Alteration of the DNA binding domain disrupts distinct functions of the C. elegans Pax protein EGL-38

The paired-domain-containing Pax transcription factors play an important role in the development of a range of organ, tissue and cell types. Although DNA binding elements and target genes for Pax proteins have been identified, how these proteins identify appropriate DNA elements and regulate different genes in different cellular contexts is not well understood. To investigate the relationship between Pax proteins and their targets, we have studied the in vivo and in vitro properties associated with wild-type and different mutant variants of the Caenorhabditis elegans Pax protein EGL-38. Here, we characterize the properties of four mutations that result in an amino acid substitution in the DNA binding domain of EGL-38. We find that animals bearing the different mutant alleles exhibit tissue-preferential defects in egl-38 function. The mutant proteins are also altered in their activity in an ectopic expression assay and in their in vitro DNA binding properties. Using in vitro selection, we have identified binding sites for EGL-38. However, we show that selected sites function poorly in vivo as EGL-38 response elements, indicating that sequence features in addition to DNA binding determine the efficacy of Pax response elements. The distinction between DNA binding and activity is consistent with the model that other factors commonly play a role in mediating Pax protein target site selection and function in vivo.