The creation of distinct tissues during embryogenesis requires the action of master regulatory genes. One class of transcription factors, the basic-helix-loop-helix-PAS (bHLH-PAS) proteins, controls the formation of a number of important tissues including the central nervous system, respiratory system, and limbs. The single-minded (sim) bHLH-PAS gene controls development of the cells that lie along the midline of the Drosophila CNS, and the related human Sim2 gene may be a factor in Down Syndrome. We have shown that Drosophila Sim forms a dimer with the Tango (Tgo) bHLH-PAS protein, and this complex enters cell nuclei and binds DNA sequence elements (the CNS midline element or CME) on target genes. Genetically, sim activates CNS midline cell gene expression and repressed lateral CNS transcription. The combination of these two events causes ectodermal cells to become CNS midline cells. The Drosophila Trachealess (Trh) bHLH-PAS protein also forms a dimer with Tgo, binds the same CME DNA element as Sim::Tgo, but activates tracheal transcription and development. The Spineless (Ss) bHLH-PAS protein also functions in a similar way to control antennal and leg identity. Mutations in ss cause antennae to become transformed into legs. Thus, Sim, Trh, and Ss each control distinct cell lineages, mechanistically function in similar ways, yet control different batteries of target genes.

Questions that we are currently pursuing involve using genetic, molecular, cellular, and transgenic approaches to understand how the bHLH-PAS:Tgo:CME regulatory casette functions to control transcription and development One project is concerned with how Sim functions as both transcriptional activator and repressor, and how sim and trh, although highly related, control different developmental decisions. Genetic screens are being pursued to identify new genes that act with sim and trh to control transcription and development. Another aspect of these screens is that we can easily identify genes involved in other aspects of CNS developoment, including nerve cell differentiation and axonogenesis. We are also pursuing an evolutionary study that seeks to understand the molecular basis for the development and organization of diverse nervous systems and respiratory systems, as well as the evolution of bHLH-PAS protein signaling pathways. Finally, bHLH-PAS proteins also control the response to hypoxia. We would like to understand the molecular and genetic basis for how organisms respond to oxygen deprivation, and explore the interesting observation that related bHLH-PAS proteins control the physiological response to oxygen and development of the respiratory system.