Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 166-175).

Thesis (Ph. D.)--West Virginia University, 2000. / Title from document title page. Document formatted into pages; contains x, 118 p. : ill. Includes abstract. Includes bibliographical references.

The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

付記する学位プログラム名: 京都大学大学院思修館 / 京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20424号 / 農博第2209号 / 新制||農||1047(附属図書館) / 学位論文||H29||N5045(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 阪井 康能, 教授 矢﨑 一史, 教授 栗原 達夫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

No description available.

Pichia pastoris, a methylotrophic yeast is widely used for recombinant protein production. It has a well characterized methanol utilization (MUT) pathway, the enzymes of which are induced when cells are cultured in the presence of methanol. In this study, we have identified an unannotated zinc finger protein, which was subsequently named ROP (repressor of phosphoenolpyruvate carboxykinase, PEPCK) and characterized its function. ROP expression is induced in P. pastoris cells cultured in biotin depleted glucose ammonium medium as well as a medium containing methanol as the sole source of carbon. In glucose-abundant, biotin depleted cultures, ROP induces the expression of a number of genes including that encoding PEPCK. Interestingly, a strain in which the gene encoding ROP is deleted (ΔROP) exhibits biotin-independent growth. Based on a number of studies, it was proposed that the ability of ΔROP to grow in the absence of biotin is due to the activation of a pyruvate carboxylase-independent pathway of oxaloacetate biosynthesis. It was also proposed that PEPCK, which normally functions as a gluconeogenic enzyme, may act as an anaplerotic enzyme involved in the synthesis of oxaloacetate. ROP was shown to be a key regulator of methanol metabolism when P. pastoris cells are cultured in YPM medium containing yeast extract, peptone and methanol but not YNBM medium containing yeast nitrogen base and methanol. In P. pastoris cells cultured in YPM, ROP functions as a transcriptional repressor of genes encoding key enzymes of the methanol metabolism such as the alcohol oxidase I. (AOXI). Deletion of the gene encoding ROP results in enhanced expression of AOXI and growth promotion while overexpression of ROP results in repression of AOXI and retardation of growth of P. pastoris cultured in YPM medium. Subcellular localization studies indicate that ROP translocates from cytosol to nucleus in cells cultured in YPM but not YNBM. To understand the mechanism of action of ROP, we examined its DNA-binding specificity. The DNA-binding domain of ROP shares 57% amino acid identity with that of Mxr1p, a master regulator of genes of methanol metabolism. We demonstrate that the DNA-binding specificity of ROP is similar to that of Mxr1p and both proteins compete with each other for binding to AOXI promoter sequences. Thus, transcriptional interference due to competition between Mxr1p and ROP for binding to the same promoter sequences is likely to be the mechanism by which ROP represses AOXI expression in vivo. Mxr1p and ROP are examples of transcription factors which exhibit the same DNA-binding specificity but regulate gene expression in an antagonistic fashion.

Thesis (MSc (Microbiology))--Stellenbosch University, 2011. / ENGLISH ABSTRACT: The link between infection with Human Papillomavirus (HPV) and the development of cervical cancer has been established by several epidemiology studies. Cervical cancer is the second most common cancer among women and it occurs at a rate of 22.8 cases per 100 000 women in South Africa. Approximately 86% of newly reported cases of cervical cancer occur in developing countries where limited access to medical facilities hampers efforts to prevent and screen for HPV infection. Two commercial virus-like particle (VLP) vaccines consisting of HPV major structural protein L1, which protect against the most common high-risk HPV-types, are currently available. The high cost and type specificity of these commercially available vaccines have necessitated the development of a low cost, broad-spectrum HPV vaccine. Inclusion of the minor structural protein L2 has been shown to induce broadly cross-neutralizing antibodies and therefore a chimera was constructed that contains an epitope of L2 inserted within the L1 sequence. This construct, renamed SAF, was shown to be highly immunogenic and thus has the potential to be used as a prophylactic cervical cancer vaccine. Methylotrophic yeasts are known to be excellent producers of recombinant proteins due to their strongly inducible promoters that allow culturing of these yeasts to very high cell densities. Pichia pastoris and Hansenula polymorpha have been employed in several studies for heterologous protein production and levels of protein higher than 1 g/L have been reported. These yeasts also have GRAS status and can therefore be used to manufacture products for use in humans. In this study, the potential of H. polymorpha and P. pastoris to produce SAF intracellularly was evaluated. The effect of increased gene dosage and peroxisomal targeting on SAF production was examined as possible strategies to increase the yield of SAF. Peroxisomal targeting was achieved by fusing the SAF gene at the C-terminal end with the Peroxisomal Targeting Sequence 1 (PTS1) which consists of a short tri-peptide: –SKL. The functionality of PTS1 was confirmed using green fluorescent protein (GFP), fluorescence microscopy and peroxisome isolation. Peroxisomal targeting was shown to have a negative effect on SAF production levels in both H. polymorpha and P. pastoris. An increase in gene dosage had no discernable effect on SAF yield in H. polymorpha which is in contrast to previous research. The highest production levels were achieved by P. pastoris KM71 (24.86 mg/L) which compares well to levels of L1 achieved by other research groups. The most significant insight emerging from this work was that all the strains that produced SAF at detectable levels were equally efficient at the production of SAF. Increased biomass was therefore the biggest contributor to high SAF levels (mg/L) in the P. pastoris strains as significantly higher cell densities were achieved during culturing of these strains. With the necessary optimisation, the methylotrophic yeasts have the potential to be used as hosts for the production of a broad-spectrum HPV vaccine. / AFRIKAANSE OPSOMMING: Die skakel tussen infeksie met Mens Papilloomvirus (HPV) en die ontwikkeling van servikale kanker is deur verskeie epidemiologiese studies bevestig. Servikale kanker is die tweede mees algemene kanker onder vroue en dit kom voor teen ‘n tempo van 22.8 gevalle per 100 000 vroue in Suid Afrika. Ongeveer 86% van alle nuwe gevalle kom voor in ontwikkelende lande waar beperkte toegang tot mediese fasiliteite pogings om HPV infeksie te voorkom en te behandel, belemmer. Twee pseudovirale-partikel (VLP) entstowwe teen HPV is tans op die mark beskikbaar en hierdie entstowwe verleen immuniteit teen die mees algemene hoë-risiko HPV tipes. Die hoë koste en nou spektrum van hierdie entstowwe het dit nodig gemaak om ‘n goedkoop, wye-spektrum HPV entstof te ontwikkel. Navorsing het bewys dat die insluiting van die strukturele L2 proteïen in die VLP entstof, lei tot die indusering van neutraliserende teenliggame, wat wye spektrum antigenisiteit tot gevolg het. ‘n Chimeriese proteïen wat ‘n epitoop van L2 binne die L1 volgorde bevat is gekonstrueer, en hierdie proteïen is benoem SAF. SAF het hoë immunogenisiteit en kan dus potensieel as ‘n voorkomende servikale kanker entstof gebruik word. Metielotrofiese giste is bekend vir hulle vermoë om hoë vlakke rekombinante proteïene te produseer as gevolg van hulle induseerbare promotors wat groei tot baie hoë sel digthede toelaat. Pichia pastoris en Hansenula polymorpha is in menigte studies gebruik om heteroloë proteïene te produseer tot vlakke bo 1 g/L. Hierdie giste en die proteïen produkte wat hulle vorm word algemeen aanvaar as veilig vir menslike gebruik. In hierdie studie het ons die potensiaal van H. polymorpha en P. pastoris om SAF intrasellulêr te produseer, geevalueer. Die effek op SAF produksie van verhoogde geen dosering asook die teiken van SAF na die peroksisoom was ondersoek as moontlike strategieë om die opbrengs van SAF te verhoog. Die teiken van SAF na die peroksisoom is behaal deur die Peroksisomale Teiken Volgorde 1 (PTS1) aan die C-terminaal van SAF te heg. Die funksionaliteit van PTS1 was bevestig deur gebruik te maak van groen fluoroserende proteïen (GFP), fluoressensie mikroskopie en isolering van peroksisome. Teiken van SAF na die peroksisoom het ‘n negatiewe uitwerking gehad op SAF uitdrukking in beide H. polymorpha en P. pastoris. ‘n Verhoging in geen dosering het geen onderskeibare effek gehad op SAF opbrengs in H. polymorpha nie wat in teenstelling is met vorige navorsing. Die hoogste produksie vlakke is opgelewer deur P. pastoris KM71 (24.86 mg/L) wat goed vergelyk met vlakke van L1 wat deur ander navorsings groepe behaal is. Die belangrikste gevolgtrekking wat gemaak kan word uit hierdie studie is dat al die rasse wat SAF geproduseer het in meetbare hoeveelhede ewe effektief was. Verhoogde biomassa was dus die grootste bydraende faktor tot hoë SAF vlakke (mg/L) in die P. pastoris rasse as gevolg van die hoë sel digthede wat hierdie rasse kan bereik. Dit is duidelik dat metielotrofiese giste, met die nodige optimisering, oor die potensiaal beskik om as gasheer sisteme te dien vir die produksie van ‘n wye spektrum HPV entstof. / The NRF and the Department of Microbiology for financial support

Os plásticos, polímeros geralmente derivados de petróleo com características bastante atraentes e valor baixo estão presentes em quase todos os objetos produzidos pelos homens, desde consumo doméstico até produtos de alta tecnologia. Em 2015, aproximadamente 320 milhões de toneladas de plásticos foram produzidas e a estimativa é que este consumo continue aumentando até 2020. No entanto, cerca de 60% do que é produzido, são plásticos não biodegradáveis, os quais são persistentes ambientalmente, afetando negativamente diversos seres vivos, inclusive os seres humanos. Diante deste cenário, e como alternativa ambientalmente correta, podemos fazer uso de biopolímeros, em especial o polihidroxibutirato (PHB). O PHB é um homopolímero biodegradável, biocompatível e possui características similares às do polipropileno, podendo servir como potencial substituto a esse polímero derivado de petróleo. No entanto, o PHB ainda não está difundido no nosso cotidiano, porque apresenta alto custo de produção e purificação, principalmente devido aos substratos utilizados, que na maioria das vezes são açúcares e chegam a representar 30% do preço final do produto. Visando diminuir o preço de produção, o objetivo deste trabalho é produzir o PHB utilizando bactérias metilotróficas, isoladas de ambiente estuarino e capazes de consumir metanol. Após isolamento seletivo, duas bactérias do gênero Methylobacterium sp. foram isoladas e identificadas por biologia molecular e espectrometria de massas (MALDI-TOF). A produção de PHB foi estudada em frascos agitados sem quaisquer ajustes de condições físico-químicas por um período de 168 horas sob 28 ºC e 180 RPM em agitador orbital de bancada e também em biorreator sob 28 °C, 180 RPM e pH 7,0 durante 96 horas. Os melhores resultados foram obtidos por M. extorquens sem ajuste de condições físico-químicas, tendo atingido produtividade do produto de 125 mg.L-1 e acúmulo de 30% de PHB em biomassa. M. rhodesianum obteve produtividade do produto de 38 mg.L-1 em seu melhor resultado, porém é uma produtora em potencial de polietileno glicol a partir de metanol. / Plastics, usually petroleum-derived polymers that have attractive characteristics and low price, are present in literally almost all products produced by humans. They are present since from home consuming to high technology products. In the year of 2015 approximately 320 million tons of plastics were produced and is estimate this consumption will continue to increase until 2020. However, about 60% of this production is non-biodegradable plastics, which makes them environmentally persistent, affecting negatively several living beings including humans. Considering this scenario, and as an environmentally correct alternative, we can make use of biopolymers, especially polyhydroxybutyrate (PHB). PHB is a biodegradable, biocompatible homopolymer and has characteristics similar to those of polypropylene, which may serve as a potential substitute for this petro derivative polymer. However, PHB is still not widespread in our daily lives, once has a high cost of production and purification, mainly due to the substrates used, which in most cases are sugars, and they can represent 30% of the final price of the product. In order to decrease the price of production, this work aims to produce PHB using methylotrophic bacteria, isolated from an estuarine environment and capable of consuming methanol. After a selective isolation, two bacteria of the genus Methylobacterium sp. were isolated and identified by molecular biology and mass spectrometry (MALDI-TOF). PHB production was studied in shake flasks without any physical-chemical adjustments for a 168 hour period under 28 ºC and 180 RPM in a rotary shaker and also in bioreactor under 28 °C, 180 RPM and pH 7.0 for 96 hours. The best results were obtained by M. extorquens without adjustment of physical-chemical conditions, reaching a product productivity of 125 mg.L-1 and accumulation of 30% of PHB in biomass. M. rhodesianum obtained product productivity of 38 mg.L-1 at its best result, but is a potential producer of polyethylene glycol from methanol.

Foram estudados a composição e o pH do meio de cultivo para a produção do fragmento de anticorpo (scFv) anti-LDL(-), expresso em Pichia pastoris recombinante. Os experimentos que definiram a composição e pH do meio assim como a concentração inicial de células na fase de indução foram realizados em agitador orbital a 250 rpm, com temperatura de 30 ºC na fase de crescimento e 20 ºC na fase de indução, durante 72 horas, com adição diária de 1% (v/v) de metanol. Para modificação do meio foi realizado um planejamento experimental empregando como variáveis independentes: extrato de soja, casaminoácidos e ureia, os quais substituíram o YNB e a biotina presentes no meio padrão (BMMY). Apesar de haver maior produção no meio com extrato de soja, o meio contendo 10 g.L-1 de casaminoácidos foi selecionado, uma vez que este favoreceu a etapa de purificação. A partir da faixa de pH estudada entre 3,0 e 8,0, determinou-se que o pH 8,0 no início da fase de indução favorece a maior produção. Finalmente, o meio BMMY-CA (pH 8,0) foi utilizado para cultivo em biorreator com volume de trabalho de 10L e a partir deste cultivo foram calculados os parâmetro cinéticos (velocidades de crescimento, de consumo de substrato e de produção, bem como produtividade). Diante do conjunto de experimentos realizados, foi possível otimizar a composição do meio de cultivo e as condições operacionais, que possibilitaram um aumento do rendimento bem como aumento do volume de produção do scFv anti-LDL(-) em biorreator. / Composition and pH culture medium for the production of anti- LDL(-) antibody fragment (scFv) were studied in recombinant yeast Pichia pastoris. The experiments that defined medium composition, pH and the initial cell concentration in the induction phase were carried out in baffled shaker flasks at 250 rpm, with temperature at 30°C for growth phase and 20°C for induction phase, during 72 hours with daily addition of 1% (v/v) methanol. A design of experiments employing for medium modification with independent variables: soy extract, casamino acids and urea, which replaced the YNB and biotin present in the standard medium (BMMY) was conducted for medium formulation. Even though, there was an increase in medium production with soy extract, the medium containing 10 g.L-1 casamino acids was selected since it favors the purification step. Through a pH range study (3.0 to 8.0), it was determined that pH 8.0 during induction phase offered higher levels. Then, the best results from shaker flask cultivation (BMMY-CA with casamino acids and pH 8.0) were carried out in 1L bioreactor, showing a biomass and a scFv production increase compared to the standard, BMMY (pH 6.0). Finally, the medium BMMY-CA (pH 8,0) was submitted to a volume scale-up into a 10L bioreactor, which was also used to evaluate kinetic parameters (rates of growth, substrate consumption and production as well as productivity). In conclusion, by optimizing culture medium and operating conditions it was possible to increase yield and scale-up the production of scFv anti-LDL(-) in bioreactor.

Os plásticos, polímeros geralmente derivados de petróleo com características bastante atraentes e valor baixo estão presentes em quase todos os objetos produzidos pelos homens, desde consumo doméstico até produtos de alta tecnologia. Em 2015, aproximadamente 320 milhões de toneladas de plásticos foram produzidas e a estimativa é que este consumo continue aumentando até 2020. No entanto, cerca de 60% do que é produzido, são plásticos não biodegradáveis, os quais são persistentes ambientalmente, afetando negativamente diversos seres vivos, inclusive os seres humanos. Diante deste cenário, e como alternativa ambientalmente correta, podemos fazer uso de biopolímeros, em especial o polihidroxibutirato (PHB). O PHB é um homopolímero biodegradável, biocompatível e possui características similares às do polipropileno, podendo servir como potencial substituto a esse polímero derivado de petróleo. No entanto, o PHB ainda não está difundido no nosso cotidiano, porque apresenta alto custo de produção e purificação, principalmente devido aos substratos utilizados, que na maioria das vezes são açúcares e chegam a representar 30% do preço final do produto. Visando diminuir o preço de produção, o objetivo deste trabalho é produzir o PHB utilizando bactérias metilotróficas, isoladas de ambiente estuarino e capazes de consumir metanol. Após isolamento seletivo, duas bactérias do gênero Methylobacterium sp. foram isoladas e identificadas por biologia molecular e espectrometria de massas (MALDI-TOF). A produção de PHB foi estudada em frascos agitados sem quaisquer ajustes de condições físico-químicas por um período de 168 horas sob 28 ºC e 180 RPM em agitador orbital de bancada e também em biorreator sob 28 °C, 180 RPM e pH 7,0 durante 96 horas. Os melhores resultados foram obtidos por M. extorquens sem ajuste de condições físico-químicas, tendo atingido produtividade do produto de 125 mg.L-1 e acúmulo de 30% de PHB em biomassa. M. rhodesianum obteve produtividade do produto de 38 mg.L-1 em seu melhor resultado, porém é uma produtora em potencial de polietileno glicol a partir de metanol. / Plastics, usually petroleum-derived polymers that have attractive characteristics and low price, are present in literally almost all products produced by humans. They are present since from home consuming to high technology products. In the year of 2015 approximately 320 million tons of plastics were produced and is estimate this consumption will continue to increase until 2020. However, about 60% of this production is non-biodegradable plastics, which makes them environmentally persistent, affecting negatively several living beings including humans. Considering this scenario, and as an environmentally correct alternative, we can make use of biopolymers, especially polyhydroxybutyrate (PHB). PHB is a biodegradable, biocompatible homopolymer and has characteristics similar to those of polypropylene, which may serve as a potential substitute for this petro derivative polymer. However, PHB is still not widespread in our daily lives, once has a high cost of production and purification, mainly due to the substrates used, which in most cases are sugars, and they can represent 30% of the final price of the product. In order to decrease the price of production, this work aims to produce PHB using methylotrophic bacteria, isolated from an estuarine environment and capable of consuming methanol. After a selective isolation, two bacteria of the genus Methylobacterium sp. were isolated and identified by molecular biology and mass spectrometry (MALDI-TOF). PHB production was studied in shake flasks without any physical-chemical adjustments for a 168 hour period under 28 ºC and 180 RPM in a rotary shaker and also in bioreactor under 28 °C, 180 RPM and pH 7.0 for 96 hours. The best results were obtained by M. extorquens without adjustment of physical-chemical conditions, reaching a product productivity of 125 mg.L-1 and accumulation of 30% of PHB in biomass. M. rhodesianum obtained product productivity of 38 mg.L-1 at its best result, but is a potential producer of polyethylene glycol from methanol.