ISSN 1607-6729, Doklady Biochemistry and Biophysics, 2009, Vol. 426, pp. 147–151. © Pleiades Publishing, Ltd., 2009. Original Russian Text © I.I. Turnaev, K.V. Gunbin, N.A. Kolchanov, 2009, published in Doklady Akademii Nauk, 2009, Vol. 426, No. 2, pp. 265–269. 147 Study of the evolution of cyclins and cyclin-depen- dent kinases (CDKs) is of special interest due to a key function of these proteins in the control of cell prolifer- ation [1]. These proteins control the proliferation through regulating the progress of temporal cell cycle phases (G1, S, G2, and M). Durations of the growth phase (G1) and G1/S transition considerably vary among the eukaryotes, being the main characteristic distinguishing between the cell types [1]. This suggests that the proteins involved in the regulation of these peri- ods play a special role in the formation of new cell types in the evolution of eukaryotes [1]. In this work, we have studied the evolutionary modes of cyclins and CDKs and determined the branches of phylogenetic trees for these protein super- families where the adaptive evolutionary events have taken place. The correlation between the evolutionary changes in the physicochemical properties (PCPs) of the proteins constituting the cyclin and CDK superfam- ilies and the total rate of the change in the number of eukaryotic cell types during the evolution was discov- ered. The protein sequences were extracted from the Gen- Bank and Ensemble databases. The sample of cyclin superfamily comprises 143 sequences, including 25 sequences of cyclin D, 17 of cyclin E, 43 of animal cyclins B1 and B2, 14 of fungal cyclin B–like proteins, 4 sequences of plant cyclin B, and 39 sequences of cyclin A. The sample of CDK superfamily consists of 64 protein sequences, namely, 14 CDK4 and CDK6, 13 CDK5, 11 CDK2 and CDK3, 15 animal CDC2, 2 fungal CDC2, and 7 plant CDC2. The activity of CDKs requires their binding to cyclins: CDK4, CDK5, and CDK6 bind to cyclin D; CDK2 and CDK3, to cyclins E and A; and CDC2, to cyclins A and B [1]. The heterodimeric complexes CDK4/cyclin D, CDK5/cyclin D, and CDK6/cyclin D control the progress through G1 phase; the complexes CDK2/cyclin E and CDK3/cyclin E control the G1/S transition; CDK2/cyclin A, the exit from S phase; and CDC2/cyclin A and CDC2/cyclin B, cell entrance in mitosis [1]. Multiple alignment of protein sequences was per- formed with the help of the MAFFT 6.240 program [2]. Phylogenetic trees were inferred using the Bayesian method (MRBAYES 3.1.2 [3]). The sequences of ancestral proteins were deduced by maximum likeli- hood estimation (FASTML 2.02 [4]) using the align- ments without deletions. The studied deletion-free pro- tein regions were highly conserved (≥60% homology in the pairwise comparisons for both superfamilies). The branches of phylogenetic trees housing the adaptive evolutionary events were searched for by a pairwise comparison of PCPs of the proteins (recon- structed or extant) located at the nearest tree nodes. Changes in the PCPs of the proteins expressed in the logarithmic units of the WAG amino acid substitution matrix [5] were assessed using the maximum likeli- hood method (TREE-PUZZLE 5.2 [6]). The conclusion on the presence of adaptive evolutionary events in a tree branch was made based on the presence of considerable alterations in the protein amino acid composition if the PCPs changed by >0.4 WAG unit * [5]. The phylogenetic analysis allowed us to divide the cyclin superfamily into two clades with different rates of protein evolution, namely, with a high (the family of cyclins D and E) and low (the family of cyclins A and B) rates (Fig. 1). The events of adaptive evolution in the near-root and terminal branches were detected in the families of cyclins D and E (Fig. 1). Individual * Corresponds to 60 units of the Grantham matrix [7]. The Evolution of Key Cell Cycle Proteins Correlates with an Increase in the Complexity of Eukaryotic Organisms I. I. Turnaev, K. V. Gunbin, and Academician N. A. Kolchanov Received December 22, 2008 DOI: 10.1134/S1607672909030065 Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Akademika Lavrent’eva 10, Novosibirsk, 630090 Russia BIOCHEMISTRY, BIOPHYSICS, AND MOLECULAR BIOLOGY