Dissertations / Theses on the topic 'Yeast cell factory'

Il ruolo principale delle biotecnologie industriali è quello di fornire soluzioni innovative per alcune delle più grandi sfide del mondo. Nonostante il potenziale e le tecniche innovative applicate, i processi microbiologici bio-based necessitano ancora di ulteriori studi per diventare pervasivi e quindi sostituire i processi di produzione tradizionali. Per rendere i processi microbici economicamente fattibili e rispettosi dell'ambiente, uno dei fattori chiave risiede nella scelta della biomassa di partenza. In una logica di bioeconomia circolare, i sottoprodotti e le biomasse residue devono essere considerati come materie prime di partenza del processo. L'uso di queste biomasse non solleva questioni etiche e allo stesso tempo è economicamente vantaggioso e orientato all'ambiente. La maggior parte di queste biomasse residue sono residui agricoli e forestali, una famiglia di biomasse caratterizzate da una struttura lignocellulosica. Il problema legato al loro utilizzo nelle bioraffinerie a base microbica è quello di trovare un pretrattamento efficiente per convertirli in zuccheri fermentabili e altri nutrienti, riducendo al minimo il rilascio di inibitori della crescita microbica. Parlando di bioraffinerie microbiche, ci sono due aspetti principali da tenere a mente durante la progettazione del processo: la biomassa di partenza e l'ospite microbico. L’host finale può essere scelto seguendo due approcci complementari: i) sfruttare la biodiversità microbica già presente in natura, scegliendo l'ospite finale in base alle sue caratteristiche innate, particolarmente vantaggiose in uno specifico processo produttivo; ii) lavorare su una cell factory già nota, customizzandola secondo le necessità. Nel Capitolo 2 è stata valutata una specifica classe di lieviti non convenzionali, denominata lieviti oleaginosi, per ottenere oli microbici (SCOs) per la produzione di biodiesel a partire da scarti dell'industria della barbabietola da zucchero. Lipomyces starkeyi è stato selezionato come cell factory per la conversione della polpa di barbabietola da zucchero e della melassa di barbabietola da zucchero per massimizzare l'accumulo di SCOs. Con questo esempio applicativo abbiamo dimostrato la possibilità di sfruttare microrganismi non convenzionali per ottenere bio-carburanti più sostenibili. D'altra parte, la scelta di Saccharomyces cerevisiae come ospite finale ha il grande vantaggio di sfruttare l'ampia conoscenza che lo circonda, compreso l’enorme numero di approcci di biologia sintetica per disegnarlo nella forma finale necessaria. Nel Capitolo 3 presento una nuova combinazione di approcci di biologia sintetica per accelerare le procedure di ingegnerizzazione, consentendo l’over-espressione e lo studio di vie biosintetiche eterologhe sempre più complesse. Inoltre, mostro l'applicazione di questo nuovo kit di strumenti alla produzione di un metabolita secondario di pianta. Nel capitolo 4 descrivo la progettazione di un nuovo vettore per migliorare le procedure di editing del genoma in S. cerevisiae. Anche in questo secondo progetto l'obiettivo finale è stato quello di velocizzare le fasi di progettazione e costruzione e le procedure di laboratorio, standardizzandole il più possibile per semplificare una parte del lavoro e lasciare più spazio alle fasi successive di test & learn. Nel Capitolo 5 propongo il concetto di co-localizzazione spaziale degli enzimi come campo d'avanguardia nella biologia sintetica per massimizzare il flusso di carbonio verso il prodotto di interesse, sfruttando l'uso di scaffold proteici sintetici e domini di interazione sintetici. La tesi qui presentata vuole porsi come esempio pratico di come le biotecnologie industriali possano essere utilizzate come potente strumento nella difficile transizione da una società basata sul petrolio e una più sostenibile.
The role of industrial biotechnology is to provide game-changing solutions for some of the world’s greatest challenges. From climate change to alternative energy sources and to sustainable productions, industrial biotechnology is fighting to find new sustainable solutions. Despite the promising potential and the innovative techniques applied, bio-based biological processes still need further studies for becoming pervasive and therefore substituting the traditional processes of production. To make microbial processes economically feasible and environmentally friendly, one of the key factors resides in the choice of the starting biomass. In a logic of circular bioeconomy, by-products and residual biomasses have to be considered as starting feedstocks of the process. The use of these biomasses does not raise ethical issues and at the same time is economically advantageous and environment oriented. Indeed, they do not compete with the food industry, as they are usually production waste. Most of these residual biomasses are agricultural and forest residues, a family of biomasses characterised by a lignocellulosic structure. The problem related to their use in microbial-based biorefineries is to find an efficient pretreatment to convert them into fermentable sugars and other nutrients, while reducing to a minimum the release of inhibitors of microbial growth. Talking about microbial-based biorefinery as a substitute to petrol-based refinery, there are two main topics to keep in mind during the process design: the starting biomass and the microbial host. The chassis which will be involved in the final production process can be chosen following two complementary approaches: i) exploiting microbial biodiversity already present in nature by picking the final host depending on its innate characteristics, particularly advantageous in a specific production process; ii) working on a well-known cell factory by customising it as needed. In this thesis both principles were followed. In Chapter 2 a specific class of non-conventional yeasts, named oleaginous yeasts, was evaluated to obtain single cell oils (SCOs) for biodiesel production starting from wastes of the sugar beet industry. Lipomyces starkeyi was selected as cell factory for the conversion of sugar beet pulp and sugar beet molasses to maximise SCOs accumulation. With this applicative example we showed the possibility to take advantage of non-conventional microorganisms to achieve a more sustainable way to produce fuels. On the other hand, choosing Saccharomyces cerevisiae as final host has the major advantage of exploiting the wide knowledge around it, starting from its genome and physiology, and arriving at the tremendous number of synthetic biology approaches to engineer it and manipulate it in the desired final form. In Chapter 3 I introduce a novel toolkit: a new combination of synthetic biology approaches to accelerate the engineering procedures allowing the overexpression and the study of more and more complex biosynthetic heterologous pathways. Moreover, I show the application of this novel toolkit to the production of a selected plant secondary metabolite. In Chapter 4 I describe the design of a new vector to improve genome editing procedures in S. cerevisiae. Even in this second project the final goal was to speed up the design and build stages and laboratory procedures, standardising them as much as possible to simplify one part of scientists' work, to leave more space to the subsequent phases of testing and learning. In Chapter 5 I propose the concept of enzyme spatial co-localisation as a forefront field in synthetic biology to maximise the carbon flux toward the product of interest, exploiting the use of protein synthetic scaffolds and synthetic interaction domains. The presented thesis wants to pose itself as a practical example on how industrial biotechnology can be used as a powerful tool in the difficult transition to a more sustainable society.

The proven ability to ferment Saccharomyces cerevisiae on a large scale presents an attractive target for producing chemicals and fuels from sustainable sources. Efficient and predominant carbon flux through to ethanol is a significant engineering issue in the development of this yeast as a multi-product cell chassis used in biorefineries. In order to evaluate diversion of carbon flux away from ethanol, combinatorial deletions were investigated in genes encoding the six isozymes of alcohol dehydrogenase (ADH), which catalyse the terminal step in ethanol production. The scarless, dominant and counter- selectable amdSYM gene deletion method was optimised for generation of a combinatorial ADH knockout library in an industrially relevant strain of S. cerevisiae. Current understanding of the individual ADH genes fails to fully evaluate genotype-by-genotype and genotype-by-environment interactions: rather, further research of such a complex biological process requires a multivariate mathematical modelling approach. Application of such an approach using the Design of Experiments (DoE) methodology is appraised here as essential for detailed empirical evaluation of complex systems. DoE provided empirical evidence that in S. cerevisiae: i) the ADH2 gene is not associated with producing ethanol under anaerobic culture conditions in combination with 25 g l-1 glucose substrate concentrations; ii) ADH4 is associated with increased ethanol production when the cell is confronted with a zinc-limited [1 μM] environment; and iii) ADH5 is linked with the production of ethanol, predominantly at pH 4.5. A successful metabolic engineering strategy is detailed which increases the product portfolio of S. cerevisiae, currently used for large-scale production of bioethanol. Heterologous expression of the cytochrome P450 fatty acid peroxygenase from Jeotgalicoccus sp., OleTJE, fused to the RhFRED reductase from Rhodococcus sp. NCIMB 978 converted free fatty acid precursors to C13, C15 and C17 alkenes (3.81 ng μl-1 total alkene concentration).

An investigation of the factors influencing the inhibitory and toxic effects of ethanol and higher alcohols, byproducts of alcoholic fermentation, on yeast, is presented. The relative potency of alcohols was found to correlate strongly with the carbon chain-length or molecular size and the lipid solubility of the respective alcohols. Higher alcohols act synergistically with each other and with ethanol in causing cell death of suspensions of non-growing Saccharomyces cerevisiae. The presence of higher alcohols in fermented broth, even at low concentrations, and other by-products of alcoholic fermentation, could explain the higher potency of ethanol produced during fermentation compared to added ethanol. The kinetics of uptake of labelled ethanol supplied at different concentrations gave no evidence of enzymic involvement in the ethanol uptake process. The rate of release of labelled ethanol by cells fed labelled glucose paralled the rate of p14sC-C0b2s release. This does not support the view that ethanol accumulates within the cells to higher concentrations than occur in the medium. Supplementation of a basal synthetic medium with various nutrients did not confer additional survival capacity on yeast against the adverse effects of alcohol. Osmotic pressure did not influence alcohol toxicity below 10% (w/v) sorbitol equivalent of osmotic pressure. Alcohol toxicity is not influenced by hydrogen ion concentration (pH) over a range of pH 5.3 to 3.5.

This work was performed in the framework of two application-oriented research projects that focus on the generation and evaluation of fluorescent Saccharomyces (S.) cerevisiae-based sensor and reporter cells for white biotechnology as well as the extension of the conventional single-cell/single-construct principle of ordinary yeast biosensor approaches. Numerous products are currently generated by biotechnological processes which require continuous and precise process control and monitoring. These demands are only partially met by physical or physiochemical sensors since they measure parameters off-line or use surrogate parameters that consequently provide only indirect information about the actual process performance. Biosensors, in particular whole cell-based biosensors, have the unique potential to near-line and long-term monitor parameters such as nutrient availability during fermentation processes. Moreover, they allow for the assessment of an analyte’s biological relevance. Prototype yeast sensor and reporter strains derived from common laboratory strains were transformed with multicopy expression plasmids that mediate constitutive or inducible expression of a fluorescence reporter gene. Performance of these cells was examined by various qualitative and quantitative detection methods – representative of putative transducer technologies. Analyses were performed on the population level by microplate reader-based fluorometry and Western blot as well as on the single-cell level by fluorescence microscopy and flow cytometry. ‘Signature’ promoters that are activated or repressed during particular nutrient-limited growth conditions were selected in order to generate yeast nutrient sensor strains for monitoring the biological availability of nitrogen, phosphorus or sulphur. For each category, at least one promoter mediating at least threefold changed green fluorescence levels between sensor cells in non-limited and nutrient-limited conditions was identified. Sensor strains were evaluated in detail regarding sensitivity, analyte selectivity and the ability to restore basic fluorescence after shift from nutrient-limited to non-limited conditions (regeneration). The applicability for bioprocess monitoring purposes was tested by growth of yeast nutrient sensor cells in microalgae media and supernatants. Despite successful proof of principle, numerous challenges still need to be solved to realise prospective implementation in this field of white biotechnology. The major drawback of plasmid-borne detection constructs is a high fluorescence variance between individual cells. By generation of a nitrogen sensor strain with a genome-integrated detection construct, uniform expression on the single-cell level and simultaneous maintenance of basic properties (ability of fluorescence induction/regeneration and lack of cross-reactivity) was achieved. However, due to the singular detection construct per cell, significantly weaker overall fluorescence was observed. The traditional single-cell/single-construct approach was expanded upon in two ways. Firstly, a practical dual-colour sensor strain was created by simultaneous, constitutive expression of a red fluorescence reporter gene in green fluorescent nitrogen sensor cells. Secondly, an innovative cellular communication and signal amplification system inspired by the natural S. cerevisiae pheromone system and mating response was established successfully. It features the yeast pheromone alpha-factor as a trigger and alpha-factor-responsive reporter cells which express a fluorescence reporter gene from the pheromone-inducible FIG1 promoter as an output signal. The system was functional both with synthetic and cell-secreted alpha-factor, provided that recombinant cells were deleted for the alpha-factor protease Bar1p. Integration of amplifier cells which secrete alpha-factor in response to stimulation with the pheromone itself could increase the system\'s sensitivity further. Signal amplification was demonstrated for phosphorus sensor cells as a proof of concept. Therefore, the alpha-factor-based cellular communication and signal amplification system might be useful in applications that suffer from poor signal yield. Due to its modular design, the system could be applied in basically any cell-based biosensor or sensor-actor system. Immobilisation of the generated sensor and reporter cells in transparent natural polymers can be beneficial considering biosensor fabrication. Functionality of sensor and reporter cells in calcium-alginate beads or nano-printed arrays was successfully demonstrated. For the latter setup, fluorescence scanning and software-assisted fluorescence quantification was applied as a new detection method. In an experiment using an agarose-based two-compartment setup proposed by Jahn, 2011, properties of the alpha-factor-based cellular communication and signal amplification system after immobilisation were tested. These studies provide an initial experimental basis for an appropriate geometry of miniaturised immobilisation matrices with fluorescent yeast sensor and reporter cells in prospective biosensor designs.

This project investigates the factors which may affect the response of yeast cells to potential mutagens and thus to optimise their response. The problem was approached from four main angles as follows: i) permeability - rendering the cells more permeable either by pre-treatment with selected chemicals or by selecting clones with cell wall defects; ii) repair capacity - preventing adequate repair of damaged DNA either by post-treatment with repair inhibitors or by using strains with defective repair genes; iii) genetic background - looking at reversion in the same gene but in a different genetic background or different genes in the same background; iv) treatment conditions - treating cells in buffer or broth, with or without exogenous activation, at 28 C or 37 C. The general conclusions which may be drawn from these studies are: a) most chemical mutagens are able to enter the yeast cells in sufficient quantities to cause damage to the DNA without pre-treating the cells to increase their permeability; b) the repair capacity of a cell is a very important factor in its response to a mutagen and if this capacity is greatly impaired, then the chances of survival of the cell after treatment with a mutagen are greatly reduced; c) the genetic background of a cell and the marker under consideration can affect the response of the cell to a mutagen; d) the conditions under which yeast cells are exposed to mutagens affect both the response of the yeast cells and the effectiveness of the mutagen itself. As for optimising the response of the yeast cells to mutagens this can only be done by gathering together all the information already known about the compound under study, and any related compounds, and analysing this data to discover what treatment conditions should be used and possibly what test.

When DNA replication is challenged, cells activate a DNA synthesis checkpoint blocking cell cycle progression until they are able to overcome the replication defects. In fission yeast, Cds1 is the effector kinase of this checkpoint, inhibiting M phase entry, stabilizing stalled replication forks and triggering transcriptional activation of S-phase genes; the molecular basis of this last effect remains largely unknown. The MBF complex controls the transcription of S-phase genes. We have purified novel interactors of the MBF complex and among them we have identified the repressor Max1. When the DNA synthesis checkpoint is activated, Max1 is phosphorylated by Cds1 resulting in the abrogation of its binding to MBF. As a consequence, MBF-dependent transcription is maintained active until cells are able to overcome this challenge.
Cuando la replicación del DNA se ve alterada, las células activan un mecanismo de control bloqueando la progresión del ciclo celular hasta que son capaces de superar el daño. En la levadura de fisión, Cds1 es la proteína kinasa efectora de dicha respuesta, mediante inhibición de la entrada en fase M, estabilización las horquillas de replicación bloqueadas, e inducción de la activación de la transcripción de los genes de fase S; siendo la base molecular de este último proceso poco conocida. El factor de transcripción MBF controla la transcripción de los genes de fase S. Hemos purificado proteínas que interaccionan con MBF, y entre ellas, hemos identificado al represor Max1. Cuando el checkpoint de síntesis de DNA es activado, Max1 es fosforilado por la kinasa Cds1, y esto se traduce en la disociación de Max1 del complejo MBF. Como consecuencia, la transcripción MBF-dependiente se mantiene activa hasta que las células son capaces de superar el daño.

Heterochromatin in the budding yeast Saccharomyces cerevisiae is composed of polymers of the SIR (Silent Information Regulator) complex bound to nucleosomal DNA. Assembly of heterochromatin requires all three proteins of the Sir complex: the histone deacetylase Sir2, and histone binding proteins Sir3 and Sir4. Heterochromatin establishment requires passage through at least one cell cycle, but is not dependent on replication. Inhibition of chromatin modifying enzymes may be a mechanism for how cells limit assembly. Dot1 dependent methylation of H3K79 is suggested to inhibit de novo assembly. Halving the levels of Sir4 in cells causes a loss of silencing, suggesting that Sir4 protein abundance regulates the assembly of heterochromatin. We examine de novo assembly using a single cell assay. Half the level of Sir4 affects establishment, but not the maintenance, of silencing at HM loci. Additional Sir4 accelerates the rate of assembly. Epistasis analysis suggests that Dot1 dependent chromatin modification may act upstream of Sir4 abundance. We hypothesize that dot1Δ mutants speed assembly by disrupting telomeric heterochromatin, which liberates Sir4 to act at the HM loci. Deletion of YKU70, which specifically disrupts telomeric silencing, also speeds de novo assembly, without altering the methylation of histone H3. Consistent with our model, we have shown that Sir4 abundance falls during pheromone and stationary phase arrests after which several cell cycles are required before silencing can be reestablished.

Modulating chromatin structure is an important step in maintaining control over the eukaryotic genome. SWI/SNF, one of the complexes belonging to the growing family of ATP-dependent chromatin remodeling enzymes, is involved in controlling the expression of a number of inducible genes whose proper regulation is vital for metabolism and progression through mitosis. The mechanism by which SWI/SNF modulates chromatin structure at the nucleosome level is an important aspect of this regulation. The work in this dissertation focuses on how the Saccharomyces cerevisiae SWI/SNF complex uses the energy of ATP-hydrolysis to alter DNA-histone contacts in nucleosomes. This has been approached in a two part fashion. First, the three-dimensional structure and subunit composition of SWI/SNF complex has been determined. From this study we have identified a potential region of the SWI/SNF complex that might [be] a site for nucleosomal interaction. Second, functional analysis of the ATPase domain of Swi2p, the catalytic subunit of SWI/SNF, has revealed that a specific conserved motif is involved in coupling ATP hydrolysis to the mechanism of chromatin remodeling. These results provide a potential model for the function of the SWI/SNF chromatin remodeling complex at the nucleosome level.

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第18326号
農博第2051号
新制||農||1022(附属図書館)
学位論文||H26||N4833(農学部図書室)
31184
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 植田 充美, 教授 喜多 恵子, 教授 栗原 達夫
学位規則第4条第1項該当

Many intricate and highly conserved mechanisms have evolved to safeguard organisms against errors in gene expression. The nonsense-mediated mRNA decay pathway (NMD) exemplifies one such mechanism, specifically by eliminating mRNAs containing premature translation termination codons within their protein coding regions, thereby limiting the synthesis of potentially deleterious truncated polypeptides. Studies in Saccharomyces Cerevisiae have found that the activity of at least three trans-acting factors, known as UPF1, UPF2/NMD2, and UPF3is necessary for the proper function of the NMD pathway. Further research conducted in yeast indicates that the degradation of substrates of the NMD pathway is dependent on their translation, and that the sub-cellular site of their degradation in the cytoplasm. Although most evidence in yeast suggests that substrates of the NMD pathway are degraded in the cytoplasm while in association with the translation apparatus, some mammalian studies have found several mRNAs whose decay appears to occur within the nucleus or before their transport to the cytoplasm has been completed. In addition, study of the mammalian TPI mRNA found that this transcript was unavailable as a substrate for the NMD pathway once it had been successfully exported to the cytoplasm, further supporting the notion that the degradation of mammalian substrates of the NMD pathway occurs in association with the nucleus, or during export from the nucleus to the cytoplasm. To determine if yeast cytoplasmic nonsense-containing mRNA can become immune to the NMD pathway we examined the decay kinetics of two NMDS substrate mRNAs in response to repressing or activating the NMD pathway. Both the ade2-1 and pgk1-UAG-2nonsense-containing mRNAs were stabilized by repressing this pathway, while activation of NMD resulted in the rapid and immediate degradation of each transcripts. These findings demonstrate that nonsense-containing mRNAs residing in the nucleus are potentially susceptible to NMD at each round of translation. The remainder of this thesis utilizes protein overexpression studies to gain understanding into the function of factors related to the processes of nonsense-mediated mRNA decay and translation in Saccharomyces cerevisiae. Overexpression of a C-terminal truncated form of Nmd3p was found to be dominant-negative for cell viability, translation and the normal course of rRNA biogenesis. Overexpression studies conducted with mutant forms of the nonsense-mediated mRNA decay protein Upf1p, found that overexpression of mutants in the ATP binding and ATP hydrolysis region ofUpflp were dominant-negative for growth in an otherwise wild-type yeast strain. Furthermore, overexpression of the ATP hydrolysis mutant of Upf1p (DE572AA), resulted in the partial inhibition of NMD and a general perturbation of the translation apparatus. These results support previous studies suggesting a general role for Upf1p function in translation.

Translation initiation factor 5A (IF5A) is an essential, highly conserved protein found within all eukaryotic (eIF5A) and archaeal (aIF5A) cells. The IF5A protein is unique in that it contains the amino acid hypusine; a two-step post translational modification of a single, conserved lysine residue. Although hypusination of eIF5A is vital for eukaryotic cell viability, the primary role of the protein and its hypusine side chain remain a mystery. eIF5A, initially identified as a translation initiation factor, is not required for global protein synthesis leading to the prevailing proposal that eIF5A is purely involved in the translation of a select subset of mRNAs. Recently a number of mutational studies have focused on the conserved, hypusine-containing loop region of eIF5A where specific residues have been found to be essential for activity without affecting hypusination. It has been postulated that eIF5A exists as a dimer (40 kDa) under native conditions and that these residues may be at the interface of dimerisation. The aim of this research was therefore to conduct a mutational analysis of the loop region in support of this hypothesis. A functional analysis of the Saccharomyces cerevisiae eIF5A mutant proteins K48D, G50A, H52A and K56A revealed that these substitutions impaired growth to varying degrees in vivo with G50A and K48D mutant proteins displaying the most convincing defects. Gel filtration profiles gave unexpected results determining eIF5A mutant and wild type proteins to have a native molecular weight of 30 to 31 kDa, suggesting that the eIF5A oligomeric state may be transitory and subject to certain conditions. The inconclusive results obtained from using gel filtration studies led to an investigation into the feasibility of producing native, hypusinated peptides for future structural studies using nuclear magnetic resonance. Hypusinated and unhypusinated eIF5A were successfully separated into their domains making this a possibility. Finally, this study proposes a role for eIF5A in eukaryotic IRES-driven translation initiation.

This study investigates endocytosis and ER export signals of the yeast α-factor receptor and the role that receptor oligomerization plays in these processes. The α-factor receptor contains signal sequences in the cytoplasmic C-terminal domain that are essential for ligand-mediated endocytosis. In an endocytosis complementation assay, I found that oligomeric complexes of the receptor undergo ligand-mediated endocytosis when the α-factor binding site and the endocytosis signal sequences are located in different receptors. Both in vitro and in vivo assays strongly suggested that ligand-induced conformational changes in one Ste2 subunit do not affect neighboring subunits. Therefore, the recognition of endocytosis signal sequence and the recognition of the ligand-induced conformational change are likely to be two independent events, where the signal sequence plays only a passive role in the ligand-induced endocytosis. Four amino acid substitutions (C59R, H94P, S141P and S145P) in TM domains I, II and III were identified that resulted in the accumulation of truncated receptors in the ER but did not block ER export of full-length receptors. The two DXE motifs in the C-terminal tail were required for export of the mutant receptors from the ER; however DXE was not essential for proper cell surface expression of wild-type receptors apparently because the receptors contain redundant ER export signals. An assay for oligomerization of receptors in the ER was developed based on the ability of truncated mutant receptors to exit the ER. The four substitutions (C59R, H94P, S141P and S145P) that caused DXE-dependent ER export failed to form homo-oligomers, suggesting that the DXE motifs and receptor oligomerization serve as independent ER export signals. Consistent with this view, two of the substitutions (S141P and S145P), when coexpressed, with wild-type receptors, formed hetero-oligomers that exited the ER. Finally, the full-length oligomer-defective mutant Ste2-S141P was sensitive to α-factor, suggesting that receptor monomers that reach the cell surface are able to activate the heterotrimeric G protein. The potential roles that TM1, 2 and 3 play in receptor oligomerization are discussed.

Nonsense-mediated mRNA decay (NMD) is an important mRNA surveillance mechanism conserved in eukaryotes. This thesis explores several interesting aspects of the NMD pathway. One important aspect of NMD which is presently the subject of intense controversy is the subcellular localization of NMD. In one set of experiments, the decay kinetics of the ade2-1 and pgk1 nonsense mRNAs (substrates for NMD) were investigated in response to activating the NMD pathway to determine if cytoplasmic nonsense mRNAs are immune to NMD in the yeast system. The results of these studies demonstrated that activation of NMD caused rapid and immediate degradation of both the ade2-1 and the early nonsense pgk1 steady state mRNA populations. The half lives of the steady state mRNA populations for both ade2-1 and pgk1 (early nonsense) were shortened from >30 minutes to approximately 7 minutes. This was not observed for pgk1mRNAs that contained a late nonsense codon demonstrating that activation of NMD specifically targeted the proper substrates in these experiments. Therefore, in yeast, nonsense mRNAs residing in the cytoplasm are susceptible to NMD. While these findings are consistent with NMD occurring in the cytoplasm, they do not completely rule out the possibility of a nuclear-associated decay mechanism. To investigate the involvement of the nucleus in NMD, the putative nuclear targeting sequence identified in Nmd2p (one of the trans-acting factors essential for NMD) was characterized. Subcellular fractionation experiments demonstrated that the majority of Nmd2p localized to the cytoplasm with a small proportion detected in the nucleus. Specific mutations in the putative nuclear localization signal (NLS) of Nmd2p were found to have adverse effects on the protein's decay function. These effects on decay function, however, could not be attributed to a failure in nuclear localization. Therefore, the residues that comprise the putative NLS of Nmd2p are important for decay function but do not appear to be required for targeting the protein to the nucleus. These results are in accordance with the findings above which implicate the cytoplasm as an important cellular compartment for NMD. This thesis then investigates the regulatory roles of the trans-acting factors involved in NMD (Upf1p, Nmd2p, and Upf3p) using a novel quantitative assay for translational suppression, based on a nonsense allele of the CAN1 gene (can1-100). Deletion of UPF1, NMD2, or UPF3 stabilized the can1-100 transcript and promoted can1-100 nonsense suppression. Changes in mRNA levels were not the basis of suppression, however, since deletion of DCP1 or XRN1 or high-copy can1-100 expression in wild-type cells caused mRNA stabilization similar to that obtained in upf/nmd cells but did not result in comparable suppression. can1-100 suppression was highest in cells harboring a deletion of UPF1, and overexpression of UPF1 in cells with individual or multiple upf/nmd mutations lowered the level of nonsense suppression without affecting the abundance of the can1-100 mRNA. These findings indicate that Nmd2p and Upf3p regulate Upf1p activity and that Upf1p plays a critical role in promoting termination fidelity that is independent of its role in regulating mRNA decay.

DNA damage is an ongoing threat to both the ability of the cell to faithfully transmit genetic information to its offspring as well as to its own survival. In order to maintain genomic integrity, eukaryotes have developed a highly conserved mechanism to detect, signal and repair damage in DNA, known as the DNA damage response (DDR). In fission yeast the two DDR pathways converge at the regulation of single transcriptional factor complex (MBF) resulting in opposite directions. We have shown that when the DNA-synthesis checkpoint is activated, Max1 is phosphorylated by Cds1 resulting in the abrogation of its binding to MBF. As a consequence, MBF-dependent transcription is maintained active until cells are able to overcome the replication challenge. In contrast, upon DNA damage, Chk1 the effector kinase of DNA damage checkpoint is activated and blocks the cell cycle progression, inducing DNA repair and repressing the MBF dependent transcription. We have revealed that Cdc10 is the target of the DNA-damage checkpoint and when cells are treated with MMS or are exposed to IR, Chk1 phosphorylates Cdc10 inducing the exit of MBF from chromatin. The consequence is that under these conditions, MBF-dependent transcription is repressed. Thus, Max1 and Cdc10 couple normal cell cycle regulation and the DNA-synthesis and DNA-damage checkpoints into MBF.

Eukaryotic ribosome synthesis is a complex process that consumes a lot of energy and involves several hundreds of trans-acting factors that transiently associate with nascent ribosomes. Biogenesis of ribosomal subunits (the small 40S and the large 60S) starts with transcription of a long precursor ribosomal RNA (pre-rRNA) by RNA polymerase I (Pol I) in the nucleolus. This is a key step that globally controls yeast ribosome synthesis. The pre-rRNA, ‘the 35S transcript’, encodes the mature sequence (18S, 5.8S, and 25S) rRNA constituents of both the 40S and 60S subunits. The 35S transcript is subsequently modified, cleaved (processed) and assembled with numerous structural ribosomal proteins and ribosome synthesis factors (trans-acting factors) to form various ribosomal particles (pre-ribosomes, precursors to the 40S and 60S subunits) along ribosome assembly pathway.

In the budding yeast Saccharomyces cerevisiae, it has been reported recently that the processing of the 35S nascent transcript and the assembly of pre-ribosomes occur concomitantly with Pol I transcription in the nucleolus. In this process, the growing Pol I transcript gradually assembles with pre-40S structural ribosomal proteins and ribosomal synthesis factors to form the so-called ‘SSU-processome’ or ‘90S pre-ribosome’, the earliest precursor of the 40S subunit. The SSU-processome/90S pre-ribosome localizes to the nucleolus and consists of the 35S pre-rRNA, the U3 small nucleolar (sno) RNA, about a dozen of 40S ribosomal proteins and more than forty ribosome synthesis factors. The U3 snoRNA and pre-40S ribosome synthesis factors are all implicated in the processing of the 35S precursor (at sites A0, A1 and A2) and therefore in the synthesis of the 18S rRNA component of the 40S subunit. Significantly, the association of the U3 snoRNA with the growing 35S transcript is important for pre-40S assembly, whereas its dissociation from the processed transcript (following cleavage at sites A0-A2) is crucial for the overall structural remodeling of the 18S rRNA and for the formation of pre-40S ribosomes from the earliest precursor 90S particles.

This thesis mostly addresses the identification and functional characterization of Esf2 and Bfr2, two novel 40S synthesis factors, components of the SSU-processome/90S pre-ribosome in yeast. Both proteins localize to the nucleolus and their genetic depletions lead to failure in the production of 40S subunits. In the absence of either factor, the 35S pre-rRNA is not processed at sites A0-A2 and the 18S rRNA is not synthesized. Also, pre-ribosome assembly is affected and pre-40S ribosomes fail to mature properly. Strikingly, in the absence of either factor, the U3 snoRNA remains associated with unprocessed 35S transcript within pre-ribosomes indicating that Esf2 and Bfr2 are required to dissociate U3 from pre-ribosomes. This process also involves RNP (ribonucleoprotein particle) unwinding activities of the putative RNA helicase Dbp8.

La biogenèse du ribosome eucaryote est un processus complexe qui consomme beaucoup d’énergie et implique plusieurs centaines de facteurs trans qui s’associent de manière transitoire avec les pré-ribosomes en cours de formation. La biogenèse des sous-unités ribosomiques (la petite sous-unité 40S et la grande sous-unité 60S) débute dans le nucléole par la synthèse d’un long précurseur d’ARN ribosomique (le pré-ARNr, dit 35S chez la levure Saccharomyces cerevisiae) par l’ARN Polymérase I (Pol I). Ceci constitue une étape clé dans le contrôle global de la synthèse du ribosome chez la levure. Le pré-ARNr 35S renferme les séquences des ARNr matures 18S (ARNr de la sous-unité 40S) et 5.8S et 25S (deux des trois ARNr de la sous-unité 60S). Le pré-ARNr 35S subit un long processus de maturation et d’assemblage au cours duquel il est modifié, clivé (on parle du « processing » du pré-ARNr) et s’assemble avec des protéines ribosomiques (« RP », composants structuraux des sous-unités ribosomiques matures) et de nombreux facteurs de synthèse (facteurs trans) pour former différentes particules pré-ribosomiques (précurseurs des sous-unités 40S et 60S).

Chez la levure S. cerevisiae, il a récemment été montré que le processing du pré-ARNr 35S et l’assemblage des pré-ribosomes se produisent de manière concomminante avec la transcription Pol I dans le nucléole. Ainsi, le transcrit Pol I en cours de synthèse s’assemble progressivement avec des facteurs de synthèse ainsi que des RP pour former le « SSU processome » ou « pré-ribosome 90S », tout premier précurseur de la petite sous-unité 40S. Le SSU processome/pré-ribosome 90S est localisé dans le nucléole et est consisté du pré-ARNr 35S naissant, du petit ARN nucléolaire (snoRNA) U3, d’une douzaine de RP de la petite sous-unité 40S et de plus de 40 facteurs de synthèse. Le snoRNA U3 et ces facteurs de synthèse sont tous impliqués dans les clivages du pré-ARNr 35S aux sites A0, A1 et A2, et donc dans la biogenèse de l’ARNr 18S. L’association du snoRNA U3 avec le pré-ARNr 35S naissant est importante pour l’assemblage du SSU processome/pré-ribosome 90S. Par ailleurs, sa dissociation après les clivages aux sites A0-A2 permet un remodelage structural général de l’ARNr 18S et la formation du « pré-ribosome 40S » à partir de la particule précoce 90S.

Au cours de cette thèse, nous avons identifié et caractérisé fonctionnelement chez la levure deux nouveaux facteurs de synthèse de la petite sous-unité 40S et composants du SSU processome/pré-ribosome 90S: Esf2 et Bfr2. Ces deux protéines sont localisées dans le nucléole. Leur déplétion entraîne une incapacité à produire la sous-unité ribosomique 40S. En l’absence d’Esf2 ou Bfr2, le pré-ARNr 35S n’est plus clivé aux sites A0-A2 et l’ARNr 18S mature n’est plus produit. L’assemblage des pré-ribosomes est aussi affecté, notamment la formation du pré-ribosome 40S. De manière importante, en l’absence de l’un ou l’autre de ces facteurs, le snoRNA U3 reste associé au pré-ARNr 35S non clivé au sein des pré-ribosomes, indiquant qu’Esf2 et Bfr2 sont requises pour la dissociation d’U3 des pré-ribosomes. Ce processus implique aussi Dbp8, une hélicase à ARN présumée.

Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished

Catharanthus roseus est une plante tropicale qui produit spécifiquement des alcaloïdes indoliques monoterpéniques (AIM) d’intérêt thérapeutique. Chez C. roseus, la branche terpénique incluant la voie du méthylérythritol phosphate (MEP) est considérée comme limitante et présente une régulation transcriptionnelle coordonnée en réponse aux hormones inductrices de l’accumulation alcaloïdique. Lors de ce travail, suite à des analyses bioinformatiques et à la caractérisation de promoteurs de gènes de la voie MEP, nous avons identifié de nouvelles familles de facteurs de transcription impliquées dans la régulation de la biosynthèse des AIM. Des membres de la famille des ZCT, des WRKY et des RR type B interagissent avec le promoteur du gène hds de la voie MEP et régulent son activité. Ces travaux ont permis d’approfondir les connaissances sur les réseaux transcriptionnels régulateurs de la biosynthèse des AIM. L’utilisation de ces nouveaux facteurs de transcription activateurs peut désormais être envisagée dans le cadre d’expériences d’ingénierie métabolique afin d’augmenter l’accumulation d’alcaloïdes d’intérêt pharmaceutique chez C. roseus
Catharanthus roseus is a tropical plant producing specifically monoterpene indole alkaloids (MIA) of high interest due to their therapeutical values. In C. roseus cells, the terpenoid branch including the methyl erythritol phosphate pathway (MEP) provides the MIA terpenoid moiety and is regarded as limited for MIA biosynthesis. This branch presents a coordinated transcriptional regulation in response to hormonal signals leading to MIA production. In this context, bioinformatic analysises and functional characterization of MEP pathway gene promoters allowed the identification of new transcription factor families involved in the MIA pathway regulation. Members of ZCT proteins, WRKY and type B RR families specifically interact with the hds promoter from the MEP pathway and regulate its activity. This work permits to gain into insight the transcriptional network controlling the MIA biosynthesis. It is possible now to consider using transcription factor that act as activators and target genes from the terpenoid branch to increase the accumulation of alkaloids of pharmaceutical interest in C. roseus by metabolic engineering approaches

碩士
國立交通大學
統計學研究所
98
Transcription factors (TFs) play critical roles in controlling gene expressions. To understand how the cell cycle-regulated genes can be transcribed just before they are needed, it is essential to identify their transcriptional regulators. We developed a novel relative R squared method to identify cell cycle TFs in yeast by integrating the ChIP-chip and cell cycle gene expression data. Our method identified 15 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining three (Hap4, Reb1 and Tye7) are putative novel cell cycle TFs. Four lines of evidence are provided to show the biological significance of our prediction. Besides, for seven of the 15 identified cell cycle TFs, we can further assign a specific cell cycle phase in which the TFs function. Most of our predictions are supported by previous experimental or computational studies. Furthermore, we show that our method performs better than five existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust.

碩士
國立臺灣海洋大學
食品科學系
95
A protein from Saccharomyces cerevisiae No.1 has been demonstrated to have the activity of glucose tolerance factor (GTF) that can enhance the glucose uptake rate of adipose cells. The aims of this research are to investigate the pH and temperature stability of the GTF extract using the differentiated 3T3-L1 cell assay model, and to investigate the efficacy of breaking methods for this yeast cells. The GTF extract is quite stable between pH 2-pH 9. The residual activities of this GTF extract after being heated at 45 ℃, 55 ℃ and 65 ℃ for 2 h are 96 %, 79 % and 35 %, respectively. Its thermal inactivation constants at 65 ℃, 75 ℃ and 85 ℃ are 8.8 x 103, 1.13 x 104, and 1.27 x 104 min-1, respectively. To reserve the GTF activity, the optimal temperature and pH value for autolysis of S. cerevisiae No.1 cells are 45℃ and pH 6.0, respectively. During cell autolysis, the addition of ethyl acetate, ammonia, citric acid or lytic enzyme could increase the amino nitrogen content and the relative GTF activity in the supernatant, among which ethyl acetate at the concentration of 5 % being the most effective. The released amino nitrogen content and the relative GTF activity were increased from 107 mmole/mL and 41 %, respectively, for the control, to 325 mmol/mL and 121 %, respectively, for 5 % ethyl acetate addition. When both 5 % ethyl acetate and protease 1 were added during cell autolysis the released amino nitrogen content could be increased 513 mmol/mL. However, the relative GTF in the supernatant were 101 %. which was less then that for 5 % ethyl acetate added along. By scanning electron microscopic observation the phenomenon of cell plasmolysis was found for cells treated with various chemical tested, while collapsed cells were monitored for cells treated with various enzymes tested.

Heat shock response (HSR) is an ancient and highly conserved signaling pathway in cells that regulates the expression of heat shock proteins (HSPs) in the presence of thermal and other environmental stresses. HSPs function to prevent the formation of non-specific protein aggregates and to assist proteins in acquiring their native structures. Although HSR has been extensively studied, key aspects of this pathway remain a mystery. In particular, how HSR is activated and regulated by the master transcription factor HSF1 is not well understood. The broad goal of this thesis is to develop a quantitative framework aimed at elucidating the HSF1-mediated activation of HSR in yeast cells. Understanding this process has important implications for development, physiology and disease. Indeed, HSF1 is conserved from yeast to human, has been shown to play an important role in stress resistance, health and disease, and is a therapeutic target for neurodegenerative diseases. Broadly, there are two putative (not mutually exclusive) models for activation in response to heat shock: (1) HSF1 dissociation from chaperone proteins and (2) hyper-phosphorylation and the subsequent activation of HSF1. However the relative contribution of each of these events in the activation process is not characterized. Thus far, there is no direct evidence linking either of these two events to activation, and the relative contribution of each mechanism to the activation process has not been quantitatively characterized. To address these issues, we develop a quantitative model of HSR in yeast cells. We use the model to make a series of quantitative predictions and, in a collaborative effort, experimentally test these predictions in a yeast model of HSR. Critically, we provide the first direct evidence for chaperone dissociation of HSF1 in response to heat shock. Moreover, we find that HSF1 phosphorylation is dispensable for activation of HSR, but is able to modulate its activity. Taken together, our work leads to a model for two “orthogonal” mechanisms regulating HSR in yeast, in which chaperone dissociation acts as an ON/OFF switch, whereas phosphorylation functions to tune the gain of the response. Finally, to complement and further test this quantitative model, we develop a novel microfluidic system to explore in more depth the behavior of individual cells in the presence of heat shock inputs. This includes (1) a microfluidic device with microscale on-chip heaters enabling programmable thermal perturbations and (2) a custom image analysis platform to follow single cells through heat shock time courses. In preliminary single-cell studies, we find a relationship between HSF1 phosphorylation state and cell-to-cell variability in HSR activation level (as measured by a transcriptional reporter). These preliminary results suggest that HSF1 phosphorylation may be generating and tuning noise in the HSR in order to promote phenotypic plasticity and increased survivability of a cell population in the face of stress.

Gene deletions are a powerful method to uncover the cellular functions of a given gene in living systems. A limitation to this methodology is that it is not applicable to essential genes. Even for non-essential genes, gene knockouts cause complete absence of gene product thereby limiting genetic analysis of the biological pathway. Alternatives to gene deletions are mutants that are conditional, for e.g, temperature sensitive (ts) mutants are robust tools to understand temporal and spatial functions of genes. By definition, products of such mutants have near normal activity at a lower temperature or near-optimal growth temperature which is called as the permissive temperature and reduced activity at a higher, non-optimal temperature called as the non-permissive temperature. Generation of ts alleles in genes of interest is often time consuming as it requires screening a large population of mutants to identify those that are conditional. Often many essential proteins do not yield ts such alleles even after saturation mutagenesis and extensive screening (Harris et al., 1992; Varadarajan et al., 1996). The limited availability of such mutants in many essential genes prompted us to adopt a biophysical approach to design temperature-sensitive missense mutants in an essential gene of fission yeast. Several studies report that mutations in buried or solvent-inaccessible amino acids cause extensive changes in the thermal stability of proteins and specific substitutions create temperature-sensitive mutants (Rennell et al., 1991; Sandberg et al., 1995). We used the above approach to generate conditional mutants in the fission yeast gene spprp18+encoding an essential predicted second splicing factor based on its homology with human and S. cerevisiae proteins. We have used a missense mutant coupled with a conditional expression system to elucidate the cellular functions of spprp18+. Further, we have employed the same biophysical principle to generate a missense mutant in spago1+ RNA silencing factor that is non-essential for viability but has critical functions in the RNAi pathway of fission yeast. Fission yeast pre-mRNA splicing: cellular functions for the protein factor SpPrp18 Pre-mRNA splicing is an evolutionarily conserved process that excises introns from nascent transcripts. Splicing reactions are catalyzed by the large ribonuclear protein machinery called the spliceosome and occur by two invariant trans-esterification reactions (reviewed in Ruby and Abelson, 1991; Moore et al., 1993). The RNA-RNA, RNA–protein and protein-protein interactions in an assembly of such a large protein complex are numerous and highly dynamic in nature. These interactions in in vitro splicing reactions show ordered recruitment of essential small nuclear ribonucleic particles snRNPs and non–snRNP components on pre-mRNA cis-elements. Further these trans acting factors recognize and poise the catalytic sites in proximity to identify and excise introns. The precision of the process is remarkable given the diversity in architecture for exons and introns in eukaryotic genes (reviewed in Burge et al., 1999; Will and Luhrmann, 2006). Many spliceosomal protein components are conserved across various organisms, yet introns have diverse features with large variations in primary sequence. We hypothesize that co-evolution of splicing factor functions occurs with changes in gene and intron architectures and argue for alternative spliceosomal interactions for spliceosomal proteins that thus enabling splicing of the divergent introns. In vitro biochemical and genetic studies in S. cerevisiae and biochemical studies with human cell lines have indicated that ScPRP18 and its human homolog hPRP18 function during the second catalytic reaction. In S. cerevisiae, ScPrp18 is non-essential for viability at growth temperatures <30°C (Vijayraghavan et al., 1989; Vijayraghavan and Abelson, 1990; Horowitz and Abelson, 1993b). The concerted action of ScSlu7 - ScPrp18 heteromeric complex is essential for proper 3’ss definition during the second catalytic reaction (Zhang and Schwer, 1997; James et al., 2002). These in vitro studies also hinted at a possible intron -specific requirement for ScPrp18 and ScSlu7 factors as they were dispensable for splicing of intron variants made in modified ACT1 intron containing transcripts (Brys and Schwer, 1996; Zhang and Schwer, 1997). A short spacing distance between branch point adenosine to 3’splice site rendered the substrate independent of Prp18 and Slu7 for the second step (Brys and Schwer, 1996; Zhang and Schwer, 1997). Extensive mutational analyses of budding yeast ScPrp18 identified two functional domains and suggested separate roles during splicing (Bacikova and Horowitz, 2002; James et al., 2002). Fission yeast with its genome harboring multiple introns and degenerate splice signals has recently emerged as a unique model to study relationships between splicing factors and their role in genomes with short introns. Previously, studies in our lab had initiated genetic and mutational analysis of S. pombe Prp18, the predicted homolog of budding yeast Prp18. Genetic analysis showed its essentiality, but a set of missense mutants based on studies of budding yeast ScPrp18 (Bacikova and Horowitz, 2002) gave either inactive null or entirely wild type phenotype for the fission yeast protein. In this study, we have extended our previous mutational analysis of fission yeast Prp18 by adopting biophysical and computational approaches to generate temperature-sensitive mutants. A missense mutant was used to understand the splicing functions and interactions of SpPrp18 and the findings are summarized below. Fission yeast SpPrp18 is an essential splicing factor with transcript-specific functions and links efficient splicing with cell cycle progression We initiated our analysis of SpPrp18 by adopting a biophysical approach to generate ts mutants. We used the PREDBUR algorithm to predict a set of buried residues, which when mutated could result in a temperature-sensitive phenotype that complements the null allele at permissive temperature. These predictions are based upon two biophysical properties of amino acids: 1) Hydrophobicity, which is calculated in a window of seven amino acids 2) Hydrophobic moment, which is calculated in a sliding window of nine amino acids in a given protein sequence. Several studies correlate these properties to protein stability and function (Varadarajan et al., 1996). One of the buried residue mutants V194R, in helix 1 of SpPrp18 conferred weak temperature- sensitivity and strong cold-sensitivity even when the protein was over expressed from a plasmid. Through semi-quantitative RT-PCR we showed splicing-defects for tfIId+ intron1 in these cells even when grown at permissive temperature. The primary phenotype was the accumulation of pre-mRNA. Further, we showed this splicing arrest is co-related with reduced levels of SpPrp18 protein, linking protein stability and splicing function. Next we examined the effects of this mutation on function by further reduction of protein levels. This was done by integrating the expression cassette nmt81:spprp18+/spprp18V194R at the leu1 chromosomal locus and by metabolic depletion of the integrated allele. Through RT-PCRs we demonstrated that depletion of wild type or missense protein has intron specific splicing defects. These findings showed its non-global and possibly substrate-specific splicing function. In the affected introns, precursor accumulation is the major phenotype, confirming prior data from our lab that hinted at its likely early splicing role. This contrasts with the second step splicing role of the human or budding yeast Prp18 proteins. Previous data from our lab showed loss of physical interaction between SpPrp18 and SpSlu7 by co-immunoprecipitation studies. This again differs from the strong and functionally important ScPrp18 and ScSlu7 interaction seen in budding yeast. We show the absence of charged residues in SpSlu7 interaction region formed by SpPrp18 helix1 and helix2 which can explain the altered associations for SpPrp18 in fission yeast. Importantly, as the V194R mutation in helix 1 shows splicing defects even at permissive temperature, the data indicate a critical role for helix 1 for splicing interactions, possibly one that bridges or stabilizes the proposed weak association of SpPrp18-SpSlu7 with a yet unknown splicing factor. We also investigated the effects of mutations in other helices; surprisingly we recovered only mutations with very subtle growth phenotypes and very mild splicing defects. Not surprisingly, stop codon at L239 residue predicted to form a truncated protein lacking helices 3, 4 and 5 conferred recessive but null phenotype implicating essential functions for other helices. Other amino acid substitutions at L239 position had near wild type phenotype at 30°C and 37°C. Helix 3 buried residue mutant I259A conferred strong cold-sensitivity when over expressed from plasmid, but semi quantitative analysis indicated no splicing defects for intron1 in the constitutively expressed transcript tfIId+. These findings indicate cold sensitivity either arises due to compromised splicing of yet unknown transcripts or that over-expressed protein has near wild type activity. We find mutations in the helix 5 buried residues L324 also conferred near WT phenotype. Earlier studies in the lab found that substitution of surface residues KR that are in helix 5 with alanine lead to null phenotypes (Piyush Khandelia and Usha Vijayraghavan unpublished data). We report stable expression of all of these mutant proteins; L239A, L239P, L239G, I259A, I259V, L324F, L324A as determined by our immunoblot analysis at 30°C and 37°C. The mild phenotypes of many buried residues can be attributed to orientation of their functional groups into a protein cavity between the helices. Lastly, our microscopic cellular and biochemical analysis of cellular phenotypes of spprp18 mutant provided a novel and direct role of this factor in G1-S transition of cell cycle. Our RT-PCR data suggest spprp18+ is required for efficient splicing of several intron containing transcripts involved in G1-S transition and subsequent activation of MBF complex (MluI cell cycle box-binding factor complex) during S-phase and shows a mechanistic link between cell cycle progression and splicing. A tool to study links between RNA interference, centromeric non-coding RNA transcription and heterochromatin formation S.pombe possesses fully functional RNA interference machinery with a single copy for essential RNAi genes ago1+, dcr1+ and rdp1+. Deletion of any of these genes causes loss of heterochromatinzation with abnormal cytokinesis, cell-cycle deregulation and mating defects (Volpe et al., 2002). In S.pombe, exogenous or endogenously generated dsRNA’s from transcription of centromeric repeats are processed by the RNaseIII enzyme dicer to form siRNA. These siRNA’s are loaded in Ago1 to form minimal RNA induced silencing complex (RISC) complex or specialized transcription machinery complex RNA induced transcriptional silencing (RITS) complex and target chromatin or complementary mRNAs for silencing. Thus as in other eukaryotes, fission yeast cells deploy RNAi mediated silencing machinery to regulate gene-expression and influence chromatin status. Several recent studies point to emerging new roles of RNAi and its association with other RNA processes (Woolcock et al., 2011; Bayane et al., 2008; Kallgren et al., 2014). Many recent reports suggest physical interactions of RISC or RITS and RNA dependent RNA polymerase complex (RDRC) with either some factors of the spliceosomal machinery, heterochromatin machinery (CLRC complex) and the exosome mediated RNA degradation machinery (Bayne et al., 2008 and Chinen et al., 2010 ; Hiriart et al., 2012; Buhler et al., 2008; Bayne et al., 2010 ). Thus we presume conditional alleles in spago1+ will facilitate future studies to probe the genetic network between these complexes as most analyses thus far rely on ago1∆ allele or have been based on proteomic pull down analyses of RISC or RITS complexes. In this study, we employed biophysical and modeling approaches described earlier to generate temperature sensitive mutants in spago1+ and spdcr1+. We tested several mutants for their ability to repress two reporter genes in a conditional manner. Our modeling studies on SpAgo1 PAZ domain indicated structural similarities with human Ago1 PAZ domain. We created site-directed missense mutants at predicted buried residues or in catalytic residues. We also analyzed the effects of random amino acid replacements in specific predicted buried or catalytic residues of SpAgoI. These ago1 mutants were screened as pools for their effects on silencing of GFP or of ura4+ reporter genes. These assays assessed post transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) activity of these mutants. We obtained three temperature sensitive SpAgo1 mutants V324G, V324S and L215V while the V324E replacement was a null allele. Based upon our modeling, a likely explanation for the phenotype of these mutants is structural distortion or mis-orientation of the functional groups caused due to these mutations, which affect activity in a temperature dependent manner. This distortion in the PAZ domain may affect binding of siRNA and thereby lead to heterochromatin formation defects that we observed. Our data on the SpAgo1 V324 mutant shows conditional centromeric heterochromatin formation confirmed by semi quantitative RT-PCR for dh transcripts levels that shows temperature dependent increase in these transcripts. We find reduced H3K9Me2 levels at dh locus by chromatin immunoprecipitation (ChIP) assay, linking the association of siRNAs for establishment of heterochromatin at this loci. The data on PTGS of GFP transcripts show SpAgo1 V324G mutation has decreased slicing activity as semi-quantitative RT-PCR for GFP transcripts show increased levels at non permissive temperature. These studies point out the importance of siRNA binding to the PAZ domain and its effect on slicing activity of SpAgo1. The mutations in Y292 showed residue loss of centromeric heterochromatin formation phenotype. Thus, we ascribe critical siRNA binding and 3’ end recognition functions to this residue of SpAgo1. These studies point out functional and structural conservation across hAgo1 and SpAgo1. Adopting the aforementioned biophysical mutational approach, we generated mutants in spdcr1+ and screened for those with conditional activity. Our modeling studies on SpDcr1 helicase domain shows it adopts the conserved helicase domain structure seen for other DEAD Box helicases. Our data on mutational analysis of a conserved buried residue I143 in the walker motif B created inactive protein. The data confirm critical functions for dicer in generation of siRNAs and also in recognition of dsRNA ends. Mutants in buried residues L1130 and I1228 of RNase IIIb domain were inactive and the proximity of these residues to the catalytic core suggest that the critical structural alignment of catalytic residues is indispensable for carrying out dsRNA cleavage to generate siRNAs. We also attribute critical catalytic functions to SpDcr1 D1185 residue for generation of siRNA and heterochromatin formation as measured by our transcriptional gene silencing assay. Our studies employing biophysical and computational approaches to design temperature-sensitive mutants have been successfully applied to an essential splicing factor SpPrp18, which was refractory for ts mutants by other methods. Using a missense mutant, we showed its intron-specific splicing function for subsets of transcripts and deduced that its ubiquitous splicing role is arguable. We have uncovered a link between the splicing substrates of SpPrp18 and direct evidence of splicing based cell cycle regulation, thus providing a mechanistic link to the cell cycle arrest seen in some splicing factor mutants. The same methodology was applied to another important biological pathway, the RNAi machinery, where central factors SpAgoI and SpDcrI were examined We report the first instance of conditional gene silencing tool by designing Ago1 ts mutants which will be useful for future studies of the global interaction network between RNAi and other RNA processing events.

This work was performed in the framework of two application-oriented research projects that focus on the generation and evaluation of fluorescent Saccharomyces (S.) cerevisiae-based sensor and reporter cells for white biotechnology as well as the extension of the conventional single-cell/single-construct principle of ordinary yeast biosensor approaches. Numerous products are currently generated by biotechnological processes which require continuous and precise process control and monitoring. These demands are only partially met by physical or physiochemical sensors since they measure parameters off-line or use surrogate parameters that consequently provide only indirect information about the actual process performance. Biosensors, in particular whole cell-based biosensors, have the unique potential to near-line and long-term monitor parameters such as nutrient availability during fermentation processes. Moreover, they allow for the assessment of an analyte’s biological relevance. Prototype yeast sensor and reporter strains derived from common laboratory strains were transformed with multicopy expression plasmids that mediate constitutive or inducible expression of a fluorescence reporter gene. Performance of these cells was examined by various qualitative and quantitative detection methods – representative of putative transducer technologies. Analyses were performed on the population level by microplate reader-based fluorometry and Western blot as well as on the single-cell level by fluorescence microscopy and flow cytometry. ‘Signature’ promoters that are activated or repressed during particular nutrient-limited growth conditions were selected in order to generate yeast nutrient sensor strains for monitoring the biological availability of nitrogen, phosphorus or sulphur. For each category, at least one promoter mediating at least threefold changed green fluorescence levels between sensor cells in non-limited and nutrient-limited conditions was identified. Sensor strains were evaluated in detail regarding sensitivity, analyte selectivity and the ability to restore basic fluorescence after shift from nutrient-limited to non-limited conditions (regeneration). The applicability for bioprocess monitoring purposes was tested by growth of yeast nutrient sensor cells in microalgae media and supernatants. Despite successful proof of principle, numerous challenges still need to be solved to realise prospective implementation in this field of white biotechnology. The major drawback of plasmid-borne detection constructs is a high fluorescence variance between individual cells. By generation of a nitrogen sensor strain with a genome-integrated detection construct, uniform expression on the single-cell level and simultaneous maintenance of basic properties (ability of fluorescence induction/regeneration and lack of cross-reactivity) was achieved. However, due to the singular detection construct per cell, significantly weaker overall fluorescence was observed. The traditional single-cell/single-construct approach was expanded upon in two ways. Firstly, a practical dual-colour sensor strain was created by simultaneous, constitutive expression of a red fluorescence reporter gene in green fluorescent nitrogen sensor cells. Secondly, an innovative cellular communication and signal amplification system inspired by the natural S. cerevisiae pheromone system and mating response was established successfully. It features the yeast pheromone alpha-factor as a trigger and alpha-factor-responsive reporter cells which express a fluorescence reporter gene from the pheromone-inducible FIG1 promoter as an output signal. The system was functional both with synthetic and cell-secreted alpha-factor, provided that recombinant cells were deleted for the alpha-factor protease Bar1p. Integration of amplifier cells which secrete alpha-factor in response to stimulation with the pheromone itself could increase the system\'s sensitivity further. Signal amplification was demonstrated for phosphorus sensor cells as a proof of concept. Therefore, the alpha-factor-based cellular communication and signal amplification system might be useful in applications that suffer from poor signal yield. Due to its modular design, the system could be applied in basically any cell-based biosensor or sensor-actor system. Immobilisation of the generated sensor and reporter cells in transparent natural polymers can be beneficial considering biosensor fabrication. Functionality of sensor and reporter cells in calcium-alginate beads or nano-printed arrays was successfully demonstrated. For the latter setup, fluorescence scanning and software-assisted fluorescence quantification was applied as a new detection method. In an experiment using an agarose-based two-compartment setup proposed by Jahn, 2011, properties of the alpha-factor-based cellular communication and signal amplification system after immobilisation were tested. These studies provide an initial experimental basis for an appropriate geometry of miniaturised immobilisation matrices with fluorescent yeast sensor and reporter cells in prospective biosensor designs.

碩士
國立成功大學
電腦與通信工程研究所
98
Reconstructing transcriptional regulatory networks (TRNs) is crucial for understanding how a cell reorganizes its gene expression patterns to respond to environmental and physiological changes. ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct TRNs. However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop computational methods which can extract a TF’s regulatory targets from its binding targets. The REgulatory Targets Extraction Algorithm (RETEA) is developed in this study, which uses partial correlation analysis on gene expression data to extract a TF’s regulatory targets from its binding targets inferred from the ChIP-chip data. We applied RETEA to yeast cell cycle microarray data and identified the plausible regulatory targets of eleven cell cycle TFs. Our predictions are validated by checking the enrichments for cell cycle genes and shared molecular functions. Moreover, we showed that RETEA performs better than three published methods (Garten et al.’s Method, MA-Network and TRIA). In summary, RETEA is capable of extracting the TF-gene regulatory relationships from the TF-promoter binding relationships (inferred by the ChIP-chip data). Thus, using RETEA to preprocess the ChIP-chip data is crucial to make the ChIP-chip data useful in systems biology studies.

CSE1, an essential Saccharomyces cerevisiae gene was initially isolated in a screen for genes important for accurate chromosome segregation. cse1 mutants have pleiotropic phenotypes including defects in the ubiquitin-mediated degradation of mitotic cyclins and in cell cycle progression. SRP1, encodes a nuclear localization signal (NLS) receptor protein involved in nuclear protein import that is an allele specific dosage suppressor of cse1-1. CSE1 can rescue certain srp1 mutant phenotypes, indicating that Cse1p and Srp1p are functionally related or have roles in similar pathways. New mutant alleles of CSE1 were generated by linker insertion mutagenesis, including a temperature sensitive allele, cse1-2, that causes arrest in G2/M, chromosome missegregation and defective mitotic cyclin degradation. Analysis of CSE1 mRNA and Cse1p indicate that their levels do not change significantly during the cell cycle and that Cse1p is not phosphorylated. Cse1p is located in the nucleus and concentrated at the nuclear periphery, probably in association with nuclear pores. Current evidence supports the model that Cse1p is required for the export of Srp1p from the nucleus. Srp1p improperly accumulates in the nuclei of both cse1-1 and cse1-2 cells. Reporter proteins that contain NLS sequences accumulate in the cytoplasm of cse1-1 and cse1-2 cells indicating that Cse1p function is also necessary for nuclear protein import. Cse1p binds the nuclear transport protein Ran/Gsp1p-GTP via a conserved amino-terminal motif. In addition, the human protein CAS, which is an export factor for importin-$\alpha,$ is 60% similar to Cse1p. Although a physical interaction between Srp1p and Cse1p has not been shown, a two-hybrid screen identified two potential Cse1p-interacting proteins, Scj1p and Yma5p. Scj1p is a DnaJ homologue involved in protein translocation, folding, and complex assembly. Yma5p is a novel non-essential protein with an as yet unknown role in these important nuclear processes.

Kluyveromyces lactis è un lievito non convenzionale ampiamente utilizzato sia nelle applicazioni industriali che nella ricerca di base. Nel nostro laboratorio stiamo studiando il gene KlMGA2, che codifica per un modulatore della risposta all’ipossia. In lavori precedenti, abbiamo mostrato come la delezione del gene KlMGA2 in K. lactis generi un ceppo vitale, ma con difetti di crescita cellulare, alterazione in quantità e composizione degli acidi grassi, respirazione difettosa e morfologia mitocondriale alterata. Con questo lavoro mostriamo come l'assenza del gene KlMGA2 causi, oltre ai fenotipi sopra citati, una maggiore resistenza allo stress ossidativo ed una longevità molto estesa, accompagnati da un aumento dell’espressione genica delle catalasi e delle superossido dismutasi. Questo potrebbe suggerire un coinvolgimento di KlMga2 come mediatore diretto non solo della risposta ipossica, ma anche nella risposta allo stress ossidativo, ipotizzando una correlazione tra ipossia, regolazione del glucosio, biosintesi degli acidi grassi e metabolismo dei ROS. In seconda analisi, con questo lavoro si è cercato di verificare una possibile risposta di K. lactis allo stress luminoso. Negli organismi unicellulari come il lievito, che non presentano tessuti specializzati per contrastare i cambiamenti dell’ambiente esterno, l’esistenza di meccanismi cellulari adattativi alle condizioni di stress risulta essere di fondamentale importanza. Precedenti studi, hanno evidenziato che in Saccharomyces cerevisiae l’impulso luminoso rappresenta una fonte di stress, in quanto provoca l’aumento intracellulare di perossido di idrogeno (H2O2). Visti i nostri studi riguardanti KlMga2 come mediatore di risposta allo stress ossidativo, abbiamo indagato sul suo possibile coinvolgimento nella trasduzione del segnale luminoso. Pertanto, tale studio permetterebbe di esaminare dei meccanismi foto-dipendenti anche in organismi apparentemente privi di domini proteici sensibili alla luce.
The yeast Kluyveromyces lactis has been widely used in both industrial applications and basic research. We previously demonstrated that deletion of the KlMGA2, coding for a hypoxic mediator in K. lactis, generated a viable strain, although suffering of several deficiencies. We also showed that glucose signaling and glucose catabolism were involved in KlMga2 regulation. In this work, we showed that, in addition to these defects, the deletion of KlMGA2 also caused increased resistance to oxidative stress and extremely extended lifespan. These phenotypes are associated with increased expression levels of catalase and superoxide dismutase genes. We propose that KlMga2 might act as a direct mediator not only of hypoxic response, but also of oxidative stress response/adaptation, thus revealing connections between hypoxia, glucose signaling, fatty acid biosynthesis and ROS metabolism. Secondly, in this work we wanted to investigate the possible light response in this yeast. In unicellular organisms like yeasts, that cannot utilize specialized tissue for protection against environmental challenges, the presence of cellular mechanisms to respond and adapt to stress conditions is fundamental. Saccharomyces cerevisiae has been reported to respond to light by increasing hydrogen peroxide (H2O2) levels. Therefore, it could be interesting to study the possible role of oxidative stress mediator KlMga2, already studied in our laboratory, in the light response of yeast.

Les protéines sont les produits finaux de la machinerie génétique. Elles jouent des rôles essentiels dans la définition de la structure, de l'intégrité et de la dynamique de la cellule afin de promouvoir les diverses transformations chimiques requises dans le métabolisme et dans la transmission des signaux biochimique. Nous savons que la doctrine centrale de la biologie moléculaire: un gène = un ARN messager = une protéine, est une simplification grossière du système biologique. En effet, plusieurs ARN messagers peuvent provenir d’un seul gène grâce à l’épissage alternatif. De plus, une protéine peut adopter plusieurs fonctions au courant de sa vie selon son état de modification post-traductionelle, sa conformation et son interaction avec d’autres protéines. La formation de complexes protéiques peut, en elle-même, être déterminée par l’état de modifications des protéines influencées par le contexte génétique, les compartiments subcellulaires, les conditions environmentales ou être intrinsèque à la croissance et la division cellulaire. Les complexes protéiques impliqués dans la régulation du cycle cellulaire sont particulièrement difficiles à disséquer car ils ne se forment qu’au cours de phases spécifiques du cycle cellulaire, ils sont fortement régulés par les modifications post-traductionnelles et peuvent se produire dans tous les compartiments subcellulaires. À ce jour, aucune méthode générale n’a été développée pour permettre une dissection fine de ces complexes macromoléculaires. L'objectif de cette thèse est d'établir et de démontrer une nouvelle stratégie pour disséquer les complexes protéines formés lors du cycle cellulaire de la levure Saccharomyces cerevisiae (S. cerevisiae). Dans cette thèse, je décris le développement et l'optimisation d'une stratégie simple de sélection basée sur un essai de complémentation de fragments protéiques en utilisant la cytosine déaminase de la levure comme sonde (PCA OyCD). En outre, je décris une série d'études de validation du PCA OyCD afin de l’utiliser pour disséquer les mécanismes d'activation des facteurs de transcription et des interactions protéine-protéines (IPPs) entre les régulateurs du cycle cellulaire. Une caractéristique clé du PCA OyCD est qu'il peut être utilisé pour détecter à la fois la formation et la dissociation des IPPs et émettre un signal détectable (la croissance des cellules) pour les deux types de sélections. J'ai appliqué le PCA OyCD pour disséquer les interactions entre SBF et MBF, deux facteurs de transcription clés régulant la transition de la phase G1 à la phase S. SBF et MBF sont deux facteurs de transcription hétérodimériques composés de deux sous-unités : une protéine qui peut lier directement l’ADN (Swi4 ou Mbp1, respectivement) et une protéine commune contenant un domain d’activation de la transcription appelée Swi6. J'ai appliqué le PCA OyCD afin de générer un mutant de Swi6 qui restreint ses activités transcriptionnelles à SBF, abolissant l’activité MBF. Nous avons isolé des souches portant des mutations dans le domaine C-terminal de Swi6, préalablement identifié comme responsable dans la formation de l’interaction avec Swi4 et Mbp1, et également important pour les activités de SBF et MBF. Nos résultats appuient un modèle où Swi6 subit un changement conformationnel lors de la liaison à Swi4 ou Mbp1. De plus, ce mutant de Swi6 a été utilisé pour disséquer le mécanisme de régulation de l’entrée de la cellule dans un nouveau cycle de division cellulaire appelé « START ». Nous avons constaté que le répresseur de SBF et MBF nommé Whi5 se lie directement au domaine C-terminal de Swi6. Finalement, j'ai appliqué le PCA OyCD afin de disséquer les complexes protéiques de la kinase cycline-dépendante de la levure nommé Cdk1. Cdk1 est la kinase essentielle qui régule la progression du cycle cellulaire et peut phosphoryler un grand nombre de substrats différents en s'associant à l'une des neuf protéines cycline régulatrice (Cln1-3, Clb1-6). Je décris une stratégie à haut débit, voir à une échelle génomique, visant à identifier les partenaires d'interaction de Cdk1 et d’y associer la cycline appropriée(s) requise(s) à l’observation d’une interaction en utilisant le PCA OyCD et des souches délétées pour chacune des cyclines. Mes résultats nous permettent d’identifier la phase(s) du cycle cellulaire où Cdk1 peut phosphoryler un substrat particulier et la fonction potentielle ou connue de Cdk1 pendant cette phase. Par exemple, nous avons identifié que l’interaction entre Cdk1 et la γ-tubuline (Tub4) est dépendante de Clb3. Ce résultat est conforme au rôle de Tub4 dans la nucléation et la croissance des faisceaux mitotiques émanant des centromères. Cette stratégie peut également être appliquée à l’étude d'autres IPPs qui sont contrôlées par des sous-unités régulatrices.
Proteins are the end-products of gene interpretative machinery. Proteins serve essential roles in defining the structure, integrity and dynamics of the cell and mediate most chemical transformations needed for everything from metabolic catalysis to signal transduction. We know that the central dogma of molecular biology, one gene = one mRNA = one protein is a gross simplification and that a protein may do different things depending on the form in which its mRNA was spliced, how and where it is post-translationally modified, what conformational state it may be in or finally, which other proteins it may interact with. Formation of protein complexes may, themselves, be governed by the states in which proteins are expressed in specific cells, cellular compartments or under specific conditions or dynamic phases such has growth or division. Protein complexes involved in mitotic cell cycle regulation are particularly challenging to dissect since they could only form during specific phases of the cell cycle, are highly regulated by post-translational modifications and can be found in any subcellular compartments. To date, no general methods have been developed to allow fine dissection of these protein complexes. The goal of this thesis was to establish and demonstrate a novel strategy for dissecting protein complexes regulating the budding yeast Saccharomyces cerevisiae (S. cerevisiae) mitotic cell cycle. In this thesis, I describe my development and optimization of a simple survival-selection Protein-fragment Complementation Assay using the prodrug-converting enzyme, yeast cytosine deaminase as reporter (OyCD PCA). I further describe, in a series of proof of principle studies, applications of the OyCD PCA to dissect the mechanism of transcriptional activation by key mitotic transcription factors and to dissect protein-protein interactions (PPIs) among regulators of the mitotic cell cycle. A key feature of the OyCD PCA is that it can be used to detect both formation and disruption of PPIs by virtue of having positive readouts for both assays. I applied the OyCD PCA in a strategy to dissect interactions between the key transcription factors of the G1/S phase: SBF and MBF. These two heterodimeric transcription factors are composed of, respectively, two distinct DNA-binding subunits named Swi4 and Mbp1 and a common transcription activation subunit called Swi6. I took advantage of the dual selection by OyCD PCA to engineer a specific mutant of Swi6 in order to demonstrate the rewiring of a transcriptional network. We isolated Swi6 with mutations found in its C-terminal domain previously identified for binding Swi4 and Mbp1 and important for SBF and MBF activities. Our results support a model where Swi6 undergoes a conformational change upon binding to Swi4 or Mbp1. In addition, this Swi6 mutant was used to dissect the regulatory mechanism that governs the entry of S. cerevisiae to a new round of cell division also known as START. We found that the SBF and MBF repressor Whi5 directly binds to the C-terminal domain of Swi6. Finally, I applied the OyCD PCA to dissect the yeast cyclin dependent kinase Cdk1-protein complexes. Cdk1 is the essential kinase that regulates cell cycle progression and can phosphorylate a large number of different substrates by teaming up with one of nine cyclin regulatory proteins (Cln1-3, Clb1-6). I describe a strategy to identify interaction partners of Cdk1 that can easily be scaled up for a genome-wide screen and associate the complexes with the appropriate cyclin(s) required for mediating the interaction using the OyCD PCA and deletion of the cyclin genes. My results allow us to postulate which phase(s) of the mitotic cell cycle Cdk1 may phosphorylate proteins and what function potential or known substrates of Cdk1 may take on during that phase(s). For example, we identified the interaction between Cdk1 and the γ-tubulin (Tub4) to be dependent upon Clb3, consistent with its role in mediating nucleation and growth of mitotic microtubule bundles on the spindle pole body. This strategy can also be applied to study other PPIs that are contingent upon accessory subunits.