Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs

We identify 101 cyclin-dependent kinases (CDKs) family members from animals, plants, yeasts and three protists with complete genome sequences. Comparative analyses suggest that cell-cycle CDKs are present in all organisms sampled in this study. In contrast, no clear orthologs of transcription-related CDKs are detected in the most putatively ancestral eukaryotes, Trypanosoma or Giardia. Kinases involved in C- terminal domain (CTD) of RNA polymerase II phosphorylation, CDK7, CDK8 and CDK9, all are recovered as well-supported and distinct orthologous families. Significantly, clear orthologs of CDK7 and CDK8 are restricted to those organisms belonging to groups in which the RNAP II CTD is strongly conserved suggesting co-evolution of the CTD and these CTD-directed CDKs. Alternatively, extensive CTD phosphorylation may occur in only a subset of eukaryotes and, when present, this interaction results in greater stabilizing selection on both CTD and CDK sequences. Overall, our results suggest that transcription-related kinases originated after cell-cycle related CDKs.