The Urchin Kinome
As part of the sequencing and analysis of the first echinoderm genome, we performed an analysis of the Strongylocentrotus purpuratus kinome.
The Sea Urchin Kinome: A First Look
Bradham, CA, Foltz, KR, Beane, WS, Arnone, MI, Rizzo, F, Coffman, JA, Mushegian, A, Goel, M, Morales, J, Geneviere, A, Lapraz, F, Robertson, AK, Kelkar, H, Loza-Coll, M, Townley, IK, Raisch, M, Rouz, MM, Legpage, T, Gache, C, McClay, DR, Manning, G. (2006).
Dev. Biol. 300:180-93. (Medline, Full Text).
Highlights of the Urchin Kinome
The urchin occupies a key evolutionary position which casts light on vertebrate evolution. It belongs to the phylum Echinodermata (Echinoderms), which are the closest invertebrates to the chordate phylum, and so a starting point to understand chordate- and vertebrate-specific features.
In our previous comparison of human, insect, and nematode kinases, it appeared that 13 kinase subfamilies were vertebrate-specific. We now find homologs of 9 of these families (BCR, G11, DNAPK, HUNK, Trio, Lmr, Tie, RIPK, NKF3) in urchin, showing that they developed earlier than expected, and that there was much less invention of new classes of kinases within vertebrates. Also, unlike both Drosophila and C. elegans, which have both lost many kinase classes found in their common ancestor, urchins appear to have lost none, making it a simple non-redundant model for vertebrate kinases.
Urchins have rich but non-redundant kinase set
The other major feature of the Urchin kinome is its simplicity. Despite having 183 of the 187 human subfamilies, it has only 353 kinases, compared with the 518 found in human. Most subfamilies have just one urchin member, but have several in vertebrates; much of this is probably due to the two rounds of whole-genome duplication that probably happened early in vertebrate evolution. Tiling array studies show that 88% of kinases are expressed in the embryo, which is experimentally well studied, and suggest that this may form a simple model system for the study of vertebrate-like signaling.
As with other kinomes, urchin does have its own idiosyncratic expansions. The largest family, called just 'Urch' has 29 members and is remote from any other family, while other unique families are found in the TK and TKL groups.
Urchin Kinases help classification of vertebrate kinases
Urchin kinases will also help subdivide complex families in human, based on orthology. For instance, the MAP2K and MAP3K (Ste7 and Ste11) families have several members in human that have not be classified into subfamilies. Urchin homologs now show that each family was split into 5 subfamilies in primitive deuterostomes. Similarly, several 'Other-Unique' singleton kinases in human are now seen to have urchin orthologs, showing that they have conserved and relatively ancient functions. These include homologs of KIS, SgK496, and SgK495. These data have enabled us to refine the kinase classification to provide family- or subfamily-level classification for all shared urchin-vertebrate homologs.
Resources
All Urchin sequences and classification are now available through our KinBase database, where domain structures and alignments can also be generated. As the genome sequence is still in draft form, many sequences have gaps and may include spurious fragments, so are not as high quality as other finished kinomes.
More information on urchins and development is available at Wikipedia and tutorials at Stanford and Davidson. More genome information is available at the Urchin Genome Project at Baylor, and at Caltech.