BMC Genomics 2004, 5:69 http://www.biomedcentral.com/1471-2164/5/69 Background Cyclin-dependent kinases (CDKs) belong to a large pro- tein family with 13 members described so far in human cells including CDKs1-11, along with PCTAIRE and PFTAIRE kinases named after conserved domain sequences [1]. These kinases are essential for cell cycle progression, and also are involved in control of transcrip- tion, DNA repair and post-mitotic cellular process [2-4]. Generally, CDKs1-6, PCTAIRE and PFTAIRE have been linked to cell cycle regulation, and CDKs7, 8 and 9 to con- trol of RNA polymerase II (RNAP II) transcription [4-8]. The functions of CDKs10 and 11 have not been defined clearly, but recent research implicates them in coordina- tion of transcription and RNA-processing [9-13]. Among the most important and broadly studied roles of CDKs in transcription is the reversible phosphorylation of the C-terminal domain (CTD) of the largest subunit (RPB1) of RNAP II. The CTD consists of multiple repeats of an evolutionarily conserved heptapeptide with the con- sensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 [14]. The number of repeats varies among different organisms, ranging from 26–27 in yeast to 52 in mammals [15,16] with 8 repeats in yeast and 28 repeats in human cells required for viability [15,17,18]. Both biochemical and genetic evidence places the CTD in a central position in the 'mRNA factory,' where it functions as a platform for interactions with processing factors and other transcrip- tion-related proteins [19,20]. More than a passive scaf- fold, reversible phosphorylation of the CTD regulates the cycling of RNAP II between a hypophosphorylated (IIO) form, which is competent to enter the preinitiation com- plex, and a hyperphosphorylated (IIA) form capable of processive transcript elongation [21]. Throughout this cycle the CTD binds essential transcription-related pro- teins that help to regulate gene expression, promote effi- cient elongation, and effectively couple transcription to pre-mRNA processing [19-24]. To date at least five of the CDKs (CDK1, 2, 7, 8 and 9) have been shown to phosphorylate the CTD in vitro; they all have been referred to as 'CTD kinases' [25-28]. Both CDK7 and CDK8 are found tightly associated with the pre-initiation complex and are involved in transcriptional regulation [29]. The CDK9 subunit of P-TEFb (positive transcription elongation factor b) induces hyper-phos- phorylation of the CTD and stimulates elongation. Unlike CDKs 7, 8 and 9, which have demonstrated interactions with the CTD in vivo, CDK1 and CDK2 are primarily cell- cycle related kinases [4]. CDK2 has been characterized functionally only human and Drosophila in mammals and its role in Tat-dependent HIV-1 transcription is still unclear [27,28]. Although phosphorylation of yeast RNAP II by CDK1 (CDC2) can inhibit transcription in vitro, the role of the CDK1 in mRNA synthesis in vivo is not, as yet, clearly understood. It has been proposed as a candidate for mitotic RNAP II inactivation by inhibition of CDK7 CTD-kinase activity [26]. In animals and yeasts, interactions between the CTD and CTD-specific kinases have become a focal point of bio- chemical and genetic investigations of RNAP II transcrip- tion and transcription-linked mRNA processing [25,26,30]. However, the ancestry and evolutionary rela- tionships among CTD kinases have not been investigated thoroughly. Evolutionary analyses of the RNAP II CTD show that canonical CTD heptads are strongly conserved only in a subset of eukaryotic groups. In evolutionary trees based on RPB1 sequences, all eukaryotic groups in which the CTD is strongly conserved appear to be descended from a single common ancestor (descendents of this ancestor have been referred to as the "CTD-clade") [31]. The reasons for differential conservation of the CTD have not been clarified, nor have evolutionary correlations been established between strong conservation of CTD structure and the presence of essential CTD/protein inter- actions. In addition, although the functions of various CDKs are reasonably well characterized in mammals and yeasts, very little is known for most other eukaryotes, and the overall evolution of CDKs has been investigated only in animals and yeasts [32]. Therefore, a comparative evo- lutionary study also can provide clues as to which CDK orthologs, and presumably CDK functions, are present over a broad range of eukaryotic diversity. Here we present a comparative genomic analysis of CDKs, using complete genomes from members of the "CTD clade" (animals, plants, yeasts and Microsporidia), as well as from other diverse eukaryotic organisms lacking a canonical CTD (Trypanosoma, Plasmodium and Giardia), to explore the evolutionary relationships between the CTD and CTD kinases. We also provide a phylogenetic distri- bution of CDKs from a wide range of organisms, suggest- ing new hypotheses regarding the emergence and evolution of different members of the CDK family. Results We identified 133 CDK family members, 123 from ani- mals, plants, yeasts, and four protists from which genome sequences have been completed, and 10 additional CDKs from incomplete genome sequences of organisms with known CTD sequences (Table 1). Although all of sequences are included in our supplemental phylogenetic analysis (additional file 1), only 101 of them are included in the major phylogenetic analysis (Fig. 1); a large plant- specific amplification of CDK9-like kinases (the phyloge- netic weight of these sequences disrupts the CDK9 sub- clade) and sequences from incomplete genomes are excluded (see Fig. 1 and additional file 1 legends for fur- ther explanation). The nomenclature for kinases from Page 2 of 13 (page number not for citation purposes)