Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

Abstract

The molecular mechanisms underlying transcriptional regulation in apicomplexan parasites remain poorly understood. Recently, the Apicomplexan AP2 (ApiAP2) family of DNA binding proteins was identified as a major class of transcriptional regulators that are found across all Apicomplexa. To gain insight into the regulatory role of these proteins in the malaria parasite, we have comprehensively surveyed the DNA-binding specificities of all 27 members of the ApiAP2 protein family from Plasmodium falciparum revealing unique binding preferences for the majority of these DNA binding proteins. In addition to high affinity primary motif interactions, we also observe interactions with secondary motifs. The ability of a number of ApiAP2 proteins to bind multiple, distinct motifs significantly increases the potential complexity of the transcriptional regulatory networks governed by the ApiAP2 family. Using these newly identified sequence motifs, we infer the trans-factors associated with previously reported plasmodial cis-elements and provide evidence that ApiAP2 proteins modulate key regulatory decisions at all stages of parasite development. Our results offer a detailed view of ApiAP2 DNA binding specificity and take the first step toward inferring comprehensive gene regulatory networks for P. falciparum.

Author Summary

Plasmodium falciparum is the main cause of the devastating human disease malaria. This parasitic organism has a complex lifecycle spanning a variety of different cell types in the mosquito vector and human host. To adapt and survive in these different environments, the parasite precisely regulates the transcription of genes throughout its lifecycle. However, the mechanisms governing transcriptional regulation in P. falciparum are poorly understood. To date, a single family of specific transcription factors, the Apicomplexan AP2 (ApiAP2) proteins, has been identified. These DNA binding proteins are likely to play a major role in coordinating the development of this parasite and are therefore of major interest. Here, we determine the DNA binding specificities for the entire P. falciparum ApiAP2 family of DNA binding proteins. Our results demonstrate that these proteins bind diverse DNA sequence motifs and co-occur in functionally related sets of genes. By mapping these sequences throughout the parasite genome, we can begin to establish a regulatory network underlying parasite development. This study represents the first characterization of a family of DNA binding proteins in P. falciparum and provides an important step towards understanding gene regulation in this parasite.