This logical model encompasses the core model (adapted from Chen et al., 2004), the morphogenesis checkpoint (MCP) module (adapted from Ciliberto et al., 2003), and a revised version of the network controlling mitotic exit (exit module, adapted from Queralt et al., 2006). + +The coupling has been done as described in (Fauré et al., in preparation) + +The resulting model preserve the dynamical properties of the original modules, while enabling the simulation of perturbations involving components that belong to several modules. + + ---------------------------------------- + +Cell viability rule in terms of sequence of events, as in the core model: firing of the origins of replication (ORI goes up), spindle alignment (SPN goes up), separase activation (or inhibition of the securin, Pds1 goes down), division (MITOSIS goes up to level 2) after the formation of a bud (BUD must have reached value 1, although it goes down afterwards before cell division), and origin relicensing (ORI goes down). + +Cell cycle phases: +G0/G1: low Clb5 and Clb2 activity (either =0 or sequestered by Sic1 / Cdc6) +S/G2: high Clb5 activity (i.e. not sequestered by the CKI), low Clb2. +M: high Clb2 activity +prophase / metaphase: low Esp1 activity (high Pds1) +anaphase / telophase: high Esp1 activity (low Pds1) (*) +(*) In the exit module, overexpressed Esp1 (Esp1=2) can overcome Pds1 inhibition.
+ +G1-cyclin, initiating Start events. + +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1.
+ +Protein initiating Start events.
+ +MBF and SBF are transcription factors. +SBF activates the transcription of Cln2. +MBF activates the transcription of Clb5.
+ +Cyclin involved in budding (represents both Cln1 and Cln2 in the model). + +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1.
+ +Transcription factor for Sic1 and Cdc6.
+ +Stoichiometric inhibitor of Cdc28/Clb2 and Cdc28/Clb5. + +Arrows directed towards Clb5 and Clb2's targets represent sequestration..
+ +Stoichiometric inhibitor of Cdc28/Clb2, but not of Cdc28/Clb5. Also a licencing factor for DNA replication. + + +Arrows directed towards Clb2's targets represent sequestration.
+ +B-type cyclins appearing late in G1, involved in DNA synthesis (represents both Clb5 and Clb6 in the model). + +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1. + +
+ +Kinase. Budding yeast homologue of Wee1. + +Activated by the MBF and inhibited by Hsl1 and Hsl7. + +Inhibits Clb2 activity by phosphorylating its Cdk partner Cdc28 on tyrosine-19.
+ +Phosphatase.Budding yeast homologue of Cdc25. + +Activates Clb2 by removing an inhibitory phosphate from Cdc28 on tyrosine-19.
+ +Activation depends on bud presence. + +Inhibits Swe1 (mecanism is unclear.)
+ +Kinase. Budding yeast homologue of Wee1. + +Activated by the MBF and inhibited by Hsl1 and Hsl7. + +Inhibits Clb2 activity by phosphorylating its Cdk partner Cdc28 on tyrosine-19.
+ +B-type cyclin essential for mitosis, present in S/G2/M phase (represents both Clb1 and Clb2 in the model). + +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1. + +Activates CDK-dependent inhibitory phosphorylation of Net1, Cdc15 and Cdh1. + +Level 1: transient level, used to monitor Clb2 degradation (activation of MITOSIS) + +
+ +Transcription factor for Clb2, Cdc20 and Swi5.
+ +Spindle assembly checkpoint protein. +"Mitosis Arrest Deficient" -- checkpoint protein that keeps Cdc20 inactive until the chromosomes are properly aligned.
+ +Activator of the APC; protein involved in Clb2, Clb5 and Pds1 proteolysis, and required for exit from mitosis. + +The APC core is considered constant throughout the cell cycle, and thus not represented.
+ +Kinase, phosphorylates Bfa1. +Essential in budding yeast for Cdc14 activation. ((Jaspersen et al., 1998; Lee et al., 2001; Stegmeier and Amon, 2004), cited in Queralt et al.)
+ +Type 2A phosphatase. +Queralt et al. (2006) refer to PP2ACdc55 as a complex consisting of Tpd3 (scaffold protein), either Pph21 or Pph22 (catalytic subunit), and Cdc55 (regulatory subunit, provide substrate specificity). +In metaphase, PP2ACdc55 prevents premature Net1 phosphorylation and Cdc14 activation. At anaphase onset, PP2ACdc55 activity is downregulated in a separase-dependent manner. (Queralt et al., 2006) +
+ +Spindle assembly checkpoint proteins. + +"Budding Uninhibited by Benomyl" -- checkpoint protein governed by spindle orientation. +
+ +GTP-GDP exchange factor. Present in the bud, and an activator of Tem1. + +Located in the daughter cell. Activates Tem1 when the later enters the bud.
+ +GTP-binding protein and a component of the MEN pathway.
+ +Kinase essential for late nuclear division and a component of the MEN pathway.
+ +Nucleolar protein and a stoichiometric inhibitor of Cdc14. +Inhibited by phosphorylation by Cdk and Cdc5/Polo. +aka: Cfi1
+ +Phosphatase required for exit of mitosis. + +Cdc14 reverses the CDK-mediated phosphorylation of Swi5, Sic1, Cdc6 and Cdh1.
+ +Activator of APC-dependent proteolysis; involved in Clb2 and Pds1 proteolysis. +Phosphorylation by the CDKs inhibits the binding to the APC. + +The APC core is considered constant throughout the cell cycle, and thus not represented.
+ +Represents the formation of a new bud when BUD = 1.
+ +Origin of replication. + +Represents the onset of DNA synthesis. + +Activates the spindle assembly checkpoint through Mad2 and Bub2-Bfa1.
+ +Spindle. + +Represents chromosomes alignment on the metaphase plate. + +Activation of this variable switches off the spindle assembly checkpoint through Mad2 and Bub2-Bfa1 inhibition.
+ +Stoichiometric inhibitor of Esp1 that prevents sister chromatid separation. +Degradation of Pds1 is necessary for release of Cdc14 from the nucleolus.
+ +Separase protein required for sister chromatid separation.
+ +Represents the mass of the cell. Boolean in this model. + +We assume that mass increase inpacts the cell cycle by increasing Cyclins concentration in the nucleus. + +In the wild-type, MASS has to cross the first threshold to initiate the cycle. + +Reset to zero when cytokinesis occurs. (Priorities are used to enforce the immediacy of the transition)
+ +In Chen et al.'s model, exit from mitosis occurs when Clb2's activity goes down a certain threshold. To represent this in the logical framework, the CYTOKINESIS variable is (pre-)activated (level 1) by high Clb2 (Clb2 = 2 or 3). Self-activating arrow keep tracks of high Clb2 pre-activation, allowing full activation when Clb2's activity is low. (i.e., making the difference between Clb2 increase and decrease.) + +Presence of the CKI has the same activating effect as low Clb2, and MASS is required to make sure the variable is inactivated after cell division. + +When CYTOKINESIS = 2, the MASS, BUD and SPN variables are reset to zero.
+ +This is a model with interactions derived from general siganling knowledge on the MAPK, PI3K, NFkB, and Wnt/beta-catenin pathways, and with Boolean equations that recapitulate
+
+All interactions are annotated with Pubmed IDs (PMID) pointing to literature references for the interaction.
+
+All nodes are annotated with the following information:
+
Gene: TP53 +Alternative gene names: P53 +Expressed in AGS. +No known mutations in AGS. + +Uniprot: P04637 (P53_HUMAN)
+ +IL1B_e is an input node marked with an auto-regulation.
+ +IFNG_e is an input node marked with an auto-regulation.
+ +IL2_e is an input node marked with an auto-regulation.
+ +IL4_e is an input node marked with an auto-regulation.
+ +IL6_e is an input node marked with an auto-regulation.
+ +IL10_e is an input node marked with an auto-regulation.
+ +IL12_e is an input node marked with an auto-regulation.
+ +IL15_e is an input node marked with an auto-regulation.
+ +IL21_e is an input node marked with an auto-regulation.
+ +IL23_e is an input node marked with an auto-regulation.
+ +IL27_e is an input node marked with an auto-regulation.
+ +TGFB_e is an input node marked with an auto-regulation.
+ +IL36_e is an input node marked with an auto-regulation.
+ +IL33_e is an input node marked with an auto-regulation.
+ +IL18_e is an input node marked with an auto-regulation.
+ +IL25_e is an input node marked with an auto-regulation.
+ +IFNB_e is an input node marked with an auto-regulation.
+ +IFNA_e is an input node marked with an auto-regulation.
+ +IL1A_e is an input node marked with an auto-regulation.
+ +IL29_e is an input node marked with an auto-regulation.
+ +APC is an input node marked with an auto-regulation.
+ +This logical model for the core cell cycle engine of the budding yeast is based on the differential published by Chen et al (2004). +This model is based on the antagonism between mitotic cyclins (Clb2 and Clb5) and G1 stabilizers (Cdh1 and the CKI). When mass increases above a certain threshold, G1 cyclins accumulate high enough to inhibit the G1 stabilizers, and thus indirectly activate the mitotic cyclins, thereby promoting entry into the S phase and mitosis. Clb2 triggers exit from mitosis and its own destruction, by activating Cdc20, and indirectly activates the G1 stabilizers through the release of the phosphatase Cdc14. +In addition, the model integrates a checkpoint mechanism that monitors DNA replication and spindle formation. + +Using well defined logical rules for the updating of each considered regulatory node, the simulation of this model qualitatively recapitulates the wild-type sequence of events the cell has to go through to be considered viable. +Over a hundred of different mutants (gene knock-outs, partial loss-of-functions, temperature-sensitive mutations, over- or ectopic expressions) or perturbations (e.g. culture in galactose- or glucose-rich medium) have been analysed experimentally and reported in the literature. + +Over 130 of these mutants have been successfully accounted for by Chen et al.'s model. In the present article, we set out to reproduce these results with our logical version of the model. Consistency of the mutant phenotypes is evaluated qualitatively in term of viability (cf infra), or arrest in a particular phase of the cell cycle. Dynamical analysis of most of the individual or multiple leads to results consistent with reported phenotypes, as well as with the results published by Chen et al.. + +Cell viability rule in terms of sequence of events: firing of the origins of replication (ORI goes up), spindle alignment (SPN goes up), separase activation (or inhibition of the securin, Pds1 goes down), division (MITOSIS goes up to level 2) after the formation of a bud (BUD must have reached value 1, although it goes down afterwards before cell division), and origin relicensing (ORI goes down). + +Cell cycle phases: +G0/G1: low Clb5 and Clb2 activity (either =0 or sequestered by Sic1 / Cdc6) +S/G2: high Clb5 activity (i.e. not sequestered by the CKI), low Clb2. +M: high Clb2 activity +prophase / metaphase: low Esp1 activity (high Pds1) +anaphase / telophase: high Esp1 activity (low Pds1) +
+ +Cln3 is the G1-cyclin, initiating Start events. +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1.
+ +The protein Bck2 initiates Start events. +
+ +MBF and SBF are transcription factors. +SBF activates the transcription of Cln2. +MBF activates the transcription of Clb5. +
+ +The cyclin Cln2 is involved in budding. +Cln2 represents both Cln1 and Cln2 in the model. +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1. +
+ +Swi 5 is transcription factor controlling Sic1 and Cdc6. + +
+ +Sic1 is a stoichiometric inhibitor of Cdc28/Clb2 and Cdc28/Clb5. +The arrows directed towards Clb5 and Clb2's targets represent sequestration. + +
+ +Cdc6 is a stoichiometric inhibitor of Cdc28/Clb2, but not of Cdc28/Clb5. +Cdc6 is also a licencing factor for DNA replication. +The arrows directed towards Clb2's targets represent sequestration.
+ +Clb5 is a B-type cyclins appearing late in G1, involved in DNA synthesis (represents both Clb5 and Clb6 in the model). +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1. +
+ +Clb2 is aB-type cyclin essential for mitosis, present in S/G2/M phase (represents both Clb1 and Clb2 in the model). +All cyclins (with different efficiencies) activate CDK-dependent inhibitory phosphorylation of Sic1, Cdc6 and Cdh1. +Level 1: transient level, used to monitor Clb2 degradation (activation of MITOSIS)
+ +Mcm1 is a transcription factor controlling the expression of Clb2, Cdc20 and Swi5.
+ +Mad2 is a spindle assembly checkpoint protein. +Mad stands for "Mitosis Arrest Deficient". +Mad2 is a checkpoint protein that keeps Cdc20 inactive until the chromosomes are properly aligned.
+ +Cdc20 is the activator of the APC; protein involved in Clb2, Clb5 and Pds1 proteolysis, and is required for exit from mitosis. +The APC core is considered constant throughout the cell cycle, and thus not represented.
+ +Unknown phosphatase hypothetised by Chen et al (2004).
+ +Spindle assembly checkpoint proteins. +Budding Uninhibited by Benomyl +Checkpoint protein governed by spindle orientation.
+ +GTP-GDP exchange factor. +Present in the bud, and an activator of Tem1. +Located in the daughter cell. +Activates Tem1 when the later enters the bud.
+ +GTP-binding protein and a component of the MEN pathway.
+ +Kinase essential for late nuclear division and a component of the MEN pathway.
+ +Nucleolar protein and a stoichiometric inhibitor of Cdc14.
+ +Phosphatase required for exit of mitosis. +Cdc14 reverses the CDK-mediated phosphorylation of Swi5, Sic1, Cdc6 and Cdh1.
+ +Activator of APC-dependent proteolysis. +Involved in Clb2 and Pds1 proteolysis. +Phosphorylation by the CDKs inhibits the binding to the APC. +The APC core is considered constant throughout the cell cycle, and thus not represented.
+ +Represents the formation of a new bud (BUD = 1).
+ +Origin of replication. +Represents the onset of DNA synthesis (ORI=1). +Activates the spindle assembly checkpoint through Mad2 and Bub2-Bfa1.
+ +Spindle. +Represents chromosomes alignment on the metaphase plate (SPN=1). +Activation of this variable switches off the spindle assembly checkpoint through Mad2 and Bub2-Bfa1 inhibition. +
+ +Stoichiometric inhibitor of Esp1 that prevents sister chromatid separation. +Degradation of Pds1 is necessary for release of Cdc14 from the nucleolus.
+ +Esp1 (separase) is a caspase, responsible for the cleavage of cohesin subunit that holds the sister chromatids together. +Esp1 is sequestered and kept inactive by Pds1.
+ +Represents the mass of the cell. Boolean in this model. +It is assumed that mass increase inpacts the cell cycle by increasing Cyclins concentration in the nucleus. +In the wild-type, MASS has to cross the first threshold to initiate the cycle. +Reset to zero when cytokinesis occurs. +Priorities are used to enforce the immediacy of the transition
+ +In the model of Chen et al (2004), exit from mitosis occurs when Clb2 activity goes down a certain threshold. To represent this in the logical framework, the CYTOKINESIS variable is (pre-)activated (level 1) by high Clb2 (Clb2 = 2 or 3). Self-activating arrow keep tracks of high Clb2 pre-activation, allowing full activation when Clb2's activity is low. (i.e., making the difference between Clb2 increase and decrease.) +Presence of the CKI has the same activating effect as low Clb2, and MASS is required to make sure the variable is inactivated after cell division. +When CYTOKINESIS = 2, the MASS, BUD and SPN variables are reset to zero. + +
+ +Nodal_In is an input node marked with an auto-regulation.
+ +Lefty_In is an input node marked with an auto-regulation.
+ +Bmp2_4_In is an input node marked with an auto-regulation.
+ +Chordin_In is an input node marked with an auto-regulation.
+ +Tolloid_In is an input node marked with an auto-regulation.
+ +Admp1_In is an input node marked with an auto-regulation.
+ +Wnt_In is an input node marked with an auto-regulation.
+ +Ag is an input node marked with an auto-regulation.
+ +cCbl is an input node marked with an auto-regulation.
+ +PIP2 is an input node marked with an auto-regulation.
+ +EGFR_stimulus is an input node marked with an auto-regulation.
+ +FGFR3_stimulus is an input node marked with an auto-regulation.
+ +DNAdamage is an input node marked with an auto-regulation.
+ +GrowthInhibitors is an input node marked with an auto-regulation.
+ +MCSF is an input node marked with an auto-regulation.
+ +IL7 is an input node marked with an auto-regulation.
+ +Delta is an input node marked with an auto-regulation.
+ +HOW TO FIND THE STABLE STATES LISTED IN TABLE 2: +1. Click on the "Stable States" of the "Actions" menu. +2. For the wild-type situation, just click on the "Run" button to get the stable state. +3. For a mutant situation, select one of the available mutations from the "Mutant Selection" list and click the "Run" button. +
+ +