Integrative Analysis of AP2 Transcription Factor Dynamics and Binding Motifs in Toxoplasma gondii

The complex life cycle of Toxoplasma gondii encompasses two infectious phases in intermediate hosts: the rapidly replicating tachyzoite and the dormant bradyzoite, responsible for acute and chronic infections, respectively. The ability of the parasite to form tissue cysts, predominantly in the brain, eyes, heart, and kidneys, and to reactivate to cause acute disease underlies its significant pathogenicity, particularly in immunocompromised individuals such as HIV patients. Despite its prevalence, effective treatments targeting cyst formation and reactivation are lacking. Our study aims to unravel the mechanisms driving the formation and reactivation of these tissue cysts, focusing on the role of AP2 transcription factors (TFs), the major family of transcription factors in Apicomplexa. AP2 TFs are implicated in controlling the gene expression necessary for the parasite's lifecycle, pathogenicity, and developmental transitions. Therefore, interaction between AP2 TFs and their DNA binding sites is very important. We constructed an integrated single-cell RNA sequencing (scRNA-seq) atlas using published data from T. gondii Type II strains, ME49 and Pru that are typically used for bradyzoite models. This atlas delineates gene expression profiles across different cell cycle phases and environmental conditions, offering a detailed map of transcriptional changes associated with the parasite's development, and highlighting the functionality of specific genes and pathways. We then investigated this atlas using the binding dynamics of AP2 TFs. Utilizing Protein Binding Microarray (PBM) data, we performed motif scanning to align AP2 binding motifs with scRNA-seq data using the MAST algorithm from MEME. We focused on mapping the expression profiles of AP2 genes and their targets within the single-cell dataset. These data implicate AP2 in both gene activation and gene repression during regulation of cell cycle progression and tachyzoite to bradyzoite differentiation. Our research provides insights into the transcriptional control in T. gondii, emphasizing the critical role of AP2 TF motifs in its adaptive life cycle. The integrative approach of mapping AP2 factor dynamics and gene expression profiles opens new avenues for therapeutic interventions, targeting the developmental transitions of T. gondii, and potentially leading to more effective treatments for toxoplasmosis.