In this thesis I describe a functional genomics resource in which each yeast gene, with its native promoter and 3’UTR, is cloned on a uniquely barcoded low-copy vector. We refer to this resource as the Molecular Barcoded Yeast ORF (MoBY-ORF) library 1.0. Each gene carried by MoBY-ORF 1.0 should mimic its native expression and thus is best suited for complementation cloning. The vector backbone of MoBY-ORF 1.0 is compatible with the mating-assisted genetically integrated cloning (MAGIC) system for recombination cloning in bacterial cells, which allows the transfer of the ORF fragment and its barcoded cassette to other vector backbones. Taking advantage of the MAGIC system, we created a multi-copy version of the library, which we refer to as MoBY-ORF 2.0. I used MoBY-ORF 1.0 to map drug resistant mutants by complementation cloning with a barcode microarray readout. I investigated several drugs with known targets in my proof-of-principle experiments and showed the feasibility of this method. I identified a single mutation that causes resistance to two different natural products, theopalauamide and stichloroside. By doing so, I was able to link these two chemicals to their cellular target, ergosterol. In fact, theopalauamide represents a new class of sterol binding chemical. I also describe the use of MoBY-ORF 2.0 to clone dosage suppressors of conditional temperature-sensitive mutants. By doing so, and combing our own data with published literature, we showed that dosage suppression interactions often overlap with protein-protein interactions and negative genetic interactions but not positive interactions; however the majority of dosage suppression interactions are unique and thus they represent an unique edge on a global functional interaction map. We also describe the first genome-wide dosage suppressor interaction map of budding yeast.

In this thesis I describe a functional genomics resource in which each yeast gene, with its native promoter and 3’UTR, is cloned on a uniquely barcoded low-copy vector. We refer to this resource as the Molecular Barcoded Yeast ORF (MoBY-ORF) library 1.0. Each gene carried by MoBY-ORF 1.0 should mimic its native expression and thus is best suited for complementation cloning. The vector backbone of MoBY-ORF 1.0 is compatible with the mating-assisted genetically integrated cloning (MAGIC) system for recombination cloning in bacterial cells, which allows the transfer of the ORF fragment and its barcoded cassette to other vector backbones. Taking advantage of the MAGIC system, we created a multi-copy version of the library, which we refer to as MoBY-ORF 2.0. I used MoBY-ORF 1.0 to map drug resistant mutants by complementation cloning with a barcode microarray readout. I investigated several drugs with known targets in my proof-of-principle experiments and showed the feasibility of this method. I identified a single mutation that causes resistance to two different natural products, theopalauamide and stichloroside. By doing so, I was able to link these two chemicals to their cellular target, ergosterol. In fact, theopalauamide represents a new class of sterol binding chemical. I also describe the use of MoBY-ORF 2.0 to clone dosage suppressors of conditional temperature-sensitive mutants. By doing so, and combing our own data with published literature, we showed that dosage suppression interactions often overlap with protein-protein interactions and negative genetic interactions but not positive interactions; however the majority of dosage suppression interactions are unique and thus they represent an unique edge on a global functional interaction map. We also describe the first genome-wide dosage suppressor interaction map of budding yeast.

The Silent Information Regulator (SIR) complex is responsible for the formation of silent chromatin domains in Saccharomyces cerevisiae, and consists of the NAD-dependent histone deacetylase Sir2, and histone binding proteins Sir3 and Sir4. The current model of silent chromatin assembly proposes that histone deacetylation by Sir2 is required to promote recruitment of Sir3 and Sir4, and assembly of full SIR complexes on chromatin. However, recent work has suggested unique roles for the histone binding proteins Sir3 and Sir4 in this process. Here we present data suggesting that Sir3 is primarily responsible for mediating the spreading of silent chromatin from sites of nucleation, while regulation of Sir4 abundance controls the rate of silencing establishment. We have also investigated a potential novel dimerization domain in Sir3, which may represent a conserved function in vertebrates. Investigations into the regulation of silent chromatin assembly in budding yeast will facilitate our understanding of the mechanisms that control heterochromatin-mediated gene repression in higher organisms.

Increasing gene dosage provides a powerful means of probing gene function, as it tends to cause a gain-of-function effect due to increased gene activity. In the budding yeast, Saccharomyces cerevisiae, systematic gene overexpression studies have shown that in wild-type cells, overexpression of a small subset of genes results in an overt phenotype. However, examining the effects of gene overexpression in sensitized cells containing mutations in known genes is a powerful means for identifying functionally relevant genetic interactions. When a query mutant phenotype is rescued by gene overexpression, the genetic interaction is termed dosage suppression. I comprehensively investigated dosage suppression genetic interactions in yeast using three approaches. First, using one of two novel plasmid libraries cloned by two colleagues and myself, I systematically performed dosage suppression screens and identified over 130 novel dosage suppression genetic interactions for more than 25 essential yeast genes. The plasmid libraries, called the molecular barcoded yeast ORF (MoBY-ORF) 1.0 and 2.0, are designed to streamline dosage analysis by being compatible with high-throughput genomics technologies that can monitor plasmid representation, including barcode microarrays and next-generation sequencing methods. Second, I describe a detailed analysis of the novel dosage suppression interactions, as well as of literature-curated interactions, and show that the gene pairs exhibiting dosage suppression are often functionally related and can overlap with physical as well as negative genetic interactions. Third, I performed a systematic categorization of dosage suppression genetic interactions in yeast and show that the majority of the dosage suppression interactions can be assigned to one of four general mechanistic classifications. With this comprehensive analysis, I conclude that systematically identifying dosage suppression genetic interactions will allow for their integration into other genetic and physical interaction networks and should provide new insight into the global wiring diagram of the cell.

Increasing gene dosage provides a powerful means of probing gene function, as it tends to cause a gain-of-function effect due to increased gene activity. In the budding yeast, Saccharomyces cerevisiae, systematic gene overexpression studies have shown that in wild-type cells, overexpression of a small subset of genes results in an overt phenotype. However, examining the effects of gene overexpression in sensitized cells containing mutations in known genes is a powerful means for identifying functionally relevant genetic interactions. When a query mutant phenotype is rescued by gene overexpression, the genetic interaction is termed dosage suppression. I comprehensively investigated dosage suppression genetic interactions in yeast using three approaches. First, using one of two novel plasmid libraries cloned by two colleagues and myself, I systematically performed dosage suppression screens and identified over 130 novel dosage suppression genetic interactions for more than 25 essential yeast genes. The plasmid libraries, called the molecular barcoded yeast ORF (MoBY-ORF) 1.0 and 2.0, are designed to streamline dosage analysis by being compatible with high-throughput genomics technologies that can monitor plasmid representation, including barcode microarrays and next-generation sequencing methods. Second, I describe a detailed analysis of the novel dosage suppression interactions, as well as of literature-curated interactions, and show that the gene pairs exhibiting dosage suppression are often functionally related and can overlap with physical as well as negative genetic interactions. Third, I performed a systematic categorization of dosage suppression genetic interactions in yeast and show that the majority of the dosage suppression interactions can be assigned to one of four general mechanistic classifications. With this comprehensive analysis, I conclude that systematically identifying dosage suppression genetic interactions will allow for their integration into other genetic and physical interaction networks and should provide new insight into the global wiring diagram of the cell.

The cell cycle of the budding yeast, Saccharomyces cerevisiae, is regulated by a complex network of chemical reactions controlling the activity of the cyclin-dependent kinases (CDKs), a family of protein kinases that drive the major events of the cell cycle. A previous mathematical model by Chen et al. (2000) described a molecular mechanism for the Start transition (passage from G1 phase to S/M phase) in budding yeast. In this thesis, my main goal is to extend Chen's model to include new information about the mechanism controlling Finish (passage from S/M phase to G1 phase). Using laws of biochemical kinetics, I transcribed the hypothetical molecular mechanism into a set of differential equations. Simulations of the wild-type cell cycle and the phenotypes of more than 60 mutants provide a thorough understanding of how budding yeast cells exit mitosis. / Master of Science

Errors in segregation of genetic materials are detrimental to all organisms. The budding yeast ensures accurate chromosome segregation by employing a system called the spindle checkpoint. The spindle checkpoint, which consists of proteins such as Mad1, Mad2, Mad3, Bub1, and Bub3, monitors the attachment of microtubules to the chromosomes and prevents cell cycle progression until all chromosomes are properly attached. To understand how the spindle checkpoint arrests cells in response to attachment errors at the chromosomes, we recruited different checkpoint proteins to an ectopic site on the chromosome by taking advantage of the binding of the lactose repressor (LacI) to the lactose operator (LacO). We found that cells expressing Bub1-LacI arrest in metaphase. The phenotype is in fact caused by dimerization of Bub1 when it is fused to LacI rather than the recruitment of Bub1 to chromosome. The cell cycle arrest by the Bub1 dimer depends on the presence of other checkpoint proteins, suggesting that the dimerization of Bub1 represents an upstream event in the spindle checkpoint pathway. The results with the Bub1 dimer inspired us to fuse checkpoint proteins to each other to mimic protein interactions that may contribute to checkpoint activation. We showed that fusing Mad2 and Mad3 arrests cells in mitosis and that this arrest is independent of other checkpoint proteins. We believe that combining Mad2 and Mad3 arrests cells because both proteins can bind weakly to Cdc20, the main target of the spindle checkpoint, and the sum of these two weak bindings creates a hybrid protein that binds tightly to Cdc20. We reasoned that if Mad3's role is to make Mad2 bind tightly, artificially tethering Mad2 directly to Cdc20 should also arrest cells and this arrest should not depend on any other checkpoint components. Our experiments confirmed these predictions, suggesting that Mad3 is required for the stable binding of Mad2 to Cdc20 in vivo, that this binding is sufficient to inhibit APC activity, and that this reaction is the most downstream event in spindle checkpoint activation. The interactions among spindle checkpoint proteins thus play an important role in cell cycle arrest and must be carefully regulated.

Yes / We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilises Rad51-DNA filaments and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although in such cells sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalised with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards interhomologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division. / Biotechnology and Biological Sciences Research Council (BB/K009346/1)

The operating principles of complex regulatory networks are more easily understood with mathematical modelling than by intuitive reasoning. In this thesis, I study the dynamics of the mitotic exit control system in budding yeast. I present a comprehensive mathematical model, which provides a system’s-level understanding of the mitotic exit process. This model captures the dynamics of classic experimental situations reported in the literature, and overcomes a number of limitations present in previous models. Analysis of the model led to a number of breakthroughs in the understanding of mitotic exit control. Firstly, numerical analysis of the model quantified the dependence of mitotic exit on the proteolytic and non-proteolytic functions of separase. It was shown that the requirement for the non-proteolytic function of separase depends on cyclin-dependent kinase activity. Secondly, APC/Cdc20 is a critical node that controls the phosphatase (Cdc14) branch and both cyclin (Clb2 and Clb5) branches of the cell cycle regulatory network. Thirdly, the model proved to be a useful tool for the systematic analysis of the recently discovered phenomenon of Cdc14 endocycles. Most proteins belonging to the cell cycle control network are regulated at the level of synthesis, degradation and activity. Presumably, these multiple layers of regulation facilitate robust cell cycle behaviour in the face of genetic and environmental perturbations. To falsify this hypothesis, I subjected the model to global parameter perturbations and tested viability against pre-defined criteria. According to these analyses, the regulated transcription and degradation of proteins make different contributions to cell cycle control. Regulated degradation confers cell cycle oscillations with robustness against perturbations, while regulated transcription plays a major role in controlling the period of these oscillations. Both regulated transcription and degradation are part of important feedback loops, that combined promote robust behaviour in the face of parametric variations.

The heterohexameric origin recognition complex (ORC) acts as a scaffold for the G1 phase assembly of pre-replicative complexes. Only the Orc1-5 subunits are required for origin binding in budding yeast, yet Orc6 is an essential protein for cell proliferation. In comparison to other eukaryotic Orc6 proteins, budding yeast Orc6 appears to be quite divergent. Two-hybrid analysis revealed that Orc6 only weakly interacts with other ORC subunits. In this assay Orc6 showed a strong ability to self-associate, although the significance of this dimerization or multimerization remains unclear. Imaging of Orc6-eYFP revealed a punctate sub-nuclear localization pattern throughout the cell cycle, representing the first visualization of replication foci in live budding yeast cells. Orc6 was not detected at the site of division between mother and daughter cells, in contrast to observations from metazoans. An essential role for Orc6 in DNA replication was identified by depleting the protein before and during G1 phase. Surprisingly, Orc6 was required for entry into S phase after pre-replicative complex formation, in contrast to what has been observed for other ORC subunits. When Orc6 was depleted in late G1, Mcm2 and Mcm10 were displaced from chromatin, the efficiency of replication origin firing was severely compromised, and cells failed to progress through S phase. Depletion of Orc6 late in the cell cycle indicated that it was not required for mitosis or cytokinesis. However, Orc6 was shown to be associated with proteins involved in regulating these processes, suggesting that it may act as a signal to mark the completion of DNA replication and allow mitosis to commence.