Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos

Mechanistic origins of temperature scaling in the early embryonic cell cycle

Temperature profoundly impacts organismal physiology and ecological dynamics, particularly affecting ectothermic species and making them especially vulnerable to climate changes. Although complex physiological processes usually involve dozens of enzymes, empirically it is found that the rates of these processes often obey the Arrhenius equation, which was originally proposed for individual chemical reactions. Here we have examined the temperature scaling of the early embryonic cell cycle, with the goal of understanding why the Arrhenius equation approximately holds and why it breaks down at temperature extremes. Using experimental data from Xenopus laevis, Xenopus tropicalis, and Danio rerio, plus published data from Caenorhabditis elegans, Caenorhabditis briggsae, and Drosophila melanogaster, we find that the apparent activation energies (E a values) for the early embryonic cell cycle for diverse ectotherms are all similar, 75 ± 7 kJ/mol (mean ± std.dev., n = 6), which corresponds to aQ 10 value at 20°C of 2.8 ± 0.2 (mean ± std.dev., n = 6). Using computational models, we find that the approximate Arrhenius scaling and the deviations from it at high and low temperatures can be accounted for by biphasic temperature scaling in critical individual components of the cell cycle oscillator circuit, by imbalances in theE a values for different partially rate-determining enzymes, or by a combination of both. Experimental studies of cycling Xenopus extracts indicate that both of these mechanisms contribute to the general scaling of temperature, and in vitro studies of individual cell cycle regulators confirm that there is in fact a substantial imbalance in theirE a values. These findings provide mechanistic insights into the dynamic interplay between temperature and complex biochemical processes, and into why biological systems fail at extreme temperatures.

Mathematical Modeling for Oscillations Driven by Noncoding RNAs

In this chapter, we first survey strategies for the mathematical modeling of gene regulatory networks for capturing physiologically important dynamics in cells such as oscillations. We focus on models based on ordinary differential equations with various forms of nonlinear functions that describe gene regulations. We next use a small system of a microRNA and its mRNA target to illustrate a recently discovered oscillator driven by noncoding RNAs. This oscillator has unique features that distinguish it from conventional biological oscillators, including the absence of an imposed negative feedback loop and the divergence of the periods. The latter property may serve crucial biological functions for restoring heterogeneity of cell populations on the timescale of days. We describe general requirements for obtaining the limit cycle oscillations in terms of underlying biochemical reactions and kinetic rate constants. We discuss future directions stemming from this minimal, noncoding RNA-based model for gene expression oscillation.

Interdependency of estradiol-mediated ERα activation and subsequent PR and GREB1 induction to control cell cycle progression

Various groups of chemicals that we encounter in every-day life are known to disrupt the endocrine system, such as estrogen mimics that can disturb normal cellular development and homeostasis. To understand the effect of estrogen on intracellular protein dynamics and how this relates to cell proliferation, we aimed to develop a quantitative description of transcription factor complexes and their regulation of cell cycle progression in response to estrogenic stimulation. We designed a mathematical model that describes the dynamics of three proteins, GREB1, PR and TFF1, that are transcriptionally activated upon binding of 17β-estradiol (E2) to estrogen receptor alpha (ERα). Calibration of this model to imaging data monitoring the expression dynamics of these proteins in MCF7 cells suggests that transcriptional activation of GREB1 and PR depends on the association of the E2-ERα complex with both GREB1 and PR. We subsequently combined this ER signaling model with a previously published cell cycle model and compared this to quantification of cell cycle durations in MCF7 cells following nuclei tracking based on images segmented with deep neural networks. The resulting model predicts the effect of GREB1 and PR knockdown on cell cycle progression, thus providing mechanistic insight in the molecular interactions between ERα-regulated proteins and their relation to cell cycle progression. Our findings form a valuable basis to further investigate the pharmacodynamics of endocrine disrupting chemicals and their influence on cellular behavior.

Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation

YAP is a transcriptional regulator that controls pluripotency, cell fate, and proliferation. How cells ensure the selective activation of YAP effector genes is unknown. This knowledge is essential to rationally control cellular decision-making. Here we leverage optogenetics, live-imaging of transcription, and cell fate analysis to understand and control gene activation and cell behavior. We reveal that cells decode the steady-state concentrations and timing of YAP activation to control proliferation, cell fate, and expression of the pluripotency regulators Oct4 and Nanog. While oscillatory YAP inputs induce Oct4 expression and proliferation optimally at frequencies that mimic native dynamics, cellular differentiation requires persistently low YAP levels. We identify the molecular logic of the Oct4 dynamic decoder, which acts through an adaptive change sensor. Our work reveals how YAP levels and dynamics enable multiplexing of information transmission for the regulation of developmental decision-making and establishes a platform for the rational control of these behaviors.

CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos

After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.

HDAC11 mediates the ubiquitin-dependent degradation of p53 and inhibits the anti-leukemia effect of PD0166285

Cytarabine-resistant acute myeloid leukemia (AML) is a common phenomenon, necessitating the search for new chemotherapeutics. WEE1 participates in cell cycle checkpoint signaling and inhibitors targeting WEE1 (WEE1i) constitute a potential novel strategy for AML treatment. HDAC (histone deacetylase) inhibitors have been shown to enhance the anti-tumor effects of WEE1i but molecular mechanisms of HDAC remain poorly characterized. In this study, the WEE1 inhibitor PD0166285 showed a relatively good anti-leukemia effect. Notably, PD0166285 can arise the expression of HDAC11 which was negatively correlated with survival of AML patients. Moreover, HDAC11 can reduced the anti-tumor effect of PD0166285 through an effect on p53 stability and the changes in phosphorylation levels of MAPK pathways. Overall, the cell cycle inhibitor, PD0166285, is a potential chemotherapeutic drug for AML. These fundings contribute to a functional understanding of HDAC11 in AML.

Pseudo-nullclines enable the analysis and prediction of signaling model dynamics

A powerful method to qualitatively analyze a 2D system is the use of nullclines, curves which separate regions of the plane where the sign of the time derivatives is constant, with their intersections corresponding to steady states. As a quick way to sketch the phase portrait of the system, they can be sufficient to understand the qualitative dynamics at play without integrating the differential equations. While it cannot be extended straightforwardly for dimensions higher than 2, sometimes the phase portrait can still be projected onto a 2-dimensional subspace, with some curves becoming pseudo-nullclines. In this work, we study cell signaling models of dimension higher than 2 with behaviors such as oscillations and bistability. Pseudo-nullclines are defined and used to qualitatively analyze the dynamics involved. Our method applies when a system can be decomposed into 2 modules, mutually coupled through 2 scalar variables. At the same time, it helps track bifurcations in a quick and efficient manner, key for understanding the different behaviors. Our results are both consistent with the expected dynamics, and also lead to new responses like excitability. Further work could test the method for other regions of parameter space and determine how to extend it to three-module systems.

Dynamic full-field optical coherence tomography module adapted to commercial microscopes allows longitudinal in vitro cell culture study

Dynamic full-field optical coherence tomography (D-FFOCT) has recently emerged as a label-free imaging tool, capable of resolving cell types and organelles within 3D live samples, whilst monitoring their activity at tens of milliseconds resolution. Here, a D-FFOCT module design is presented which can be coupled to a commercial microscope with a stage top incubator, allowing non-invasive label-free longitudinal imaging over periods of minutes to weeks on the same sample. Long term volumetric imaging on human induced pluripotent stem cell-derived retinal organoids is demonstrated, highlighting tissue and cell organization processes such as rosette formation and mitosis as well as cell shape and motility. Imaging on retinal explants highlights single 3D cone and rod structures. An optimal workflow for data acquisition, postprocessing and saving is demonstrated, resulting in a time gain factor of 10 compared to prior state of the art. Finally, a method to increase D-FFOCT signal-to-noise ratio is demonstrated, allowing rapid organoid screening.

The super-enhancer-driven lncRNA LINC00880 acts as a scaffold between CDK1 and PRDX1 to sustain the malignance of lung adenocarcinoma

Super-enhancers (SEs) are regulatory element clusters related to cell identity and disease. While the studies illustrating the function of SE-associated long noncoding RNAs (lncRNAs) in lung adenocarcinoma (LUAD) remains few. In our research, a SE-driven lncRNA, LINC00880, was identified, which showed higher expression in LUAD compared to normal tissues and indicated worse outcomes in stage I LUADs. We found that the transcription factor (TF) FOXP3 could simultaneously occupy the promoter and SE regions of LINC00880 to promote its transcription. The oncogenic function of LINC00880 was validated both in vitro and in vivo. Mechanically, LINC00880 binds to the protein CDK1 to increase its kinase activity, which rely on the phosphorylation state of pT161 in CDK1. LINC00880 also promotes the interaction between CDK1 and PRDX1. Moreover, LINC00880 interacts with PRDX1, which indicates that LINC00880 acts as a protein scaffold between CDK1 and PRDX1 to form a ternary complex, thereby resulting in the activation of PI3K/AKT to promote malignancy. Our results reveal that the SE-associated lncRNA LINC00880 regulates the CDK1/PRDX1 axis to sustain the malignancy of LUAD, providing a novel therapeutic target.

Cell cycle oscillations driven by two interlinked bistable switches

Regular transitions between interphase and mitosis during the cell cycle are driven by changes in the activity of the enzymatic protein complex cyclin B with cyclin-dependent kinase 1 (Cdk1). At the most basic level, this cell cycle oscillator is driven by negative feedback: active cyclin B-Cdk1 activates the anaphase-promoting complex/cyclosome, which triggers the degradation of cyclin B. Such cell cycle oscillations occur fast and periodically in the early embryos of the frog Xenopus laevis, where several positive-feedback loops leading to bistable switches in parts of the regulatory network have been experimentally identified. Here, we build cell cycle oscillator models to show how single and multiple bistable switches in parts of the underlying regulatory network change the properties of the oscillations and how they can confer robustness to the oscillator. We present a detailed bifurcation analysis of these models.

Establishment of the body condition score for adult female Xenopus laevis

The assessment of animals' health and nutritional status using a Body Condition Score (BCS) has become a common and reliable tool in lab-animal science. It enables a simple, semi-objective, and non-invasive assessment (palpation of osteal prominences and subcutaneous fat tissue) in routine examination of an animal. In mammals, the BCS classification contains 5 levels: A low score describes a poor nutritional condition (BCS 1-2). A BCS of 3 to 4 is considered optimum, whereas a high score (BCS = 5) is associated with obesity. While BCS are published for most common laboratory mammals, these assessment criteria are not directly applicable to clawed frogs (Xenopus laevis) due to their intracoelomic fat body instead of subcutaneous fat tissue. Therefore, this assessment tool is still missing for Xenopus laevis. The present study aimed to establish a species-specific BCS for clawed frogs in terms of housing refinement in lab-animal facilities. Accordingly, 62 adult female Xenopus laevis were weighed and sized. Further, the body contour was defined, classified, and assigned to BCS groups. A BCS 5 was associated with a mean body weight of 193.3 g (± 27.6 g), whereas a BCS 4 ranged at 163.1 g (±16.0 g). Animals with a BCS = 3 had an average body weight of 114.7 g (±16.7 g). A BCS = 2 was determined in 3 animals (103 g, 110 g, and 111 g). One animal had a BCS = 1 (83 g), equivalent to a humane endpoint. In conclusion, individual examination using the presented visual BCS provides a quick and easy assessment of the nutritional status and overall health of adult female Xenopus laevis. Due to their ectothermic nature and the associated special metabolic situation, it can be assumed that a BCS ≥3 is to be preferred for female Xenopus laevis. In addition, BCS assessment may indicate underlying subclinical health problems that require further diagnostic investigation.

The midbody component Prc1-like is required for microtubule reorganization during cytokinesis and dorsal determinant segregation in the early zebrafish embryo

We show that the zebrafish maternal-effect mutation too much information (tmi) corresponds to zebrafish prc1-like (prc1l), which encodes a member of the MAP65/Ase1/PRC1 family of microtubule-associated proteins. Embryos from tmi homozygous mutant mothers display cytokinesis defects in meiotic and mitotic divisions in the early embryo, indicating that Prc1l has a role in midbody formation during cell division at the egg-to-embryo transition. Unexpectedly, maternal Prc1l function is also essential for the reorganization of vegetal pole microtubules required for the segregation of dorsal determinants. Whereas Prc1 is widely regarded to crosslink microtubules in an antiparallel conformation, our studies provide evidence for an additional function of Prc1l in the bundling of parallel microtubules in the vegetal cortex of the early embryo during cortical rotation and prior to mitotic cycling. These findings highlight common yet distinct aspects of microtubule reorganization that occur during the egg-to-embryo transition, driven by maternal product for the midbody component Prc1l and required for embryonic cell division and pattern formation.

A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems

In this article, we consider a double phosphorylation cycle, a ubiquitous signaling component, having the ability to display bistability, a behavior strongly related to the existence of positive feedback loops. If this component is connected to other signaling elements, it very likely undergoes some sort of protein-protein interaction. In several cases, these interactions result in a non-explicit negative feedback effect, leading to interlinked positive and negative feedbacks. This combination was studied in the literature as a way to generate relaxation-type oscillations. Here, we show that the two feedbacks together ensure two types of oscillations, the relaxation-type ones and a smoother type of oscillations functioning in a very narrow range of frequencies, in such a way that outside that range, the amplitude of the oscillations is severely compromised. Even more, we show that the two feedbacks are essential for both oscillatory types to emerge, and it is their hierarchy what determines the type of oscillation at work. We used bifurcation analyses and amplitude vs. frequency curves to characterize and classify the oscillations. We also applied the same ideas to another simple model, with the goal of generalizing what we learned from signaling models. The results obtained display the wealth of oscillatory dynamics that exists in a system with a bistable module nested within a negative feedback loop, showing how to transition between different types of oscillations and other dynamical behaviors such as excitability. Our work provides a framework for the study of other oscillatory systems based on bistable modules, from simple two-component models to more complex examples like the MAPK cascade and experimental cases like cell cycle oscillators.

Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems

We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures have been discussed. The biological applications ranging from protein folding, biomolecular recognition, specificity, biomolecular evolution and design for equilibrium systems as well as cell cycle, differentiation and development, cancer, neural networks and brain function, and evolution for nonequilibrium systems, cross-scale studies of genome structural dynamics and experimental quantifications/verifications of the landscape and flux are illustrated. Together, this gives an overall global physical and quantitative picture in terms of the landscape and flux for the behaviors, dynamics and functions of biological systems.

Cell cycle involvement in cancer therapy; WEE1 kinase, a potential target as therapeutic strategy

Mitosis is the process of cell division and is regulated by checkpoints in the cell cycle. G1-S, S, and G2-M are the three main checkpoints that prevent initiation of the next phase of the cell cycle phase until previous phase has completed. DNA damage leads to activation of the G2-M checkpoint, which can trigger a downstream DNA damage response (DDR) pathway to induce cell cycle arrest while the damage is repaired. If the DNA damage cannot be repaired, the replication stress response (RSR) pathway finally leads to cell death by apoptosis, in this case called mitotic catastrophe. Many cancer treatments (chemotherapy and radiotherapy) cause DNA damages based on SSBs (single strand breaks) or DSBs (double strand breaks), which cause cell death through mitotic catastrophe. However, damaged cells can activate WEE1 kinase (as a part of the DDR and RSR pathways), which prevents apoptosis and cell death by inducing cell cycle arrest at G2 phase. Therefore, inhibition of WEE1 kinase could sensitize cancer cells to chemotherapeutic drugs. This review focuses on the role of WEE1 kinase (as a biological macromolecule which has a molecular mass of 96 kDa) in the cell cycle, and its interactions with other regulatory pathways. In addition, we discuss the potential of WEE1 inhibition as a new therapeutic approach in the treatment of various cancers, such as melanoma, breast cancer, pancreatic cancer, cervical cancer, etc.

Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos

The active site of the essential CDK1 kinase is generated by core structural elements, among which the PSTAIRE motif in the critical αC-helix, is universally conserved in the single CDK1 ortholog of all metazoans. We report serial CDK1 duplications in the chordate, Oikopleura. Paralog diversifications in the PSTAIRE, activation loop substrate binding platform, ATP entrance site, hinge region, and main Cyclin binding interface, have undergone positive selection to subdivide ancestral CDK1 functions along the S-M phase cell cycle axis. Apparent coevolution of an exclusive CDK1d:Cyclin Ba/b pairing is required for oogenic meiosis and early embryogenesis, a period during which, unusually, CDK1d, rather than Cyclin Ba/b levels, oscillate, to drive very rapid cell cycles. Strikingly, the modified PSTAIRE of odCDK1d shows convergence over great evolutionary distance with plant CDKB, and in both cases, these variants exhibit increased specialization to M-phase.

Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast

Networks of interacting molecules organize topology, amount, and timing of biological functions. Systems biology concepts required to pin down 'network motifs' or 'design principles' for time-dependent processes have been developed for the cell division cycle, through integration of predictive computer modeling with quantitative experimentation. A dynamic coordination of sequential waves of cyclin-dependent kinases (cyclin/Cdk) with the transcription factors network offers insights to investigate how incompatible processes are kept separate in time during the eukaryotic cell cycle. Here this coordination is discussed for the Forkhead transcription factors in light of missing gaps in the current knowledge of cell cycle control in budding yeast. An emergent design principle is proposed where cyclin waves are synchronized by a cyclin/Cdk-mediated feed-forward regulation through the Forkhead as a transcriptional timer. This design is rationalized by the bidirectional interaction between mitotic cyclins and the Forkhead transcriptional timer, resulting in an autonomous oscillator that may be instrumental for a well-timed progression throughout the cell cycle. The regulation centered around the cyclin/Cdk-Forkhead axis can be pivotal to timely coordinate cell cycle dynamics, thereby to actuate the quantitative model of Cdk control.

Regulation of Myt1 kinase activity via its N-terminal region in Xenopus meiosis and mitosis

Immature animal oocytes are naturally arrested at the first meiotic prophase (Pro-I), which corresponds to the G2 phase of the cell cycle. In Xenopus oocytes, Myt1 kinase phosphorylates and inactivates cyclin-dependent kinase 1 (Cdk1) at Pro-I, thereby preventing oocytes from entering meiosis I (MI) prematurely. Previous studies have shown that, upon resuming MI, Cdk1 and p90rsk, which is a downstream kinase of the Mos-MAPK pathway, in turn phosphorylate the C-terminal region of Myt1, to suppress its activity, thereby ensuring high Cdk1 activity during M phase. However, the roles of the N-terminal region of Myt1 during meiosis and mitosis remain to be elucidated. In the present study, we show that the N-terminal region of Myt1 participates in the regulation of Myt1 activity in the Xenopus cell cycle. In particular, we found that a short, conserved sequence in the N-terminal region, termed here as the PAYF motif, is required for the normal activity of Myt1 in oocytes. Furthermore, multiple phosphorylations by Cdk1 at the Myt1 N-terminal region were found to be involved in the negative regulation of Myt1. In particular, phosphorylations at Thr11 and Thr16 of Myt1, which are adjacent to the PAYF motif, were found to be important for the inactivation of Myt1 in the M phase of the cell cycle. These results suggest that in addition to the regulation of Myt1 activity via the C-terminal region, the N-terminal region of Myt1 also plays an important role in the regulation of Myt1 activity.

A modular approach for modeling the cell cycle based on functional response curves

Modeling biochemical reactions by means of differential equations often results in systems with a large number of variables and parameters. As this might complicate the interpretation and generalization of the obtained results, it is often desirable to reduce the complexity of the model. One way to accomplish this is by replacing the detailed reaction mechanisms of certain modules in the model by a mathematical expression that qualitatively describes the dynamical behavior of these modules. Such an approach has been widely adopted for ultrasensitive responses, for which underlying reaction mechanisms are often replaced by a single Hill function. Also time delays are usually accounted for by using an explicit delay in delay differential equations. In contrast, however, S-shaped response curves, which by definition have multiple output values for certain input values and are often encountered in bistable systems, are not easily modeled in such an explicit way. Here, we extend the classical Hill function into a mathematical expression that can be used to describe both ultrasensitive and S-shaped responses. We show how three ubiquitous modules (ultrasensitive responses, S-shaped responses and time delays) can be combined in different configurations and explore the dynamics of these systems. As an example, we apply our strategy to set up a model of the cell cycle consisting of multiple bistable switches, which can incorporate events such as DNA damage and coupling to the circadian clock in a phenomenological way.

Bistability plays an important role in many biochemical processes and typically emerges from complex interaction patterns such as positive and double negative feedback loops. Here, we propose to theoretically study the effect of bistability in a larger interaction network. We explicitly incorporate a functional expression describing an S-shaped input-output curve in the model equations, without the need for considering the underlying biochemical events. This expression can be converted into a functional module for an ultrasensitive response, and a time delay is easily included as well. Exploiting the fact that several of these modules can easily be combined in larger networks, we construct a cell cycle model consisting of multiple bistable switches and show how this approach can account for a number of known properties of the cell cycle.

Cell cycle control during early embryogenesis

Understanding the mechanisms of embryonic cell cycles is a central goal of developmental biology, as the regulation of the cell cycle must be closely coordinated with other events during early embryogenesis. Quantitative imaging approaches have recently begun to reveal how the cell cycle oscillator is controlled in space and time, and how it is integrated with mechanical signals to drive morphogenesis. Here, we discuss how the Drosophila embryo has served as an excellent model for addressing the molecular and physical mechanisms of embryonic cell cycles, with comparisons to other model systems to highlight conserved and species-specific mechanisms. We describe how the rapid cleavage divisions characteristic of most metazoan embryos require chemical waves and cytoplasmic flows to coordinate morphogenesis across the large expanse of the embryo. We also outline how, in the late cleavage divisions, the cell cycle is inter-regulated with the activation of gene expression to ensure a reliable maternal-to-zygotic transition. Finally, we discuss how precise transcriptional regulation of the timing of mitosis ensures that tissue morphogenesis and cell proliferation are tightly controlled during gastrulation.

Temporal Gradients Controlling Embryonic Cell Cycle

Simple Summary

Embryonic cells sense temporal gradients of regulatory signals to determine whether and when to proceed or remodel the cell cycle. Such a control mechanism is allowed to accurately link the cell cycle with the developmental program, including cell differentiation, morphogenesis, and gene expression. The mid-blastula transition has been a paradigm for timing in early embryogenesis in frog, fish, and fly, among others. It has been argued for decades now if the events associated with the mid-blastula transition, i.e., the onset of zygotic gene expression, remodeling of the cell cycle, and morphological changes, are determined by a control mechanism or by absolute time. Recent studies indicate that multiple independent signals and mechanisms contribute to the timing of these different processes. Here, we focus on the mechanisms for cell cycle remodeling, specifically in Drosophila, which relies on gradual changes of the signal over time. We discuss pathways for checkpoint activation, decay of Cdc25 protein levels, as well as depletion of deoxyribonucleotide metabolites and histone proteins. The gradual changes of these signals are linked to Cdk1 activity by readout mechanisms involving thresholds.

Abstract

Cell proliferation in early embryos by rapid cell cycles and its abrupt pause after a stereotypic number of divisions present an attractive system to study the timing mechanism in general and its coordination with developmental progression. In animals with large eggs, such as Xenopus, zebrafish, or Drosophila, 11–13 very fast and synchronous cycles are followed by a pause or slowdown of the cell cycle. The stage when the cell cycle is remodeled falls together with changes in cell behavior and activation of the zygotic genome and is often referred to as mid-blastula transition. The number of fast embryonic cell cycles represents a clear and binary readout of timing. Several factors controlling the cell cycle undergo dynamics and gradual changes in activity or concentration and thus may serve as temporal gradients. Recent studies have revealed that the gradual loss of Cdc25 protein, gradual depletion of free deoxyribonucleotide metabolites, or gradual depletion of free histone proteins impinge on Cdk1 activity in a threshold-like manner. In this review, we will highlight with a focus on Drosophila studies our current understanding and recent findings on the generation and readout of these temporal gradients, as well as their position within the regulatory network of the embryonic cell cycle.

The Apparent Requirement for Protein Synthesis during G2 Phase Is due to Checkpoint Activation

Protein synthesis inhibitors (e.g., cycloheximide) block mitotic entry, suggesting that cell cycle progression requires protein synthesis until right before mitosis. However, cycloheximide is also known to activate p38 mitogen-activated protein kinase (MAPK), which can delay mitotic entry through a G2/M checkpoint. Here, we ask whether checkpoint activation or a requirement for protein synthesis is responsible for the cycloheximide effect. We find that p38 inhibitors prevent cycloheximide-treated cells from arresting in G2 phase and that G2 duration is normal in approximately half of these cells. The Wee1 inhibitor MK-1775 and Wee1/Myt1 inhibitor PD0166285 also prevent cycloheximide from blocking mitotic entry, raising the possibility that Wee1 and/or Myt1 mediate the cycloheximide-induced G2 arrest. Thus, protein synthesis during G2 phase is not required for mitotic entry, at least when the p38 checkpoint pathway is abrogated. However, M phase progression is delayed in cycloheximide-plus-kinase-inhibitor-treated cells, emphasizing the different requirements of protein synthesis for timely entry and completion of mitosis.

Protein synthesis inhibitors have long been known to prevent G2 phase cells from entering mitosis. Lockhead et al. demonstrate that this G2 arrest is due to the activation of p38 MAPK, not insufficient protein synthesis, arguing that protein synthesis in G2 phase is not absolutely required for mitotic entry.

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions

Bistability is a common mechanism to ensure robust and irreversible cell cycle transitions. Whenever biological parameters or external conditions change such that a threshold is crossed, the system abruptly switches between different cell cycle states. Experimental studies have uncovered mechanisms that can make the shape of the bistable response curve change dynamically in time. Here, we show how such a dynamically changing bistable switch can provide a cell with better control over the timing of cell cycle transitions. Moreover, cell cycle oscillations built on bistable switches are more robust when the bistability is modulated in time. Our results are not specific to cell cycle models and may apply to other bistable systems in which the bistable response curve is time-dependent.

Many systems in nature show bistability, which means they can evolve to one of two stable steady states under exactly the same conditions. Which state they evolve to depends on where the system comes from. Such bistability underlies the switching behavior that is essential for cells to progress in the cell division cycle. A quick switch happens when the cell jumps from one steady state to another steady state. Typical of this switching behavior is its robustness and irreversibility. In this paper, we expand this viewpoint of the dynamics of the cell cycle by considering bistable switches which themselves are changing in time. This gives the cell an extra layer of control over transitions both in time and in space, and can make those transitions more robust. Such dynamically changing bistability can appear very naturally. We show this in a model of mitotic entry, in which we include a nuclear and cytoplasmic compartment. The activity of a crucial cell cycle protein follows a bistable switch in each compartment, but the shape of its response is changing in time as proteins are imported into and exported from the nucleus.

Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation

The phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activation of the cyclin-dependent kinase Cdk1. However, more recently it has been suggested that bistability also arises from positive feedback in the regulation of the Cdk1-counteracting phosphatase PP2A-B55. Here, we demonstrate biochemically using Xenopus laevis egg extracts that the Cdk1-counter-acting phosphatase PP2A-B55 functions as a bistable switch, even when the bistability of Cdk1 activation is suppressed. In addition, Cdk1 regulates PP2A-B55 in a biphasic manner; low concentrations of Cdk1 activate PP2A-B55 and high concentrations inactivate it. As a consequence of this incoherent feedforward regulation, PP2A-B55 activity rises concurrently with Cdk1 activity during interphase and suppresses substrate phosphorylation. PP2A-B55 activity is then sharply downregulated at the onset of mitosis. During mitotic exit, Cdk1 activity initially falls with no obvious change in substrate phosphorylation; dephosphorylation then commences once PP2A-B55 spikes in activity. These findings suggest that changes in Cdk1 activity are permissive for mitotic entry and exit but that the changes in PP2A-B55 activity are the ultimate trigger.

Mitotic transitions are accompanied by drastic changes in the phosphorylation state of proteins. Kamenz et al. demonstrate biochemically that the major mitotic phosphatase PP2A-B55 is regulated by incoherent feedforward and double-negative feedback loops to promote rapid and switch-like mitotic entry and exit.

Bifurcation and oscillatory dynamics of delayed CDK1-APC feedback loop

Extensive experimental evidence has been demonstrated that the dynamics of CDK1-APC feedback loop play crucial roles in regulating cell cycle processes, but the dynamical mechanisms underlying the regulation of this loop are still not completely understood. Here, the authors systematically investigated the stability and bifurcation criteria for a delayed CDK1-APC feedback loop. They showed that the maximum reaction rate of CDK1 inactivation by APC can drive sustained oscillations of CDK1 activity ([inline-formula removed]) and APC activity ([inline-formula removed]), and the amplitude of these oscillations is increasing with the increase of the reaction rate over a wide range; a certain range of the self-activation rate for CDK1 is also significant for generating these oscillations, for too high or too low rates the oscillations cannot be generated. Moreover, they derived the sufficient conditions to determine the stability and Hopf bifurcations, and found that the sum of time delays required for activating CDK1 and APC can induce [inline-formula removed] and [inline-formula removed] to be oscillatory, even when the [inline-formula removed] and [inline-formula removed] settle in a definite stable steady state. Furthermore, they presented an explicit algorithm for the properties of periodic oscillations. Finally, numerical simulations have been presented to justify the validity of theoretical analysis.

Nuclei determine the spatial origin of mitotic waves

Traveling waves play an essential role in coordinating mitosis over large distances, but what determines the spatial origin of mitotic waves remains unclear. Here, we show that such waves initiate at pacemakers, regions that oscillate faster than their surroundings. In cell-free extracts of Xenopus laevis eggs, we find that nuclei define such pacemakers by concentrating cell cycle regulators. In computational models of diffusively coupled oscillators that account for nuclear import, nuclear positioning determines the pacemaker location. Furthermore, we find that the spatial dimensions of the oscillatory medium change the nuclear positioning and strongly influence whether a pacemaker is more likely to be at a boundary or an internal region. Finally, we confirm experimentally that increasing the system width increases the proportion of pacemakers at the boundary. Our work provides insight into how nuclei and spatial system dimensions can control local concentrations of regulators and influence the emergent behavior of mitotic waves.

Network mechanisms and dysfunction within an integrated computational model of progression through mitosis in the human cell cycle

The cellular protein-protein interaction network that governs cellular proliferation (cell cycle) is highly complex. Here, we have developed a novel computational model of human mitotic cell cycle, integrating diverse cellular mechanisms, for the purpose of generating new hypotheses and predicting new experiments designed to help understand complex diseases. The pathogenic state investigated is infection by a human herpesvirus. The model starts at mitotic entry initiated by the activities of Cyclin-dependent kinase 1 (CDK1) and Polo-like kinase 1 (PLK1), transitions through Anaphase-promoting complex (APC/C) bound to Cell division cycle protein 20 (CDC20), and ends upon mitotic exit mediated by APC/C bound to CDC20 homolog 1 (CDH1). It includes syntheses and multiple mechanisms of degradations of the mitotic proteins. Prior to this work, no such comprehensive model of the human mitotic cell cycle existed. The new model is based on a hybrid framework combining Michaelis-Menten and mass action kinetics for the mitotic interacting reactions. It simulates temporal changes in 12 different mitotic proteins and associated protein complexes in multiple states using 15 interacting reactions and 26 ordinary differential equations. We have defined model parameter values using both quantitative and qualitative data and using parameter values from relevant published models, and we have tested the model to reproduce the cardinal features of human mitosis determined experimentally by numerous laboratories. Like cancer, viruses create dysfunction to support infection. By simulating infection of the human herpesvirus, cytomegalovirus, we hypothesize that virus-mediated disruption of APC/C is necessary to establish a unique mitotic collapse with sustained CDK1 activity, consistent with known mechanisms of virus egress. With the rapid discovery of cellular protein-protein interaction networks and regulatory mechanisms, we anticipate that this model will be highly valuable in helping us to understand the network dynamics and identify potential points of therapeutic interventions.

Incoherent Inputs Enhance the Robustness of Biological Oscillators

Robust biological oscillators retain the critical ability to function in the presence of environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive what peripheral modifications to the core contribute to this functional variation. Here, we have generated a complete atlas of two- and three-node oscillators computationally, then systematically analyzed the association between network structure and robustness. We found that, while certain core topologies are essential for producing a robust oscillator, local structures can substantially modulate the robustness of oscillations. Notably, local nodes receiving incoherent or coherent inputs respectively promote or attenuate the overall network robustness in an additive manner. We validated these relationships in larger-scale networks reflective of real biological oscillators. Our findings provide an explanation for why auxiliary structures not required for oscillation are evolutionarily conserved and suggest simple ways to evolve or design robust oscillators.

Involvement of Myt1 kinase in the G2 phase of the first cell cycle in Xenopus laevis

During cleavage of Xenopus laevis, the first mitotic cell cycle immediately following fertilization is approximately 90 min and consists of S, G2, and M phases. In contrast, the subsequent eleven cell cycles are approximately 30 min and consist mostly of S and M phases. The balance between Cdc25 and Wee1A/Myt1 is thought to be crucial for Xenopus first cell cycle progression; however, the role of Myt1 in this period has not been fully investigated. In this study, we examined the roles of Myt1, Wee1A, and Cdc25A in the first cell cycle of Xenopus laevis. Inhibition of Cdc25A with antisense morpholino oligonucleotides lengthened the duration of the first cell cycle to some extent, whereas it was slightly shortened by ectopic Cdc25A expression, suggesting that the low concentration of Cdc25A during the first cell cycle does not fully account for the long duration of this cycle. Using the Wee1A antisense morpholino oligonucleotide and neutralizing antibody against Myt1, we found that Myt1 phosphorylates and inhibits Cdk1 much more effectively than Wee1A during the first cell cycle in Xenopus. Taken together, these results suggest that the activity of Myt1 is predominantly responsible for the duration of the long G2 phase in the first mitotic cell cycle in Xenopus.

Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes

Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.

Techniques for Studying Decoding of Single Cell Dynamics

Cells must be able to interpret signals they encounter and reliably generate an appropriate response. It has long been known that the dynamics of transcription factor and kinase activation can play a crucial role in selecting an individual cell's response. The study of cellular dynamics has expanded dramatically in the last few years, with dynamics being discovered in novel pathways, new insights being revealed about the importance of dynamics, and technological improvements increasing the throughput and capabilities of single cell measurements. In this review, we highlight the important developments in this field, with a focus on the methods used to make new discoveries. We also include a discussion on improvements in methods for engineering and measuring single cell dynamics and responses. Finally, we will briefly highlight some of the many challenges and avenues of research that are still open.

Induction of a Spindle-Assembly-Competent M Phase in Xenopus Egg Extracts

Normal mitotic spindle assembly is a prerequisite for faithful chromosome segregation and unperturbed cell-cycle progression. Precise functioning of the spindle machinery relies on conserved architectural features, such as focused poles, chromosome alignment at the metaphase plate, and proper spindle length. These morphological requirements can be achieved only within a compositionally distinct cytoplasm that results from cell-cycle-dependent regulation of specific protein levels and specific post-translational modifications. Here, we used cell-free extracts derived from Xenopus laevis eggs to recapitulate different phases of the cell cycle in vitro and to determine which components are required to render interphase cytoplasm spindle-assembly competent in the absence of protein translation. We found that addition of a nondegradable form of the master cell-cycle regulator cyclin B1 can indeed induce some biochemical and phenomenological characteristics of mitosis, but cyclin B1 alone is insufficient and actually deleterious at high levels for normal spindle assembly. In contrast, addition of a phosphomimetic form of the Greatwall-kinase effector Arpp19 with a specific concentration of nondegradable cyclin B1 rescued spindle bipolarity but resulted in larger-than-normal bipolar spindles with a misalignment of chromosomes. Both were corrected by the addition of exogenous Xkid (Xenopus homolog of human Kid/KIF22), indicating a role for this chromokinesin in regulating spindle length. These observations suggest that, of the many components degraded at mitotic exit and then replenished during the subsequent interphase, only a few are required to induce a cell-cycle transition that produces a spindle-assembly-competent cytoplasm.

Ca2+-Induced Mitochondrial ROS Regulate the Early Embryonic Cell Cycle

While it is appreciated that reactive oxygen species (ROS) can act as second messengers in both homeostastic and stress response signaling pathways, potential roles for ROS during early vertebrate development have remained largely unexplored. Here, we show that fertilization in Xenopus embryos triggers a rapid increase in ROS levels, which oscillate with each cell division. Furthermore, we show that the fertilization-induced Ca²⁺ wave is necessary and sufficient to induce ROS production in activated or fertilized eggs. Using chemical inhibitors, we identified mitochondria as the major source of fertilization-induced ROS production. Inhibition of mitochondrial ROS production in early embryos results in cell-cycle arrest, in part, via ROS-dependent regulation of Cdc25C activity. This study reveals a role for oscillating ROS levels in early cell cycle regulation in Xenopus embryos.

Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling

All living systems function out of equilibrium and exchange energy in the form of heat with their environment. Thus, heat flow can inform on the energetic costs of cellular processes, which are largely unknown. Here, we have repurposed an isothermal calorimeter to measure heat flow between developing zebrafish embryos and the surrounding medium. Heat flow increased over time with cell number. Unexpectedly, a prominent oscillatory component of the heat flow, with periods matching the synchronous early reductive cleavage divisions, persisted even when DNA synthesis and mitosis were blocked by inhibitors. Instead, the heat flow oscillations were driven by the phosphorylation and dephosphorylation reactions catalyzed by the cell-cycle oscillator, the biochemical network controlling mitotic entry and exit. We propose that the high energetic cost of cell-cycle signaling reflects the significant thermodynamic burden of imposing accurate and robust timing on cell proliferation during development.

Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts

Real-time measurement of oscillations at the single-cell level is important to uncover the mechanisms of biological clocks. Although bulk extracts prepared from Xenopus laevis eggs have been powerful in dissecting biochemical networks underlying the cell-cycle progression, their ensemble average measurement typically leads to a damped oscillation, despite each individual oscillator being sustained. This is due to the difficulty of perfect synchronization among individual oscillators in noisy biological systems. To retrieve the single-cell dynamics of the oscillator, we developed a droplet-based artificial cell system that can reconstitute mitotic cycles in cell-like compartments encapsulating cycling cytoplasmic extracts of Xenopus laevis eggs. These simple cytoplasmic-only cells exhibit sustained oscillations for over 30 cycles. To build more complicated cells with nuclei, we added demembranated sperm chromatin to trigger nuclei self-assembly in the system. We observed a periodic progression of chromosome condensation/decondensation and nuclei envelop breakdown/reformation, like in real cells. This indicates that the mitotic oscillator functions faithfully to drive multiple downstream mitotic events. We simultaneously tracked the dynamics of the mitotic oscillator and downstream processes in individual droplets using multi-channel time-lapse fluorescence microscopy. The artificial cell-cycle system provides a high-throughput framework for quantitative manipulation and analysis of mitotic oscillations with single-cell resolution, which likely provides important insights into the regulatory machinery and functions of the clock.

Cyclin A-cdk1-Dependent Phosphorylation of Bora Is the Triggering Factor Promoting Mitotic Entry

Mitosis is induced by the activation of the cyclin B/cdk1 feedback loop that creates a bistable state. The triggering factor promoting active cyclin B/cdk1 switch has been assigned to cyclin B/cdk1 accumulation during G2. However, this complex is rapidly inactivated by Wee1/Myt1-dependent phosphorylation of cdk1 making unlikely a triggering role of this kinase in mitotic commitment. Here we show that cyclin A/cdk1 kinase is the factor triggering mitosis. Cyclin A/cdk1 phosphorylates Bora to promote Aurora A-dependent Plk1 phosphorylation and activation and mitotic entry. We demonstrate that Bora phosphorylation by cyclin A/cdk1 is both necessary and sufficient for mitotic commitment. Finally, we identify a site in Bora whose phosphorylation by cyclin A/cdk1 is required for mitotic entry. We constructed a mathematical model confirming the essential role of this kinase in mitotic commitment. Overall, our results uncover the molecular mechanism by which cyclin A/cdk1 triggers mitotic entry.

Expression variation and covariation impair analog and enable binary signaling control

Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. Such high variation is beneficial for population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here, we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5-15%, compatible with accurate single-cell transmission. Focusing on bimodal ERK signaling, we show that variation and covariation in MEK and ERK expression improves controllability of the percentage of activated cells, demonstrating how variation and covariation in expression enables population-level control of binary cell-fate decisions. Together, our study argues for a control principle whereby low expression variation enables accurate control of analog single-cell signaling, while increased variation, covariation, and numbers of pathway components are required to widen the stimulus range over which external inputs regulate binary cell activation to enable precise control of the fraction of activated cells in a population.

A robust and tunable mitotic oscillator in artificial cells

Single-cell analysis is pivotal to deciphering complex phenomena like heterogeneity, bistability, and asynchronous oscillations, where a population ensemble cannot represent individual behaviors. Bulk cell-free systems, despite having unique advantages of manipulation and characterization of biochemical networks, lack the essential single-cell information to understand a class of out-of-steady-state dynamics including cell cycles. Here, by encapsulating Xenopus egg extracts in water-in-oil microemulsions, we developed artificial cells that are adjustable in sizes and periods, sustain mitotic oscillations for over 30 cycles, and function in forms from the simplest cytoplasmic-only to the more complicated ones involving nuclear dynamics, mimicking real cells. Such innate flexibility and robustness make it key to studying clock properties like tunability and stochasticity. Our results also highlight energy as an important regulator of cell cycles. We demonstrate a simple, powerful, and likely generalizable strategy of integrating strengths of single-cell approaches into conventional in vitro systems to study complex clock functions.

Chemical waves in cell and developmental biology

Many biological events, such as the propagation of nerve impulses, the synchronized cell cycles of early embryogenesis, and collective cell migration, must be coordinated with remarkable speed across very large distances. Such rapid coordination cannot be achieved by simple diffusion of molecules alone and requires specialized mechanisms. Although active transport can provide a directed and efficient way to travel across subcellular structures, it cannot account for the most rapid examples of coordination found in biology. Rather, these appear to be driven by mechanisms involving traveling waves of chemical activities that are able to propagate information rapidly across biological or physical systems. Indeed, recent advances in our ability to probe the dynamics of signaling pathways are revealing many examples of coordination of cellular and developmental processes through traveling chemical waves. Here, we will review the theoretical principles underlying such waves; highlight recent literature on their role in different contexts, ranging from chemotaxis to development; and discuss open questions and future perspectives on the study of chemical waves as an essential feature of cell and tissue physiology.

Delay models for the early embryonic cell cycle oscillator

Time delays are known to play a crucial role in generating biological oscillations. The early embryonic cell cycle in the frog Xenopus laevis is one such example. Although various mathematical models of this oscillating system exist, it is not clear how to best model the required time delay. Here, we study a simple cell cycle model that produces oscillations due to the presence of an ultrasensitive, time-delayed negative feedback loop. We implement the time delay in three qualitatively different ways, using a fixed time delay, a distribution of time delays, and a delay that is state-dependent. We analyze the dynamics in all cases, and we use experimental observations to interpret our results and put constraints on unknown parameters. In doing so, we find that different implementations of the time delay can have a large impact on the resulting oscillations.

Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development

The early Xenopus laevis embryo is replete with dynamic spatial waves. One such wave, the cell division wave, emerges from the collective cell division timing of first tens and later hundreds of cells throughout the embryo. Here, we show that cell division waves do not propagate between neighboring cells and do not rely on cell-to-cell coupling to maintain their division timing. Instead, intrinsic variation in division period autonomously and gradually builds these striking patterns of cell division. Disrupting this pattern of division by placing embryos in a temperature gradient resulted in highly asynchronous entry to the midblastula transition and misexpression of the mesodermal marker Xbra. Remarkably, this gene expression defect is corrected during involution, resulting in delayed yet normal Xbra expression and viable embryos. This implies the existence of a previously unknown mechanism for normalizing mesodermal gene expression during involution.

Chk1 Inhibition of the Replication Factor Drf1 Guarantees Cell-Cycle Elongation at the Xenopus laevis Mid-blastula Transition

The early cell divisions of many metazoan embryos are rapid and occur in the near absence of transcription. At the mid-blastula transition (MBT), the cell cycle elongates and several processes become established including the onset of bulk transcription and cell-cycle checkpoints. How these events are timed and coordinated is poorly understood. Here we show in Xenopus laevis that developmental activation of the checkpoint kinase Chk1 at the MBT results in the SCF^β-TRCP-dependent degradation of a limiting replication initiation factor Drf1. Inhibition of Drf1 is the primary mechanism by which Chk1 blocks cell-cycle progression in the early embryo and is an essential function of Chk1 at the blastula-to-gastrula stage of development. This study defines the downregulation of Drf1 as an important mechanism to coordinate the lengthening of the cell cycle and subsequent developmental processes.

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Activation of Chk1 at the Xenopus MBT results in the degradation of Drf1

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Drf1 degradation is SCF^β-TRCP dependent

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Chk1 blocks the cell cycle in the early embryo through inhibition of Drf1

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Inhibition of Drf1 is an essential function of Chk1 during gastrulation

The Design Space of the Embryonic Cell Cycle Oscillator

One of the main tasks in the analysis of models of biomolecular networks is to characterize the domain of the parameter space that corresponds to a specific behavior. Given the large number of parameters in most models, this is no trivial task. We use a model of the embryonic cell cycle to illustrate the approaches that can be used to characterize the domain of parameter space corresponding to limit cycle oscillations, a regime that coordinates periodic entry into and exit from mitosis. Our approach relies on geometric construction of bifurcation sets, numerical continuation, and random sampling of parameters. We delineate the multidimensional oscillatory domain and use it to quantify the robustness of periodic trajectories. Although some of our techniques explore the specific features of the chosen system, the general approach can be extended to other models of the cell cycle engine and other biomolecular networks.

Stat3/Cdc25a-dependent cell proliferation promotes embryonic axis extension during zebrafish gastrulation

Cell proliferation has generally been considered dispensable for anteroposterior extension of embryonic axis during vertebrate gastrulation. Signal transducer and activator of transcription 3 (Stat3), a conserved controller of cell proliferation, survival and regeneration, is associated with human scoliosis, cancer and Hyper IgE Syndrome. Zebrafish Stat3 was proposed to govern convergence and extension gastrulation movements in part by promoting Wnt/Planar Cell Polarity (PCP) signaling, a conserved regulator of mediolaterally polarized cell behaviors. Here, using zebrafish stat3 null mutants and pharmacological tools, we demonstrate that cell proliferation contributes to anteroposterior embryonic axis extension. Zebrafish embryos lacking maternal and zygotic Stat3 expression exhibit normal convergence movements and planar cell polarity signaling, but transient axis elongation defect due to insufficient number of cells resulting largely from reduced cell proliferation and increased apoptosis. Pharmacologic inhibition of cell proliferation during gastrulation phenocopied axis elongation defects. Stat3 regulates cell proliferation and axis extension in part via upregulation of Cdc25a expression during oogenesis. Accordingly, restoring Cdc25a expression in stat3 mutants partially suppressed cell proliferation and gastrulation defects. During later development, stat3 mutant zebrafish exhibit stunted growth, scoliosis, excessive inflammation, and fail to thrive, affording a genetic tool to study Stat3 function in vertebrate development, regeneration, and disease.

During vertebrate embryogenesis, cell proliferation, fate specification and cell movements are key processes that transform a fertilized egg into an embryo with head, trunk and tail. Cell proliferation is orchestrated by maternal and zygotic functions of conserved regulators including Cdc25a, and has generally been considered dispensable for embryonic axis elongation. Stat3 transcriptional factor, a known promoter of cell proliferation, is associated with human scoliosis, inflammation and cancer. Based on morpholino-mediated downregulation of Stat3 during zebrafish embryogenesis, Stat3 was previously proposed to regulate convergence and extension cell movements that narrow the embryonic body and elongate it from head to tail partially through planar cell polarity signaling and unknown transcriptional targets. Here, we report that zebrafish mutants lacking maternal and zygotic Stat3 expression exhibit normal convergence movements and planar cell polarity signaling, but transient axis elongation defect due to insufficient number of cells resulting largely from reduced cell proliferation and increased cell death. Accordingly, pharmacologic inhibition of cell proliferation also hinders axis elongation. Further experiments indicate that Stat3 promotes head- to -tail axis elongation by stimulating cell proliferation in part via upregulation of Cdc25a expression during oogenesis. During later development, zebrafish stat3 mutants exhibit scoliosis and inflammation, potentially affording a new tool to study related human diseases.

The Botrytis cinerea PAK kinase BcCla4 mediates morphogenesis, growth and cell cycle regulating processes downstream of BcRac

Rac proteins are involved in a variety of cellular processes. Effector proteins that interact with active Rac convey the GTPase-generated signal to downstream developmental cascades and processes. Here we report on the analysis of the main effector and signal cascade downstream of BcRac, the Rac homolog of the grey mold fungus Botrytis cinerea. Several lines of evidence highlighted the p21-activated kinase Cla4 as an important effector of Rac in fungi. Analysis of Δbccla4 strains revealed that the BcCla4 protein was sufficient to mediate all of the examined BcRac-driven processes, including hyphal growth and morphogenesis, conidia production and pathogenicity. In addition, the Δbccla4 strains had altered nuclei content, a phenomenon that was previously observed in Δbcrac isolates, thus connecting the BcRac/BcCla4 module with cell cycle control. Further analyses revealed that BcRac/BcCla4 control mitotic entry through changes in phosphorylation status of the cyclin dependent kinase BcCdk1. The complete cascade includes the kinase BcWee1, which is downstream of BcCla4 and upstream of BcCdk1. These results provide a mechanistic insight on the connection of cell cycle, morphogenesis and pathogenicity in fungi, and position BcCla4 as the most essential effector and central regulator of all of these processes downstream of BcRac.

Regulation of Cell Division

The challenging task of mitotic cell divisions is to generate two genetically identical daughter cells from a single precursor cell. To accomplish this task, a complex regulatory network evolved, which ensures that all events critical for the duplication of cellular contents and their subsequent segregation occur in the correct order, at specific intervals and with the highest possible fidelity. Transitions between cell cycle stages are triggered by changes in the phosphorylation state and levels of components of the cell cycle machinery. Entry into S-phase and M-phase are mediated by cyclin-dependent kinases (Cdks), serine-threonine kinases that require a regulatory cyclin subunit for their activity. Resetting the system to the interphase state is mediated by protein phosphatases (PPs) that counteract Cdks by dephosphorylating their substrates. To avoid futile cycles of phosphorylation and dephosphorylation, Cdks and PPs must be regulated in a manner such that their activities are mutually exclusive.

Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis

From cyanobacteria to human, sustained oscillations coordinate important biological functions. Although much has been learned concerning the sophisticated molecular mechanisms underlying biological oscillators, design principles linking structure and functional behavior are not yet fully understood. Here we explore design principles of biological oscillators from a multiobjective optimization perspective, taking into account the trade-offs between conflicting performance goals or demands. We develop a comprehensive tool for automated design of oscillators, based on multicriteria global optimization that allows two modes: (i) the automatic design (forward problem) and (ii) the inference of design principles (reverse analysis problem). From the perspective of synthetic biology, the forward mode allows the solution of design problems that mimic some of the desirable properties appearing in natural oscillators. The reverse analysis mode facilitates a systematic exploration of the design space based on Pareto optimality concepts. The method is illustrated with two case studies: the automatic design of synthetic oscillators from a library of biological parts, and the exploration of design principles in 3-gene oscillatory systems.

Bistability of mitotic entry and exit switches during open mitosis in mammalian cells

Mitotic entry and exit are switch-like transitions that are driven by the activation and inactivation of Cdk1 and mitotic cyclins. This simple on/off reaction turns out to be a complex interplay of various reversible reactions, feedback loops, and thresholds that involve both the direct regulators of Cdk1 and its counteracting phosphatases. In this review, we summarize the interplay of the major components of the system and discuss how they work together to generate robustness, bistability, and irreversibility. We propose that it may be beneficial to regard the entry and exit reactions as two separate reversible switches that are distinguished by differences in the state of phosphatase activity, mitotic proteolysis, and a dramatic rearrangement of cellular components after nuclear envelope breakdown, and discuss how the major Cdk1 activity thresholds could be determined for these transitions.

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.