of rifins and 4 also have overlapping ESTs. Further analysis showed that several sequences associated with var genes have the capacity to encode small peptides. A previous report has shown that upstream peptides can regulate the expression of var genes hence we propose that these conserved GC-rich sequences may play roles in regulation of gene expression.

Keywords: Plasmodium; antigenic variation; comparative genomics; genome bias; regulatory elements.

Figure 1

Sequence alignment of proximal upstream regions of upsB var genes. Notes: The box shows that conserved GC-rich sequences contain the putative upstream ORF MYATI. Grey highlights show-conserved sequences, indicating that sequences flanking the putative uORF are less conserved than the regions encoding the uORF. The annotated start codon is highlighted in grey.

Figure 2

BLAST result of PfNC12.4var against the Plasmodium reichenowi genome. Note: The regions of conservation are shown with stars and the uORF is highlighted in grey.