pathogens Review ApiAP2 Transcription Factors in Apicomplexan Parasites Myriam D. Jeninga 1 , Jennifer E. Quinn 1 and Michaela Petter 1,2,* 1 Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany; [email protected] (M.D.J.); [email protected] (J.E.Q.) 2 Department of Medicine, The University of Melbourne, Melbourne, VIC 3010, Australia * Correspondence: [email protected] Received: 28 February 2019; Accepted: 28 March 2019; Published: 7 April 2019 Abstract: Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites. Keywords: Apicomplexa; Plasmodium; Toxoplasma; Cryptosporidium; malaria; gene regulation; transcription factor; ApiAP2; differentiation 1. Introduction Apicomplexan parasites, like Plasmodium spp., Toxoplasma gondii, or Cryptosporidium spp. cause devastating diseases in humans and their eradication is still far away. Plasmodium falciparum parasites alone accounted for about 435,000 deaths in 2017 and small children under the age of five, in particular, are affected by the disease [1]. T. gondii causes many deaths in immunocompromised patients and it has detrimental effects when newly acquired during pregnancy [2], and Cryptosporidium spp. are one of the leading causes of infant diarrhoea in developing countries [3]. With emerging drug resistance in Plasmodium and other apicomplexan parasites, treatment options are becoming limited [4,5], and it is clear that there is a need for better and innovative drugs. This will be greatly aided by a profound understanding of the parasites’ biology. The apicomplexan parasites have complex life cycles, which are marked by several differentiation steps that are associated with significant switches in the transcriptome [6–10]. In Plasmodium and Toxoplasma, epigenetic regulation via histone modifications and histone variants has been implicated in the control of gene expression (reviewed in [11]), but also, generally, specific transcription factors (TFs) are of major importance in the developmental regulation of transcription in eukaryotes [12]. For a long time, only few conserved DNA binding domains of specific TFs were identified in the apicomplexan lineage, including myb (myeloblastosis), PREBP (Prx Regulatory Element binding protein), HMGB (high mobility group b), C2H2 zinc fingers, and E2F (only in Cryptosporidium) domains [13–20]. However, in 2005, Balaji et al. first described a class of putative TFs in Apicomplexa that carried a domain presenting similarity to the Apetala2/ERF (ethylene response factor) (AP2/ERF) integrase DNA binding domain, which is present in many plant TFs [21,22]. Thus, this novel family of putative TFs was dubbed ApiAP2 (apicomplexan AP2). The Pathogens 2019, 8, 47; doi:10.3390/pathogens8020047 www.mdpi.com/journal/pathogens Pathogens 2019, 8, x FOR PEER REVIEW 2 of 23 Pathogens 2019, 8, 47 2 of 24 of putative TFs was dubbed ApiAP2 (apicomplexan AP2). The putative acquisition of an ancestral putativeAP2/ERF acquisition TF from the of plant an ancestral lineage AP2/ERFby horizontal TF from gene thetransfer plant was lineage in line by with horizontal the hypothesis gene transfer that a wasred inalga line of with rhodophyte the hypothesis origin was that an a redendosymbiont alga of rhodophyte in the apicomplexan origin was an parasites endosymbiont ancestor in, from the apicomplexanwhich the apicoplast parasites organelle ancestor, originated from which [23 the–26 apicoplast]. organelle originated [23–26]. P.P. falciparum falciparumcodes codes for for 27 27 putative putative ApiAP2 ApiAP2 TFs, TFs, while while in T. in gondii T. gondiiand C. and parvum C. parvum, there, arethere more are thanmore 60than and 60 10 and ApiAP2 10 ApiAP2 annotated annotated genes, respectively genes, respectively [27]. Some [27] of. the Some ApiAP2 of the TFs ApiAP2 are widely TFs conservedare widely amongconserved the apicomplexanamong the apicomplexan families and theirfamilies close and relative theirPerkinsus close relative marinus Perkinsus[28], suggesting marinus that[28], theirsuggesting common that chromalveolate their common ancestor chromalveolat could alreadye ancestor have could had about already 9 to have 18 AP2 had domain about 9 containing to 18 AP2 TFs,domain while containing the more TFs, species while specific the more factors species likely specific evolved factors through likely independentevolved through lineage-specific independent expansionlineage-specific after theexpansion divergence after ofthe the divergence Apicomplexan of the Apicomplexan species [21,28 ].species Gene [21,28] expression. Gene data expression from P.data falciparum from Pand. falciparumC. parvum andindicated C. parvum that indicated different that ApiAP2 different family ApiAP2 members family were members expressed were in differentexpressed stages in different during parasitestages during development, parasite development, suggesting that suggesting they might that be they involved might in be life involved cycle progressionin life cycle andprogression differentiation and differentiation processes, like processes their plant, like their homologues plant homo [21,logues29]. Numerous [21,29]. Numerous studies havestudies since have corroborated since corroborated this hypothesis this hypothesis and demonstrated and demonstrated the critical the importance critical importance of ApiAP2 of ApiAP2 TFs in apicomplexanTFs in apicomplexan biology. biology. 2.2. Structure Structure of of ApiAP2 ApiAP2 Transcription Transcription Factors Factors TheThe ApiAP2 ApiAP2 TFs TFs can can comprise comprise one one to to four four AP2 AP2 domains domains as as well well as as additional additional functional functional regions regions andand they they greatly greatly vary vary in size,in size from, from approximately approxima 200tely to200 several to several thousand thousand amino amino acids (Figure acids 1(Figure). There 1). isT generallyhere is generally little sequence little sequence homology homology outside o ofutside the AP2 of the domains. AP2 domains Apart. from Apart the from AP2 the domain, AP2 domain, other proteinother protein domains domains that are that present are inpresent some in of some the ApiAP2s of the ApiAP2s in Plasmodium in Plasmodiumspp. include spp. a include DNA binding a DNA domainbinding called domain AT-hook, called AT a zinc-hook, finger a zinc domain, finger domain, an Acyl-CoA-N-acetyltransferase an Acyl-CoA-N-acetyltransferase domain, domain, as well as aswell a pentapeptide-repeat-like as a pentapeptide-repeat domain-like (Figuredomain1 ).(Figure Several 1) ApiAP2. Several TFs ApiAP2 in P. falciparum TFs in additionallyP. falciparum containadditionally a conserved contain motif a conserved that was motif named that the was ACDC named domain the ACDC (AP2-coincident domain (A domainP2-coincident mainly domain at the C-terminus),mainly at the but C- theterminus), function but of the this function domain isof unknownthis domain thus is farunknown [30]. thus far [30]. Figure 1. Apicomplexan AP2 (ApiAP2)-domain-containig proteins in P. falciparum. The proteins are Figure 1. Apicomplexan AP2 (ApiAP2)-domain-containig proteins in P. falciparum. The proteins are organised by size, ApiAP2-domains are marked in red, ACDC (AP2-coincident domain mainly at the organised by size, ApiAP2-domains are marked in red, ACDC (AP2-coincident domain mainly at the C-terminus) domains in pink, AT hooks in black, zinc finger in blue, Acyl-CoA-N-acyltransferase in C-terminus) domains in pink, AT hooks in black, zinc finger in blue, Acyl-CoA-N-acyltransferase in light blue, pentapeptide-repeat-like domains in yellow. light blue, pentapeptide-repeat-like domains in yellow. Pathogens 2019, 8, 47 3 of 24 AP2 domains are about 60 amino acids in size and they normally consist of 3 β-strands and one C-terminal α-helix that stabilises the β-strands [21,31]. An insert is present between strand 2 and 3 that might stand out as a hairpin-like structure, which is positively charged. This positive charge probably enables the nonspecific interaction with the DNA backbone, enhancing the affinity of the ApiAP2 TF to the DNA. When comparing multiple AP2 domains from plants and other organisms, it was shown that 12 amino acid residues were highly conserved, which are implicated in the formation of specific DNA contacts with GCC boxes and DNA backbone contact [21]. In plants, the residues corresponding to R150, R152, W154, E160, R162, R170, and W172 (in the AP2 domain of the plant TF ATERF) mediate the specific binding to the GCC boxes. In ApiAP2s, the R150 residue is often changed to be Y or S and the R152 residue, rather, is found to be D or N, with both