Browsing by Subject "Cell cycle"

Cell division is a biological process fundamental to all life. One aspect of the process that is still under investigation is whether or not cells in a lineage are correlated in their cell-cycle progression. Data on cell-cycle progression is typically acquired either in lineages of single cells or in synchronized cell populations, and each source of data offers complementary information on cell division. To formally assess dependence in cell-cycle progression, I develop a hierarchical statistical model of single-cell measurements and extend a previously proposed model of population cell division in the budding yeast, Saccharomyces cerevisiae. Both models capture correlation and cell-to-cell heterogeneity in cell-cycle progression, and parameter inference is carried out in a fully Bayesian manner. The single-cell model is fit to three published time-lapse microscopy datasets and the population-based model is fit to simulated data for which the true model is known. Based on posterior inferences and formal model comparisons, the single-cell analysis demonstrates that budding yeast mother and daughter cells do not appear to correlate in their cell-cycle progression in two of the three experimental settings. In contrast, mother cells grown in a less preferred sugar source, glycerol/ethanol, did correlate in their rate of cell division in two successive cell cycles. Population model fitting to simulated data suggested that, under typical synchrony experimental conditions, population-based measurements of the cell-cycle were not informative for correlation in cell-cycle progression or heterogeneity in daughter-specific G1 phase progression.

The cell division cycle is the process in which the entirety of a cell's contents is duplicated completely and then equally segregated into two identical daughter cells. The order of the steps in the cell cycle must be followed with fidelity to guarantee two viable cells. Understanding the regulatory mechanisms that control cell-cycle events remains to be a fundamental question in cell biology. In this dissertation, I explore the mechanisms that coordinate and regulate cell-cycle progression in the budding yeast, Saccharomyces cerevisiae.

Cell-cycle events have been shown to be triggered by oscillations in the activity of cyclin dependent kinases (CDKs) when bound to cyclins. However, several studies have shown that some cell-cycle events, such as periodic transcription, can continue in the absence of CDK activity. How are periodic transcription and other cell-cycle events coupled to each other during a wild-type cell cycle? Currently, two models of cell-cycle regulation have been proposed. One model hypothesizes that oscillations in CDK activity controls the timing of cell-cycle events, including periodic transcription. The second model proposes that a transcription factor (TF) network oscillator controls the timing of cell-cycle events, via proper timing of gene expression, including cyclins. By measuring global gene expression dynamics in cells with persistent CDK activity, I show that periodic transcription continues. This result fits with the second model of cell-cycle regulation. Further, I show that during a wild-type cell cycle, checkpoints are responsible for arresting the bulk of periodic transcription. This finding adds a new layer of regulation to the second model, providing a mechanism that coordinates cell-cycle events with a TF network oscillator. Taken together, these data provide further insight into the regulation of the cell cycle.

Cell division and growth are complex processes fundamental to all living organisms. In the budding yeast, Saccharomyces cerevisiae, these two processes are known to be coordinated with one another as a cell's mass must roughly double before division. Moreover, cell-cycle progression is dependent on cell size with smaller cells at birth generally taking more time in the cell cycle. This dependence is a signature of size control. Systems biology is an emerging field that emphasizes connections or dependencies between biological entities and processes over the characteristics of individual entities. Statistical models provide a quantitative framework for describing and analyzing these dependencies. In this dissertation, I take a statistical systems biology approach to study cell division and growth and the dependencies within and between these two processes, drawing on observations from richly informative microscope images and time-lapse movies. I review the current state of knowledge on these processes, highlighting key results and open questions from the biological literature. I then discuss my development of machine learning and statistical approaches to extract cell-cycle information from microscope images and to better characterize the cell-cycle progression of populations of cells. In addition, I analyze single cells to uncover correlation in cell-cycle progression, evaluate potential models of dependence between growth and division, and revisit classical assertions about budding yeast size control. This dissertation presents a unique perspective and approach towards comprehensive characterization of the coordination between growth and division.

The cell cycle is a series of ordered events that culminates in a single cell dividing into two daughter cells. These events must be properly coordinated to ensure the faithful passage of genetic material. How cell cycle events are carried out accurately remains a fundamental question in cell biology. In this dissertation, I investigate mechanisms orchestrating cell-cycle events in the yeast, Saccharomyces cerevisiae.

Cyclin dependent kinase (CDK) activity is thought to both form the fundamental cell-cycle oscillator and act as an effector of that oscillator, regulating cell-cycle events. By measuring transcript dynamics over time in cells lacking all CDK activity, I show that transcriptional oscillations are not dependent on CDK activity. This data indicates that CDKs do not form the underlying cell-cycle oscillator. I propose a model in which a transcription factor network rather than CDK activity forms the cell-cycle oscillator. In this model, CDKs are activated by the periodic transcription of cyclin genes and feedback on the network increasing the robustness of network oscillations in addition to regulating cell-cycle events.

I also investigate CDK-dependent and -independent mechanism regulating the duplication of the yeast centrosome, the spindle pole body (SPB). It is critical for the formation of a bipolar spindle in mitosis that the SPB duplicates once and only once per cell cycle. Through a combination of genetic and microscopic techniques I show that three distinct mechanisms regulate SPB duplication, ensuring its restriction to once per cell cycle.

Together, the data presented in this dissertation support a model in which CDKs, periodic transcription, and a TF-network oscillator are all important cell-cycle regulatory mechanisms that collaborate to regulate the intricate collection of events that constitute the cell cycle.

Bud formation by Saccharomyces cerevisiae is a fundamental process for yeast proliferation. Bud emergence is initiated by the polarization of the cytoskeleton, leading to local secretory vesicle delivery and gulcan synthase activity. The master regulator of polarity establishment is a small Rho-family GTPase – Cdc42. Cdc42 forms a clustered patch at the incipient budding site in late G1 and mediates downstream events which lead to bud emergence. Cdc42 promotes morphogenesis via its various effectors. PAKs (p21-activated kinases) are important Cdc42 effectors which mediate actin cytoskeleton polarization and septin filament assembly. The PAKs Cla4 and Ste20 share common binding domains for GTP-Cdc42 and they are partially redundant in function. However, we found that Cla4 and Ste20 behaved differently during the polarization and this depended on their different membrane interaction domains. Also, Cla4 and Ste20 compete for a limited number of binding sites at the polarity patch during bud emergence. These results suggest that PAKs may be differentially regulated during polarity establishment.

Morphogenesis of yeast must be coordinated with the nuclear cycle to enable successful proliferation. Many environmental stresses temporarily disrupt bud formation, and in such circumstances, the morphogenesis checkpoint halts nuclear division until bud formation can resume. Bud emergence is essential for degradation of the mitotic inhibitor, Swe1. Swe1 is localized to the septin cytoskeleton at the bud neck by the Swe1-binding protein Hsl7. Neck localization of Swe1 is required for Swe1 degradation. Although septins form a ring at the presumptive bud site prior to bud emergence, Hsl7 is not recruited to the septins until after bud emergence, suggesting that septins and/or Hsl7 respond to a “bud sensor”. Here we show that recruitment of Hsl7 to the septin ring depends on a combination of two septin-binding kinases: Hsl1 and Elm1. We elucidate which domains of these kinases are needed, and show that artificial targeting of those domains suffices to recruit Hsl7 to septin rings even in unbudded cells. Moreover, recruitment of Elm1 is responsive to bud emergence. Our findings suggest that Elm1 plays a key role in sensing bud emergence.

The cell cycle is one of the fundamental processes in all living organisms, and all cells arise from the division of existing cells. To better understand the regulation of the cell cycle, synchrony experiments are widely used to monitor cellular dynamics during this process. In such experiments, a large population of cells is generally arrested or selected at one stage of the cycle, and then released to progress through subsequent division stages. Measurements are then taken in this population at a variety of time points after release to provide insight into the dynamics of the cell cycle. However, due to cell-to-cell variability and asymmetric cell division, cells in a synchronized population lose synchrony over time. As a result, the time-series measurements from the synchronized cell populations do not accurately reflect the underlying dynamics of cell-cycle processes.

In this thesis, we introduce a deconvolution algorithm that learns a more accurate view of cell-cycle dynamics, free from the convolution effects associated with imperfect cell synchronization. Through wavelet-basis regularization, our method sharpens signal without sharpening noise, and can remarkably increase both the dynamic range and the temporal resolution of time-series data. Though it can be applied to any such data, we demonstrate the utility of our method by applying it to a recent cell-cycle transcription time course in the eukaryote Saccharomyces cerevisiae. We show that our method more sensitively detects cell-cycle-regulated transcription, and reveals subtle timing differences that are masked in the original population measurements. Our algorithm also explicitly learns distinct transcription programs for both mother and daughter cells, enabling us to identify 82 genes transcribed almost entirely in the early G1 in a daughter-specific manner.

In addition to the cell-cycle deconvolution algorithm, we introduce DOMAIN, a protein-protein interaction (PPI) network alignment method, which employs a novel direct-edge-alignment paradigm to detect conserved functional modules (e.g., protein complexes, molecular pathways) from pairwise PPI networks. By applying our approach to detect protein complexes conserved in yeast-fly and yeast-worm PPI networks, we show that our approach outperforms two widely used approaches in most alignment performance metrics. We also show that our approach enables us to identify conserved cell-cycle-related functional modules across yeast-fly PPI networks.

The neocortex expanded spectacularly during human origins. That expansion is thought to form the foundation for our cognitive faculties underlying abstract reasoning and socialization. The human neocortex differs from that of other great apes in several notable regards including altered cell cycle, prolonged corticogenesis, and massively increased size. However, despite decades of effort, little progress has been made in uncovering the genetic contributions that underlie these differences that distinguish our species from closely related primate, such as chimpanzees. A subset of highly conserved non-coding regions that show rapid sequence changes along the human lineage are candidate loci for the development and evolution of uniquely human traits. Several studies have identified human-accelerated enhancers, but none have linked an expression difference to a organismal traits, such as brain sizes. Here we report the discovery of a human-accelerated regulatory enhancer (HARE5) near the Wnt receptor FRIZZLED-8 (FZD8). Using a variety of approaches, we demonstrate dramatic differences in human and chimpanzee HARE5 activity, with human HARE5 driving significantly strong expression. We show that HARE5 likely regulates FZD8 and that expression differences influence cell cycle kinetics, cortical layers, and brain size. At present, this would provide the first evidence of a human-chimpanzee genetic difference influencing the evolution of brain size.

The majority of breast tumors express the estrogen receptor (ER), and more than half of these cancers also express the progesterone receptor (PR). While the actions of ER on breast cancer pathogenesis are well understood, those of PR are still unclear. The Women's Health Initiative trial in 2002 brought into focus the alarming result that women receiving both estrogen and progestins as hormone replacement therapy are at greater risk for breast cancer than women receiving estrogen alone. Thus, there is considerable interest in defining the mechanisms that underlie the pharmacological actions of progestins in the normal and malignant breast.

Progestins facilitate cell cycle progression through multiple mechanisms, one of which is the induction of phosphorylation of the tumor suppressor retinoblastoma (Rb) protein. Stimulation by growth factors induces the transcription of Cyclin D1 which in turn activates the cyclin dependent kinases (CDKs). The Cyclin D1- Cdk4/6 complex phosphorylates the Rb protein, leading to the release of E2F1, which then binds and activates other target genes, leading to G1-S transition of the cell cycle. Given the reported action of PR to activate MAPK signaling, we initially thought that the progestin-induced Rb phosphorylation was mediated by this pathway. However, we turned to an alternate hypothesis based on our data using MEK inhibitors demonstrating that this was not the case.

Given the primacy of Cyclin D1 in cell cycle control, we then turned our attention to defining the mechanism by which Cyclin D1 expression is regulated by PR. Interestingly, it was determined that progestin mediated up- regulation of Cyclin D1 is rapid, peaking at 6hrs post hormone addition followed by a decrease in expression reaching a nadir at 18hrs. Unexpectedly, we found that contrary to what has been published before, the induction of Cyclin D1 mRNA expression was a primary transcriptional event and we have demonstrated the specific interaction of PR with PREs (progesterone response elements) located on this gene. We have further determined that the half-life of Cyclin D1 mRNA is decreased significantly by progestin addition explaining how the levels of this mRNA following the addition of hormone are quickly attenuated. Thus, when taken together, our data suggest that progestins exert both positive and negative effects on Cyclin D1 mRNA, the uncoupling of which is likely to impact the pathogenesis of breast cancer

The observation that PR reduces the Cyclin D1 mRNA stability led us to investigate the effects of PR on RNA binding proteins, especially those which are involved in RNA stability. We discovered that PR induces the expression of several RNA binding proteins. Although the work to determine the effects of these RNA binding proteins on CyclinD1 mRNA stability is still ongoing, we have discovered a role for one of the PR-induced RNA binding proteins tristetraprolin (TTP), in the suppression of the inflammation pathway in breast cancer. We found that while TTP was not required for the PR-mediated decrease in Cyclin D1 mRNA stability, overexpression of this tumor suppressive protein was able to inhibit IL-1β-mediated stimulation of inflammatory genes in our breast cancer model. Since it is established that the upregulation of the inflammatory pathway is oncogenic, we are currently exploring the intersection of PR and TTP-mediated signaling on the inflammation transcriptome in breast cancer.

Thus, collectively these data provide us with a better picture of the poorly understood actions of PR on breast cancer proliferation and tumorigenesis. We believe that further investigation of the studies developed in this thesis will lead to novel and better-targeted approaches to the use of PR as a therapeutic target in the clinic.

Cell polarity is critical for essential functions in many types of cells. Rho-family GTPases are master regulators of cell polarity. Thus, mechanisms for controlling the activity of Rho GTPases are of both academic interest and practical concern. While much has been discovered about regulation of Rho GTPase activity by partners like GEFs, GAPs, and GDIs, there are still many things which remain unclear about how their behavior is enforced in cells of various kinds.

The budding yeast, Saccharomyces cerevisiae, has long been a model for studying cell polarity. Its Rho GTPase Cdc42 is responsible for defining a single polarity site for the purpose of either mating with a single partner or making a single bud. Other types of yeasts, however, can generate multiple polarity sites utilizing the same core polarity machinery. What are the rules which allow for such differences in behavior while using a similar set of proteins? We highlight key design principles established in mathematical models for Rho GTPase polarity machineries and show that they apply in budding yeast cells: strains featuring specific genetic perturbations which increase the total amount of polarity proteins can go from making one bud, to making multiple buds.

Bud emergence in yeast is enabled by cell cycle activity in G1. It is known that bud emergence also requires cytoskeletal changes which are orchestrated by Cdc42 and its effectors. How are these changes coordinated with cell cycle progression? It seems likely that G1 CDK activity regulates many aspects of Cdc42 polarization. We use live-cell fluorescence microscopy to reveal one such avenue whereby input from the cell cycle is required for many Cdc42 effector proteins to localize to sites with active Cdc42, thus restricting bud formation until the time is right.

Early development in most metazoans is characterized by remarkably fast and coordinated cell cycles. Nonetheless, it is unclear what organizational principles underlie cell cycle synchronization across a large developing embryo. We found that cell cycle synchronization in Drosophila arises through the self-organized positioning of nuclei, which is regulated by the spatiotemporal dynamics of the cell cycle, cortical contractions, and cytoplasmic streaming. First, local Cdk1 downregulation at mitotic exit initiates the damped spreading of PP1 activity, which is responsible for recruiting myosin II to cortical regions that surround the nuclei, where gradients of contractility are generated. These gradients drive cortical and cytoplasmic flows that properly position the nuclei across the embryo. Uniform positioning of nuclei across the embryo is required for the emergence of synchronous cell cycles. Once at the surface of the embryo, nuclei undergo four metachronous cell cycles, which spread in a wave-like manner with remarkable speed across the large distance of the egg. Using a Cdk1 biosensor, we found that travelling waves of Cdk1 activity propagate through the embryo and synchronize the cell cycle during S-phase through an active mechanism, while mitotic events simply follow S-phase synchronization with a delay. Taken together, a self-organized mechanism that spreads nuclei uniformly is required early on in development to give rise to synchronous divisions. Cell cycle synchrony is then maintained by waves of Cdk1 activity, ensuring that all nuclei initiate the mid-blastula transition simultaneously. This work highlights the importance of chemical waves and cytoplasmic flows in the spatiotemporal regulation of the cell cycle of large embryos.

Cellular dynamics arise from intricate interactions among diverse components, such as metabolites, RNAs, and proteins. An in-depth understanding of these interactions requires an integrated approach to the investigation of biological systems. This task can benefit from a combination of mathematical modeling and experimental validations, which is becoming increasingly indispensable for basic and applied biological research.

Utilizing a combination of modeling and experimentation, we investigate mammalian cell cycle entry. We begin our investigation by making predictions with a mathematical model, which is constructed based on the current knowledge of biology. To test these predictions, we develop experimental platforms for validations, which in turn can be used to further refine the model. Such iteration of model predictions and experimental validations has allowed us to gain an in-depth understanding of the cell cycle entry dynamics.

In this dissertation, we have focused on the Myc-Rb-E2F signaling pathway and its associated pathways, dysregulation of which is associated with virtually all cancers. Our analyses of these signaling pathways provide insights into three questions in biology: 1) regulation of the restriction point (R-point) in cell cycle entry, 2) regulation of the temporal dynamics in cell cycle entry, and 3) post-translational regulation of Myc by its upstream signaling pathways. The well-studied pathways can serve as a foundation for perturbations and tight control of cell cycle entry dynamics, which may be useful in developing cancer therapeutics.

We conclude by demonstrating how a combination of mathematical modeling and experimental validations provide mechanistic insights into the regulatory networks in cell cycle entry.

In the plant innate immune system, diverse signals from a wide range of pathogens converge on the same output, effector triggered immunity (ETI) and the associated programmed cell death (PCD). Past genetic studies have succeeded in uncovering the role of R-genes in recognizing the presence of pathogen effectors, and in identifying a number of downstream executors of the immune response. However, the gap between effector recognition and phenotype regulation remains poorly understood, with each signaling component only contributing a minor quantitative effect to the phenotype of ETI-PCD. In this dissertation, my goal is to fill in a portion of that gap.

I demonstrate that there is a prolonged nuclear increase of calcium ions during ETI, and that that nuclear calcium signal is essential for PCD. I also utilize cpr5, a point mutant identified for its constitutive defense response and programmed cell death lesions, to identify a new role for cell cycle regulators in regulating ETI-PCD. I show that phosphorylation of the cell cycle regulator Retinoblastoma-Related 1 (RBR1) is responsive to ETI. The RBR1 target transcription factors E2Fa, E2Fb, and E2Fc have an additive role regulating ETI, and a triple e2fabc mutant is susceptible to pathogens. Using a reverse genetics approach in e2fabc, I identify repression of nonphotochemical quenching in the chloroplasts as a key step in ETI-PCD regulation.

Together, these studies emphasize the role of organelles in PCD regulation, with the nucleus serving as a hub of second messenger signaling and transcription and the chloroplasts responding to ETI by remodeling to serve a new role as a platform for ROS production. In addition, they define a new pathway of ETI regulation that contributes quantitatively to ETI-PCD.

The successful completion of many critical biological processes depends on the proper execution of complex spatial and temporal gene expression programs. With the advent of high-throughput microarray technology, it is now possible to measure the dynamics of these expression programs on a genome-wide level. In this thesis we present work focused on utilizing this technology, in combination with novel computational techniques, to examine the role of transcriptional regulatory mechanisms in controlling the complex gene expression programs underlying two fundamental biological processes---the cell cycle and the development and differentiation of an organ.

We generate a dataset describing the genomic expression program which occurs during the cell division cycle of Saccharomyces cerevisiae. By concurrently measuring the dynamics in both wild-type and mutant cells that do not express either S-phase or mitotic cyclins we quantify the relative contributions of cyclin-CDK complexes and transcriptional regulatory networks in the regulation the cell cell expression program. We show that CDKs are not the sole regulators of periodic transcription as contrary to previously accepted models; and we hypothesize an oscillating transcriptional regulatory network which could work independent of, or in tandem with, the CDK oscillator to control the cell cell expression program.

To understand the acquisition of cellular identity, we generate a nearly complete gene expression map of the Arabidopsis Thaliana root at the resolution of individual cell-types and developmental stages. An analysis of this data reveals a representative set of dominant expression patterns which are used to begin defining the spatiotemporal transcriptional programs that control development within the root.

Additionally, we develop computational tools that improve the interpretability and power of these data. We present CLOCCS, a model for the dynamics of population synchrony loss in time-series experiments. We demonstrate the utility of CLOCCS in integrating disparate datasets and present a CLOCCS based deconvolution of the cell-cycle expression data. A deconvolution method is also developed for the Arabidopsis dataset, increasing its resolution to cell-type/section subregion specificity. Finally, a method for identifying biological processes occurring on multiple timescales is presented and applied to both datasets.

It is through the combination of these new genome-wide expression studies and computational tools that we begin to elucidate the transcriptional regulatory mechanisms controlling fundamental biological processes.

Homeostatic maintenance of cellular mitochondria requires a dynamic balance between fission and fusion, and disruptions in this balance have been implicated in multiple pathological conditions, including Charcot-Marie-Tooth, Parkinson's, and Alzheimer's diseases. Whereas deregulated fission and fusion can be detrimental to health and survival, controlled changes in morphology are important for processes like cellular division and apoptosis. Specifically, regulated mitochondrial fission occurs closely with cytochrome c release during apoptosis and upon entry into mitosis during the cell cycle. Using cell culture-based assays, microscopy, and fly genetics, we examine how changes in the mitochondrial network are mediated at the molecular level during apoptosis and the cell cycle.

First, we report that the fly protein Reaper induces mitochondrial fragmentation in mammalian cells, likely through inhibition of the mitochondrial fusion protein Mfn2. Reaper colocalizes with and binds to Mfn2 and its fly orthologue dMFN, and the colocalization of the two proteins is necessary for Reaper-induced mitochondrial fission. Moreover, the overexpression of dMFN inhibits Reaper-induced killing both in vitro and in vivo.

Our data and work in a number of experimental systems demonstrate a requirement for mitochondrial fragmentation during apoptosis that is conserved from worms to flies to mammals. Our findings indicate that Reaper may function to inactivate mitochondrial metabolic function and/or to facilitate mitochondrial elimination during apoptosis.

Secondly, we characterize Drp1 degradation by the APC/C during mitotic exit and interphase. We provide evidence that APC/CCdh1-mediated degradation of Drp1 underlies both the morphological changes that occur during progression through the cell cycle and changes in mitochondrial metabolism during interphase. Inhibition of Cdh1-mediated Drp1 ubiquitylation and proteasomal degradation during interphase prevents the normal regrowth of mitochondrial networks after mitosis, prevents cyclin E accumulation, and alters the profile of lipid-derived metabolites. Our findings describe a novel role for APC/CCdh1-mediated Drp1 degradation in cell cycle-dependent changes in mitochondrial morphology and metabolic function and suggest that the APC/CCdh1complex may regulate the distinct bioenergetic needs of a growing cell during synthetic phases of the cell cycle.

In the past decade, a challenge to the canonical model of cell cycle transcriptional control has been posed by a series of high-throughput gene expression studies in budding yeast. Using genetic methods to inhibit or lock the activity of the cyclin-CDK/APC oscillator, these population studies demonstrated that a significant proportion of cell cycle transcription persists in the absence of cyclin-CDK/APC oscillations. To account for these findings, a network of serially activating transcription factors with sources of negative feedback from transcriptional repressors (referred to as a \say{TF network}) was proposed to drive cyclin-CDK/APC independent gene expression.

However, population studies of cell cycle gene expression are limited due to loss of phase synchrony that limits the timescale of measurement of gene expression and due to expression averaging that limits assessment of heterogeneity of expression within the population. To circumvent these limitations I used a single-cell timelapse microscopy approach to assess transcriptional dynamics of cell cycle regulated genes during extended cell cycle arrests in both the Gl/S and early mitosis (metaphase) phases of the cell cycle.

During G1/S arrest, transcriptional dynamics of four cell cycle regulated genes was assessed and activation of out-of-phase cell cycle transcription was observed in two of these genes. Though budding oscillations were observed in G1/S arrested cells, robust transcriptional oscillations were not seen for any of the four genes and budding dynamics were uncoupled from transcriptional dynamics after the first bud emergence. During cell cycle arrest in early mitosis, transcriptional dynamics of ten cell cycle regulated genes was assessed and activation of out-of-phase transcription was observed for four genes. All four genes activated once with canonical ordering but robust oscillations were not observed during mitotic arrest. Together these studies demonstrate activation, but not oscillation, of cell cycle transcription in the absence of cyclin-CDK/APC oscillations.

Cell proliferation is one of the elementary operations involved in building and maintaining the bodies of organisms, and animal development employs diverse regulatory strategies to ensure that it happens in the correct spatial and temporal arrangements. This dissertation is a study of some of the mechanisms involved in timing the early cell cycles of the embryo of Drosophila melanogaster. In chapter 1, we introduce many of the important concepts and provide the reader with background on developmental regulation of the cell cycle. In chapter 2, we turn our focus to the problems associated with the cell-cycle transitions that accompany the maternal-to-zygotic transition. Specifically, it had been shown that slowing of the cell cycle following the initial rapid cleavage divisions is linked to the downregulation of protein phosphatase Cdc25/Twine activity. We pursue this problem with a structure-function analysis of Cdc25/Twine. In chapter 3, we turn our attention to the fourteenth round of cell divisions, which form exquisite spatio-temporal patterns called mitotic domains. Six heterochronic genes (btd, ems, kni, slp1, h, and hkb) had been identified that have dosage-sensitive effects on the timing of cell division in mitotic domain 2 (MD2). We tag two of these factors with GFPs using BAC trangenesis and measure their dynamics in MD2 and other head domains. We find that btd is expressed in a gradient that anticipates the mitotic schedule of MD2, and that slp1 is a powerful repressor of mitosis in the head domains. We conclude that these two factors contribute to the timing of MD2 via a mixed hourglass model that involves both activator-accumulation and repressor-depletion.

The cell cycle is arguably one of the most conserved regulatory networks within Eukaryotes. Despite the animals and fungi are sibling “kingdoms” within the Opisthokont supergroup, the core transcription factors that control commitment to cell division (E2F and SBF, respectively) and their repressors (Rb and Whi5, respectively) do not appear to have a shared molecular origin. My thesis work has focused on understanding how the networks that regulate cell cycle decisions have changed and rewired through evolutionary time.

By using comparative genomics, I found that the main fungal regulator (SBF) was acquired very early in the evolution of fungi by horizontal gene transfer from a viral origin. I also showed that this viral-derived transcription factor still coexists with the ancestral E2F in the zooporic fungus Spizellomyces punctatus, forming a hybrid cell cycle control network. I hypothesize a viral-derived regulator (SBF) hijacked cell cycle control in the dawn of Fungi by binding the promoters regulated by the ancestral counterpart (E2F), pushing cells to proliferation. This requires the invading SBF to be able to bind regulatory regions controlled by E2F. Using a high-throughput analyses of the DNA-binding properties of the SBF and E2F-family across Eukaryotic lineages I found that E2F and SBF share binding preferences, but that these are not completely overlapping, which could permit the evolutionary conservation of the hybrid E2F/SBF network in Spizellomyces. I then proceeded to test the potential differences \textit{in vivo} in accessibility to E2F and SBF binding sites by coupling in vitro DNA-binding information with nucleosomal and TF-footprints generated from MNase-seq data.

Finally, I developed Agrobacterium-mediated transformation in Spizellomyces, allowing me to describe basic characteristics of its developmental program using live-cell and fluorescence microscopy. By following nuclear dynamics with a fluorescently tagged histone I found that mitosis only initiates after germination, and that nuclei divide synchronously during sporogenesis. Furthermore, by following actin dynamics with LifeAct I showed that zoospores use actin-filled pseudopods to crawl, much like amoeba or animal cells, and that sporangia rely on complex actin dynamics during the formation of zoospores that are reminiscent of animal cellularization processes. This work highlights the importance of non-model systems for finding new solutions to longstanding questions in biology. This is a first step towards establishing Spizellomyces as a model system to study the evolution of key animal and fungal traits, particularly cell cycle regulation and development.

Within individual cells, the opposing processes of proliferation and apoptosis are precisely regulated. When this regulatory balance is interrupted, cells may become abnormal or even transformed. Understanding how to reverse or avoid these detrimental transformative processes begins with an intimate knowledge of the processes governing the cell cycle and apoptosis. Cell proliferation is governed by the cell cycle machinery. The cell cycle is driven by Cyclin-dependent kinase (Cdk) activity, which is dependent on the availability of specific Cyclin binding partners. The amount of available Cyclin is tightly controlled by a ubiquitin ligase protein complex called the anaphase promoting complex/cyclosome (APC/C.) This complex mediates the timely ubiquitylation and degradation of cell cycle regulators in order to control mitotic exit, the G1/S transition and to respond to signals emanating from spindle assembly checkpoint.

Given the importance of the APC/C, cells develop many ways to regulate APC/C activity. Post-translational modifications of the APC/C have been shown to alter its functionality, and many pseudosubstrate-based inhibitors have been discovered. Moreover, inhibitors such as Emi1 and Emi2, have been showed to inhibit the APC/C through their own intrinsic ubiquitin E3 ligase activities. Utilizing the Xenopus egg extract system, our laboratory has previously demonstrated that the RING domain-containing ubiquitin E3 ligase Xnf7 can inhibit Xenopus APC/C activity. In the thesis, we have identified TRIM39 as an Xnf7-related human regulator of the APC/C. Our study showed that TRIM39 restrains the ability of the APC/C to ubiquitylate Cyclin B in vitro and attenuates the degradation of Cyclin B and geminin when TRIM39 is incubated in cell lysates. Notably, it has been reported that TRIM39 activity is responsible for the accumulation of the Bax-interacting protein (and activator) MOAP-1 following etoposide-induced DNA damage. Our data indicated that MOAP-1 is a novel APC/C substrate, and that the ligase activity of TRIM39 appears to be essential for preventing its degradation. We further demonstrated that decreased levels of the APC/C activator Cdh1 induces MOAP-1 protein accumulation, thereby promoting DNA damage-induced apoptosis in 293T, PC3 and H1299 cells. This study illustrates a potential function for the APC/C in DNA damage induced apoptosis and also demonstrates that TRIM39 regulates both the cell cycle and apoptosis via APC/C inhibition.

To extend our observations regarding the role for TRIM39 in APC/C regulation, we investigated effects on the cell cycle via real-time imaging microscopy. We found cells arrest at G1/S in TRIM39 depleted RPE cells, a cell line which is commonly used for cell cycle analysis. This arrest phenotype is not observed in 293T, PC3 and H1299 cells which bear mutant p53 alleles. Further analysis showed that TRIM39 depleted RPE cells upregulate many genes that function downstream of p53 activity, such as the cdk inhibitor p21--thus, arresting cells at G1/S and reducing proliferation. The reduced growth can be rescued by p53 knockdown. Mechanistically, TRIM39 interacts with p53 and promotes destruction of p53 by ubiquitylation. This ubiquitylation is independent of the activity of the most intensively studied p53-directed E3 ligase, MDM2; depletion of both MDM2 and TRIM39 has a synergistic effect on p53 accumulation. This elevated p53 leads to more apoptosis in cancer cells bearing wildtype p53. Consequently, TRIM39 depletion might be employed as a combination treatment with MDM2 inhibitor, such as nutlin-3a, to stimulate tumor cell death.

In the thesis, we have found TRIM39 inhibits both the APC/C and p53. Both are essential regulators of cell cycle and apoptosis. Moreover, we have determined that the inhibitory activity of TRIM39 requires its E3 ligase activity. Future experiments will be directed towards investigating how TRIM39 protein stability and ligase activity are regulated to understand more fully the physiological situations in which TRIM39 is able to exert its ability to modulate the cell cycle and apoptosis. I will also discuss some preliminary data regarding changes in TRIM39 ligase activity induced by Chk1 and changes in TRIM39 protein abundance regulated by polo-like kinase 1(Plk1). Chk1 and Plk1 are essential kinases for cell cycle checkpoint and progression. Connecting Chk1 and Plk1 to TRIM39 may provide a more thorough understanding of TRIM39's ability to control the APC/C inhibition and p53 ubiquitylation in response to cell cycle or cell damage cues. Since the APC/C and p53 both can regulate cell cycle and apoptosis, further investigations into the involvement of TRIM39 in the life-or-death decision will be of great interest.