Dissertations / Theses on the topic 'Pichia Pastoris Fermentation'

The high cell density fermentation of recombinant Pichia pastoris for human serum albumin (HSA) production is a high oxygen demand process. The oxygen demand is usually met by increased agitation rate and use of oxygen-enriched air. Microbubble fermentation however can supply adequate oxygen to the microorganisms at relatively low agitation rates because of improved mass transfer of the microbubbles used for the sparging. Conventionally sparged fermentations were conducted for the production of HSA using P. pastoris at agitation rates of 350, 500, and 750 rpm, and were compared to MBD sparged fermentation at 150, 350, and 500 rpm agitation rates. The MBD improved the volumetric oxygen transfer coefficient (kLa) and subsequently increased the cell mass and protein production compared to conventional fermentation. Cell production in MBD fermentation at 350 rpm was 4.6 times higher than that in conventional fermentation at 350 rpm, but similar to that in the conventional 750 rpm. Maximum cell mass productivity in the conventional 350 rpm was only 0.37 g / (Lâ ¢h), while the maximum value in MBD 350 rpm was 2.0 g / (Lâ ¢h), which was similar to 2.2 g / (Lâ ¢h) in the conventional 750 rpm. Biomass yield on glycerol Ys (g cell/ g glycerol) was 0.334 g / g in the conventional 350 rpm, 0.431 g / g in MBD 350 rpm and 0.438 g / g in the conventional 750 rpm. Protein production in MBD 350 rpm was 7.3 times higher than that in the conventional 350 rpm, but similar to the conventional 750 rpm. Maximum protein productivity in the conventional 350 rpm was 0.37 mg / (Lâ ¢h), 2.8 mg / (Lâ ¢h) in MBD 350 rpm, and 3.3 mg / (Lâ ¢h) in the conventional 750 rpm. Protein yield on methanol Yp (mg protein / g methanol) was 1.57 mg /g in the conventional 350 rpm, 5.02 in MBD 350 rpm, and 5.21 in the conventional 750 rpm. The volumetric oxygen transfer coefficient kLa was 1011.9 h-1 in MBD 350 rpm, which was 6.1 times higher than that in the conventional 350 rpm (164.9 h-1) but was similar to the conventional 750 rpm (1098 h-1). Therefore, MBD fermentation results at low agitation of 350 rpm were similar to those in the conventional fermentation at high agitation of 750 rpm. There was considerable improvement in oxygen transfer to the microorganism using MBD sparging relative to the conventional sparging. Conventional fermentations were conducted both in a Biostat Q fermenter (small) at 500 rpm, 750 rpm, and 1000 rpm, and in a Bioflo III fermenter (large) at 350 rpm, 500 rpm, and 750 rpm. At the same agitation rate of 500 rpm, cell production in the large reactor was 3.8 times higher than that in the small one, and no detectable protein was produced in the small reactor at 500 rpm. At the same agitation rate of 750 rpm, both cell production and protein production in the large reactor were 4.6 times higher than the small reactor. Thus, the Bioflo III fermenter showed higher oxygen transfer efficiency than the Biostat Q fermenter, because of the more efficient aeration design of the Bioflo III fermenter.
Master of Science

The methylotrophic yeast Pichia pastoris has become an efficient expression system for heterologous protein production. Different methods have been studied to enhance cell growth as well as the production of products of interest. Two of the major strategies for improving the product or biomass yields are optimizing bioprocess controls and cultivation conditions. In this work, the characteristics of this yeast system and of its different promoters are discussed, and the effect of operational strategies on cell growth and recombinant protein expression is also studied. The effect of different feeding strategies were studied and optimized for pGAP (glyceraldehyde-3-phosphate dehydrogenase)-regulated phytase production in P. pastoris. Alternative carbon sources were screened and the feasibility of using citric acid as a carbon source for recombinant protein production was also investigated. The effects of parameters such as the carbon source concentration and culture pH were studied using shake-flasks, and the effect of different feeding profiles on bioreactor performance was also investigated. Three feeding strategies, Stepwise feeding, Exponential feeding and DO-stat feeding were tested and DO-stat was found to be more efficient and led to a high phytase activity. A modified DO-stat method was investigated to overcome the oxygen limited condition in the standard DO-stat method. For the carbon source, citric acid showed promise in improving phytase expression. Further experiments in bioreactors performed with the presence of certain amount of citric acid showed that less glycerol could be used to achieve the same level of phytase activity.

Abstract Potential lethal diarrhoea caused by enterotoxigenic Escherichia coli strains is one of the most common diseases in young pigs. It can be cured by single-chain antibody fragments (scFv), which can be produced in recombinant microorganisms. Pichia pastoris, a methylotrophic yeast, is generally considered an interesting production system candidate, as it can secrete properly folded proteins. These proteins accumulate in high concentrations during fermentation, reducing the cost for product recovery. Strong inducible AOX1 promoter, widely used in P. pastoris for fast, inexpensive production, is typically induced by methanol. The high oxygen demand of methanol metabolism makes oxygen supply a major parameter in cultivations requiring special process design strategies. In standard fed-batch cultivation, dissolved oxygen concentration inside a bioreactor is kept at a certain level by pumping air and pure oxygen into the reactor. There are safety concerns over the handling of oxygen, especially at a large scale. Therefore, there is a need to develop a production process under oxygen-limited conditions. This dissertation studies the development of a cost-efficient production process of scFv in P. pastoris. Both methanol and oxygen parameters influence the production process and the objective was to find a robust production process. Fed-batch cultivations were performed in a 10 L scale bioreactor. The effects of lower oxygen level, methanol concentration, glycerol feeding duration and specific substrate-uptake rates on product formation were studied. A P. pastoris GS115 his4 strain under an AOX1 promoter system expressing scFv was used in this study. The fed-batch fermentations were carried out in a bioreactor with basal salt media. In this doctoral dissertation, a process was developed for a single-chain antibody fragment (scFv) production in P. pastoris. The product levels of 3.5 g L-1 scFv in culture supernatant were achieved and a production process was designed without additional need of pure oxygen, thus relieving safety requirements and lowering the amount of methanol. The process developed during this research may potentially be utilised by both academia and industry having interests in expressing proteins in P. pastoris. The methanol-uptake control strategy is beneficial for those products that suffer from degradation or modification during limited feeding of methanol
Tiivistelmä Enterotoksigeenisten E.coli kantojen aiheuttama ripuli on porsaiden tavallisimpia tauteja, joka voi johtaa jopa kuolemaan. Tautia voidaan hoitaa yhdistelmä-DNA-tekniikalla tuotetuilla vasta-ainefragmenteilla (scFv). Metylotrofista Pichia pastoris hiivaa pidetään kiinnostavana vasta-ainefragmenttien tuottoisäntänä, koska se pystyy erittämään oikealla tavalla laskostuneita proteiineja. Näitä proteiineja kertyy fermentointiprosessissa solujen ulkopuolelle korkeina pitoisuuksina, mikä vähentää tuotteiden talteenottokustannuksia. Vahva metanolilla indusoituva AOX1-promoottori on laajassa käytössä P. pastoris tuottosysteemissä tuoton nopeuden ja alhaisten kustannusten ansiosta. Metanolin aineenvaihdunta vaatii paljon happea, joten riittävän tehokas hapen liuottaminen on tärkeimpiä fermentointiparametreja ja vaatii erityisiä prosessin toteutusstrategioita. Perinteisessä fed-batch-fermentoinnissa liuenneen hapen pitoisuus bioreaktorissa pidetään halutulla tasolla lisäämällä ilmaa ja puhdasta happea reaktoriin. Koska hapen käsittelyyn liittyy turvallisuusriskejä erityisesti teollisuusmittakaavassa, happirajoitteisissa olosuhteissa toimiva tuotantoprosessi olisi hyödyllinen. Tässä väitöstutkimuksessa kehitettiin kustannustehokasta prosessia scFv-:n tuottoon P. pastoris hiivalla. Metanoliin ja happeen liittyvät parametrit ovat olennaisia prosessiin vaikuttavia tekijöitä. Tavoite oli kehittää yksinkertainen ja käytännöllinen prosessi. Työssä tutkittiin alhaisen happitason, metanolin pitoisuuden, glyserolisyötön keston ja substraattien spesifisten kulutusnopeuksien vaikutuksia tuotteen muodostumiseen 10 litran bioreaktorissa. Isäntäkantana oli P. pastoris GS115 his4, jossa scFv-ekspressiota säädeltiin AOX1 promoottorilla. Fed-batch fermentointien kasvatusalustana käytettiin Basal Salt Medium alustaa (BSM). Väitöstyössä kehitettiin tavoitteiden mukainen vasta-ainefragmenttien tuottoprosessi P.pastoris hiivalle. Menetelmällä saavutettiin tuotepitoisuus 3,5 g L-1 kasvatusliemen supernatantissa ilman puhtaan hapen lisäystarvetta, ja siten metanolin kulutus väheni ja prosessiturvallisuus parani verrattuna perinteisiin prosesseihin. Kehitetty prosessi soveltuu käytettäväksi sekä akateemisessa tutkimuksessa että teollisuudessa tuotettaessa erilaisia proteiineja P. pastoris hiivalla. Metanolin kulutuksen säätöstrategia on erityisen hyödyllinen tuotteille, joilla ongelmana on proteolyysi tai muokkautuminen metanolirajoitteisessa fermentoinnissa

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Protease inhibitors have a broad biotechnological application, which goes since the development of several drugs to your utilization as a bioinsecticide, antifungal and as an antibacterial agent. However, those are found in small quantities in their natural sources, which unfeasible it utilization in industrial scale. Therefore, the heterologous production ends up as a method that allows the increase of scale production of those proteins. The Inga laurina Trypsin Inhibitor (ILTI) previously characterized showed an inhibitory effect in proteases extracted from the midgut of insects, besides reducing its larval developments by up to 84%, therefore, boing a candidate to be used as a potential bioinsecticide. Thus, the present work aimed at the heterologous production of ILTI in Komagataella phaffii (Pichia pastoris), followed by the optimization of the culture modes in a bioreactor with the objective of maximizing the production of the recombinant protein. For this, the gene that codifies ILTI were cloned in the expression vector pPIC9K, followed by your insertion on the strain GS115 by electroporation. PCR analysis showed that the recombinant vector was integrated into the genome of the yeast, and all the clones obtained had MutS genotype. The expression was performed for 96 hours by adding 0.5% methanol. An analysis of the proteins on the supernatant of the recombinant strain culture, by SDS-PAGE, confirmed the production of a protein with a size close to 20 KDa. Data from MALDI-TOF confirmed that the obtained protein is, in fact, the recombinant ILTI. Furthermore, inhibitory assays showed that the produced protein had activity against trypsin. Thus, culture in bioreactors was performed to optimize the production of this heterologous protein. In order to increase its expression, fed-batch was performed where on the batch phase the biomass production was favored, and the feeding phase was programmed to continuously supply methanol, based on the methanol specific consumption and its specific growth velocity, using methanol as carbon source. During the fermentations, 351.27 UIT were obtained in the extract of crude fermentation broth, and a specific activity of 2.07 UIT/mg protein. Although widely used as a host for the production of heterologous proteins, studies of the production of protease inhibitors in K. phaffii are still very limited. Until the moment, there is no report in the optimization of the production of serine protease inhibitors in K. phaffii, making this study pioneering and essential for the beginning of scaling up the process of this technology.
Os inibidores de protease possuem uma ampla aplica????o biotecnol??gica que vai desde o desenvolvimento de diversos f??rmacos at?? sua utiliza????o como bioinseticidas, antif??ngicos e como agentes antibacterianos. Por??m, estes s??o encontrados em pequenas quantidades nas suas fontes naturais, o que inviabiliza sua utiliza????o em escala industrial. Sendo assim, a produ????o heter??loga acaba sendo um m??todo que permite o aumento da escala de produ????o dessas prote??nas. O inibidor de tripsina de Inga laurina (ILTI) foi caracterizado previamente e mostrou possuir efeito inibit??rio em proteases extra??das do trato digestivo de insetos, al??m de diminuir em at?? 84% seu desenvolvimento larval, sendo, portanto, um candidato a ser utilizado como um poss??vel bioinseticida. Dessa forma, o presente trabalho teve como objetivo a produ????o heter??loga do inibidor ILTI, em Komagataella phaffii (Pichia pastoris), seguido da otimiza????o dos modos de cultivo em biorreator com o objetivo de maximizar a produ????o da prote??na recombinante. Para isso, o gene que codifica o ILTI foi clonado no vetor de express??o pPIC9K seguindo de sua inser????o na cepa GS115 por eletropora????o. An??lises de PCR mostraram que o vetor recombinante foi integrado ao genoma da levedura e que todos os clones obtidos possu??am gen??tipo MutS. A indu????o da express??o foi realizada durante 96 horas por meio da adi????o de metanol ?? 0,5%. A an??lise de prote??nas presentes no sobrenadante da cultura da cepa recombinante, por meio de SDS-PAGE, confirmou a produ????o de uma prote??na com tamanho pr??ximo a 20 KDa. Dados obtidos em MALDI-TOF confirmaram que a prote??na obtida ?? de fato ILTI recombinante. Al??m disso, ensaios inibit??rios mostraram que a prote??na produzida possui atividade contra tripsina. Dessa forma, cultivo em biorreatores foram realizados com a finalidade de otimizar a produ????o dessa prote??na heter??loga. A fim de aumentar sua express??o foram realizadas bateladas alimentadas, onde durante a fase de batelada foi favorecida a produ????o de biomassa, e a fase de alimenta????o programada para fornecer metanol de forma cont??nua, com base nos dados de velocidade espec??fica de consumo de metanol e velocidade de crescimento espec??fica nesta fonte de carbono. Ao longo das fermenta????es realizadas foi obtido 351,27 UIT no extrato bruto do caldo fermentado e uma atividade espec??fica de 2,07 UIT/mg de prote??na. Apesar de ser amplamente utilizada como hospedeira para a produ????o de prote??nas heter??logas, estudos da produ????o de inibidores em K. phaffii ainda s??o muito limitados. At?? o momento n??o existem relatos de otimiza????o da produ????o de inibidores de serinoproteases em K. phaffii, sendo esse estudo pioneiro e essencial para o in??cio do processo de escalonamento dessa tecnologia.

Recombinant Candida antarctica lipase B was successfullyproduced in the methylotropic yeast Pichia pastoris. Thespecific activities of Candida antarctica lipase B produced inPichia pastoris and commercial Candida antarctica lipase B fromNovozymes were the same. In shake-flask cultivations theexpression levels were about 25 mg L-1. Production levels couldbe increased to 1.5 g L-1, using a fermentor. A model tosimulate growth and oxygen consumption was described. The highcell density growth could be explained by the low maintenancecoefficient of Pichia pastoris. Enrichment of the aeration withoxygen increased the recombinant protein production. The lipasewas also produced as a fusion to a cellulose binding module.The cellulose binding module did not interfere with thespecific activity of the lipase. With this fusion proteincatalytic reactions can be performed in close proximity to acellulose surface. The binding module can also function as anaffinity tag for purification. Establishment of the Candidaantarctica lipase B production system allowed the engineeringof Candida antarctica lipase B variants. Four differentvariants were produced in order to investigate if electrostaticinteractions contributed to enantioselectivity. Theenantioselectivity of two halogenated secondary alcohols wasdoubled for the Ser47Ala variant. Thisimplied thatelectrostatic interactions are important forenantioselectivity. The Trp104His variant showed a decrease inenantioselectivity for all tested substrates. This was causedby an increase in the size of the stereoselectivity pocket.Symmetrical secondary alcohols of different size were used tomap the stereoselectivity pocket. A substituent as large as apropyl or isopropyl could be accommodated in the pocket of theTrp104His variant. In the wild-type lipase thestereoselectivity pocket was estimated to fit an ethyl group.The enzyme variants were subjected to a thermodynamic study, toelucidate changes in the enthalpic and entropic contributionsto enantioselectivity. The enthalpic and entropic contributionschanged for the different lipase variants and werecompensatory. The compensation was not perfect, allowing forchanges in enantioselectivity.

In general one can conclude that rational design of newenzyme properties, in order to change the substrateselectivity, is feasible if based on a thorough model ofsubstrate enzyme interactions.

Key words:Protein expression, Candida antarctica lipaseB, Pichia pastoris, sitedirected mutagenesis, fermentation,selectivity

This thesis focuses on the study of the influence of selected parameters on the course of microbial cultivation and evaluation of bioprocess. It is divided into two parts. The first part deals with the production of mutant forms of the protein cryptogein yeast Pichia pastoris. The theoretical part summarizes the findings of the yeast P. pastoris and its expression. It also deals with cryptogein that induces defense reactions in plants. In the experimental part was produced mutant cryptogein X24, in which the concentration of each fraction and the ability to transfer sterols. The second part of this thesis is focused on aerobic and anaerobic oxidation of elemental sulfur by Acidithiobacillus ferrooxidans. In the theoretical section, our knowledge on A. ferrooxidans, its metabolism and the importance of ATP in cell metabolism was summarized. In the experimental part, the above bioprocess was monitored using pH, biomass concentration, the rate of oxidation of elemental sulfur the cellular ATP content.

Les proteines de transfert de lipides (ltp) sont des proteines des faible masse moleculaire qui sont capables de realiser in vitro un transfert de lipides entre deux membranes. Dans le ble, les genes de ltp forment une famille mutigenique et il existe au moins cinq genes de ltp exprimes dans le grain de ble. Dans un premier temps, nous avons utilise le systeme d'expression levurien pichia pastoris pour produire quatre isoformes de ltp de ble dur (triticum durum) et de ble tendre (triticum aestivum). Ce systeme permet de secreter trois ltp recombinantes solubles dans le milieu de culture en quantite variable (1,1 g/l, 700 mg/l et 80 mg/l). Quand l'acide amine n-terminal de la proteine deduite de l'adnc est un residu alanine et non un residu isoleucine, la maturation de la ltp recombinante correspondante est optimale. Nos resultats ont montre qu'il y a une grande diversite de production selon le clone considere et les conditions de cultures utilisees. Dans un deuxieme temps, nous avons suivi l'expression des genes de ltp de ble au cours de la maturation et de la germination du grain de ble dur, et l'effet de stress abiotiques sur l'expression de ces memes genes dans des plantules de ble dur. Au cours de la maturation, ce sont les transcrits des genes ltp4. 90 et ltp8. 3 qui sont les plus abondants. Apres application des stress abiotiques, une variation de la quantite de transcrits des genes ltp6. 48 et ltpd2 est observee dans les pousses. Chaque gene de ltp de ble etudie semble avoir une expression spatiale et temporelle specifique.

In this study, it was aimed to develop a bioprocess using the Pichia pastoris expression system as an alternative to the mammalian system used in industry, for production of the therapeutically important glycoprotein, erythropoietin, and to form stoichiometric and kinetic models. Firstly, the human EPO gene, fused with a polyhistidine-tag and factor-Xa protease target site, in which cleavage produces the native termini of EPO, was integrated to AOX1 locus of P. pastoris. The Mut+ strain having the highest rHuEPO production capacity was selected. The glycosylation profile of rHuEPO was characterized by MALDI-ToF MS and Western blotting. The native polypeptide form of human EPO was obtained for the first time in P. pastoris expression system, after affinity-purification, deglycosylation and factor-Xa protease digestion. Thereafter, effects of medium components and pH on rHuEPO production and cell growth were investigated in laboratory-scale bioreactors. Sorbitol was shown to increase production efficiency when added as a co-substrate. Moreover, a cheap alternative nutrient, the byproduct of biodiesel industry, crude-glycerol, was suggested for the first time for P. pastoris fermentations. Furthermore, methanol feeding strategy was investigated in fed-batch pilot-scale bioreactors, producing 70 g L-1 biomass and 130 mg L-1 rHuEPO at t=24h. Moreover, metabolic flux analysis by using the stoichiometric model formed, which consisted of m=102 metabolites and n=141 reactions, proved useful in further understanding the P. pastoris metabolism. Finally, the first structured kinetic model formed for r-protein production with P. pastoris successfully predicted cell growth, substrate consumption and r-product production rates, where rHuEPO production kinetics was associated with AOX production and proteolytic degradation.

In recent years, several industrial yeasts, owing to their robust growth and certain other characteristics, have been developed as recombinant host systems for commercial production of heterologous proteins. One such yeast Pichia pastoris has proven to be an excellent host for production of secreted and intracellular proteins (Cereghino and Cregg. 2000). The increasing popularity of this particular expression system can be attributed to several factors, most importantly: (1) the simplicity of techniques needed for the molecular genetic manipulation of Pichia pastoris and their similarity to those of Saccharomyces cerevisiae, one of the most well-characterized experimental systems in modern biology;(2) the ability of Pichia pastoris to produce foreign proteins at high levels, either intracellularly or extracellularly; and (3) the capability of performing many eukaryotic post-translational modifications, such as glycosylation, disulfide bond formation and proteolytic processing. The expression level for a given recombinant protein produced by Pichia pastoris seems to be determined largely by its inherent properties such as amino acid sequence, the tertiary structure and the site for expression (Sreekrishna et al.,1997). The attempts on increasing the protein expression levels by far are focused on genetic manipulations to enhance the gene expression and protein stability. Although this is crucial, there is ample scope to improve the productivity of Pichia pastoris fermentations by undertaking a systematic program of optimizing the entire fermentation process. This work aims at undertaking such a program by focusing on strategy to identify and to characterize trends in the behavior of the system. It can be expected that by addressing the process as a whole, rather than narrowly focusing on the protein expression alone, the methodology proposed here can simplify process scale-up and can be applied to several products made by the same host. Pichia pastoris is methylotrophic yeast. In the Pichia pastoris fermentation, the limiting carbon source is glycerol, method or mixture of both. It can grow on methanol as a sole carbon and energy source. It possesses a highly inducible methanol utilization pathway. The first step in the metabolism of methanol is the oxidation of methanol to formaldehyde using molecular oxygen by alcohol oxidase (AOX). AOX, the first enzyme of the pathway, accounts for up to 35% of the total protein in cells grown on limited amounts of methanol. The enzymes undetectable in cells grown on glucose, ethanol or glycerol. There are two genes in Pichia pastoris that code for AOX: AOXI. The AOXI gene product accounts for the majority of alcohol oxidase activity in the cell. This highly inducible and stringently regulated AOXI promoter has been used to construct expression vectors for the production of heterologous proteins in Pichia pastoris. Although some foreign proteins have expressed well in shake-flask cultures, expression levels are typically low compared to fomenter cultures. There are several key aspects of Pichia pastoris fermentations: 1. Fed-batch operation – Controlled addition of glycerol, methanol or mixture thereof. In general, strains are grown initially in a defined medium containing glycerol as its carbon source (growth phase). During this phase, biomass accumulates but heterogonous gene expression is fully repressed. Upon depletion of glycerol, a transition phase is initiated in which additional glycerol is fed to the culture at a growth-limiting rate. Finally, method a mixture of glycerol and methanol is fed to the culture to induce expression (induction phase). The duration of individual substrate feeds, the amount and mode of feeding are critical to optimal fermentation performance. 2.Online measurement and control-One of the most important key parameters in Pichia pastor is expression system is the methanol concentration. Monitoring and controlling this variable are important because high levels of this inductor substrate can be toxic to the cells and low levels of methanol may not be enough to initiate the AOX transcription (Cereghino and Cregg, 2000) This research work aims at investigation the above mentioned aspects by conduction an in depth engineering analysis of the Pichia Pastoris fermentations.

In recent years, several industrial yeasts, owing to their robust growth and certain other characteristics, have been developed as recombinant host systems for commercial production of heterologous proteins. One such yeast Pichia pastoris has proven to be an excellent host for production of secreted and intracellular proteins (Cereghino and Cregg. 2000). The increasing popularity of this particular expression system can be attributed to several factors, most importantly: (1) the simplicity of techniques needed for the molecular genetic manipulation of Pichia pastoris and their similarity to those of Saccharomyces cerevisiae, one of the most well-characterized experimental systems in modern biology;(2) the ability of Pichia pastoris to produce foreign proteins at high levels, either intracellularly or extracellularly; and (3) the capability of performing many eukaryotic post-translational modifications, such as glycosylation, disulfide bond formation and proteolytic processing. The expression level for a given recombinant protein produced by Pichia pastoris seems to be determined largely by its inherent properties such as amino acid sequence, the tertiary structure and the site for expression (Sreekrishna et al.,1997). The attempts on increasing the protein expression levels by far are focused on genetic manipulations to enhance the gene expression and protein stability. Although this is crucial, there is ample scope to improve the productivity of Pichia pastoris fermentations by undertaking a systematic program of optimizing the entire fermentation process. This work aims at undertaking such a program by focusing on strategy to identify and to characterize trends in the behavior of the system. It can be expected that by addressing the process as a whole, rather than narrowly focusing on the protein expression alone, the methodology proposed here can simplify process scale-up and can be applied to several products made by the same host. Pichia pastoris is methylotrophic yeast. In the Pichia pastoris fermentation, the limiting carbon source is glycerol, method or mixture of both. It can grow on methanol as a sole carbon and energy source. It possesses a highly inducible methanol utilization pathway. The first step in the metabolism of methanol is the oxidation of methanol to formaldehyde using molecular oxygen by alcohol oxidase (AOX). AOX, the first enzyme of the pathway, accounts for up to 35% of the total protein in cells grown on limited amounts of methanol. The enzymes undetectable in cells grown on glucose, ethanol or glycerol. There are two genes in Pichia pastoris that code for AOX: AOXI. The AOXI gene product accounts for the majority of alcohol oxidase activity in the cell. This highly inducible and stringently regulated AOXI promoter has been used to construct expression vectors for the production of heterologous proteins in Pichia pastoris. Although some foreign proteins have expressed well in shake-flask cultures, expression levels are typically low compared to fomenter cultures. There are several key aspects of Pichia pastoris fermentations: 1. Fed-batch operation – Controlled addition of glycerol, methanol or mixture thereof. In general, strains are grown initially in a defined medium containing glycerol as its carbon source (growth phase). During this phase, biomass accumulates but heterogonous gene expression is fully repressed. Upon depletion of glycerol, a transition phase is initiated in which additional glycerol is fed to the culture at a growth-limiting rate. Finally, method a mixture of glycerol and methanol is fed to the culture to induce expression (induction phase). The duration of individual substrate feeds, the amount and mode of feeding are critical to optimal fermentation performance. 2.Online measurement and control-One of the most important key parameters in Pichia pastor is expression system is the methanol concentration. Monitoring and controlling this variable are important because high levels of this inductor substrate can be toxic to the cells and low levels of methanol may not be enough to initiate the AOX transcription (Cereghino and Cregg, 2000) This research work aims at investigation the above mentioned aspects by conduction an in depth engineering analysis of the Pichia Pastoris fermentations.

Recombinant Pichia pastoris is one of the important methylotropic yeast due to its robustness and ability to produce hormones like human chorionic gonadotropin (hCG), luteinizing hormone (LH) extracellularly. High growth on glycerol and strong protein expression on methanol by insertion of alcohol oxidase (AOX) promoter demand the fermentation to be a multistage operation. Methylotropic pathway demands more oxygen as methanol has to be converted to formaldehyde with half mole of oxygen. Moreover as fermentation progresses cell density in the reactor also increases. In case of Pichia pastoris fermentation cell density usually reaches very high (above 100 gm/lit) at the end of fermentation. Both these contribute in the increased oxygen demand in the fermentation and oxygen transfer turns out to be a limiting step. The present study focuses on the oxygen transfer process and its improvement in the fermentation. Oxygen transfer in bioreactor is a multistep process and involves different kinetic as well as mass transfer steps. In case of fermentation especially at high cell densities, oxygen transfer from bubbles to the broth becomes limiting step. The interface transport is governed by many physical as well as kinetic parameters. It is essential to screen these parameters from the whole set to identify the key parameters. Sensitivity analysis is carried out by using Metabolic Control Analysis (MCA) to quantify the effects of different parameters. It is found that bubble size and oxygen partial pressure are two such key parameters which can be manipulated. Use of pure oxygen to increase partial pressure and thereby solubility of oxygen in broth is a common approach. This work focuses on bubble size manipulation to increase the oxygen transfer rates.The idea behind this work is on to generate micron sized bubbles and utilize them effectively in the fermentation. There are many techniques reported to generate microbubble dispersions. In this work ’Spinning Disc microbubble Generator’ is fabricated to generate microbubbles. A flat disc surrounded by baffles with 5 mm gap in between, when subjected to 5000 rpm generates microbubbles. Some modifications are done to the set up to achieve desired properties of the bubbles. The bubbles generated fall in the range of 30-300 micron with mean size of about 60 micron. Use of Tween-20 surfactant stabilize the bubbles and hence offer a good resistance to coalescence and breakage. The liquid fraction in the bubbles can be as high as 40%. Contineous addition of this dispersion unnecessarily can dilute the fermentation broth. To overcome this volume constrain, a recirculation system is designed. Microbubble dispersion is added contineously to the reactor and equivalent fermentation broth is pumped back to the microbubble generator to achieve steady state to the liquid volume in both the vessels. Mass transfer studies with microbubbles show the potential of microbubble dispersion (MBD) to enhance mass transfer significantly. Decrease in volumetric mass transfer coefficient (KLa) due to surfactant is overcompensated by the increase in the interfacial area and net effect is, potential enhancement in KLa. The enhance- ment factor, that is, ratio of mass transfer coefficient with MBD to mass transfer coefficient with conventional sparging, is obtained to be about 4 to 5. Prior to utilization of bubbles in the recirculation system, cells are checked for the shear sensitiveness. Negligible lysis losses and almost no effect on growth patterns in shake flask culture confirm that the cells used are mechanically stable at operating conditions. Better growth patterns in shake flask are observed when microbubbles are pumped for predetermined duration in the broth. It shows possible use of MBD as oxygen carriers. Glycerol batch phase with MBD and conventional sparging is studied at different initial cell densities. Conventional sparging fails to grow the cells and Dissolved Oxygen (DO) levels close to zero suggest high oxygen demands which can not be sustained by conventional sparging. The same batch is run using MBD. Reasonably good growth patterns are observed. DO levels are well above 70% for most of the time during operation. High oxygen demand which can not be sustained by conventional sparging alone can be sustained by MBD. In this way in high den- sity cultures utilization of MBD can be a good alternative to fulfill required oxygen demand in fermentation.

Recombinant Pichia pastoris is one of the important methylotropic yeast due to its robustness and ability to produce hormones like human chorionic gonadotropin (hCG), luteinizing hormone (LH) extracellularly. High growth on glycerol and strong protein expression on methanol by insertion of alcohol oxidase (AOX) promoter demand the fermentation to be a multistage operation. Methylotropic pathway demands more oxygen as methanol has to be converted to formaldehyde with half mole of oxygen. Moreover as fermentation progresses cell density in the reactor also increases. In case of Pichia pastoris fermentation cell density usually reaches very high (above 100 gm/lit) at the end of fermentation. Both these contribute in the increased oxygen demand in the fermentation and oxygen transfer turns out to be a limiting step. The present study focuses on the oxygen transfer process and its improvement in the fermentation. Oxygen transfer in bioreactor is a multistep process and involves different kinetic as well as mass transfer steps. In case of fermentation especially at high cell densities, oxygen transfer from bubbles to the broth becomes limiting step. The interface transport is governed by many physical as well as kinetic parameters. It is essential to screen these parameters from the whole set to identify the key parameters. Sensitivity analysis is carried out by using Metabolic Control Analysis (MCA) to quantify the effects of different parameters. It is found that bubble size and oxygen partial pressure are two such key parameters which can be manipulated. Use of pure oxygen to increase partial pressure and thereby solubility of oxygen in broth is a common approach. This work focuses on bubble size manipulation to increase the oxygen transfer rates.The idea behind this work is on to generate micron sized bubbles and utilize them effectively in the fermentation. There are many techniques reported to generate microbubble dispersions. In this work ’Spinning Disc microbubble Generator’ is fabricated to generate microbubbles. A flat disc surrounded by baffles with 5 mm gap in between, when subjected to 5000 rpm generates microbubbles. Some modifications are done to the set up to achieve desired properties of the bubbles. The bubbles generated fall in the range of 30-300 micron with mean size of about 60 micron. Use of Tween-20 surfactant stabilize the bubbles and hence offer a good resistance to coalescence and breakage. The liquid fraction in the bubbles can be as high as 40%. Contineous addition of this dispersion unnecessarily can dilute the fermentation broth. To overcome this volume constrain, a recirculation system is designed. Microbubble dispersion is added contineously to the reactor and equivalent fermentation broth is pumped back to the microbubble generator to achieve steady state to the liquid volume in both the vessels. Mass transfer studies with microbubbles show the potential of microbubble dispersion (MBD) to enhance mass transfer significantly. Decrease in volumetric mass transfer coefficient (KLa) due to surfactant is overcompensated by the increase in the interfacial area and net effect is, potential enhancement in KLa. The enhance- ment factor, that is, ratio of mass transfer coefficient with MBD to mass transfer coefficient with conventional sparging, is obtained to be about 4 to 5. Prior to utilization of bubbles in the recirculation system, cells are checked for the shear sensitiveness. Negligible lysis losses and almost no effect on growth patterns in shake flask culture confirm that the cells used are mechanically stable at operating conditions. Better growth patterns in shake flask are observed when microbubbles are pumped for predetermined duration in the broth. It shows possible use of MBD as oxygen carriers. Glycerol batch phase with MBD and conventional sparging is studied at different initial cell densities. Conventional sparging fails to grow the cells and Dissolved Oxygen (DO) levels close to zero suggest high oxygen demands which can not be sustained by conventional sparging. The same batch is run using MBD. Reasonably good growth patterns are observed. DO levels are well above 70% for most of the time during operation. High oxygen demand which can not be sustained by conventional sparging alone can be sustained by MBD. In this way in high den- sity cultures utilization of MBD can be a good alternative to fulfill required oxygen demand in fermentation.

碩士
國立臺灣大學
生化科技學系
104
T4 endonuclease V (T4N5) is a DNA repair enzyme isolated from T4 bacteriophage. It can specifically recognize and remove cyclobutane pyrimidine dimer which is resulted from the UV-induced DNA damage and might cause skin cancer. In previous reports, in conjunction of recombinant T4N5 expressed by Escherichia coli and liposome, T4N5 liposome lotion effectively penetrated into skin in vivo and clinical trials also indicated its potential for UV-induced DNA damage treatment. In order to extensive application of T4N5 in skin care products such as sunscreen, it’s important to develop a method for large-scale production recombinant T4N5 with low expenses. The major recombinant T4N5 are currently produced by E. coli. However, the procedures include cell lysis and protein purification, which may increase the production cost. Moreover, it is at risk due to endotoxins. Pichia pastoris is a well-defined expression system which can be cultivated at high cell density at low cost. In this study, P. pastoris KM71H was used as a heterologous expression system, and methanol was added to induce recombinant T4N5 expression. In flask, we have successfully expressed extracellular T4N5 with correct conformation and function. The T4N5 activity in supernatant of flask culture reached up to 0.47±0.05 U/µL. When using 5 L fermenter, methanol fed at 2.6 mL//L/h induced cell lysis and release of cellular proteases, while reducing methanol feeding rate led to low yield of target protein yield. Therefore, it’s necessary to modify other induction conditions. In this study, we found that reduction of the induction temperature from 30oC to 23oC improved recombinant protein yield remarkably at the same methanol feeding rate. The amount of proteases in the culture decreased, and methanol dissimilation is improved.

碩士
國立臺灣科技大學
化學工程系
90
Abstract Murine granulocyte-macrophage colony-stimulating factors (mGM-CSF) have advanced cell proliferation function for the different precursor cells become mature granulocyte cells and macrophage cells. In the recently years, due to maturity technological development of genetic engineering,mGM-CSF could be integrated to the chromosome of Pichia pastoris The AOX1 promoter controlled mGM-CSF gene could be induced to express by methanol. The recombinant strain of P. pastoris X-33/mGM-CSF was cultrivated using fermentation basal salts medium . In order to reach high cell density fed-batch fermentation was carried our using D.O. stat as feeding strateqy. Different feeding medium 4﹪glycerol,4﹪glycerol with 0.5﹪(w/v) of casamino acid, and YPG were employed. At the end of high cell density fermentation,cell concentration reached 142 O.D.,about 120g/L wet cell weight and protein concentration was 1.04g/L. The 6× His tagged mGM-CSF expressed in fermentation broth was recovered by using and its concentration was immobilized metal affinity chromatography concentrated 50 fold.

碩士
國立成功大學
生物化學研究所
97
Integrins are a family of heterodimeric receptors and modulate many cellular processes, including growth, death, adhesion, and migration. Rhodostomin (Rho) is a potent platelet aggregation inhibitor and belongs to the family of disintegrins. Rho consists of 68 amino acids with a 48PRGDM53P motif and six disulfide bonds. In previous study we expressed Rho in Pichia pastrois (P. pastoris) and used it as the scaffold to design integrin αvβ3-specific drugs. In this study I optimized the fermentation culture condition to increase the protein production of Rho mutants expressed in P. pastoris. The protein production of Rho mutants using shake-flask culture is ~100 mg/L. I increased the production of a Rho mutant, HSA-ARLDDL, up to 9-fold with a yield of ~900 mg/L by optimizing pH, temperature, medium composition, and oxygen level of the fermentation process. The final yields of proteins produced from shake-flask and fermentation cultures after purification were 30 mg/L and 170 mg/L, respectively. The recovery of proteins produced from shake-flask and fermentation cultures after purification were 30% and 17%, respectively. It is likely due to higher mis-folding proteins produced from the fermentation process. In our previous study we found that Rho mutants with a 39KKKRTICR47I linker sequence affected their binding affinity and selectivity to integrins α5β1, αvβ3, and αIIbβ3. Therefore, I have successfully expressed three Rho mutants with the 39KKKRT linker sequence (R46A, I47R, and R46A/I47R mutants) and one mutant with the 39SRAGK linker sequence (R46A mutant). The analysis of platelet aggregation and cell adhesion assays showed that the R46A mutant with the 39SRAGK linker sequence exhibited 5.4-, 7.6-, 2.2-, and 5.6-fold decreases in their inhibitory activity to platelet aggregation and integrins αIIbβ3,αvβ3, and α5β1, respectively. In addition, the R46A mutant with the 39KKKRT linker sequence exhibited 4.1-, 24.8-, 1.8-, and 1.8-fold decreases in their inhibitory activity to platelet aggregation and integrins αIIbβ3, αvβ3, and α5β1. In contrast, the I47R mutant with the 39KKKRT linker sequence exhibited 3- and 7-fold increases in their inhibitory activity to integrins αvβ3 and α5β1, respectively. Interestingly, we found that Rho mutant containing the 39KKKRTICARARGDN53P sequence inhibited integrins αIIbβ3, αvβ3, and α5β1 with the IC50 values of 956.0, 5.7, and 6.6 nM, respectively. The finding indicated that this mutant can abolish its activity to integrin αIIbβ3. The mutational study on Rho will provide new insight into design potent integrin-specific disintegrins, and the optimization of fermentation condition of HSA-ARLDDL will serve the basis to produce integrin-specific disintegrins expressed in P. pastoris.

碩士
大同大學
生物工程學系(所)
107
In this study, SuperPro Designer software was used to simulate Pichia pastoris for the production β-glucosidase using glycerol as the carbon source. The same software was also used to evalulate the total investment, the cross margin, the return on investment, the payback time, the return on investment (after taxes). This study was partitioned into two sections: one section compared the total activity and specific activity derived from original medium, improved medium, optimized medium and optimal medium; the other section used SuperPro Designer to evaluate the economic benefits from two-1.5T and one-20 T production lines. The simulated results indicated that using the optimized medium and one-20 T production line was the better choice. Using the one-20 T production line, pNPG was 44.7 U/ml and spec. pNPG reached 174.5 U/mg. The gross margin was 39.7 %, the return on investment was 42.2 %, the payback time was 2.4 years, and the return on investment (after taxes) was 61.5 %.

碩士
大同大學
生物工程學系(所)
106
In this study, the production of recombinant protein β-glucosidase through high cell density fermentation by exogenous gene expression strain of Pichia pastoris （carrying with GAP promoter system）. Metabolism of the carbon source by P. pastoris could produce glyceraldehyde-3-phosphate dehydrogenase （GAPDH） to initiate foreign gene expression and continuous expression of the exogenous protein. Therefore, the design of carbon source will have a significant impact on the expression of the system. This study used fed-batch fermentation with glycerol as the primary carbon source with the addition of different sugars for evaluation. The fermentation mode adopts a two-stage fermentation strategy. In the pre-fermentation stage, the culture temperature and pH value were adjusted to facilitate the rapid growth of the cells, then the temperature and pH were adjusted after the fermentation at 48 hrs to facilitate enzyme production. The results showed that the maximum enzyme activity of the five groups of fermentation experiments from low to high values were 16.2 U/ml （control group, without adding sugar）, 30 U/ml （adding molasses）, 51 U/ml （adding sugar cane liquid）, 58.3 U/ml （adding maltodextrin）, and 104 U/ml （adding brown sugar）, respectively. Among of all sugars additions, brown sugar achieved the highest enzyme activity, which also reached the maximum cell concentration of 125 g/L at 240 hrs and the maximum protein amount of 590 mg/L at 432 hrs. The maximum enzyme activity of this result was 104 U/ml,that was 6.4 times of the control group （without adding sugar）, and the maximum specific enzyme activity was 176 U/mg, which was 6.3 times of the control group.

碩士
國立臺灣科技大學
化學工程系
92
High cell density fermentation of recombinant yeasts Saccharomyces cerevisiae and Pichia pastoris were studied. Both recombinant yeasts strains carry glucose oxidase(GOD) gene of Aspergius niger and constitutively express this extracellular enzyme. Among the carbon sources screened, fructose is the one very suitable for cultivating both GOD expressing recombinant yeasts. Fed-batch cultivation was employed to achieve high cell density fermentation. When 20﹪(w/v) fructose was used in the feeding nutrient and exponential feeding strategy was employed for S. cerevisiae high cell density cultivation, 200 OD600 was obtained after 66 hours cultivation and the final GOD activity was 107 U/ml. Under the same cultivation condition, cell concentration of P. pastoris could reach 220 OD600 and the GOD activity could only reach 40 U/ml. In order to prevent the extracellular GOD from being degraded by protease, 1﹪ casmino acid was employed in the medium. The cell density of P. pastoris could be increased further to 365 OD600 , when 40﹪ fructose was used in the feeding medium. The GOD activity of 85 U/ml was obtained. GOD from S. cerevisiae and P. pastoris had very different glycosylation extent. Glycosylation degree of GOD(S. cerevisiae) and GOD(P. pastoris) were 104﹪ and 25﹪, respectively. The high glycosylation extent of GOD(S. cerevisiae) make it has broader pH and temperature stability range than that of GOD(P. pastoris). The molecular weight of GOD(S. cerevisiae) and GOD(P. pastoris) were determined to be about 140 KDa and 90 KDa , respectively.