Sequence of a conserved region of a new sea urchin homeobox gene from the NK family.

The partial sequence of a novel homeobox-containing gene from Paracentrotus lividus is described. Both cDNA and genomic DNA were screened using probes from the vnd/NK-2 homeobox gene found in Drosophila melanogaster. The new DNA sequence found in P. lividus encodes a protein fragment that is closely related to the NK family of homeodomain transcriptional regulators originally discovered in the fruit fly. This study thus represents the first finding of a homeobox gene from the NK family in sea urchin. The DNA that was sequenced includes the most highly conserved region of the NK genes and contains the 180 basepair homeobox (i.e. the DNA segment that encodes the homeodomain), the NK-2 box that encodes the NK-2-specific domain (NK-2 SD), and the acidic box that encodes an acidic domain, but which is found only in a limited subset of the NK genes. In this deduced sequence, the 60 amino acid residue homeodomain contains tyrosine in position 54 and leucine in position 7, which implies that the protein will bind to an unusual sequence of DNA that contains 5'-CAAGTG-3' as its core. The presence of tyrosine in position 54 identifies the gene as a member of the NK-2 class of homeobox genes. Positions 37 and 56 of the homeodomain contain isoleucine and leucine, respectively, which is the first finding in the NK family of homeodomains of these particular amino acid residues in those positions. The presence of the NK-2 box is consistent with identification of the gene as a member of the NK-2 class, and suggests an important role for the C-terminal portion of the protein in transcriptional activation. The sequence homology of the NK-2 box and the spacing between it and the homeobox further suggest that this gene is a member of the NKx-2.2 subclass, whose genes typically are expressed in brain and play a role in axonal guidance, and whose full lengths often are of the order of 900 bases. Homologous NK genes have been found in such diverse invertebrate and vertebrate species, such as Amphioxus sp., Xenopus sp., Caenorhabditis elegans, zebra fish, chicken, hamster, mouse and humans. The finding of this new gene together with sequence comparisons suggests possible evolutionary relationships between sea urchins and vertebrates in the developmental pathways of their body plans.