A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle

Abstract

Precise timing of cell division is achieved by coupling waves of cyclin-dependent kinase (Cdk) activity with a transcriptional oscillator throughout cell cycle progression. Although details of transcription of cyclin genes are known, it is unclear which is the transcriptional cascade that modulates their expression in a timely fashion. Here, we demonstrate that a Clb/Cdk1-mediated regulation of the Fkh2 transcription factor synchronizes the temporal mitotic CLB expression in budding yeast. A simplified kinetic model of the cyclin/Cdk network predicts a linear cascade where a Clb/Cdk1-mediated regulation of an activator molecule drives CLB3 and CLB2 expression. Experimental validation highlights Fkh2 as modulator of CLB3 transcript levels, besides its role in regulating CLB2 expression. A Boolean model based on the minimal number of interactions needed to capture the information flow of the Clb/Cdk1 network supports the role of an activator molecule in the sequential activation, and oscillatory behavior, of mitotic Clb cyclins. This work illustrates how transcription and phosphorylation networks can be coupled by a Clb/Cdk1-mediated regulation that synchronizes them.

Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models

“…This model was converted to a Boolean logic, where a prior knowledge network (PKN) with four nodes—comprehending the cyclins Clb5, Clb3 and Clb2, and the CKI Sic1—was generated (Linke et al. 2017) incorporating the novel interactions found experimentally (Barberis et al. 2012).…”

“…Among these six models, only two were able to match the experimental profile of CLB2 overexpression (Linke et al. 2017). Intriguingly, regardless of the number of interactions within these two models, a common, novel regulatory design is identified that connects the three Clb cyclins, which allows for their timely occurrence in a wave-like fashion.…”

“…That is, all Clb/Cdk1 complexes phosphorylate the transcription factor Fkh2 by a linear regulation, where Fkh2 in turn transcribes for both CLB3 and CLB2 genes, thus coordinating the timely appearance of waves of Clb cyclins (Linke et al. 2017). …”

“…The model of Barberis and colleagues was validated against the Clb2 overexpression phenotype, showing that an increase of Clb2 level upon a certain threshold leads to a reduction in the number of Clb waves (Linke et al. 2017). This outcome is compatible with the inhibition of mitotic exit, as experimentally observed (Cross et al.…”

“…Furthermore, the model predicted that waves of expression of mitotic CLB cyclin genes are the result of cyclin/Cdk1-dependent linear regulation on the transcription factor Fkh2 (Linke et al. 2017), which is the main regulator of CLB2 transcription (Koranda et al. 2000; Kumar et al.…”