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Budding yeast

Budding yeast cell cycle (adapted from Irons, 2009)

Summary: 

This model is a direct transcription of the Boolean model published by Irons [1], except for the specific temporisation system. Synchronous simulation of this model recovers the results obtained by Irons in absence of time delays (Fig. 3B in [1]), i.e. a single, cyclic attractor qualitatively consistent with available kinetic data.


References

  1. Irons DJ.  2009.  Logical analysis of the budding yeast cell cycle. Journal of theoretical biology. 257(4):543-59.
Curation
Submitter: 
Adrien Fauré (C. Chaouiya)

Budding yeast cell cycle (Orlando et al. 2008)

Summary: 

This model is a direct transcription of the Boolean model published by Orlando et al. [1]. Synchronous simulation of this model yields a cyclic attractor gathering most trajectories in the state transition graph, which is robust to parameter choice, as reported in [1]. However, asynchronous simulations all lead to a stable state with all variables OFF, whatever the parameter set proposed by the authors, indicating that the oscillations observed in the synchronous simulations may not be sustained. See [2] for more details.


References

Curation
Submitter: 
Adrien Fauré (C. Chaouiya)

Budding yeast exit module

Summary: 

This logical model (cf. figure below and [1]) focuses on the network controlling mitotic exit in budding yeast. It is inspired by the work of Queralt et al. (2006) [2], which emphasises the role of PP2A down-regulation by separase in the triggering of Cdc14 activation during anaphase. These authors developed a quantitative model for mitotic exit, integrating evidence on the roles of FEAR (Cdc Fourteen Early Anaphase Release) components Cdc5Polo, PP2ACdc55 and Esp1.

This model was then used to update our model for budding yeast core cycling engine, that relied on an hypothetical inhibitor of Cdc14, called PPX, activated by Pds1, in place of the FEAR reaction. Our logical model qualitatively accounts for available data on the wild-type cell cycle, as well as for nine different cycle perturbations described in Queralt et al, in terms of Cdc14 activation.

See also:


References

Curation
Submitter: 
Adrien Fauré (C. Chaouiya)

Morphogenetic checkpoint of the budding yeast cell cycle

Summary: 

In budding yeast, the morphogenetic checkpoint (MCP) relies upon inhibitory phosphorylation of Cdc2/Cyclin B by Swe1 to condition entry into mitosis to the formation of a bud. Taking inspiration in the ODE model published by Ciliberto et al. (2003) [1], we have developed a logical model of the MCP, with the aim to plug it to our core engine of the budding yeast cell cycle (cf. [2]).

The activity of Cdc28/Clb2 is controlled by the balance between Swe1 and Mih1. Swe1, the budding yeast homologue of the tyrosine kinase wee1, inhibits Cdc28 by phosphorylation, whereas the phosphatase Mih1 (homologue of Cdc25) removes the inhibitory phosphate. Swe1 itself is inhibited by phosphorylation by Cdc28/Clb2, in a positive feed-back loop. Based on Ciliberto's model, we assume that Swe1 is also somehow modified by Hsl1, a protein kinase activated by bud formation, and that this modification of unknown nature - as Swe1 does not appear to be a substrate of Hsl1- has an inhibitory effect on Swe1. The checkpoint is reinforced by a MAPK pathway that inhibits Mih1 through Mpk1 activity in absence of a bud. An important point of the MCP is the possibility for the cell to undergo adaptation, that is to evade the checkpoint and enter mitosis in absence of a bud after some time. Ciliberto's model supports the hypothesis that failure to make a bud creates a second threshold for mass for the G2-M transition (the first threshold being at Start). Mass impacts cell progression by increasing the synthesis of the cyclins, and in particular CycB that is required for entry into mitosis (see the core model -LINK- for details). Here, we have introduced a second threshold for the MASS variable, to represent the idea that increased CycB synthesis can yield enough CycB activity to overcome inhibition by Swe1. Our model accounts for the wild-type as well as 14 mutants phenotypes described by Ciliberto et al. and in Harrison et al (2001) [3] in terms of entry into mitosis – monitored by Clb2 activation. This model has then been to our model of the core cell cycle engine of the budding yeast (see coupled model).


References

Curation
Submitter: 
Adrien Fauré (C. Chaouiya)

Core engine controlling the budding yeast cell cycle

Summary: 

Leaning on the differential model published by Chen et al. in 2004 [1], we have delineated a discrete, logical model that reproduces the main qualitative results reported in this study, in terms of cycle viability or arrest in a particular stable state, for the wild type as well as over one hundred mutant conditions [2]. In a first step, we have defined a regulatory graph encompassing the main documented interactions between core regulators of the cell cycle (Cdk/cyclins, APC, Cdk inhibitors).
For proper logical rules, in the wild type situation, our model accounts for the following sequence of events: firing of the origins of replication (ORI goes up), spindle alignment (SPN goes up), inhibition of the securin (Pds1 goes down), division (MITOSIS goes up to level 2) after the formation of a bud (BUD must reach at least transiently the level 1), and origin relicensing (ORI goes down). This sequence serves as a criterion to evaluate the viability of the cell. Based on the levels of activity of key variables (Clb5, Clb2, Pds1), we can divide the cycle into three different phases: G0/G1 (low Clb5 and Clb2 activity, either OFF or sequestered by Sic1/Cdc6), S/G2 (high Clb5 activity, i.e. not sequestered by the CKI, and low Clb2), and M (high Clb2 activity). The M phase is itself subdivided into prophase/metaphase (high Pds1, low Esp1, sister chromatids not separated) and anaphase/telophase (low Pds1, high Esp1). These rules are used to characterised cell arrests in various mutants. Although the logical formalism is particularly well suited to represent information fluxes (activation, inhibition), it is not adapted to the representation of mass flow, reactant consumption, or complex formation. Consequently, we represent the complexes implicitly: a complex is considered present if all its components are present; all components, whether regulatory or enzymatic subunits, regulate the targets of the enzymatic member, with a logical AND rule (or AND NOT in the case of sequestration). For example, in the case of the inhibition of the Clbs by the CKI, we have represented inhibition of the Clbs by introducing arrows from the CKI towards the Clbs targets, so that inhibition of the Clbs is represented by an inhibition of the components they activate and by an activation of the components they inhibit. In Chen's model, cytokinesis was triggered by a fall of clb2's activity below a certain threshold. To formulate this rule in the logical formalism, we introduced a multilevel CYTOKINESIS variable. This variable is fully activated (level 2) only when CycB is inactivated, either by a decrease of CycB level from level 2 to level 1, or by an increase of the CKI activity when Clb2 is still high. To differentiate between a rise and a fall of CycB activity, CYTOKINESIS has to be pre-activated (up to level 1) by high Clb2 activity before being allowed to reach level 2. Our model simulations qualitatively agree with the behaviour reported for the wild-type Yeast, as well as for over one hundred mutant conditions. This led us to further develop this model by defining additional regulatory modules such as the morphogenetic checkpoint. We also developed a model for mitotic exit based on more recent evidence. The resulting logical models are presented as separate entries of our model repository. In conclusion, our core cell cycle model served as a benchmark to assess the power of logical modelling applied to a complex oscillatory system, as well as the first step towards the development of a more comprehensive model of the budding yeast cell cycle network.


References

Curation
Submitter: 
Adrien Fauré (C. Chaouiya)

Budding yeast cell cycle (Fauré et al. 2009)

Summary: 

Leaning on former models, we have defined a logical model for three regulatory modules involved in the control of the mitotic cell cycle in budding yeast, namely the core cell cycle module, the morphogenetic checkpoint, and a module controlling the exit from mitosis. Consistency with available data has been assessed through a systematic analysis of model behaviours for various genetic backgrounds and other perturbations. See:

Here, we take advantage of compositional facilities of the logical formalism to combine these three models in order to generate a single comprehensive model involving over thirty regulatory components. The resulting logical model preserves all relevant characteristics of the original modules, while enabling the simulation of more sophisticated experiments (cf. [1]).

Chen et al (2004) [2] discussed the possibility to graft the model of the morphogenesis checkpoint published in a “companion study” by Ciliberto et al (2003) [3] to their model of the cell cycle, and to replace the hypothetical PPX by a more accurate version of the network controlling mitotic exit. We have adapted all three modules in the logical formalism, and coupled them together.

Coupling of the MCP module to the core cycling engine model

We have kept and left unchanged all components that were specific of the MCP module (Mih1, Swe1, Mpk1 and Hsl1), and similarly, all components specific of the core model. Among the components that were shared by both modules, MASS, MBF and the BUD received no input from the variables specific of the MCP, while their regulation amounted to a simplification of what had been proposed in the core cycling engine model. Hence, we kept these variables and their regulation from the core model and left them unchanged in the coupled model. In contrast, in the coupled model, CycB get inputs from components specific of each of the two modules. Moreover, in the MCP module, CycB is Boolean, whereas it is multilevel in the core model. Based on the parameters of CycB in each of the modules, we determined that CycB would have to satisfy the two sets of conditions to be active in the coupled model. Consequently, the logical formula giving the conditions of activation of CycB in the coupled model amounts to a logical AND between its formulas in the core cycling engine and in the MCP module. The main characteristics of the behaviour of the two original modules are conserved in the coupled model, in the case of the wild-type as for the different mutations simulated.

Coupling of the exit module to the core cycling engine model

The next step was to fuse the exit module to the core cycling engine. We followed the same method as with the coupling of the MCP. The first step was to identify which components and interactions were to be kept in the coupled model. Obviously, we chose to discard the hypothetical PPX, along with the parameters of the components of the exit network that were present in the core model (Net1, Cdc14, Tem1, Bub2-Bfa1, Cdc15 and Pds1), to replace them with their equivalents from the new exit module, including the SeparaseEsp1, PP2ACdc55 and Cdc5Polo that were not present in the core model. The logical rules for Clb2, Cdh1 and Cdc20 in the exit module amount to simplifications of their counterparts in the core model, so we kept the core model wiring and regulation in the coupled model for these components. Last but not least, we added regulation from Sic1 and Cdc6 towards Clb2 new targets to represent sequestration of the cyclins by the CKI (see the core cycling engine model for more details). The resulting model fits the more recent data used to built the exit module, and the behaviour of the core model is preserved. Still, one difficulty arose regarding mutant simulations for the exit module: the two mutants involving Cdk inhibition (see Queralt [i]et al.[/i], supplementary figure S6.4 [4]) could not be simulated in the coupled model, as inhibition of Cdk1 / Clb2 is the signal for cytokinesis in this model. This points out towards the “TARGET model” hypothesis discussed in Chen et al, where the trigger for cytokinesis would involve both a decrease of Cdk1 / Clb2 kinase activity and an increase in Cdc14 phosphatase activity.


References

Curation
Submitter: 
Adrien Fauré (C. Chaouiya)
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