Biol Cell (1990) 70, 1-8 © Elsevier, Paris l Original article Sequence analysis of cell cycle control (cdc2) protein kinases among protein serine/threonine kinases Marie-Anne Guerrucci ~, Henri Soldano ~' 2, Robert Bell6 3 ILaboratoire de Bio-informatique, Institut Curie Section Physique-Chimie, 11, rue Pierre et Marie Curie, 75005 Paris; 2LIPN, Universitd Paris-Nord, ave JB-Cldment, 94430 Villetanneuse; 3Laboratoire de Physiologic de la Reproduction, UPMC, CNRS UA 555, INRA, 4, place Jussieu, 75256 Paris Cedex 05, France (Received 16 July 1990; accepted 30 October 1990) Summary - Among protein serine/threonine kinases, the CDC2 proteins are both well characterized as protein serine/threonine kinases and are functionally involved in the control of cell division. Protein serine/threonine kinase sequences were analysed using Fourier transform of the coded sequences. Characteristic code/frequency pairs were extracted from a set of well defined protein serine/threonine kinases. The characteristic frequencies 0.179, 0.250 and 0.408 distinguished protein serine/threonine kinases from proteins which did not have the biological activity. Pertinent patterns in the sequence, responsible for the code/frequency pairs detec- tion were searched and found to be correlated with the putative catalytic domain of the proteins. Protein serine/threonine kinases involved in cell division control, CDC2 protein kinases, were compared to the other protein serine/threonine kinases. Specific code/frequency pairs were extracted from the sequences and could be related to the function or regulation of the kinases in cell division. Two CDC2 related proteins CDC2(Mm) from mice and CDC2(Gg) from chicken were shown to fit well with the CDC2 proteins, whereas KIN28, PHO85 and PSKJ3, which skare sequence homology but not functional activity with the CDC2 proteins, were clearly excluded from the CDC2 proteins by the characteristic code/frequency pairs. Pertinent patterns in the CDC2 proteins were analysed and mapped on the CDC2 related protein sequences. Four patterns were correlated with the code/frequency detection and therefore, could be associated to the regulation of the CDC2-related proteins. sequence analysis / cdc2 protein kinases / protein serine-threonine kinases / cell cycle control Introduction Phosphorylation and dephosphorylation of proteins cata- lyzed by protein kinases and protein phosphatases are recognized as major processes for regulating cellular func- tions [8, 12, 15, 27]. During the last decade, there has been a veritable explosion in the number of identified protein kinases, resulting largely from molecular cloning of pro- tein kinase genes rather from enzyme purification. Two main classes of protein kinases can be differentiated, de- pending on the different amino-acid specificities of the en- zymes; protein serine/threonine kinases and protein thyrosine kinases [12, 15]. Protein serine/threonine kinases occur in families classified on their regulation such as cyclic-nucleotide-regulated, calmodulin-regulated, diacylglycerol-regulated and others, showing striking similarities in their sequences [12, 15]. Among the protein serine/threonine kinases, some have been shown to be in- volved in cell division control. Genetic analysis of fission yeast, Shizosaccharomyces pombe, has identified a gene called cdc2 whose product (p34 cd¢2) is required for traver- sal of both the G~ and G 2 cell-cycle control points. p34 cdc2 was demonstrated to be a protein serine/threo- nine kinase [29]. An homolog of cdc2 gene has been described in budding yeast, Saccharomyces cerevisae (cdc28) whose product is clearly involved at the "start" point in G I and which is also a protein serine/threonine kinase [25]. The cdc2 and cdc28 genes are functionally in- terchangeable [3]. A human homolog of cdc2/cdc28 was cloned by expression of a human cDNA library [19] ; the cdc2(Hs) gene characterized encodes a protein with simi- lar biochemical properties to that encoded by cdc2 [6] and functionally identical [19]. Interestingly, products of cdc2 homologs have been biologically and biochemically charac- terized in Amphibian and Starfish oocytes, also involved in meiotic and mitotic cell division [1, 7, 9, 18]. Altogether, cdc2 homologs involved in cell division control have been characterized from yeast to man [14, 20, 22] ; cdc2 from fission yeast as well as cdc28 from budding yeast and cdc2(Hs) from human cells have been sequenced and are proved to be protein serine/threonine kinases. Two other sequenced cdc2 homologs must so far be considered as putative; a mice CDC2, CDC2(Mm) [22] and a chicken homolog, CDC2(Gg) [17]. Although they are both func- tionaly equivalent to cdc2, they have not been proven to possess the kinase activity. The aim of this work was to analyse the CDC2 protein serine/threonine kinase family using a novel approach de- veloped by Viari et al [35] which does not require sequence alignment but computing analysis of sequences by Fouri- er transform [35]. We have taken advantage of the large number of known protein serine/threonine kinases which were sequenced and of the well-defined function of the CDC2 protein kinase family. Materials and methods Protein kinase sequences The protein serine/threonine kinases used were cAPK: cAMP- dependent protein kinase, fl form [28] ; cGPK : cGMP-dependent