Isolation of Cladonema Pax-B genes and studies of the DNA-binding properties of cnidarian Pax paired domains

Par genes encode nuclear transcription factors that are involved in develop mental control. They contain a conserved DNA-binding domain, the paired dom ain. The DNA-binding specificity of paired domains is directly related to t he gene regulation function of Pax proteins. Par genes were previously divi ded into five groups on the basis of a phylogenetic analysis of paired doma ins. In this study, two highly similar cnidarian Pax-B genes from Cladonema californicum, a jellyfish with eyes, were found and sequenced. In an effor t to understand the function of the cnidarian Pax genes isolated in this an d a previous study, we characterized the consensus DNA sequences bound by t he cnidarian paired domains using a PCR-based method and electrophoretic mo bility shift assays. The consensus DNA sequences obtained are very similar to those bound by mammalian Pax proteins. Comparison of known consensus seq uences indicates that they are all partially palindromic, but this characte ristic is most prominent in cnidarians, which suggests that the DNA sequenc es bound by the ancestral paired domain could have been palindromic. Also, cnidarian paired domains, like those of Pax-2/5/8, possess a broader bindin g specificity than other paired domains, which implies that the common ance stor of Pax-2/5/8 and Pax-4/6 paired domains could also have had a similar broad DNA-binding specificity. Thus fail a definitive Pax-6 gene has not be en found in several cnidarian species examined, which is consistent with a later origin of the Pax-6 gene and raises two possibilities: the Pay genes of cnidarians are multifunctional and control two or more developmental pat hways, including eye development, or they use a Pax-independent pathway for eye development. Whether this pathway does exist and is unique to cnidaria ns or it whether it represents a true master control under which Pax-6 was later included remains to be determined.