| 1. |
- Ask, Magnus, 1983
(författare)
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Towards More Robust Saccharomyces cerevisiae Strains for Lignocellulosic Bioethanol Production: Lessons from process concepts and physiological investigations
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dwindling oil reserves and the negative impacts of fossil fuels on the environment call for more sustainable energy sources. First-generation bioethanol produced from sugar cane and corn has met some of these needs, but it competes with the food supply for raw materials. Lignocellulosic biomass is an abundant non-edible raw material that can be converted to ethanol using the yeast Saccharomyces cerevisiae. However, due to the inherent recalcitrance to degradation of lignocellulosic raw materials, harsh pretreatment methods must be used to liberate fermentable sugars, resulting in the release of compounds such as acetic acid, furan aldehydes and phenolics, that inhibit yeast metabolism. This thesis research aimed to identify bottlenecks in terms of inhibitory compounds related to ethanol production from two lignocellulosic raw materials, Arundo donax and spruce, and furthermore to harness the physiological responses to these inhibitors to engineer more robust yeast strains. A comparative study of separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) revealed that acetic acid limits xylose utilization in pretreated Arundo donax, whereas the furan aldehydes furfural and 5-hydroxymethyl-2-furaldehyde (HMF) were hypothesized to be key inhibitors in pretreated spruce. The impacts of furfural and HMF on the redox and energy metabolism of S. cerevisiae were studied in detail in chemostat and batch cultivations. After adding the inhibitors to the feed medium of chemostat cultivations, the intracellular levels of NADH, NADPH, and ATP were found to decrease by 40, 75, and 19%, respectively, suggesting that furan aldehydes drain the cells of reducing power. A strong effect on redox metabolism was also observed after pulsing furfural and HMF in the xylose consumption phase in batch cultures. The drainage of reducing power was also observed in a genome-wide study of transcription that found that genes related to NADPH-requiring processes, such as nitrogen and sulphur assimilation, were significantly induced. The redox metabolism was engineered by overproducing the protective metabolite and antioxidant glutathione. Strains with an increased intracellular level of reduced glutathione were found to sustain ethanol production for longer duration in SSF of pretreated spruce, yielding 70% more ethanol than did the wild type strain.
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| 2. |
- Ylitervo, Päivi
(författare)
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Concepts for improving ethanol productivity from lignocellulosic materials : encapsulated yeast and membrane bioreactors
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lignocellulosic biomass is a potential feedstock for production of sugars, which can be fermented into ethanol. The work presented in this thesis proposes some solutions to overcome problems with suboptimal process performance due to elevated cultivation temperatures and inhibitors present during ethanol production from lignocellulosic materials. In particular, continuous processes operated at high dilution rates with high sugar utilisation are attractive for ethanol fermentation, as this can result in higher ethanol productivity. Both encapsulation and membrane bioreactors were studied and developed to achieve rapid fermentation at high yeast cell density. My studies showed that encapsulated yeast is more thermotolerant than suspended yeast. The encapsulated yeast could successfully ferment all glucose during five consecutive batches, 12 h each at 42 °C. In contrast, freely suspended yeast was inactivated already in the second or third batch. One problem with encapsulation is, however, the mechanical robustness of the capsule membrane. If the capsules are exposed to e.g. high shear forces, the capsule membrane may break. Therefore, a method was developed to produce more robust capsules by treating alginate-chitosan-alginate (ACA) capsules with 3-aminopropyltriethoxysilane (APTES) to get polysiloxane-ACA capsules. Of the ACA-capsules treated with 1.5% APTES, only 0–2% of the capsules broke, while 25% of the untreated capsules ruptured within 6 h in a shear test. In this thesis membrane bioreactors (MBR), using either a cross-flow or a submerged membrane, could successfully be applied to retain the yeast inside the reactor. The cross-flow membrane was operated at a dilution rate of 0.5 h-1 whereas the submerged membrane was tested at several dilution rates, from 0.2 up to 0.8 h-1. Cultivations at high cell densities demonstrated an efficient in situ detoxification of very high furfural levels of up to 17 g L-1 in the feed medium when using a MBR. The maximum yeast density achieved in the MBR was more than 200 g L-1. Additionally, ethanol fermentation of nondetoxified spruce hydrolysate was possible at a high feeding rate of 0.8 h-1 by applying a submerged membrane bioreactor, resulting in ethanol productivities of up to 8 g L-1 h-1. In conclusion, this study suggests methods for rapid continuous ethanol production even at stressful elevated cultivation temperatures or inhibitory conditions by using encapsulation or membrane bioreactors and high cell density cultivations.
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| 3. |
- Westman, Johan
(författare)
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Ethanol production from lignocellulose using high local cell density yeast cultures. Investigations of flocculating and encapsulated Saccharomyces cerevisiae
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Efforts are made to change from 1st to 2nd generation bioethanol production, using lignocellulosics as raw materials rather than using raw materials that alternatively can be used as food sources. An issue with lignocellulosics is that a harsh pretreatment step is required in the process of converting them into fermentable sugars. In this step, inhibitory compounds such as furan aldehydes and carboxylic acids are formed, leading to suboptimal fermentation rates. Another issue is that lignocellulosics may contain a large portion of pentoses, which cannot be fermented simultaneously with glucose by Saccharomyces cerevisiae. In this thesis, high local cell density has been investigated as a means of overcoming these two issues. Encapsulation of yeast in semi-permeable alginate-chitosan capsules increased the tolerance towards furan aldehydes, but not towards carboxylic acids. The selective tolerance can be explained by differences in the concentration of compounds radially through the cell pellet inside the capsule. For inhibitors, gradients will only be formed if the compounds are readily convertible, like the furan aldehydes. Conversion of inhibitors by cells close to the membrane leads to decreased concentrations radially through the cell pellet. Thus, cells closer to the core experience subinhibitory levels of inhibitors and can ferment sugars. Carbohydrate gradients also give rise to nutrient limitations, which in turn trigger a stress response in the yeast, as was observed on mRNA and protein level. The stress response is believed to increase the robustness of the yeast and lead to improved tolerance towards additional stress. Glucose and xylose co-consumption by a recombinant strain, CEN.PK XXX, was also improved by encapsulation. Differences in affinity of the sugar transporters normally result in that glucose is taken up preferentially to xylose. However, when encapsulated, cells in different parts of the capsule experienced high and low glucose concentrations simultaneously. Xylose and glucose could thus be taken up concurrently. This improved the co-utilisation of the sugars by the system and led to 50% higher xylose consumption and 15% higher final ethanol titres. A protective effect by the capsule membrane itself could not be shown. Hence, the interest in flocculation was triggered, as a more convenient way to keep the cells together. To investigate whether flocculation increases the tolerance, like encapsulation, recombinant flocculating yeast strains were constructed and compared with the non-flocculating parental strain. Experiments showed that strong flocculation did not increase the tolerance towards carboxylic acids. However, the tolerance towards a spruce hydrolysate and especially against furfural was indeed increased. The results of this thesis show that high local cell density yeast cultures have the potential to aid against two of the major problems for 2nd generation bioethanol production: inhibitors and simultaneous hexose and pentose utilisation.
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| 4. |
- Nickel, David, 1990
(författare)
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Process development for platform chemical production from agricultural and forestry residues
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- As part of a bio-based economy, biorefineries are envisaged to sustainably produce platform chemicals via biochemical conversion of agricultural and forestry residues. However, supply risks, the recalcitrance of lignocellulosic biomass, and inhibitor formation during pretreatment impair the economic feasibility of such biorefineries. In this thesis, process design and assessment were developed with the aim of addressing these hurdles and improving the cost-effectiveness of lignocellulose-derived platform chemicals. To expand the feedstock base and reduce operational costs, logging residues served as underutilised and inexpensive raw material. The major impediment in converting logging residues was their high recalcitrance and low cellulose content, which resulted in low attainable ethanol titres during simultaneous saccharification and co-fermentation (SSCF). Pretreatment optimisation reduced inhibitor formation and recalcitrance, and led to enzymatic hydrolysis yields at par with those obtained for stem wood, despite the less favourable chemical composition. Upgrading logging residues with carbohydrate-rich oat hulls increased ethanol titres to >50 g/L using batch SSCF at 20% WIS loadings, demonstrating the potential to further decrease downstream processing costs. To alleviate the toxicity of inhibitors generated during pretreatment, preadaptation was applied to Saccharomyces cerevisiae . Exposure to the inhibitors in the pretreated liquid fraction improved ethanol production during subsequent fermentation. Transferring the concept of preadaptation to lactic acid production by Bacillus coagulans cut the process times by half and more than doubled the average specific lactic acid productivity, showcasing how preadaptation could decrease operational costs. To assess the performance and robustness of process designs against process input variations, a multi-scale variability analysis framework was developed. The framework included models for bioprocess, flowsheet, techno-economic, and life cycle assessment. In a case study, multi-feed processes, in which solids and cells are fed to the process using model-based predictions, were more robust against variable cellulolytic activities than batch SSCFs in a wheat straw-based ethanol biorefinery. The developed framework can be used to identify robust biorefinery process designs, which simultaneously meet technological, economic, and environmental goals.
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| 5. |
- Alm, Tove, 1977-
(författare)
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Interaction engineered three-helix bundle domains for protein recovery and detection
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- HTML clipboard The great advances in DNA technology, e.g. sequencing and recombinant DNA techniques, have given us the genetic information and the tools needed to effectively produce recombinant proteins. Recombinant proteins are valuable means in biotechnological applications and are also emerging as alternatives in therapeutic applications. Traditionally, monoclonal antibodies have been the natural choice for biotechnological and therapeutic applications due to their ability to bind a huge range of different molecules and their natural good affinity. However, the large size of antibodies (150 kDa) limits tissue penetration and the recombinant expression is complicated. Therefore, alternative binders with smaller sizes have been derived from antibodies and alternative scaffolds.In this thesis, two structurally similar domains, Zbasic and ABDz1, have been used as purification tags in different contexts. They are both three-helical bundles and derived from bacterial surface domains, but share no sequence homology. Furthermore, by redesign of the scaffold used for ABDz1, a molecule intended for drug targeting with extended in-vivo half-life has been engineered. In Papers I and II, the poly-cationic tag Zbasic is explored and evaluated. Paper I describes the successful investigation of Zbasic as a purification handle under denaturating conditions. Moreover, Zbasic is evaluated as an interaction domain in matrixassisted refolding. Two different proteins were successfully refolded using the same setup without individual optimization. In Paper II, Zbasic is further explored as a purification handle under non-native conditions in a multi-parallel setup. In total, 22 proteins with varying characteristics are successfully purified using a multi-parallel protein purification protocol and a robotic system. Without modifications, the system can purify up to 60 proteins without manual handling. Paper I and II clearly demonstrate that Zbasic can be used as an interaction domain in matrix-assisted refolding and that it offers a good alternative to the commonly used His6-tag under denaturating conditions. In paper III, the small bifunctional ABDz1 is selected from a phage display library. Endowed with two different binding interfaces, ABDz1 is capable of binding both the HSA-sepharose and the protein A-derived MabSelect SuRe-matrix. The bifunctionality of the domain is exploited in an orthogonal affinity setup. Three target proteins are successfully purified using the HSA-matrix and the MabSelect SuRe-matrix. Furthermore, the purity of the target proteins is effectively improved by combining the two chromatographic steps. Thus, paper III shows that the small ABDz1 can be used as an effective purification handle and dual affinity tag without target specific optimization. Paper IV describes the selection and affinity maturation of small bispecific drug-targeting molecules. First generation binders against tumor necrosis factor-α are selected using phage display. Thereafter on-cell surface display and flow cytometry is used to select second-generation binders. The binding to tumor necrosis factor-α is improved up to 30 times as compared to the best first generation binder, and a 6-fold improvement of the binding strength was possible with retained HSA affinity. Paper III and IV clearly demonstrate that dual interaction surfaces can successfully be grafted on a small proteinaceous domain, and that the strategy in paper IV can be used for dual selection of bifunctional binders.
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| 6. |
- Hanora, Amro
(författare)
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Primary Recovery of Biologically Active Compounds Using Macroporous Monolithic Hydrogels
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The completion of sequencing of human and other mammalian genomes opens a new era for drug development. New approaches have been proposed for tackling diseases such as development of small molecule therapies based on understanding of human genome and proteome, new proteinous based therapies, where the therapeutic protein can inhibit or modify a certain metabolic pathway or DNA-based therapies delivering a gene into the cell (e.g., cancer cells) to correct or inhibit the imperfect gene function. The possibility of production of novel therapeutics (small, proteinous and DNA based substances) in biotechnological processes utilising mammalian cells or microorganisms such as bacteria or yeast, presents new challenges for the separation processes. Moreover, new methods for high throughput screening are needed to identify potentially important lead molecules within the large molecular libraries. Indeed, designing downstream process (DSP) of biologically active compounds depends on the nature and intended use of such compounds. Commodity compounds that are produced in tons need fast and cheap purification methods. However, high molecular weight molecules intended for pharmaceutical applications, need careful design of DSP to meet the legislator demands such as removal of contaminants and toxic substances. Two examples were demonstrated for the design of DSP purification process for small and large molecular weight compounds. Lactic acid was purified from cell broth using composite ion exchanger in expanded bed chromatographic format. Plasmid DNA was captured directly from cell lysate using monolithic macroporous hydrogel, so called cryogel, grafted with different polycations. Using cryogels with coupled specific ligands, bacterial endotoxin was successfully removed from protein solutions and captured from disposed cell homogenate. Fast parallel screening of complex samples containing target substance was demonstrated using affinity minicryogel columns in 96-well format plate.
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| 7. |
- Soares, Ana
(författare)
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Biodegradation of the Recalcitrant Endocrine Disruptor Nonylphenol
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Currently, over 100 high-volume chemicals have been classified as endocrine disrupters. One of these is nonylphenol, which was used as the model compound in this study. This substance originates mainly from the degradation of non-ionic surfactants (nonylphenol ethoxylates) which are widely used in industrial and domestic applications. Hence, nonylphenol is widespread in the environment. Under anaerobic conditions the degradation of nonylphenol with 10 ethoxylate groups was observed to take place through sequential removal of ethoxylate groups, resulting in the formation of nonylphenol (up to 11 mg/kg dw) and nonylphenol ethoxylate with 1-3 ethoxylate groups that were accumulated on the sludge. Due to its harmful effects and recalcitrance, the investigation of organisms that can metabolize nonylphenol is important. This was performed by acclimatization and enrichment of selected inocula with nonylphenol as the only carbon source. Suitable bacteria were only found in soil contaminated with ethoxylated non-ionic surfactants collected in an industrial area in Gothenburg, Sweden. The bacteria isolated were classified as Stenotrophomonas sp., Pseudomonas mandelii and Pseudomonas veronii, and were able to grow at low temperatures, with an optimum at 10?C for the two Pseudomonas spp. and they were thus classified as cold-adapted microorganisms. These are, to the best of our knowledge, the first reported cold-adapted organisms that can degrade nonylphenol.. The enriched culture was used to inoculate a lab-scale packed-bed bioreactor fed with mineral salt medium saturated with nonylphenol in order to simulate contaminated water/groundwater. Nonylphenol was degraded by 99-100%, at rates of 43 mg/l?day at 10?C and 22 mg/l?day at temperatures of 5.5?C and 15?C. Removal of endocrine-disrupting activity was also observed. The same type of bioreactor was inoculated with a pure strain of Sphingomonas sp. TTPN3, known to biodegrade nonylphenol and classified as a mesophilic organism. The degradation rate achieved at reactor removal yields of 99-100% was 33 mg nonylphenol/l?day at room temperature (22?2?C), which was lower than the rate obtained at 10?C. These results indicate that the low degradation rates usually observed at low temperatures, common in most of the industrialized countries, can be overcome by the use of adapted organisms. This underlines the relevance of studying cold-adapted organisms which are poorly known, according to FISH analysis performed, in favour of mesophilic organisms. Besides bacteria, white-rot fungi, Trametes versicolor and Bjerkandera sp. BOL13 were screened, among other fungi, for their ability to remove nonylphenol from liquid matrices. Removal rates of 6.6 mg nonylphenol/l?day and 6.1 mg nonylphenol/l?day were observed after 25 days of incubation by Trametes versicolor and Bjerkandera sp. BOL13, respectively. These rates could be increased to 9.7 mg nonylphenol/l?day for Bjerkandera sp. BOL13 by raising the concentration of active biomass in the inoculum and reducing mass transfer limitations by agitating the cultures. However, the removal of nonylphenol was not clearly correlated with the production of extracellular enzymes. For Trametes versicolor, nonylphenol removal was closely related with laccase production. This fungus was inhibited at nonylphenol concentrations above 15 mg/l, indicating the toxic effects of nonylphenol on this fungal strain. Nonylphenol removal from soil was also attempted by washing artificially contaminated soil at 40?C. The leachate was then fed into a packed-bed bioreactor where nonylphenol was successfully degraded. However, when real contaminated soil was used, the removal of nonylphenol from the soil decreased, showing the limitation of this method in aged soils where adsorption restricted the extraction process. White-rot fungi are potential soil colonizers with high surface growth rates, and are able to reach pollutants in soil in ways bacteria can not. Trametes versicolor and Bjerkandera sp. BOL13 degraded approximately 430 mg nonylphenol/kg in artificially contaminated soil after 5 weeks of incubation. These results could not be repeated with real contaminated soil due to the high pH of the soil used and the presence of other contaminants which interfered with the growth of the fungi.
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| 8. |
- Dahlin, Andreas, 1980
(författare)
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Nanoplasmonic Biosensors compatible with Artificial Cell Membranes
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Within life science, there is currently an intense search for novel techniques that enable efficient and reliable analysis of biomolecular interactions. Such methods have future applications within medical diagnostics and drug development, as well as within proteomic research in general. Lately, several concepts have emerged that are based on monitoring molecular binding to surfaces via optical, mechanical or electrical signal transduction. In particular, the plasmons associated with metallic nanoparticles are of interest since they offer a convenient way to monitor biomolecular interactions, also in a miniaturized format, by optical spectroscopy.This thesis describes the development of a biosensor based on the optical properties of nanoscale apertures in continuous metal films. The fabrication and characterization of the nanostructure is described, as well as surface modification protocols based on thiol chemistry for material-specific functionalization. In addition, an experimental setup for spectroscopy is presented together with data analysis algorithms for minimizing noise.It is emphasized that, from an experimental sensing perspective, nanoholes and nanoparticles have essentially the same plasmonic properties. However, the nanoholes offer several advantages because of the fact that the structure is physically different. In particular, it is shown how various artificial cell membranes can be spontaneously formed inside nanoholes. This makes the sensor compatible with studies of processes related to biological membranes. In this context, membrane-bound proteins are of special interest since they constitute a third of our genome and represent the target of half of the most common medical drugs. Potential future applications of the artificial membranes on the plasmonic nanostructures are discussed, with focus on probing transport across the membrane.
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| 9. |
- Zamani, Akram
(författare)
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Superabsorbent Polymers from the Cell Wall of Zygomycetes Fungi
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The present thesis presents new renewable, antimicrobial and biodegradable superabsorbent polymers (SAPs), produced from the cell wall of zygomycetes fungi. The cell wall was characterized and chitosan, being one of the most important ingredients, was extracted, purified, and converted to SAP for use in disposable personal care products designed for absorption of different body fluids. The cell wall of zygomycetes fungi was characterized by subsequent hydrolysis with sulfuric and nitrous acids and analyses of the products. The main ingredients of the cell wall were found to be polyphosphates (4-20%) and copolymers of glucosamine and N-acetyl glucosamine, i.e. chitin and chitosan (45-85%). The proportion of each of these components was significantly affected by the fungal strain and also the cultivation conditions. Moreover, dual functions of dilute sulfuric acid in relation to chitosan, i.e. dissolution at high temperatures and precipitation at lowered temperatures, were discovered and thus used as a basis for development of a new method for extraction and purification of the fungal chitosan. Treatment of the cell wall with dilute sulfuric acid at room temperature resulted in considerable dissolution of the cell wall polyphosphates, while chitosan and chitin remained intact in the cell wall residue. Further treatment of this cell wall residue, with fresh acid at 120°C, resulted in dissolution of chitosan and its separation from the remaining chitin/chitosan of the cell wall skeleton which was not soluble in hot acid. Finally, the purified fungal chitosan (0.34 g/g cell wall) was recovered by precipitation at lowered temperatures and pH 8-10. The purity and the yield of fungal chitosan in the new method were significantly higher than that were obtained in the traditional acetic acid extraction method. As a reference to pure chitosan, SAP from shellfish chitosan, was produced by conversion of this biopolymer into water soluble carboxymethyl chitosan (CMCS), gelation of CMCS with glutaraldehyde in aqueous solutions (1-2%), and drying the resultant gel. Effects of carboxymethylation, gelation and drying conditions on the water binding capacity (WBC) of the final products, were investigated. Finally, choosing the best condition, a biological superabsorbent was produced from zygomycetes chitosan. The CMCS-based SAPs were able to absorb up to 200 g water/g SAP. The WBC of the best SAP in urine and saline solutions was 40 and 32 g/g respectively, which is comparable to the WBC of commercially acceptable SAPs under identical conditions (34-57 and 30-37 g/g respectively).
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| 10. |
- Löfdahl, Per-Åke, 1959-
(författare)
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On bacterial formats in protein library technology
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Millions of years of evolution have resulted in an immense number of different proteins, which participate in virtually every process within cells and thus are of utmost importance for allknown forms of life. In addition, there are several examples of natural proteins which have found use in applications outside their natural environment, such as the use of enzymes infood industry and washing powders or the use of antibodies in diagnostic, bioseparation or therapeutic applications. To improve the performance of proteins in such applications, anumber of techniques, all collectively referred to as ‘protein engineering’, are performed in thelaboratory.Traditionally, methods involving ‘rational design’, where a few alterations are introduced atspecific protein locations to hopefully result in expected improvements have been applied.However, the use of more recent techniques involving a simultaneous construction of a large number of candidate variants (protein libraries) by various diversification principles, fromwhich rare clones showing enhanced properties can be isolated have contributed greatly to thefield of protein engineering.In the present thesis, different protein traits of biotechnological importance have beenaddressed for improvements by the use of such methods, in which there is a crucial need tomaintain a clonal link between the genotype and the phenotype to allow an identification of protein library members isolated by virtue of their functional properties. In all protein library investigations included in this thesis this coupling has been obtained by Escherichia coli bacterialcell-membrane compartmental confinement.In a first study, a combination of error prone PCR and gene-shuffling was applied to the Tobacco Etch Virus (TEV)-protease gene in order to produce collections from which genesencoding variants showing an enhanced soluble expression of the enzyme frequently used inbiotechnology to cleave fusion proteins were identified. Using Green Fluorescence Protein(GFP)-based cell fluorescence analysis, a clone with a five-fold increase in the yield of solubly produced protein was successfully isolated. In a second study, a novel and different GFPbased selection system, in addition also involving targeted in vivo protein degradation principles,was employed for investigations of the substrate sequence space of the same protease. In two additional studies, a selection system denoted Protein Fragment Complementation Assay(PCA), based on the affinity driven structural complementation of a genetically split β-lactamase enzyme was used to identify variants having desired target protein binding abilities,including both specificity and affinity. Using Darwinian principles concerning clonal growth advantages, affibody binding proteins showing sub-nanomolar dissociation constants to thehuman cytokine TNF-α were isolated. Taken together, these studies have shown that the bacterial format is very well suited for use in various aspects of protein library selection.
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