In Search of Transcription Factors: An Exciting Case for Malaria

Source: De Silva et al. (2008). Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc Natl Acad Sci, in press (available online).

This is an outstanding study by our neighbors (Llinas lab) in the Lewis-Sigler Institute. As always, I asked Erandi to write a summary of her paper for me to post here which she accepted. Here it comes...

Our lab studies the malaria-causing Apicomplexan parasite Plasmodium falciparum. Bioinformatic analysis of the parasite genome demonstrates a dearth of specific transcription factors that could modulate the periodic gene expression cascade seen during the red blood cell stages of development. Furthermore, computational prediction of cis-regulatory elements has proven difficult given the extensive A-T content of intergenic regions (approaching 90%) in this unusual organism. Up to now, only a handful of regulatory elements sufficient to drive gene expression have been experimentally characterized in P. falciparum, and their cognate DNA-binding proteins remain unknown. Our recent work characterizes the in vitro DNA-binding specificities of two members of a recently identified Apicomplexan AP2 (ApiAP2) family of putative transcriptional regulators from Plasmodium falciparum. The ApiAP2 proteins contain AP2 domains homologous to the well-characterized plant AP2 family of transcriptional regulators, which play key roles in development and environmental stress response pathways. We assayed ApiAP2 protein-DNA interactions using protein binding microarray technology (Berger et al, 2006. Nat Biotechnol 11:1429–1435) and combined these results with computational predictions of co-expressed target genes to couple these putative trans factors to corresponding cis-regulatory motifs in Plasmodium. We also showed that the protein-DNA sequence specificity is conserved in orthologous proteins between phylogenetically distant Apicomplexan species. Remarkably, our experimentally-derived cis-regulatory motifs closely match independent computational predictions for motifs involved in stage-specific gene regulation in P. falciparum (Elemento et al, 2007. Mol Cell 28:337–350). This study represents the first characterization of the DNA-binding specificities of putative transcriptional regulators in Plasmodium and lays the foundation for the exploration of the role of ApiAP2 proteins during parasite development.

DNA motifs specifically bound by AP2 domains predicted using protein-binding microarrays (PBMs) and computational analysis. (A) The core nucleotides (boxed) in the motif specifically bound by the P. falciparum AP2 domain of PF14_0633 are identical to those bound by its Cryptosporidium parvum ortholog cgd2_3490 (top two rows). The motifs determined from the PBM correspond to motifs predicted by computational analysis of 5’ upstream regions of co-expressed genes (bottom row). (B) The PBM-predicted motif bound by the tandem AP2 domains of PFF0200C (top row) is identical to the motif bound by the first domain alone (middle row). Domain 2 of PFF0200C did not bind a specific DNA motif (data not shown). Both PBM-predicted motifs for PFF0200C match the computationally predicted motif (bottom row).