Transcription factors important for starting the cell cycle in yeast

Experimental testing of a new integrated model of the budding yeast Start transition

Mathematical modeling of the cell cycle has unveiled recurrent features and emergent behaviors of cellular networks. Constructing new mutants and performing experimental tests during development of a new model of the budding yeast cell cycle yields a more efficient modeling process and results in several testable hypotheses.

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1–S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1–S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model’s simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network.

Control of cell cycle transcription during G1 and S phases

The accurate transition from G1 phase of the cell cycle to S phase is crucial for the control of eukaryotic cell proliferation, and its misregulation promotes oncogenesis. During G1 phase, growth-dependent cyclin-dependent kinase (CDK) activity promotes DNA replication and initiates G1-to-S phase transition. CDK activation initiates a positive feedback loop that further increases CDK activity, and this commits the cell to division by inducing genome-wide transcriptional changes. G1-S transcripts encode proteins that regulate downstream cell cycle events. Recent work is beginning to reveal the complex molecular mechanisms that control the temporal order of transcriptional activation and inactivation, determine distinct functional subgroups of genes and link cell cycle-dependent transcription to DNA replication stress in yeast and mammals.

Design principles of the yeast G1/S switch

A hallmark of the G1/S transition in budding yeast cell cycle is the proteolytic degradation of the B-type cyclin-Cdk stoichiometric inhibitor Sic1. Deleting SIC1 or altering Sic1 degradation dynamics increases genomic instability. Certain key facts about the parts of the G1/S circuitry are established: phosphorylation of Sic1 on multiple sites is necessary for its destruction, and both the upstream kinase Cln1/2-Cdk1 and the downstream kinase Clb5/6-Cdk1 can phosphorylate Sic1 in vitro with varied specificity, cooperativity, and processivity. However, how the system works as a whole is still controversial due to discrepancies between in vitro, in vivo, and theoretical studies. Here, by monitoring Sic1 destruction in real time in individual cells under various perturbations to the system, we provide a clear picture of how the circuitry functions as a switch in vivo. We show that Cln1/2-Cdk1 sets the proper timing of Sic1 destruction, but does not contribute to its destruction speed; thus, it acts only as a trigger. Sic1's inhibition target Clb5/6-Cdk1 controls the speed of Sic1 destruction through a double-negative feedback loop, ensuring a robust all-or-none transition for Clb5/6-Cdk1 activity. Furthermore, we demonstrate that the degradation of a single-phosphosite mutant of Sic1 is rapid and switch-like, just as the wild-type form. Our mathematical model confirms our understanding of the circuit and demonstrates that the substrate sharing between the two kinases is not a redundancy but a part of the design to overcome the trade-off between the timing and sharpness of Sic1 degradation. Our study provides direct mechanistic insight into the design features underlying the yeast G1/S switch.

The mitotic Clb cyclins are required to alleviate HIR-mediated repression of the yeast histone genes at the G1/S transition

The histone genes are an important group of cell cycle regulated genes whose transcription is activated during the G1/S transition and repressed in early G1, late S, and G2/M. The HIR complex, comprised of Hir1, Hir2, Hir3 and Hpc2, regulates three of the four histone gene loci. While relief of repression at the G1/S boundary involves the HIR complex, as well as other cofactors, the mechanism by which this derepression occurs remains unknown. To better understand how transcriptional repression contributes to periodic expression in the cell cycle, we sought to identify the cell cycle signals required to alleviate HIR-mediated repression of the histone genes. By measuring histone gene transcription in strains with various combinations of clb mutations, we found that the mitotic Clb1/Clb2 cyclins are required to alleviate Hir-mediated repression during the G1/S transition and that Clb2 physically interacts with the HIR complex. While the HIR complex regulates histone gene transcription in combination with two other histone H3/H4 chaperones, Asf1 and Rtt106, our data demonstrate that the mitotic Clb cyclins are necessary to specifically alleviate the repressive action of the HIR complex itself in order to allow proper expression of the histone genes in late G1/early S phase.

Cell size at S phase initiation: an emergent property of the G1/S network

The eukaryotic cell cycle is the repeated sequence of events that enable the division of a cell into two daughter cells. It is divided into four phases: G₁, S, G₂, and M. Passage through the cell cycle is strictly regulated by a molecular interaction network, which involves the periodic synthesis and destruction of cyclins that bind and activate cyclin-dependent kinases that are present in nonlimiting amounts. Cyclin-dependent kinase inhibitors contribute to cell cycle control. Budding yeast is an established model organism for cell cycle studies, and several mathematical models have been proposed for its cell cycle. An area of major relevance in cell cycle control is the G₁ to S transition. In any given growth condition, it is characterized by the requirement of a specific, critical cell size, P_S, to enter S phase. The molecular basis of this control is still under discussion. The authors report a mathematical model of the G₁ to S network that newly takes into account nucleo/cytoplasmic localization, the role of the cyclin-dependent kinase Sic1 in facilitating nuclear import of its cognate Cdk1-Clb5, Whi5 control, and carbon source regulation of Sic1 and Sic1-containing complexes. The model was implemented by a set of ordinary differential equations that describe the temporal change of the concentration of the involved proteins and protein complexes. The model was tested by simulation in several genetic and nutritional setups and was found to be neatly consistent with experimental data. To estimate P_S, the authors developed a hybrid model including a probabilistic component for firing of DNA replication origins. Sensitivity analysis of P_S provides a novel relevant conclusion: P_S is an emergent property of the G₁ to S network that strongly depends on growth rate.

A major property of living cells is their ability to maintain mass homeostasis throughout cell divisions. It has been proposed that in order to achieve such homeostasis, some critical event(s) in the cell cycle will take place only when the cell has grown beyond a critical cell size. In the budding yeast Saccharomyces cerevisiae, a widely used model for the study of the eukaryotic cell cycle, a large body of evidence indicates that cells have to reach a critical size before they start to replicate their DNA and to form bud, which will give rise to the daughter cell. This critical cell size is modulated by growth rate, hence by nutritional conditions and the multiplicity of genetic material (i.e., ploidy). The authors present a mathematical model of the regulatory molecular network acting at the G₁ to S transition. The major novel features of this model compared with previous models of this process are (1) the accounting for cell growth (i.e., the increase in cell volume); (2) the explicit consideration of the fact that cells have a nucleus and a cytoplasm, and that key cell cycle regulatory molecules must move between these different compartments and can only react or regulate each other if they are in the same compartment; and (3) the requirement of sequential overcoming of two molecular thresholds given by a cyclin-dependent kinase/cyclin and a cyclin-dependent kinase inhibitor. The model was tested by simulating the processes during G₁ to S transition for different growth conditions or for different mutants and by comparing the results with experimental data. A parameter sensitivity analysis (i.e., testing the model predictions when parameters are varied), newly indicates that the critical cell size is an emergent property of the G₁ to S network. The model leads to a unified interpretation of seemingly disparate experimental observations and makes predictions to be experimentally verified.

Distinct mechanisms control the stability of the related S-phase cyclins Clb5 and Clb6

The yeast S-phase cyclins Clb5 and Clb6 are closely related proteins that are synthesized late in G1. Although often grouped together with respect to function, Clb5 and Clb6 exhibit differences in their ability to promote S-phase progression. DNA replication is significantly slowed in clb5Delta mutants but not in clb6Delta mutants. We have examined the basis for the differential functions of Clb5 and Clb6 and determined that unlike Clb5, which is stable until mitosis, Clb6 is degraded rapidly at the G1/S border. N-terminal deletions of CLB6 were hyperstabilized, suggesting that the sequences responsible for directing the destruction of Clb6 reside in the N terminus. Clb6 lacks the destruction box motif responsible for the anaphase promoting complex-mediated destruction of Clb5 but contains putative Cdc4 degron motifs in the N terminus. Clb6 was hyperstabilized in cdc34-3 and cdc4-3 mutants at restrictive temperatures and when S/T-P phosphorylation sites in the N terminus were mutated to nonphosphorylatable residues. Efficient degradation of Clb6 requires the activities of both Cdc28 and Pho85. Finally, hyperstabilized Clb6 expressed from the CLB6 promoter rescued the slow S-phase defect exhibited by clb5Delta cells. Taken together, these findings suggest that the SCF(Cdc4) ubiquitin ligase complex regulates Clb6 turnover and that the functional differences exhibited by Clb5 and Clb6 arise from the distinct mechanisms controlling their stability.

Evidence that Spt10 and Spt21 of Saccharomyces cerevisiae play distinct roles in vivo and functionally interact with MCB-binding factor, SCB-binding factor and Snf1

Mutations in SPT10 and SPT21 of Saccharomyces cerevisiae have been previously shown to cause two prominent mutant phenotypes: (1) defects in transcription of particular histone genes and (2) suppression of Ty and delta-insertion mutations (Spt(-) phenotype). The requirement for Spt10 and Spt21 for transcription of particular histone genes suggested that they may interact with two factors previously shown to be present at histone loci, SBF (Swi4 and Swi6) and MBF (Mbp1 and Swi6). Therefore, we have studied swi4Delta, mbp1Delta, and swi6Delta mutants with respect to histone gene transcription and for interactions with spt10Delta and spt21Delta. Our results suggest that MBF and SBF play only modest roles in activation of histone gene transcription. In addition, we were surprised to find that swi4Delta, mbp1Delta, and swi6Delta mutations suppress the spt21Delta Spt(-) phenotype, but not the spt21Delta defect in histone gene transcription. In contrast, both swi4Delta and mbp1Delta cause lethality when combined with spt10Delta. To learn more about mutations that can suppress the spt21Delta Spt(-) phenotype, we performed a genetic screen and identified spt21Delta suppressors in seven additional genes. Three of these spt21Delta suppressors also cause lethality when combined with spt10Delta. Analysis of one spt21Delta suppressor, reg1, led to the finding that hyperactivation of Snf1 kinase, as caused by reg1Delta, suppresses the Spt(-) phenotype of spt21Delta. Taken together, these genetic interactions suggest distinct roles for Spt21 and Spt10 in vivo that are sensitive to multiple perturbations in transcription networks.

Functional domains of rep2, a transcriptional activator subunit for Res2-Cdc10, controlling the cell cycle "start"

In the fission yeast Schizosaccharomyces pombe, passage from G1 to S-phase requires the execution of the transcriptional factor complex that consists of the Cdc10 and Res1/2 molecules. This complex activates the MluI cell cycle box cis-element contained in genes essential for S-phase onset and progression. The rep2(+) gene, isolated as a multicopy suppressor of a temperature-sensitive cdc10 mutant, has been postulated to encode a putative transcriptional activator subunit for the Res2-Cdc10 complex. To identify the rep2(+) function and molecularly define its domain organization, we reconstituted the Res2-Cdc10 complex-dependent transcriptional activation in Saccharomyces cerevisiae. Reconstitution experiments, deletion analyses using one and two hybrid systems, and in vivo Res2 coimmunoprecipitation assays show that the Res2-Cdc10 complex itself can recognize but cannot activate MluI cell cycle box without Rep2, and that consistent with its postulated function, Rep2 contains 45-amino acid Res2 binding and 22-amino acid transcriptional activation domains in the middle and C terminus of the molecule, respectively. The functional essentiality of these domains is also demonstrated by their requirement for rescue of the cold-sensitive rep2 deletion mutant of fission yeast.

A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase

In budding yeast genes that encode G1 cyclins and proteins involved in DNA synthesis are transcriptionally activated in late G1. A transcription factor, called SBF, is composed of Swi4 and Swi6 proteins and activates transcription of G1 cyclin genes. A different, but related, complex called MBF binds to MCB elements (Mlu I cell cycle box) found in the promoter of most DNA synthesis genes. MBF contains Swi6 and a 120-kilodalton protein (p120). MBF was purified and the gene encoding p120 (termed MBP1) was cloned. A deletion of MBP1 was not lethal but led to deregulated expression of DNA synthesis genes, indicating a direct regulatory role for MBF in MCB-driven transcription. Mbp1 is related to Swi4. Strains deleted for both MBP1 and SWI4 were inviable, demonstrating that transcriptional activation by MBF and SBF has an important role in the transition from G1 to S phase.