DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum
Open Access
- Author:
- Bonnell, Victoria
- Graduate Program:
- Biochemistry, Microbiology, and Molecular Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- February 15, 2023
- Committee Members:
- Elizabeth Mcgraw, Outside Unit & Field Member
Shaun Mahony, Major Field Member
Scott Lindner, Major Field Member
Manuel Llinas, Chair & Dissertation Advisor
Wendy Hanna-Rose, Program Head/Chair
Lu Bai, Major Field Member
B. Franklin Pugh, Special Member - Keywords:
- Molecular Parasitology
Gene Regulation
Transcription Factor Binding
Malaria
Sequence-specific Transcription Factors - Abstract:
- Malaria, caused by protozoan parasites of the genus Plasmodium, remains a major global health burden, with 247 million cases and killing 619,000 in 2021 alone. In Plasmodium falciparum, the deadliest human malaria parasite, about 90% of the protein-coding genes are transcribed in a periodic fashion over the 48-hour intraerythrocytic development cycle (IDC), with the peak transcript abundance generally occurring just before the protein is required. The periodicity of transcription forms a genome-wide cascade of continuous gene expression, which is believed to be finely regulated by a limited number of transcriptional regulators, including the 30-member Apicomplexan APETALA2 (ApiAP2) family of sequence-specific transcription factors (TFs). Interestingly, this family of proteins has AP2 DNA-binding domains only evolutionarily conserved in plant-linage genomes and Apicomplexan parasites, making them potential drug targets for novel antimalarial therapeutics in humans. The current literature is focused only on identifying regulatory networks controlled by the ApiAP2 TFs; however, dissecting the molecular mechanisms of their genome-wide binding pattern is still understudied. Knowing mechanisms of binding site selection of putative drug targets is critical to identifying essential interactions or features to be blocked. This dissertation elucidates the biological function and binding specificity of a subset of ApiAP2 TFs, which each recognize similar DNA sequence motifs in vitro, along with their chromatin-remodeling interaction partners. This project applies in vitro, in vivo, and in silico approaches to identify how sequence preferences are established during parasite development by probing the effects of cis- and trans- regulation on TF binding, in addition to dissecting the function of these TFs in parasite development. In higher eukaryotes, TFs with similar binding preferences can carry out different regulatory functions in a given cell type, work synergistically or antagonistically, perform similar functions in different cell types, or can be fully redundant and only necessary in the event that the primary factor cannot function. The occurrence of multiple TFs recognizing similar DNA sequence motifs in P. falciparum is intriguing since functional gene redundancy is not often evolutionarily conserved in pathogens. Therefore, despite the similar DNA binding motifs of these proteins, we predict that they carry out distinct regulatory functions in the parasite. There are several established features investigated by this work that can modulate binding specificity of a TF such as: DNA sequence context/intrinsic DNA shape, interaction with cofactors, histone post-translational modification, and chromatin accessibility. It is critical to understand which features, or combinations thereof, influence binding specificity of transcriptional regulators in P. falciparum to inform future antimalarial drug development.