TheCryptosporidium parvumApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems

Abstract

We provide the first comprehensive analysis of any transcription factor family in Cryptosporidium, a basal-branching apicomplexan that is the second leading cause of infant diarrhea globally. AP2 domain-containing proteins have evolved to be the major regulatory family in the phylum to the exclusion of canonical regulators. We show that apicomplexan and perkinsid AP2 domains cluster distinctly from other chromalveolate AP2s. Protein-binding specificity assays of C. parvum AP2 domains combined with motif conservation upstream of co-regulated gene clusters allowed the construction of putative AP2 regulons across the in vitro life cycle. Orthologous Apicomplexan AP2 (ApiAP2) expression has been rearranged relative to the malaria parasite P. falciparum, suggesting ApiAP2 network rewiring during evolution. C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation. C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5′-TGCAT-3′, 5′-CACACA-3′ and G-box motifs (5′-G[T/C]GGGG-3′). Many overrepresented motifs in C. parvum upstream regions are not AP2 binding motifs. We propose that C. parvum is less reliant on ApiAP2 regulators in part because it utilizes E2F/DP1 transcription factors. C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination.

Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi

“…It is possible that proteins containing multiple AP2 domains are able to bind to distinct DNA regions either separately or simultaneously, thus adding increasing functional versatility for these molecules. In general, and consistent with what was found for other AP2 proteins, there is low sequence identity or similarity among the AP2 proteins, and, thus, their similarities are just restricted to the conserved 60 amino acid domain [8, 22, 24]. The percent identities found among the full AP2 proteins after their alignment is shown in S1 Table.…”

“…In addition, gene expression can also be regulated at the post-transcriptional and translational levels. Key advances in understanding mechanisms involved in gene regulation have so far been achieved in the more studied Babesia -related Plasmodium , Theileria annulata , and Toxoplasma , among others [8]. These studies serve as a model for characterization of similar and generally conserved gene regulatory mechanisms in Babesia and closely related parasites.…”

“…bovis T2Bo strain genome resulted in the annotation of 18 genes encoding for AP2 domain-containing proteins [3]. However, Oberstaller et al [8], using a highly sensitive Hidden Marcov Model (HMM), recently identified four additional genes encoding for AP2 proteins, thus extending the number of genes encoding for AP2 domain-containing proteins to a total of 22. General features of the 22 B .…”

Sexual development in Plasmodium parasites: knowing when it's time to commit

“…To date, seven ApiAP2 proteins have been identified as regulators of stage-specific development, including liver-stage maturation (AP2-L) 71 , salivary gland sporozoite formation (AP2-Sp) 73 , ookinete development (AP2-O) 72 and gametocyte commitment (AP2-G) 47,50 in Plasmodium spp., as well as bradyzoite development (AP2IX-9 and AP2XI-4) 125,126 , virulence and host invasion (AP2XI-5) in the related apicomplexan parasite Toxoplasma gondii 127 . Many ApiAP2 proteins are also predicted to be involved in the regulation of the parasite cell cycle 75,[128][129][130][131] .…”

“…Although the function of many ApiAP2 proteins remains to be determined, the binding specificities for many of the AP2 domains from P. falciparum 75 , T. gondii 126 and Cryptosporidium parvum 131 have been determined in vitro using protein-binding microarrays, capturing a diverse repertoire of DNA-binding interactions for this protein family. Although these sequences enable the prediction of target genes regulated by specific ApiAP2 factors, further experimental work using chromatin immunoprecipitation followed by sequencing will be required to specifically determine the regulatory network for each of these proteins.…”