Dynamics of Cdk1 Substrate Specificity during the Cell Cycle

Abstract

SummaryCdk specificity is determined by the intrinsic selectivity of the active site and by substrate docking sites on the cyclin subunit. There is a long-standing debate about the relative importance of these factors in the timing of Cdk1 substrate phosphorylation. We analyzed major budding yeast cyclins (the G1/S-cyclin Cln2, S-cyclin Clb5, G2/M-cyclin Clb3, and M-cyclin Clb2) and found that the activity of Cdk1 toward the consensus motif increased gradually in the sequence Cln2-Clb5-Clb3-Clb2, in parallel with cell cycle progression. Further, we identified a docking element that compensates for the weak intrinsic specificity of Cln2 toward G1-specific targets. In addition, Cln2-Cdk1 showed distinct consensus site specificity, suggesting that cyclins do not merely activate Cdk1 but also modulate its active-site specificity. Finally, we identified several Cln2-, Clb3-, and Clb2-specific Cdk1 targets. We propose that robust timing and ordering of cell cycle events depend on gradual changes in the substrate specificity of Cdk1.

Among B-Type Cyclins Only CLB5 and CLB6 Promote Premeiotic S Phase in Saccharomyces cerevisiae

“…One explanation for the inability of CLB1 or CLB3 to promote premeiotic DNA replication when expressed under regulation of the CLB5 promoter, even when combined with swe1 deletion, is that they may be less effective than Clb5 at interacting with substrates required for premeiotic DNA replication. While some Cdk1 substrates are effectively phosphorylated by either Clb3-Cdk1 or Clb5-Cdk1, a subset of protein substrates displays very strong preference for either Clb3 or Clb5 (Koivomagi et al 2011). Additionally, both twohybrid and proteomic screens have identified distinct arrays of interacting proteins for Clb3 and Clb5 with surprisingly little overlap (Ito et al 2001;Archambault et al 2004).…”

“…A growing body of evidence supports the contention that cyclins target Cdk activity to the correct substrates and hence the cyclin provides specificity to the Cdk activity (Cross et al 1999;Roberts 1999;Loog and Morgan 2005;Bhaduri and Pryciak 2011;Koivomagi et al 2011;Pagliuca et al 2011). In addition to interaction with protein substrates, the specificity of cyclins for particular functions can be imparted by the timing of accumulation, the activity of cyclin-CDK inhibitors, and by subcellular localization (Draviam et al 2001;Miller and Cross 2001;Moore et al 2003;Carlile and Amon 2008).…”

“…Similarly, S. cerevisiae deficient in the Sphase cyclins Clb5 and Clb6 display a delay in DNA replication, and even overproduction of Clb1 or Clb2 or the expression of CLB3 under control of the CLB5 promoter does not fully suppress this defect (Hu and Aparicio 2005). Additionally, many B-type cyclin-Cdk complexes display substrate preferences in vitro (Peeper et al 1993;Higashi et al 1995;Loog and Morgan 2005;Joshi et al 2009;Koivomagi et al 2011). Thus, while there is considerable overlap between the activity and function of various cyclins, the substrate specificity of cyclin-CDK complexes remains a central mechanism that regulates cell cycle progression.…”

Cdk1: A kinase with changing substrate specificity

“…We recently presented a detailed study on the specificity of budding yeast cyclinCdk1 complexes and outlined the general mechanisms underlying changes in Cdk1 specificity during the cell cycle. 10 We found that the sequentially appearing cyclins gradually increase the specificity of Cdk1 toward the optimal Cdk consensus site (Fig. 1).…”

Coordinating cell cycle progression via cyclin specificity

“…6 Therefore, in addition to binding certain targets with varying affinities, cyclins also appear to be able to modulate the behavior of the cdk kinase partner toward those proteins. It will be interesting to extend these studies to human cyclins and Cdks.…”