Intermediary Metabolism
Complete reconstruction of the pathways and metabolic fluxes through them is beyond the scope of this initial analysis. In the rest of this paper, however, we present the examples of findings that clarify the status of individual molecular functions or selected pathways in sea urchin.
Cholesterol biosynthesis
Addition of cholesterol to animals' diet is often considered beneficial for sea urchin cultivation. We were able, however, to identify all genes of the trunk mevalonate pathway and of cholesterol synthesis from mevalonate in S. purpuratus (Supplementary Tables 2A and B). Expression of some of these genes has been reported earlier, in the course of analysis of S. purpuratus ESTs (Poustka et al., 2003). The presence of the complete cholesterol biosynthetic pathway indicates that sea urchin must be capable of cholesterol biosynthesis at least under some conditions. Synthesis of small amounts of cholesterol has been reported in another sea urchin species, Echinus esculentus (Smith and Goad, 1974).
Urea metabolism
Sea urchin is an ammonotelic animal-unlike terrestrial animals, it does not secrete urea as the nitrogenous waste (Ruppert et al., 2003). Nonetheless, all enzymes of the urea cycle are found in the genome of sea urchin (Supplementary Table 2C), as well as in genomes of other marine organisms (Armbrust et al., 2004). This suggests that urea has other functions in marine, if not in all, animals. One such function may be osmotic homeostasis, which requires a distinct type of glutamine-dependent carbamoyl-phosphate synthetases, CPS-III (Withers, 1998). SPU_002174 is a candidate for CPS-III function in sea urchin. In the phylogenetic tree, this sequence appears to be equidistant from the known CPS-III and from the alternative, paralogous ammonia-dependent CPS-I sequences, but the presence of a signature cysteine residue in position 292 (Hong et al., 1994) suggests that SPU_002174 may have a CPS-III like activity. The presence of this gene indicates that sea urchin may use urea as a balancing osmolyte.
We have also identified several predicted urea transporters. SPU_004849 and SPU_010793 represent two such genes with significant protein sequence similarity to solute carrier family 14 members, which are found in vertebrates and play a role in urea transport (Shayakul and Hediger, 2004). The two conserved motifs diagnostic of the known urea transporters (Bagnasco, 2003) appear to be modified in these proteins. Interestingly, SPU_011497 and SPU_004180 are gene fragments similar to, respectively, N-terminus and C-terminus of fungal Dur3p urea transporter. An EST database search with sea urchin Dur3p-like protein finds matches to proteins only from fungi. Thus, sea urchin genome may have functionally and evolutionarily unusual repertoire of urea transporters.