New eukaryotic systematics: a phylogenetic perspective of developmental gene expression in the Apicomplexa.

The phylum Apicomplexa consists of obligate intracellular protistan parasites, some of which are responsible for global disease causing serious morbidity and mortality in humans and animals. Understanding the mechanisms of gene expression that drive the cellular changes required to complete their life cycles will be critical in combating infection and disease. Plasmodium spp. and Toxoplasma gondii have served as good models for growth and development in the Apicomplexa. Elucidating developmental gene expression relies on comparisons with known mechanisms and their DNA, RNA and protein components. Transcriptional profiling across asexual development suggests a model where a cascade of gene expression results in a "just-in-time" production process that makes products only when needed. Some mechanisms that control transcription such as chromatin/histone modification are highly conserved in the phylum compared with the traditional model organisms, yeast, worms, flies and mammals. Studies exploiting this phenomenon show great potential for both investigating the effects of chromatin structure on developmental gene expression, and helping to identify genes that are expressed in a stage-specific manner. Transcription factors and their cognate cis-acting binding sites have been difficult to identify. This may be because the DNA binding motifs that have evolved to act as transcription factors in the Apicomplexa, e.g. the AP2 family, may be more like plants than the traditional model organisms. A new eukaryotic phylogenetic model comprised of six super-groups divides the traditional model organisms, plants and the Apicomplexa into separate super-groups. This phylogenetic model helps explain why basic functions such as transcriptional regulation appear be a composite of mechanisms in the Apicomplexa compared with what is known from other eukaryotes.