Pitx genes in development and disease.

Homeobox genes encode sequence-specific transcription factors (SSTFs) that recognize specific DNA sequences and regulate organogenesis in all eukaryotes. They are essential in specifying spatial and temporal cell identity and as a result, their mutations often cause severe developmental defects. Pitx genes belong to the PRD class of the highly evolutionary conserved homeobox genes in all animals. Vertebrates possess three Pitx paralogs, Pitx1, Pitx2, and Pitx3 while non-vertebrates have only one Pitx gene. The ancient role of regulating left-right (LR) asymmetry is conserved while new functions emerge to afford more complex body plan and functionalities. In mouse, Pitx1 regulates hindlimb tissue patterning and pituitary development. Pitx2 is essential for the development of the oral cavity and abdominal wall while regulates the formation and symmetry of other organs including pituitary, heart, gut, lung among others by controlling growth control genes upon activation of the Wnt/ß-catenin signaling pathway. Pitx3 is essential for lens development and migration and survival of the dopaminergic neurons of the substantia nigra. Pitx gene mutations are linked to various congenital defects and cancers in humans. Pitx gene family has the potential to offer a new approach in regenerative medicine and aid in identifying new drug targets.

Pax genes: regulators of lineage specification and progenitor cell maintenance.

Pax genes encode a family of transcription factors that orchestrate complex processes of lineage determination in the developing embryo. Their key role is to specify and maintain progenitor cells through use of complex molecular mechanisms such as alternate RNA splice forms and gene activation or inhibition in conjunction with protein co-factors. The significance of Pax genes in development is highlighted by abnormalities that arise from the expression of mutant Pax genes. Here, we review the molecular functions of Pax genes during development and detail the regulatory mechanisms by which they specify and maintain progenitor cells across various tissue lineages. We also discuss mechanistic insights into the roles of Pax genes in regeneration and in adult diseases, including cancer.

PAX proteins and fables of their reconstruction.

The PAX proteins derive their name from the "paired box," a region of homology first described between the Drosophila paired (Prd) and gooseberry (Gsb) proteins and later found to encode a sequence-specific DNA-binding activity. Both Prd and Gsb also contain a homeodomain, and this combination of DNA-binding domains is conserved in ancestral predecessors, reflecting an early "homeodomain-capturing" event. In addition, the prototypic PAX protein was thought to contain 2 additional features, namely the octapeptide (or eh1) motif and PHT (or OAR) domain-both modulate PAX regulatory activity but are not unique to the PAX family. Together with gene duplications and mutagenesis, a domain loss model accounts for the distinct architecture and sequence of extant PAX proteins. Despite the disparate evolutionary history of these 4 conserved motifs, there is a remarkable level of interplay that is modulated by discrete sequences elsewhere in the protein. Here, the implications with respect to the evolution of PAX protein structure and activity are discussed, it is suggested that the sum of these constituent domains is more than the contribution of individual parts. When combined with alternative splicing and posttranslational modifications, this model confers an extraordinary degree of functional diversity to even highly related PAX proteins.

Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses.

The functional equivalence of Pax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo-devo studies is based. In this study, we show that Pax4, in addition to Pax6, is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy] gene, unique to Insecta). Molecular phylogenetic trees published to date placed the Pax4 gene outside the Pax6/eyeless subgroup as if the Pax4 gene originated from a gene duplication before the origin of bilaterians. However, Pax4 genes had only been reported for mammals. Our molecular phylogenetic analysis, including previously unidentified teleost fish pax4 genes, equally supported two scenarios: one with the Pax4-Pax6 duplication early in vertebrate evolution and the other with this duplication before the bilaterian radiation. We then investigated gene compositions in the genomic regions containing Pax4 and Pax6, and identified (1) conserved synteny between these two regions, suggesting that the Pax4-Pax6 split was caused by a large-scale duplication and (2) its timing within early vertebrate evolution based on the duplication timing of the members of neighboring gene families. Our results are consistent with the so-called two-round genome duplications in early vertebrates. Overall, the Pax6/eyeless ortholog is merely part of a 2:2 orthology relationship between vertebrates (with Pax4 and Pax6) and the fly (with eyeless and toy). In this context, evolution of transcriptional regulation associated with the Pax4-Pax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time.

Evolution of the gene families forming the Pax/Six regulatory network: isolation of genes from primitive animals and molecular phylogenetic analyses.

Some members of the Pax (paired box) and Six (sine oculis homeobox) gene families function as components of a gene regulatory network controlling eye development. To investigate the early evolution of the genetic interaction between Pax and Six genes, we identified and sequenced members of the Pax and Six gene families from primitive animals. Molecular phylogenetic analyses of the two gene families revealed that all gene duplications that gave rise to different subfamilies occurred before the divergence of cnidarians (ctenophorans) and bilaterians and most of these duplications antedate the sponge-eumetazoan split. Based on the fact that members of Six-1/2 subfamily have genetic interactions with several types of Pax genes from three different subfamilies, it is possible that transcriptional regulation between the Pax and Six genes was established in the common ancestor of all metazoans.