Dissertations / Theses on the topic 'Proteins – Biotechnology'

Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94%) appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1) a dimer interface motif found in voltage-gated chloride channels, (2) a proton transfer motif found in heme-copper oxidases, and (3) a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

The aim of this thesis was to produce DNA expression constructs and use them to investigate the feasibility of recombinantly expression proteins for future interaction studies between human RBBP6 and p53 and pRb proteins.

Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94%) appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1) a dimer interface motif found in voltage-gated chloride channels, (2) a proton transfer motif found in heme-copper oxidases, and (3) a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

While the advances of the scientific community have enabled extraordinary improvements in the capabilities of synthetic biology, there is a continued desire in biotechnology for enhanced or entirely novel biological functions. As proteins are either directly or indirectly responsible for the vast majority of naturally occurring biological activities, the modification of peptide structures constitutes a promising approach to address the ambitions of biotechnology. Central to the work in this thesis is the recognition that naturally occurring protein structures are intangibly complex due to the relics of evolutionary processes, accumulated from years of blind natural selection. Chapter 1 introduces de novo protein design strategies that circumvent the use of naturally occurring peptide scaffolds, offering examples of tractable systems that have been generated to perform various biological functions, thus forming the justification for the experimental approach undertaken here. The experimental work detailed in chapters 3 and 4 aimed to develop a system that would enable the incorporation of carotenoids and acenes into the internal cavity of de novo-designed 'maquette' proteins by hydrophobic partitioning alone. The results of these sections demonstrated that the protein chassis had little or no effect in the photophysical properties of the incorporated chromophores, whilst providing enhanced stability and solubility in entirely aqueous solutions. Conversely, the experimental strategy outlined in chapter 5 aimed to introduce nuclei of high atomic mass into the maquette proteins in order to directly affect the photophysical properties of the bound chromophores through the spin-orbit coupling interaction. The results of the final experimental chapter demonstrated that de novo designed proteins could effectively interface with native biological systems and provide a mechanism to enable cofactor incorporation in vivo. Where appropriate, the results of each experimental section are discussed in relation to their impact on specific areas of research and potential applications in biotechnology.

The unicellular yeast, Pichia pastoris has currently emerged as one of the most popular host systems for heterologous proteins due to its relatively cheap cost, easy genetic manipulability, ability to perform post-translational modifications on proteins, and respiratory growth capabilities which allow it to be cultured in very high concentrations. Over 700 foreign proteins have been recombinantly expressed using P. pastoris. Although P. pastoris appears to be an ideal host system, its main drawback is its inability to efficiently export some heterologous proteins into the extracellular medium. The incorporation of S. cerevisiae's MATα pre-pro signal leader (MATα) has led to increased protein secretion in most cases. MATα is thus used in the production of 90% of all proteins secreted in P. pastoris. However secretion efficiency still remains a problem. It has been suspected that low secretion may be attributed to improper extracellular targeting (a function of MATα). In order to address these issues there has been a precedent for performing limited mutagenesis of a signal leader peptide (like MATα) to increase protein secretion. In one study the insertion of a 10 amino-acid residue into MATα resulted in a 5-fold increase in secretion of bacterial phytase, an important industrial enzyme. Despite this success there have been no systematic mutagenesis processes which would help elucidate the reason behind this case of increased secretion. In our study, we performed a series of mutagenesis events, both random and site directed, with the intent of illuminating the mechanisms of MATα that contribute to secretion. As a result were able to create a novel secretion signal (pLL3) with enhanced secretion levels of our reporter protein HRP.

A novel metal-inducible and amplifiable metallothionein (MT) expression system, pNK, was firstly optimised and characterised for the production of a reporter protein, human growth hormone (hGH) in a suspension CHO cell line grown in a serum-free media. The pNK-based hGH production was demonstrated in cadmium-free condition under various fermentation modes (batch, fed-batch and perfusion) and scales (flask to bench-top bioreactor). Improvement of specific productivity of recombinant protein from pNK was shown to be possible by addition of butyrate or substrate substitution of glutamine by glutamate. Combination of fed-batch and butyrate addition strategies resulted in more than one gram per litre of hGH being obtained from the pNK expression system in a bioreactor. In the second part of the project, based on a statistical approach suggested by Plackett-Burman (P-B), a chemically-defined and protein-free medium, named Super-CHO protein-free (SPF), was developed to support a Super-CHO cell line, C2.8-325, to grow as a single-cell suspension culture with comparable growth rate and viable cell number as observed in a commercial medium containing undefined additives. Using Dulbecco's Modified Eagle's Medium/Ham's F12 1:1 mixture (DMEM/F12) as the basal medium, a P-B design matrix screened 10 nutritional components. Components shown potentially beneficial for cell growth rate and viable cell number were supplemented to DMEM/F12 to formulate the SPF medium. Finally, the pNK expression system and the Super-CHO cell line were applied simultaneously in an attempt to express a humanised anti-CD48 monoclonal antibody (MAb), IgG1-N2A (N2A-MAb). This aimed to test C2.8-SPF grown in newly developed SPF medium for transfection, clone development and recombinant protein production. A stable and N2A-MAb expressing C2.8-SPF cell line was successfully constructed, and N2A MAb expression was subsequently amplified and demonstrated in various cultivation scales (flask and bioreactor). This project demonstrated that the novel metal-inducible and - amplifiable mammalian expression system, pNK, and the novel mammalian host cell-line, Super-CHO C2.8-SPF, capable of growing as a single-cell suspension culture in a chemically-defined protein-free medium, SPF, could be utilised in combination to provide a new, low-cost, and regulatory-compliant recombinant protein expression platform, suitable for the biopharmaceutical industry to use in the manufacture of therapeutic recombinant proteins.

Being able to control protein function directly and in real time is attractive. In this thesis, I discuss controlling protein activity using alternating current electric fields on the order of 1 MV/m. Since protein structures result in localized and/or protein-wide charge gradients, it is expected that a sufficiently high electric field applied across a protein should result in structural distortions which can temporarily alter or halt protein function. The field is set to oscillate above the influences of the electrochemical double layer effects (1 kHz) and below the level needed for hydrodynamic rotation of proteins (10 MHz). A device is used to pass this field across a small volume of sample while allowing the solution to still be observed. Through application of high electric fields, we are able to temporarily reduce the activity of a bioluminescent luciferase reaction. Activity is inferred by measurement of the intensity and wavelength of the light emitted by the luciferase reaction. As this process is explored further, it could lead to the ability to electrically control protein function.

A METHOD BASED ON CONSERVED MULTIPLE AMINO ACID PROPERTIES TO PREDICT AMINO ACID SUBSTITUTIONS WHICH MAINTAIN THE PROTEIN STRUCTURE Avinash M. Baktula September 16, 2004 1-117 Directed by: Claire A. Rinehart, Doug McElroy and Sigrid Jacobshagen Department of Biology Western Kentucky University Proteins often contain several domains, each with a distinct structure. Such domains have evolved as units that, when combined in various arrangements, produce proteins of unique structure. This study was conducted to identify amino acid substitutions that don’t change structure. Amino acid properties which were conserved in proteins with identical structures were used to predict a set of amino acids profiles at each sequence position that can serve as viable substitutions. To test this analysis ten different protein sets were taken from the Conserved Domain Database of National Center for Biotechnology Information (NCBI). An amino acid index database of numerical indices representing various physicochemical and biochemical properties of amino acids were mapped onto the amino acid sequences in each dataset and these were used to select properties common to the proteins with the same structure. Based on these conserved properties, a substitution index percentage (SI%) was calculated to represent the relative ability of an amino acid to substitute at a given position and still maintain a protein structure. Amino acid profiles from different SI% ranges were used to create a set of substitutions into the consensus sequence of each dataset (AASCS). The AASCS from each SI% range were submitted to two validation programs, RPS-BLAST and PSI-PRED. The number of matches between the AASCS and the primary data set sequences for each SI% range was used to select the substitution profile ranges that best maintained the structure. It was concluded that amino acid, substitutions with SI% greater than 90% consistently conserved the structure of the protein. This method may prove useful in predicting the structure of proteins with induced mutations (site-directed mutagenesis), and in studies pertaining to protein engineering.

Thesis (Ph. D.)--University of Kentucky, 2004.
Title from document title page (viewed on June 22, 2006). Document formatted into pages; contains viii, 116 p. : ill. (some col.). Includes abstract and vita. Includes bibliographical references (p. 103-114).

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O fungo Neurospora crassa é um organismo amplamente utilizado como organismo modelo na compreensão de aspectos fundamentais da biologia dos eucariotos. Nosso laboratório tem utilizado este fungo para estudar os mecanismos bioquímicos e moleculares envolvidos na regulação do metabolismo do glicogênio. A avaliação de uma coleção de linhagens mutantes individualmente nocauteadas em genes que codificam fatores de transcrição permitiu identificar várias proteínas potencialmente envolvidas na regulação do metabolismo do glicogênio neste organismo modelo. As linhagens mutantes selecionadas apresentaram alterações no perfil de acúmulo de glicogênio e expressão do gene que codifica a enzima glicogênio sintase (gsn) durante a situação de estresse térmico. Entre estas, as linhagens mutantes nas ORFS NCU03043, NCU01629 e NCU04731, anotadas como proteínas hipotéticas no banco de dados do genoma do fungo, foram selecionadas para o presente estudo. Através de análises de Blast, a proteína codificada pela ORF NCU04731 mostrou ser homóloga ao grupo de fator de transcrição SREBPs (Sterol Regulatory Element Binding Protein) de mamíferos, que atuam como principal regulador da síntese de colesterol. Estas proteínas possuem domínio transmembrana e são ativadas após clivagem. Uma proteína ortóloga a SREBP (Sre1) foi identificada em Schizosaccharomyces pombe, entretanto, enquanto a habilidade de resposta a esteróis é conservada, as SREBPs de fungo regulam genes envolvidos na resposta transcricional à hipóxia, sendo necessárias para o crescimento em baixas concentrações de oxigênio. A proteína codificada pela ORF NCU03043 mostrou homologia a proteínas FlbC e FLE1 de fungos, as quais estão envolvidas na conidiação e desenvolvimento asexual. A linhagem flbCKO de N. crassa apresentou defeitos na progressão...
The fungus Neurospora crassa has been widely used as a model organism for fundamental aspects of eukaryotic biology. We have been studying the biochemical and molecular mechanisms involved in glycogen metabolism regulation in this fungus. The screening of a set of knocked-out strains in genes encoding transcription factors was previously performed as an attempt to identify transcription factors regulating glycogen metabolism in N. crassa. Mutant strains presenting changes in glycogen accumulation and glycogen synthase gene (gsn) expression under normal growth temperature and under heat shock stress were selected. Among them, the mutant strains in the ORFs NCU03043, NCU01629 and NCU04731, annotated as hypothetical proteins in the fungus genome database were studied in the present work. By Blast analysis, the proteins NCU04731 showed homology to a group of mammalian transcription factors SREBPs (Sterol Regulatory Element Binding Protein), which act as regulators of cholesterol synthesis and requiring cleavage from the membrane for activation. A SREBP orthologue was identified in Schizosaccharomyces pombe (Sre1), however while the ability to respond to sterol is conserved, fungal SREBPs regulates genes involved in the transcriptional response to hypoxia and are required for growth under low-oxygen conditions. The proteins encoded by the ORF NCU03043 showed homology to the fungal proteins FlbC and FLE1 involved in conidiation and asexual development. The N. crassa flbCKO strain presented defects in cell cycle progression and morphology. FLBC protein is necessary for proper induction of conidiation and is important for growth and development in N. crassa. flbC gene expression was highly induced in the early times of conidia germination confirming the importance of this protein to the fungus... (Complete abstract click electronic access below)

The ability of members of the hsp70 family to bind to peptides in vivo and in vitro suggests that they may be involved in the processing of antigens for binding to Major Histocompatibility (MHC) class I and/or class n molecules. The aims of this thesis have been to provide evidence for the involvement of hsp70s in antigen processing and to characterise the binding of peptides by hspTOs by structural and functional studies. Firstly, the peptide-binding domains of two hsp70s, hsp70hom and PBP74, were expressed in isolation from the rest of the molecule for structure determination. Both of these hsp70s were implicated in antigen processing: hsp70hom in the class I pathway, due to its cytoplasmic localisation and constitutive expression, and the presence of its gene in the MHC; and PBP74 in the class n pathway because published work indicated that it was localised to endosomes and that antibodies against it inhibited antigen processing. The expression and purification of both peptide-binding domains was very successful, and one dimensional NMR experiments indicated that they were folded. However, it was not possible to determine their structures by NMR spectroscopy or X-ray crystallography because they aggregated in solution at high concentrations. Instead, the structure of the C-terminal region of hsp70hom, which includes its peptidebinding domain, was modelled based on the known structure of the equivalent portion of dnaK, the hsp70 of E.coli. The structure of hsp70hom is predicted to be very similar to that of dnaK, and modelling studies suggest that it is likely to bind peptides in a closely related fashion. The modelling of complexes between hsp70hom and two peptides suggest that the peptide-binding groove is very versatile, accounting for the broad peptide-binding specificity of hsp70s. The interactions of hsp70hom and PB74 with peptides were investigated using plate binding assays and isothermattitration calorimetry. A biotinylated peptide bound to the peptide-binding domain of hsp70hom, immobilised in plastic wells, with a Kd of <25 μM, which is within the range of Kds reported for other hsp70-peptide complexes (0.1-100 μM). In solution, isothermal titration calorimetry showed that the binding of peptides to the peptide-binding domains of hsp70hom and PBP74 was likely to be entropically rather than enthalpically driven, and, therefore, the interactions involved are likely to be predominantly hydrophobic. Secondly, PBP74, an hsp70 thought to be involved in the class II antigen processing pathway in endosomes, was localised by immunofluorescence microscopy. It was shown to be a mitochondrial protein, and is, therefore, unlikely to be involved in antigen processing. The presence of other members of the hsp70 family in lysosomes purified from a B cell line by Percoll density gradient centrifugation was investigated using antibodies that reacted with many Afferent members of the hsp70 family. No hsp70s were detected in these late endocytic compartments, even after heat shock or serum starvation. However, the presence of an hsp70 in endosomes, or of a member of this family not detected by the antibodies used, in lysosomes, cannot be ruled out. A third approach investigated the induction of the three hsp70 genes found in the MHC by four cytokines. The hsp70-l and hsp70-2 genes are induced at the mRNA level by IFN-γ and IL- 1, while TNF induces hsp70-2 alone. This data supports a role for the heat-inducible hsp70 in MHC class I antigen processing, as it appears to be coregulated with known members of this antigen processing pathway. The expression of hsp70hom was unaffected by any of the four cytokines examined. In addition, the mitochondrial hsp70 (which is not encoded in the MHC) appears to be induced by IFN-γ at the protein level. The research presented in this thesis provides a greater understanding of the peptide-binding properties of two hsp70s. Further work is necessary to show conclusively whether any of the hsp70s is involved in antigen processing.

This thesis covers studies on endogenous proteolytic enzymes and their impact on fish muscle proteins and texture. The studies have been performed using Atlantic salmon (Salmo salar) and cod (Gadus morhua) subjected to different treatments and storage conditions.

The textural properties were very different in the two species. Salmon fillets were significantly softer and less resilient than cod fillets, and the properties changed somewhat differently during storage experiments. Different proteolytic enzymes have been reported to participate in muscle softening. Some of these enzymes were investigated, and specific proteolytic activities were detected throughout the storage periods. Collagenase-like enzymes seem to be the most important for cod muscle texture. Microorganisms and/or microbial enzymes seem not to be important for changes in salmon muscle texture. Results suggest that the cathepsin B-like enzymes are important for salmon texture. The activities of the proteolytic enzymes may be greatly affected by the muscle pH, and by the treatment(s) the fish are subjected to. In any case, changes caused by differences in proteolytic activities may need some time to be detectable or have significant impact on fish quality.

When cod fillets are stored in ice, it is highly recommended to keep the temperature low. Even a relatively mild temperature abuse was sufficient to result in less favorable textural characteristics, and make the fillets seem older than their days of storage.

Salmon fillets are often subjected to cold-smoking. The smoking temperature was important for the solubility properties of the muscle proteins, and for their composition, but did not affect the proteolytic activity. The effects of the processing parameters were most important early in the product’s shelf life, as the differences caused by the different smoking temperatures were reduced by further storage of the smoked samples.

Paper II and III are reprinted with kind permission of Elsevier, sciencedirect.com

Foam separation is a simple and economic method for separation of surface-active molecules such as proteins and enzymes from aqueous solutions. In this study, lactic acid broth, spent brewer&rsquo
s yeast extract and residual beer was used to investigate the applicability and efficiency of foam separation technique in partial purification of fermentation products and recovery of valuable components from industrial waste streams. The effects of the process variables initial feed concentration, air flow rate, foaming time, liquid pool height and temperature on separation performance were studied and optimum conditions for removal of proteins from lactic acid broth was determined. Highest enrichment (172.2) and separation ratio (314) with a high protein recovery (45.2 %) were obtained by foaming 200 ml of lactic acid broth with an initial feed concentration of 0.018 mg/ml at an air flow rate of 38.5 cm3/min. Selectivity of foam separation in protein purification, and its effect on protein structure was investigated in brewery wastes using SDS-PAGE and native PAGE, respectively.

Thesis (MSc)--Stellenbosch University, 2003.
ENGLISH ABSTRACT: Protein secretion and intracellular transport are highly regulated processes and involve the interplay of a multitude of proteins. A unique collection of thermosensitive secretory mutants allowed scientists to demonstrate that the secretory pathway of the yeast Saccharomyces cerevisiae is very similar to that of the higher eukaryotes. All proteins commence their journey in the endoplasmic reticulum, where they undergo amino-linked core glycosyl modification. After passage through the Golgi apparatus, where the remodelling of the glycosyl chains is completed, proteins are transported to their final destinations, which are either the cell surface, periplasmic space or the vacuole. Proteins destined for secretion are usually synthesised with a transient amino-terminal secretion leader of varying length and hydrophobicity, which plays a crucial role in the targeting and translocation of their protein cargo. Considerable effort has been made to elucidate the molecular mechanisms involved in these processes, especially due to their relevance in a rapidly expanding biotech industry. The advantages of S. cerevisiae as a host for the expression of recombinant proteins are well documented. Unfortunately, S. cerevisiae is also subject to a number of drawbacks, with a relative low product yield being one of the major disadvantages. Bearing this in mind, different secretion leaders were compared with the aim of improving the secretion of the LKA 1 and LKA2 a-amylase enzymes from the S. cerevisiae secretion system. The yeast Lipomyces kononenkoae is well known for its ability to degrade raw starch and an improved secretion of its amylase enzymes from S. cerevisiae paves the way for a potential one-step starch utilisation process. Three sets of constructs were prepared containing the LKA 1 and LKA2 genes separately under secretory direction of either their native secretion leader, the S. cerevisiae mating pheromone a-factor (MFa1) secretion leader, or the MFa1 secretion leader containing a synthetic C-terminal spacer peptide (EEGEPK). The inclusion of a spacer peptide in the latter set of constructs ensured improved Kex2p proteolytic processing of the leader/protein fusion. Strains expressing the amylase genes under their native secretion leaders resulted in the highest saccharolytic activity in the culture medium. In contrast to this, strains utilising the synthetic secretion leader produced the highest fermentation yield, but had a lower than expected extracellular activity. We hypothesise that the native amylase leaders may function as intramolecular chaperones in the folding and processing of their passenger proteins, thereby increasing processing efficiency and concomitant enzyme activity.
AFRIKAANSE OPSOMMING: Proteïensekresie en intrasellulêre transport is hoogs gereguleerde prosesse en betrek die onderlinge wisselwerking van 'n verskeidenheid proteïene. 'n Unieke versameling van temperatuur-sensitiewe sekresiemutante het wetenskaplikes in staat gestelom die ooreenkoms tussen die sekresiepad van die gis Saccharomyces cerevisiae en dié van komplekser eukariote aan te toon. Alle proteïene begin hul reis in die endoplasmiese retikulum, waartydens hulle ook amino-gekoppelde kernglikosielveranderings ondergaan. Nadat die proteïene deur die Golgi-apparaat beweeg het, waar die laaste veranderings aan die glikosielkettings plaasvind, word hulle na hul finale bestemmings, waaronder die seloppervlak, die periplasmiese ruimte of die vakuool, vervoer. Proteïene wat vir sekresie bestem is, word gewoonlik met 'n tydelike, amino-eindpuntsekresiesein, wat 'n kritiese rol in die teiken en translokasie van hul proteïenvrag speel, gesintetiseer. Heelwat pogings is in hierdie studie aangewend om die molekulêre meganismes betrokke by hierdie prosesse te ontrafel, veral as gevolg van hul toepaslikheid in 'n vinnig groeiende biotegnologiebedryf. Die voordele van S. cerevisiae as 'n gasheer vir die uitdruk van rekombinante proteïene is alombekend. S. cerevisiae het egter ook verskeie nadele, waaronder die relatiewe lae produkopbrengs die belangrikste is. Teen hierdie agtergrond, is verskillende sekresieseine met mekaar vergelyk met die doelom die sekresie van die LKA 1 en LKA2 a-amilasegene vanuit die S. cerevisiae-uitdrukkingsisteem te verbeter. Die gis Lipomyces kononenkoae is bekend vir sy vermoeë om rou stysel af te breek en 'n verbeterde sekresie van sy amilasegene vanuit S. cerevisiae baan die weg vir 'n moontlike een-stap styselgebruiksproses. Drie stelle konstrukte is gemaak wat die LKA 1- en LKA2- gene onafhanklik onder sekresiebeheer van onderskeidelik hul inheemse sekresiesein, die S. cerevisiae paringsferomoonsekresiesein (MFa1) of die MFa1-sekresiesein met 'n sintetiese koppelingspeptied aan die C-eindpunt (EEGEPK), plaas. Die insluiting van 'n koppelingspeptied in die laasgenoemde stel konstrukte verseker verbeterde Kex2p proteolitiese prosessering van die sein/proteïenfusie. Rasse wat die amilasegene onder beheer van hul inheemse sekresieseine uitdruk, het die beste saccharolitiese aktiwiteit in die kultuurmedia getoon. In teenstelling hiermee, het rasse wat van die sintetiese sekresiesein gebruik maak, die beste fermentasie-opbrengs getoon, maar met 'n laer as verwagte ekstrasellulêre aktiwiteit. Ons vermoed dat die inheemse amilaseseine as intramolekulêre begeleiers optree in die vou en prosessering van hul proteïenpassasiers, wat lei tot verbeterde prosessering en ensiemaktiwiteit.

Exocyst positive organelle (EXPO) is a newly discovered double membrane organelle involved in exocytosis and likely other vesicle trafficking processes. EXPO is likely generated from the ER, fused with plasma membrane and released a single membrane vesicle to cell exterior. The Arabidopsis protein Exo70E2 was found to be associated with EXPO and therefore is considered as a marker of EXPO and might play a role in EXPO-mediated vesicle trafficking. Understanding the biological function of AtExo70E2 (abbreviated as E2 in this thesis) will be very helpful in unraveling the function of EXPO. The aim of this work was to use various molecular, genetic and physiological approaches to determine the possible role of Arabidopsis Exo70E2 in biological pathways. By using the Exo70E2pro:GUS line, the expression pattern of Exo70E2 was determined. Exo70E2 was expressed mainly in roots, especially in root tips and epidermal cells in the division and elongation zones of roots. Its expression level was induced when the seedlings were treated with Flg22, a peptide derived from bacterial flagillin protein that induces the plant defense response. The tissue subcellular localization of Exo70E2 was also studied using the 35S:Exo70E2-eYFP and Exo70E2pro:Exo70E2-GFP reporter lines. The GFP fusion protein was found primarily in the epidermal cells of roots even in the 35S:Exo70E2-eYFP lines. For phenotypic analysis resulting from mutations of the Exo70E2 gene, I obtained three T-DNA insertion mutant lines and generated its overexpression lines. The two mutant alleles, e2-2 and e2-3 are in the Columbia ecotype background and further characterized. e2-2 which has a T-DNA insertion in an exon is likely a knock out line as Exo70E2 gene transcript could not be detected. e2-3, which carries a T-DNA insertion in its promoter region, was found to accumulate a higher level of the transcript, suggesting that the insertion causes its enhanced expression of Exo70E2. There was no obvious difference between wild type and e2-2 in their phenotypes under different conditions tested in this study. However, e2-3 had a retarded growth phenotype when grown in soil or on MS medium. The seedlings of e2-3 on MS medium also had a yellowish color although such a phenotype was not obvious when they were grown in soil. When supplementing the MS medium with sucrose, glucose or mannitol, the growth of e2-3 was more reduced compared to wild type under these conditions. However, on the medium with NaCl or under phosphate deficiency, the yellowish phenotype of e2-3 was rescued and the mutant seedlings became relatively healthier than the seedlings under the regular MS medium. A proteomics approach was taken to compare protein secreted from the seedlings of wild type and the mutants. Proteins secreted by seedlings to the liquid medium were collected, concentrated and subjected to MS analysis. Comparison of the profiles of secreted proteins between the wild type and the mutants leaded to identification of candidate proteins whose secretion might be affected by the mutation. My study indicates that Exo70E2 and EXPO are involved in transporting proteins (likely also metabolites) to the exterior of cells and the rhizosphere and might play an important role in stress responses.

Human malaria is an economically important disease caused by single-celled parasites of the Plasmodium genus whose biology displays great evolutionary adaptation to both its mammalian host and transmitting vectors. This thesis details the 70 kDa heat shock protein (Hsp70) and J protein chaperone complements in malaria parasites affecting humans, primates and rodents. Heat shock proteins comprise a family of evolutionary conserved and structurally related proteins that play a crucial role in maintaining the structural integrity of proteins during normal and stress conditions. They are considered future therapeutic targets in various cellular systems including Plasmodium falciparum. J proteins (Hsp40) canonically partner with Hsp70s during protein synthesis and folding, trafficking or targeting of proteins for degradation. However, in P. falciparum, these classes of proteins have also been implicated in aiding the active transport of parasite proteins to the erythrocyte cytosol following erythrocyte entry by the parasite. This host-parasite “cross-talk” results in tremendous modifications of the infected erythrocyte, imparting properties that allow it to adhere to the endothelium, preventing splenic clearance. The genome of P. falciparum encodes six Hsp70 homologues and a large number of J proteins that localize to the various intracellular compartments or are exported to the infected erythrocyte cytosol. Understanding the Hsp70-J protein interactions and/or partnerships is an essential step for drug target validation and illumination of parasite biology. A review of these chaperone complements across the Plasmodium species shows that P. falciparum possesses an expanded Hsp70-J protein complement compared to the rodent and primate infecting species. It further highlights how unique the P. falciparum chaperone complement is compared to the other Plasmodium species included in the analysis. In silico analysis showed that the genome of P. falciparum encodes approximately 49 J proteins, 19 of which contain a PEXEL motif that has been implicated in routing proteins to the infected erythrocyte. Most of these PEXEL containing J proteins are unique with no homologues in the human system and are considered as attractive drug targets. Very few of the predicted J proteins in P. falciparum have been experimentally characterized. To this end, cell biological and biochemical approaches were employed to characterize PFB0595w and PFD0462w (Pfj1) J proteins. The uniqueness of Pfj1 and the controversy in literature regarding its localization formed the basis for the experimental work. This is the first study showing that Pfj1 localizes to the mitochondrion in the intraerythrocytic stage of development of P. falciparum and has further proposed PfHsp70-3 as a potential Hsp70 partner. Indeed, attempts to heterologously express and purify Pfj1 for its characterization are described. It is also the first study that details the successful expression and purification of PfHsp70-3. Further, research findings have described for the first time the expression and localization of PFB0595w in the intraerythrocytic stages of P. falciparum development. Based on the cytosolic localization of both PFB0595w and PfHsp70-1, a chaperone – cochaperone partnership was proposed that formed the basis for the in vitro experiments. PFB0595w was shown for the first time to stimulate the ATPase activity of PfHsp70-1 pointing to a functional interaction. Preliminary surface plasmon spectroscopy analysis has revealed a potential interaction between PFB0595w and PfHsp70-1 but highlights the need for further related experiments to support the findings. Gel filtration analysis showed that PFB0595w exists as a dimer thereby confirming in silico predictions. Based on these observations, we conclude that PFB0595w may regulate the chaperone activity of PfHsp70-1 in the cytosol while Pfj1 may play a co-chaperoning role for PfHsp70-3 in the mitochondrion. Overall, this data is expected to increase the knowledge of the Hsp70-J protein partnerships in the erythrocytic stage of P. falciparum development, thereby enhancing the understanding of parasite biology.

The purity of heterologous recombinant proteins is of utmost importance to the pharmaceutical sector since most are consumed as therapeutic agents by humans. Variability caused by co- and posttranslational modifications is a major concern in pharmaceutical production. In order to develop strategies which guarantee a homogeneous product in a robust production process, it is important to better understand the metabolic basis of the synthesis of related non-canonical amino acids. So far, studies have identified high glucose fluxes in connection to oxygen limitation and overexpression of leucine-rich proteins as possible reasons for the production of non-canonical amino acids and their incorporation into heterologous proteins expressed in Escherichia coli. The results presented in this work provide evidence that oscillations in the concentrations of glucose and oxygen as they occur in inhomogeneous industrial scale bioreactors potentiate the synthesis and incorporation of norvaline into the leucine-rich protein IL-2, heterologously expressed in E. coli W3110M, as observed in well-mixed homogenous cultures and perturbed shake flask cultivations. In order to represent the heterogeneities existing in large-scale bioreactors, two experimental setups were applied, using a simple shake flask scale-down model developed to monitor dissolved oxygen and pH online during a batch and fed-batch cultivation phases. Results here show that by applying repeated glucose pulses to the glucose limited culture, which consequently induce oscillations in dissolved oxygen, norvaline is accumulated. Analysis of inclusion bodies that resulted from the expressed IL-2 revealed the presence of norvaline in the protein. A higher concentration of norvaline was observed in the oscillating scale-down model compared to the non-perturbed culture, which suggests that the conditions as they typically occur in large scale bioreactors may be critical for product quality. The results and tools, developed in this work are a solid basis for future cell engineering approaches to overcome the challenges in view of product quality.

The methylotrophic yeast. Pichia pastoris, is a powerful, adaptable, and inexpensive recombinant expression system commonly used to secrete heterologous protein. Although P. pastoris is a popular host organism, secretion inefficiency continues to be a major hurdle in its ability to produce high levels of foreign protein. Optimization of cis- and trans-acting factors has greatly enhanced the secretory capabilities of P. pastoris, however protein-specific engineering of a host organism is costly and not always effective. P. pastoris' secretion inefficiency is commonly due to trans-acting factors. Strains of S. cerevisiae have been engineered, through random genomic mutation, that are capable of overcoming these /ram-acting factors to secrete high levels of foreign protein. The Lin-Cereghino laboratory at University of the Pacific has developed a screen to identify mutations in P. pastoris capable of circumventing secretion obstacles. The P. pastoris genome was randomly disrupted through restriction enzyme-mediated integration of an antibiotic resistance marker. Supersecretion mutants were identified by their ability to secrete β-galactosidase, a reporter enzyme not natively secreted by P. pastoris. Sixteen β-galactosidase secretion (bgs) mutants were initially isolated by the Lin-Cereghino lab. This research focused on characterizing one of the resultant bgs mutants, ///. Initial sequencing and alignment studies identified the predicted LI1p sequence to be homologous to S. cerevisiae protein kinase C (PKC). Considering the role of PKC in the Cell Wall Integrity pathway of S. cerevisiae. the cell wall and secretory organelles of III were closely examined using transmission electron microscopy. Additionally, a qualitative alkaline phosphatase assay was used to evaluate the cell wall integrity of ///. Finally, the secretory phenotype of 111 was examined using a group of structurally and functionally diverse reporter proteins. In characterizing the bgs mutant, III, this research contributes to an understanding of cellular components that limit protein secretion in the yeast, P. pastoris.

elevação da expectativa de vida e a diminuição no índice de natalidade têm como consequência o envelhecimento da população mundial, com aumento da incidência de doenças neurodegenerativas. Pessoas acometidas por esses males dispõem atualmente de limitados recursos terapêuticos. Estes muitas vezes são só paliativos, com baixa ou nula perspectiva quanto à reversão dos danos instalados. Por isso, o estudo de substâncias possivelmente neuroprotetoras, que apresentam potencial aplicação como novas drogas, tem sido alvo de pesquisas. Estudos realizados a partir das toxinas produzidas por lagartas da mariposa Lonomia obliqua, as quais têm causado inúmeros acidentes na região Sul do Brasil, identificaram uma proteína presente na hemolinfa com atividade antiapoptótica. A mesma demonstrou provável atuação na manutenção do potencial elétrico de membrana mitocondrial elevado, evitando a morte celular por mecanismo apoptótico. Desta forma, este estudo tem como objetivo avaliar o perfil proteico e efeito da hemolinfa bruta e fração cromatográfica sobre a viabilidade celular de cultura primária de neurônios hipocampais de ratos após a indução de apoptose. Para avaliação do perfil proteico em amostras da hemolinfa bruta e frações de 3 lotes de lagartas de origens distintas, foi utilizada a abordagem proteômica shotgun, semi-quantitativa. Foram identificadas 76 proteínas totais, sendo 71 na hemolinfa e 40 nas frações. Na avaliação do extrato bruto da hemolinfa predominaram proteínas do tipo antiviral, serino proteases, hemolinas e inibidores de proteases. Já nas frações avaliadas, foram identificadas proteínas dos grupos hemolinas, serino proteases e inibidores de proteases. Os lotes apresentaram diferenças quali e quantitativas nas proteínas identificadas entre si. Em relação à viabilidade celular, não foram encontradas diferenças estatisticamente significativas (p<0,05) nas células tratadas com hemolinfa ou frações e induzidas ao dano oxidativo. Porém o tratamento das células com a fração na concentração de 0,05 e 0,1% (v/v) por 24 h foi capaz de manter a viabilidade celular significativamente maior em relação ao controle positivo (p<0,05 e p<0,01 respectivamente). Estes resultados podem contribuir na identificação de proteínas com potencial aplicação como neuroprotetoras.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.
Increased life expectancy and the decline in births results in aging population, with increasing of neurodegenerative diseases incidence. The therapeutic is limited, often only palliative, with low or no prospect damage reversal. Study of substances with potentially neuroprotective has been the focus of research. Toxic proteins of Lonomia obliqua caterpillars, which have caused several accidents in southern Brazil, were identified in the hemolymph with anti-apoptotic activity. This protein had demonstrated the maintaining of high electric potential of mitochondrial membrane, preventing cell death by apoptosis mechanism. This study aims the evaluation of the protein profile and effect of hemolymph and fraction on cell viability of rats primary cultured hippocampal neurons after induction of apoptosis. Semi-quantitative shotgun proteomics approach was used to evaluate the protein profile of 3 lots of different origin, 71 in hemolymph and 40 in fractions, in a total of 76 proteins. Antiviral protein predominated in crude extract of hemolymph, following by serine proteases, hemolines and protease inhibitors. In fractions were identified hemolines, serine proteases and protease inhibitors. No statistics differences were found (p<0.05) in the cell viability induced of oxidative damage, which were treated with hemolymph or fractions. However, the treatment with the fraction at concentration of 0.05 and 0.1% (v/v) for 24 hours, was able to maintain cell viability significantly higher than positive control (p<0.05 and p<0.01 respectively). These results may contribute to the identification of proteins with potential use as neuroprotective in degenerative conditions.

Orientador: Maria Célia Bertolini
Banca: Cleslei Fernando Zanelli
Banca: Iran Malavazi
Resumo: O fungo Neurospora crassa é um organismo amplamente utilizado como organismo modelo na compreensão de aspectos fundamentais da biologia dos eucariotos. Nosso laboratório tem utilizado este fungo para estudar os mecanismos bioquímicos e moleculares envolvidos na regulação do metabolismo do glicogênio. A avaliação de uma coleção de linhagens mutantes individualmente nocauteadas em genes que codificam fatores de transcrição permitiu identificar várias proteínas potencialmente envolvidas na regulação do metabolismo do glicogênio neste organismo modelo. As linhagens mutantes selecionadas apresentaram alterações no perfil de acúmulo de glicogênio e expressão do gene que codifica a enzima glicogênio sintase (gsn) durante a situação de estresse térmico. Entre estas, as linhagens mutantes nas ORFS NCU03043, NCU01629 e NCU04731, anotadas como proteínas hipotéticas no banco de dados do genoma do fungo, foram selecionadas para o presente estudo. Através de análises de Blast, a proteína codificada pela ORF NCU04731 mostrou ser homóloga ao grupo de fator de transcrição SREBPs (Sterol Regulatory Element Binding Protein) de mamíferos, que atuam como principal regulador da síntese de colesterol. Estas proteínas possuem domínio transmembrana e são ativadas após clivagem. Uma proteína ortóloga a SREBP (Sre1) foi identificada em Schizosaccharomyces pombe, entretanto, enquanto a habilidade de resposta a esteróis é conservada, as SREBPs de fungo regulam genes envolvidos na resposta transcricional à hipóxia, sendo necessárias para o crescimento em baixas concentrações de oxigênio. A proteína codificada pela ORF NCU03043 mostrou homologia a proteínas FlbC e FLE1 de fungos, as quais estão envolvidas na conidiação e desenvolvimento asexual. A linhagem flbCKO de N. crassa apresentou defeitos na progressão... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The fungus Neurospora crassa has been widely used as a model organism for fundamental aspects of eukaryotic biology. We have been studying the biochemical and molecular mechanisms involved in glycogen metabolism regulation in this fungus. The screening of a set of knocked-out strains in genes encoding transcription factors was previously performed as an attempt to identify transcription factors regulating glycogen metabolism in N. crassa. Mutant strains presenting changes in glycogen accumulation and glycogen synthase gene (gsn) expression under normal growth temperature and under heat shock stress were selected. Among them, the mutant strains in the ORFs NCU03043, NCU01629 and NCU04731, annotated as hypothetical proteins in the fungus genome database were studied in the present work. By Blast analysis, the proteins NCU04731 showed homology to a group of mammalian transcription factors SREBPs (Sterol Regulatory Element Binding Protein), which act as regulators of cholesterol synthesis and requiring cleavage from the membrane for activation. A SREBP orthologue was identified in Schizosaccharomyces pombe (Sre1), however while the ability to respond to sterol is conserved, fungal SREBPs regulates genes involved in the transcriptional response to hypoxia and are required for growth under low-oxygen conditions. The proteins encoded by the ORF NCU03043 showed homology to the fungal proteins FlbC and FLE1 involved in conidiation and asexual development. The N. crassa flbCKO strain presented defects in cell cycle progression and morphology. FLBC protein is necessary for proper induction of conidiation and is important for growth and development in N. crassa. flbC gene expression was highly induced in the early times of conidia germination confirming the importance of this protein to the fungus... (Complete abstract click electronic access below)
Mestre

Clustered, regularly interspaced, short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) constitute a bacterial and archaeal adaptive immune system. The ongoing arms race between prokaryotic hosts and their invaders such as phages led to the emergence of anti-CRISPR proteins as countermeasures against the potent antiviral defense. Since the first examples of anti-CRISPRs were shown in a subset of CRISPR-Cas systems, we endeavored to uncover these naturally-occurring inhibitors that inactivate different types of CRISPR-Cas systems. In the first part of my thesis, we have identified and characterized Type II anti-CRISPR proteins that inactivate several Cas9 orthologs. We share mechanistic insights into anti-CRISPR inhibition and show evidence of its potential utility as an off-switch for Cas9-mediated mammalian genome editing. Although the RNA programmability of Cas9 enables facile genetic manipulation with great potential for biotechnology and therapeutics, limitations and safety issues remain. The advent of anti-CRISPR proteins presents opportunities to exploit the inhibitors to exert temporal, conditional, or spatial control over CRISPR. In the second part of my thesis, we demonstrate that anti-CRISPR proteins can serve as useful tools for Cas9 genome editing. In particular, we have demonstrated that anti-CRISPRs are effective as genome editing off-switches in the tissues of adult mammals, and we further engineered anti-CRISPR proteins to achieve tissue-specific editing in vivo. Taken together, my thesis research aimed to mine for natural anti-CRISPR protein inhibitors and repurpose these proteins to complement current Cas9 technologies in basic and clinical research.

Rodent-borne hantaviruses (family Bunyaviridae) cause two distinct human infections; hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). HFRS is a common viral zoonosis, characterized by fever, renal dysfunction and hemostatic imbalance. Four HFRS-associated hantaviruses have been described: Hantaan virus and Seoul virus mainly found in Asia, Dobrava virus, encountered in the Balkan region and Puumala virus (PUU), causing mild HFRS (nephropathia epidemica; NE) in Europe. HPS, recently discovered in the Americas, involves adult respiratory distress syndrome with a high mortality rate and is caused by Sin Nombre virus. Hantaviruses are enveloped and carry a RNA genome which encodes a polymerase, two glycoproteins and a nucleocapsid protein. The latter elicits a strong humoral immune response in infected patients. The clinical diagnosis of hantavirus infections has until recently relied on serological confirmation by immunofluorescense assay (IFA) and enzyme-linked immunosorbent assay (ELISA) using cell culture derived viral antigens. Due to the hazardous nature of hantaviruses and variable virus yield in cell culture we aimed at using recombinant hantavirus proteins for serological purposes. We expressed PUU N in E. coli (PUU rN) and found that high levels of IgM to this protein could be detected at onset of NE. This indicated that it was useful as the sole antigen for serodiagnosis. Our finding was confirmed by comparing IFA and PUU rN ELISA using 618 sera collected at the regional diagnostic laboratory. Full-length PUU rN is difficult to purify due to aggregation to E. coli remnants. We therefore located the important domain for the humoral immune response by utilizing truncated PUU rN proteins to its amino-terminal region (amino acid 7-94). Amino acid 1-117 of N of the five major human hantavirus pathogens were produced in E. coli. Serological assays based on them could detect IgM and IgG serum responses in 380 HFRS and HPS patients from Sweden, Finland, Slovenia, China, Korea and the USA with high sensitivity. In an epidemiological investigation of hantavirus serum responses in European Russia we unexpectedly found antibody responses to the hantaviruses found in east Asia and the Balkan region in 1.5 %, speaking in favour for the presence of such virus in this region. The degree of cross reactivity within the hantavirus genus was adressed by following the serum responses in NE patients. We found an increase of cross reactivity during the maturation of the immune response from onset of disease up to three years by comparing the IgG reactivity towards the hantavirus aminoterminal rN proteins. The first human isolate of the causative agent of NE in Scandinavia was recovered in cell culture from phytohemagglutinin stimulated leukocytes. Serological analysis revealed that this virus belongs to the PUU hantavirus serotype, distinct from the rodent prototype PUU Sotkamo. The human PUU Umeå is unique but genetically similar to rodent isolates from northern Sweden.
digitalisering@umu.se

Abiotic stress leads to a change in the water content of plants. Salinity and osmotic stress affect both the morphology and physiology of plants. Plants have therefore responded to these environmental changes by adapting and tolerating them. The SABP2-interacting proteins (SIP) 428-silenced RNAi transgenic tobacco lines were subjected to various abiotic stresses (salinity, osmotic, and drought). The effect of SIP428-silencing on the tobacco plants subjected to these abiotic stresses was monitored. The results from the root growth data show that the sip428-silenced lines exhibit enhanced tolerance to the stressors compared to the wild-type plants. Interestingly, results of the relative chlorophyll content show no significant difference between the wild-type plants and sip428-silenced transgenic plants. In summary, based on the results presented in this study it could be concluded that SIP428 is a negative regulator of salinity, osmotic and drought stresses. Further studies are required to understand the mechanism.

Expanding upon our understanding of plant defense is critical, particularly with the perilous threats of climate change and overpopulation to our food security, health and well-being. In this study, we focused on plant defense using two distinct approaches. First, we performed a proteomic analysis of plant exosome-like nanoparticles in order to elucidate their defense related protein cargo. Secondly, we used a wheat antimicrobial protein, puroindoline, as a fusion partner for the expression of recombinant proteins in rice endosperm. Plant exosome-like nanoparticles (ELP) were isolated from fresh tomato and subjected to mass spectrometry (MS) analysis. The ELPs were compared to fresh pressed tomato juice, and the proteins that were significantly upregulated in the ELPs were analyzed for their defensive properties. Bioinformatic analysis identified 30 proteins upregulated in the ELPs, with a majority of these being involved in plant defense. Puroindoline is a protein found in soft wheat varieties. A unique feature of this protein is the presence of a tryptophan-rich domain, which causes it to localize and tether onto starch granule surfaces; a property we are seeking to exploit for recombinant protein isolation. We hypothesized that when expressed in a pin-null crop, such as rice, puroindoline along with its fusion partner will localize and adhere to starch granule surfaces. PIN fusions were expressed in rice, and their subcellular localization was determined by immunolocalization. It was observed that PIN localizes to rice starch ii granules in vitro and in planta, and retains its starch granule binding abilities as a fusion partner. To identify other possible starch granule binding fusion partners, an anhydrous cleavage method was developed that can scan dry biological materials for associated proteins, in this case the starch granule surface. Incubation of our cleavage reagent with isolated rice starch granules yielded several cleavage products as determined through SDS-PAGE. These cleavage products were compared with previous proteomic data of trypsin digested rice starch granules.

Main purpose of this study was to increase protein expression in Chinese hamster ovary (CHO) cells by improving protein secretion of translated proteins. The goal was to find signal peptides from the screening of signal peptide libraries for improvement of protein secretion using a CHO-cell express selection system. Biopharmaceutical products, proteins such as monoclonal antibodies (mAbs), are most commonly produced using mammalian expression systems such as the expression in CHO cells. The posttranslational modifications of the proteins being expressed in CHO cells are similar to the expressional modifications in human cells, why the CHO cells are suitable for production of proteins used for human therapy. The expression of proteins in the cell is a complex mechanism, fundamentally depending on the DNA sequences in the cell nucleus. Secretion of translated proteins has been showed to be a bottleneck when improving expression. Secretion is initiated by the signal peptide, a n-terminal prolongation of the protein that is recognized by a signal recognition particle (SRP) when being translated by the ribosome. The sequence and structure of the signal peptide has been proved to affect secretion and altering the signal peptide could improve secretion even when changing signal peptide between different species. Designing variants of the signal peptides and analyzing protein expression might lead to improvements of the construct design and more protein produced from the cells, which would save time, money and material for the producer. To construct plasmids containing the gene of interest (GOI) and different signal peptides, several gene cloning methods were used. The plasmids were amplified using Escherichia coli (E. coli) transformation. The constructs were expressed by transfection into the CHO cell genome, and expression were analyzed using flow cytometry. When analyzing expression of a Fc-fusion protein with 5 different signal peptides, the signal peptide Azurocidin is the one showing highest expression levels in this study. In addition, IgG kapa and Albumin signal peptides did not show as high protein expression levels, even if they were better than the L1d and H5b signal peptides. Since signal peptides are exchangeable between proteins and species, it might be that Azurocidin is improving secretion and protein expression with other proteins than Fc-fusion proteins which would be an interesting aspect for further studies. When altering signal peptides with library sequences, the experimental challenges were crucial for the protein expression results and due to these issues, no library sequence could be seen to conquer others when it comes to protein expression levels. Transfection and cultivation procedures needs to be studied and improved before being able to draw conclusions about which signal peptide library sequences that might improve secretion and increase the protein expression.

Fluorescence resonance energy transfer (FRET)-based biosensors have been designed to fluorometrically detect everything from proteolytic activity to receptor-ligand interactions and structural changes in proteins. While a wide variety of fluorophores have demonstrated effectiveness in FRET probes, several potential sensor components are particularly notable. Semiconductor quantum dots (QDs) are attractive FRET donors because they are rather bright, exhibit high quantum yields, and their nanoparticulate structure enables the attachment of multiple acceptor molecules. Fluorescent proteins (FPs) are also of particular interest for fluorescent biosensors because design elements necessary for signal transduction, probe assembly, and device delivery and localization for intracellular applications can all be genetically incorporated into the FP polypeptide. The studies described in this thesis elucidate the important parameters for concerted QD-FP FRET probe design. Experimental results clarify issues of FRET pair selection, probe assembly, and donor-acceptor distance for the multivalent systems. Various analysis approaches are compared and guidelines asserted based on the results. To demonstrate the effectiveness of the QD-FP FRET probe platform, a ratiometric pH sensor is presented. The sensor, which uses the intrinsic pH-sensitivity of the FP mOrange to modulate the FP/QD emission ratio, exhibits a 20-fold change in its ratiometric measurement over a physiologically interesting pH range, making it a prime candidate for intracellular imaging applications.

Det uppskattas att 15% av alla par världen över lider avinfertilitet. Ungefär hälften beror på manlig infertilitet och 40% av dessa fall kan ännu inte förklaras. Därmed är nuvarande metoder för att diagnostisera manlig infertilitet otillräckliga och ytterligare tekniker behövs. En lyckad befruktning kräver att spermierna uttrycker membranproteinet Izumo1 som måste känna igen dess receptorprotein Juno, belägen vid ytan av äggmembranet. Bindningen mellan Juno och Izumo1 är essentiell för befruktning hos däggdjur då den bidrar till att gameternabinder och skapar en ny distinkt organism. Juno är ett relativt nyupptäckt protein och mekanismen med Izumo1 är fortfarande okänd. Ett nystartat företag vid namn Spermosens vill mäta interaktionen mellan Juno ochIzumo1 i ett nytt diagnostikverktyg som ska diagnostisera manlig infertilitet. Tanken är att Juno ska immobiliseras på guld-nanopartiklar och användas för att mätainteraktionen med spermaprover. Det nya verktyget ska hjälpa par att fastställa felet i befruktningen, vilket som en följd skulle hjälpa paret att välja lämplig assisteradreproduktionsmetod. I utvecklingen av det nya diagnostikverktyget behöver det konfirmeras att den Juno som används i enheten kan binda korrekt till mänskligt Izumo1. Därför måste interaktionerna mellan de mänskliga, rekombinanta proteinerna Juno och Izumo1 mätas och karakteriseras. Syftet med detta projekt var att utveckla en metod för att immobilisera Juno på guldnanopartiklar och sedan mäta interaktionerna med Izumo1 genom UV-Visspektroskopi. Detta är teoretiskt möjligt eftersom guld-nanopartiklarna framkallar ett fenomen som kallas lokaliserad ytplasmonresonans som varierar beroende påstorleken på guld-nanopartikelkomplexet. Immobiliseringsmetoden var en process som involverade flera steg som designades, polerades och förbättrades underarbetets gång. Dithiobis(C2-NTA) konjugerades till guldytan och koboltjonerkonjugerades till NTA. Det sista steget som innebar konjugering av Juno till kobolt genom en His-tag lyckades inte, och interaktionerna kunde därför inte mätas genom denna metod. Istället mättes protein-protein-interaktionen genom SPR-mätningar med Biacore, ett instrument som också är baserat på ytplasmonresonans. Interaktioner mellan Izumo1 och Juno kunde uppmätas både vid användning av Juno producerad från E. coli ochfrån däggdjursceller. Dissociationskonstanten (Kd) beräknades till 7-33 nM (för Junooch Izumo1 producerade i däggdjursceller) vilket kan jämföras med ett experimentfrån 2016 där 48 nM beräknades. Ett mer exakt Kd kunde inte fastställas och entrolig anledning till detta var att regenereringen av sensorytan som utfördes med NaOH varierade i effektivitet, vilket ledde till en osäkerhet då ytförhållandena kan ha varierat mellan mätningarna. De två Juno-proteinerna, som är producerade i olika organismer, visade två skilda affinitetsprofiler med Izumo1 vilket tyder på att glykosyleringen påverkar bindningsmekanismen mellan Juno och Izumo1.
It is estimated that 15% of all couples worldwide suffer from infertility. Roughly half is male-factor infertility and 40% of these cases cannot be explained. Thus, current methods for diagnosing male infertility are not enough and further techniques are needed. To have a successful fertilisation event, it is required that the sperm expresses membrane surface-protein Izumo1 which must recognise its counterpart protein Juno, located at the surface of the egg membrane. The recognition step between Juno and Izumo1 is essential in mammalian fertilisation for the gametes to bind and start the creation of a new distinct organism, but the molecular mechanism is still unknown.A start-up company named Spermosens want to measure the Juno-Izumo1 interaction in a new diagnostic device designed to diagnose male infertility. The idea is to have Juno immobilised on gold nanoparticles and measure the interaction between Juno and various semen samples. The new device is supposed to help couples pin-point the procreation issue which would help in the selection of suitable assisted reproductive technology. In the development of the new device, it had to be established that the Juno used in the device will bind correctly to human Izumo1. Therefore, the interactions between the human recombinant proteins Juno and Izumo1 had to be measured and characterized.The objectives of this project were to develop a method to immobilise Juno on gold nanoparticles and then measure the interactions with Izumo1 using UV-vis spectroscopy. This is theoretically possible since the gold nanoparticles exhibit a phenomenon called localized surface plasmon resonance that vary depending on the size of the gold nanoparticle-complex. The immobilisation procedure was a process involving several steps that were designed, polished and improved along the way. Dithiobis(C2-NTA) was conjugated to the gold surface and a cobalt ion was conjugated to the NTA. The last step involving conjugation of Juno to the cobalt through a His-tag was not succeeded, and the interactions could therefore not be measured this way.Instead, the protein-protein interaction was measured through SPR-measurements using Biacore, an instrument that is based on surface plasmon resonance as well. Interactions between Izumo1 and Juno could be detected using Juno produced in E. coli and in mammalian cells. The dissociation constant (Kd) could be calculated to 7-33 nM which can be compared to a previously published Kd of 48 nM. A more precise Kd could not be established, possibly due to that the regeneration of the sensor surface with NaOH varied in efficiency, leading to changing surface conditions during the measurements. The two Juno proteins, that were produced in different hosts, showed two different affinity profiles with Izumo1, which contributes to the suggestion that the glycosylation plays a role in the binding mechanism between Juno and Izumo1.

Les protéines associées aux membranes sont d'une importance cruciale pour la cellule. Cependant, en raison d'une plus grande difficulté de manipulation, les données biochimiques les concernant sont très lacunaires, notamment au point de vue de la formation de complexes entre ces protéines.

L'objectif global de notre travail consiste à combler ces lacunes et à préciser les interactions entre protéines membranaires chez la levure Saccharomyces cerevisiae et plus précisément, entre les transporteurs. Nous avons commencé notre travail par l'étude d'un jeu de données d'interactions à grande échelle entre toutes les perméases détectées par une méthode de double hybride spécialement adaptée aux protéines insolubles (split ubiquitin). Premièrement, la qualité des données a été estimée en étudiant le comportement global des données et des témoins négatifs et positifs. Les données ont ensuite été standardisées et filtrées de façon à ne conserver que les plus significatives. Ces interactions ont ensuite été étudiées en les modélisant dans un réseau d'interactions que nous avons étudié par des techniques issues de la théorie des graphes. Après une évaluation systématique de différentes méthodes de clustering, nous avons notamment recherché au sein du réseau des groupes de protéines densément interconnectées et de fonctions similaires qui correspondraient éventuellement à des complexes protéiques. Les résultats révélés par l'étude du réseau expérimental se sont révélés assez décevants. En effet, même si nous avons pu retrouver certaines interactions déjà décrites, un bon nombre des interactions filtrées semblait n'avoir aucune réalité biologique et nous n'avons pu retrouver que très peu de modules de protéines de fonction semblable hautement inter-connectées. Parmi ceux-ci, il est apparu que les transporteurs d'acides aminés semblaient interagir entre eux.

L'approche expérimentale n'ayant eu que peu de succès, nous l'avons contournée en utilisant des méthodes de génomique comparative d'inférence d'interactions fonctionnelles. Dans un premier temps, malgré une évaluation rigoureuse, l'étude des profils phylogénétiques (la prédiction d'interactions fonctionnelles en étudiant la corrééélation des profils de présence - absence des gènes dans un ensemble de génomes), n'a produit que des résultats mitigés car les perméases semblent très peu conservées dès lors que l'on considère d'autres organismes que les \
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

Thesis (MScAgric (Viticulture and Oenology. Wine Biotechnology))--University of Stellenbosch, 2010.
ENGLISH ABSTRACT: Agriculture worldwide is under great pressure to produce enough food in order to sustain the ever-growing world population. Among the many challenges faced by food producers, crop losses and damage caused by fungal plant pathogens is a major problem. The study of fungal pathogens and the interaction between plants and fungi is therefore essential, and has been carried out for many years. Much has been learned in this time, but the full mechanisms of the various modes of fungal attack and plant defence have still not been elucidated. Many fungi rely on the action of cell-wall degrading enzymes (CWDEs) to breach the plant cell wall and facilitate access to the nutrients within. CWDEs are among the very first enzymes to be secreted at the start of fungal attack, and many of them are considered to be essential pathogenesis factors. Endopolygalacturonases (ePGs) are CWDEs that cleave the homogalacturonan stretches of the plant cell wall and are vital virulence factors for a number of fungi, including Botrytis cinerea. An important defence mechanism of plants involves the inhibition of CWDEs in order to halt or slow down the fungal attack. Plant polygalacturonaseinhibiting proteins (PGIPs) are cell wall associated CWDE-inhibiting proteins that specifically act on fungal ePGs. Many different PGIPs from a number of diverse plant species have been described to date. They are known to have differential inhibition capabilities that often result from only a few key amino acid changes within the leucine-rich repeat (LRR) active domains. Previously, the first grapevine PGIP was isolated and characterised from Vitis vinifera cultivar Pinotage (Vvpgip1). This Vvpgip1 gene was overexpressed in the tobacco species Nicotiana tabacum, and was shown to be very effective in reducing the susceptibility of tobacco towards B. cinerea. The combined results confirmed transgene overexpression, increased PGIP activity and a strong resistance response against Botrytis, leading to the characterisation of these lines as having PGIP-specific resistance phenotypes. In a subsequent transcriptomic analysis of these lines it was found that they display differential expression of cell wall metabolism genes and biochemical characteristics that might indicate possible cell wall strengthening compared to wild-type tobacco under uninfecting conditions. The V. vinifera cultivars are all very susceptible to fungal attack, whereas other grapevine species, specifically the North American Vitis species, are known for their strong resistance and even immunity against many fungal pathogens. Thirty seven PGIPs have previously been isolated from these more resistant species. The amino acid sequences of the active domains of these PGIPs were previously aligned with that of VvPGIP1, and the proteins were found to be highly homologous with each other and with VvPGIP1. The different nonvinifera PGIPs separated into 14 subgroups based on their active domain sequences. For this study, one PGIP from each group was selected for functional analysis in tobacco. The selected PGIP-encoding genes were transformed into tobacco by means of Agrobacterium tumefaciens. Analyses of the putatively transformed plantlets were performed to test for transgene presence, transgene expression, and PGIP activity: final transgenic tobacco populations consisting of three to twelve individually transformed lines of nine different nonvinifera PGIPs were obtained. A subset of the resultant transgenic lines was infected with B. cinerea in two independent whole plant infections over 11-14 days in order to investigate the disease resistance afforded by the various PGIPs towards this fungus. A line from the previously characterised VvPGIP1 population was included as reference; all the infections were contrasted to the WT tobacco. All the infected lines overexpressing the non-vinifera PGIPs displayed very strong disease reduction in comparison to the WT control: after initial primary lesion formation, the spread of fungal infection was contained and halted in these lines, while wild-type tobacco plants were severely affected. Although the VvPGIP1 line displayed the characteristic PGIP-defense response, the non-vinifera PGIP plants displayed smaller lesions, indicating very strong resistance phenotypes. The characterised non-vinifera PGIP overexpressing lines, together with the VvPGIP1 line and the WT control were also used to further evaluate the previous observation that overexpression might lead to changes in expression of cell wall genes. Analysis of the expression of a xyloglucan endotransglycosylase (xth) gene in the transgenic population showed that this gene was down-regulated in healthy uninfected tissue from all the transgenic lines tested. This confirmed previous results and have confirmed in all grapevine PGIP overexpressing lines tested so far that this gene is downregulated. XTH is typically involved in cell wall metabolism and specifically in controlling the strength and elasticity of the plant cell wall. From previous work it is known that downregulation of this gene leads to strengthening of the wall. The results obtained in this study showed that the PGIP-specific resistance phenotype seen for VvPGIP1-overexpressing tobacco could be confirmed in transgenic tobacco overexpressing non-vinifera PGIPs from more resistant grapevine species as well. The fact that these PGIPs lines all performed even better than the VvPGIP1 lines in conferring resistance towards B. cinerea provides an interesting angle for further investigation into the structural differences between the non-vinifera PGIPs and VvPGIP1. The transgenic lines are also excellent material to study the in vivo functions of PGIPs further in the context of plant-pathogen interactions.
AFRIKAANSE OPSOMMING: Die landboubedryf is wêreldwyd onder groot druk om genoeg voedsel te produseer vir die groeiende wêreldbevolking. Een van die grootste probleme wat die bedryf ondervind, is die groot skade wat aan gewasse aangerig word deur patogeniese swamme. Dit is dus noodsaaklik om swamme en die interaksie tussen plante en swamme te bestudeer, en dit word al vir jare gedoen. Hoewel daar al baie geleer is in hierdie tydperk, is die volle meganismes van die verskeie maniere hoe swamme aanval en hoe plante hulleself verdedig, nog nie bekend nie. Verskeie swamme maak staat op die aktiwiteit van selwand-afbrekende ensieme (SWAEe) om deur die plantselwand te breek en sodoende toegang tot voedingstowwe in die plantsel te fasiliteer. SWAEe is van die eerste ensieme wat tydens die begin van patogeniese aanval deur swamme afgeskei word en verskeie SWAEe word as noodsaaklike patogeniese faktore beskou. Endopoligalakturonases (ePGs) is SWAEe wat die homogalakturoniese dele van die plantselwand verteer en is noodsaaklike virulensie faktore vir ‘n aantal swamme, onder andere Botrytis cinerea. ‘n Belangrike weerstandsmeganisme van plante behels die inhibering van swam SWAEe om sodoende die patogeen-aanval te stop of te vertraag. Die poligalakturonase-inhiberende proteïne (PGIPs) van plante is selwand-geassosieerde SWAEinhiberende proteïne wat spesifiek teen swam ePGs optree. Verskeie verskillende PGIPs vanuit verskillende plantspesies is tot dusver beskryf. Dit is bekend dat hulle differensiële inhiberende vermoëns het wat dikwels toegeskryf kan word aan slegs ‘n paar belangrike aminosuurvolgordeverskille in die leusien-ryke herhalende (LRH) aktiewe areas. Die eerste wingerd PGIP is vantevore geïsoleer vanuit Vitis vinifera kultivar Pinotage (Vvpgip1) en gekarakteriseer. Hierdie Vvpgip1 geen is ooruitgedruk in die tabakspesie Nicotiana tabacum en was baie effektief om die weerstand van tabak teen die swam Botrytis cinerea te verhoog. Die ooruitdrukking van die transgeen, verhoogde PGIP aktiwiteit en goeie weerstand teen Botrytis cinerea is bevestig, en het gelei daartoe dat die transgeniese VvPGIP1 plantlyne geklassifiseer is as lyne met PGIP-spesifieke weerstandsfenotipes. ‘n Daaropvolgende transkriptomiese analise van die plantlyne het gewys dat hulle differensiële uitdrukking van selwand-geassosieerde gene het, asook biochemiese eienskappe, wat ‘n moontlike selwandversterking aandui in vergelyking met wilde-tipe tabak in die afwesigheid van infeksie. Die V. vinifera kultivars is hoogs vatbaar vir swamme, terwyl ander wingerdspesies, spesifiek die Noord-Amerikaanse spesies, bekend is vir hoë weerstand en selfs immuniteit teenoor verskeie patogeniese swamme. Sewe-en-dertig PGIPs is vantevore geïsoleer vanuit hierdie meer weerstandbiedende spesies. Die aminosuurvolgordes van die aktiewe areas van hierdie PGIPs is vantevore vergelyk met die van VvPGIP1 en dit is gevind dat hierdie proteïne hoogs homoloog is aan mekaar, sowel as aan VvPGIP1. Die verskillende nie-vinifera PGIPs het in 14 groepe verdeel na aanleiding van die homologie van hulle aktiewe areas. Vir hierdie studie is een PGIP vanuit elkeen van hierdie groepe gekies vir verdere funksionele analise in tabak. Die 14 nie-vinifera PGIP-koderende gene is stabiel oorgedra na tabak deur middel van Agrobacterium tumefaciens. Die vermeende transgeniese plante is geanaliseer vir die teenwoordigheid van die transgeen, die uitdrukking daarvan en PGIP aktiwiteit: bevestigde transgeniese tabak populasies wat wissel van drie tot 12 individuele getransformeerde lyne kon verkry word vir nege van die verskillende nie-vinifera PGIPs. ‘n Aantal van die transgeniese lyne is geïnfekteer met B. cinerea in twee onafhanklike heelplantinfeksies vir 11-14 dae om die siekteweerstand van hierdie PGIPs teenoor die swam te evalueer. ‘n Plantlyn van die VvPGIP1-populasie is as ‘n verwysing ingesluit en al die infeksies is vergelyk met die wilde-tipe tabak. Al die geïnfekteerde lyne wat die nie-vinifera PGIPs ooruitdruk het ‘n baie sterk afname in siektesimptome getoon in vergelyking met die wilde-tipe kontrole: na aanvanklikle primêre lesies gevorm het, is die verspreiding van die infeksie ingeperk en gestop in hierdie lyne, terwyl die wilde-tipe plante baie erg geaffekteer is. Terwyl die VvPGIP1 lyn ook die tipiese PGIPweerstandsrespons getoon het, het die nie-vinifera PGIPe kleiner lesies ontwikkel, wat dui op baie sterk weerstandsfenotipes. Die gekarakteriseerde nie-vinifera PGIP ooruitdrukkende lyne, asook die VvPGIP1 lyn en die wilde-tipe kontrole, is gebruik om die vorige waarneming dat die ooruitdrukking kan lei tot veranderinge in selwandgeen-uitdrukking verder te ondersoek. Analise van die uitdrukking van ‘n xiloglukaan-endotransglikosilase (xth) geen in die transgeniese populasie het getoon dat hierdie geen afgereguleer is in gesonde, oninfekteerde weefsel van al die transgeniese lyne wat getoets is. Dit het vorige resultate bevestig en het ook bevestig dat hierdie geen afgereguleer is in alle wingerd PGIP-ooruitdrukkende lyne wat tot dusver getoets is. XTH is tipies betrokke by selwandmetabolisme, spesifiek by die beheer van selwandsterkte en selwandelastisiteit. Dit is uit vorige werk bekend dat die afregulering van hierdie geen lei tot versterking van die plantselwand. Die resultate verkry tydens hierdie studie het gewys dat die PGIP-spesifieke weerstand fenotipe van VvPGIP1-ooruitdrukkende tabak ook bevestig kon word in transgeniese tabak wat nie-vinifera PGIPs vanuit meer weerstandbiedende wingerdspesies ooruitdruk. Die feit dat hierdie PGIP lyne almal selfs beter weerstand teen B. cinerea bied as VvPGIP1 lyne is ‘n interessante invalshoek vir opvolgende ondersoeke na die belang van strukturele verskille tussen die nie-vinifera PGIPs en VvPGIP1. Hierdie transgeniese lyne is ook uitstekende hulpbronne om die in vivo funksies van PGIPs verder te bestudeer in die konteks van plantpatogeen interaksies.

The purpose of this project was to identify and evaluate nucleotide sequences enhancing translation of proteins in Chinese hamster ovary (CHO) cells. Candidate sequences were placed in the 5´-untranslated region (UTR) or 3´ UTR respectively and evaluated in a CHO-based expression system with a fluorescent Fc-fusion protein as a model protein.Five plasmid vectors were constructed, two of which designed to have a randomized nucleotide library in their 5´ and 3´ UTR respectively, and three of which designed to hold varying repeats of a known enhancing translation (ET) sequence in their 5´ or 3´ UTR. The plasmid constructs were transfected into CHO cells and the protein expression was analyzed both by fluorescence intensity in single cells using flow cytometry and in bulk by monoclonal antibody titer analysis based on Protein A affinity.The main result is that both flow cytometry and titer analysis indicate that insertion of five repeats of the ET in the 5´UTR has a negative effect on protein expression as compared to the control which had no ET repeats. Results related to the insertion of three ETs in the 5´ UTR were ambiguous. The titer analysis indicated that it had a negative effect on the protein expression compared to the control which had no ET repeats, whereas the flow cytometry results suggest that the effect is negligible. Transfection of library plasmids was unsuccessful; hence no library expression analysis results were achieved. Due to the time constraints of the project, the reason for the unsuccessful transfection of library plasmids was not investigated, but the LTX transfection method is stated as a highly plausible cause.Based on the outcome of this study, two recommendations for future work are suggested. The first one is to continue the focus on UTR sequences in terms of library screening, and to improve the method of transfecting library plasmid constructs into CHO cells using lipofection. The second suggestion for further studies is to test different UTR sequence lengths without involving potential ETs, to rule out the effect and positions of the ETs and investigate the expressional effect of UTR length solely.

Advances in the biomedical field require functional materials and processes that can lead to devices that are biocompatible, and biodegradable while maintaining high performance and mechanical conformability. In this context, a current shift in focus is towards natural polymers as not only the structural but also functional components of such devices. This poses material-specific functionalization and fabrication related questions in the design and fabrication of such systems. Silk protein biopolymers from the silkworm show tremendous promise in this regard due to intrinsic properties: mechanical performance, optical transparency, biocompatibility, biodegradability, processability, and the ability to entrap and stabilize biomolecules. The unique ensemble of properties indicates opportunities to employ this material into numerous biomedical applications. However, specific processing, functionalization, and fabrication techniques are required to make a successful transition from the silk cocoon to silk-based devices. This research is focused on these challenges to form silk-based functional material and devices for application in areas of therapeutics, bio-optics, and bioelectronics. To make silk proteins mechanically conformable to biological tissues, the first exploration is directed towards the realization of precisely micro-patterned silk proteins in flexible formats. The optical properties of silk proteins are investigated by showing the angle-dependent iridescent behavior of micropatterned proteins, and developing soft micro-optical devices for light concentration and focusing. The optical characteristics and fabrication process reported in the work can lead to the future application of silk proteins in flexible optics and electronics. The microfabrication process of silk proteins is further extended to form shape-defined silk protein microparticles. Here, the specificity of shape and the ability to form monodisperse shapes can be used as shape encoded efficient cargo and contrast agents. Also, these particles can efficiently entrap and stabilize biomolecules for drug delivery and bioimaging applications. Next, a smart confluence of silk sericin and a synthetic functional polymer PEDOT:PSS is shown. The composite materials obtained have synergistic effects from both polymers. Silk proteins impart biodegradability and patternability, while the intrinsically conductive PEDOT:PSS imparts electrical conductivity and electrochemical activity. Conductive micro architectures on rigid as well as flexible formats are shown via a green, water-based fabrication process. The applications of the composite are successfully demonstrated by realizing biosensing and energy storage devices on rigid or flexible forms. The versatility of the approach will lead to the development of a variety of applications such as in bio-optics, bioelectronics, and in the fundamental study of cellular bio electrogenic environments. Finally, to expand the applicability of reported functional polymers and composites beyond the microscale, a method for silk nano-patterning via electron beam lithography is explored. The technique enables one-step fabrication of user defined structures at the submicron and nano-scales. By virtue of acrylate chemistry, a very low energetic beam and dosage are required to form silk nano-architectures. Also, the process can form both positive and negative features depending on the dosage. The fabrication platform can also form nano scale patterns of the conductive composite. The conductive measurements confirm the formation of conductive nanowires and the ability of silk sericin to entrap PEDOT:PSS particles in nanoscale features.

La transglutaminasa (TGasa) és un enzim que catalitza modificacions postraduccionals de proteïnes mitjançant enllaços ε-(γ-glutamil) i ponts covalents d’amida. En plantes, aquest enzim està poc estudiat, i només ha estat clonat el gen TGasa de Zea mays (tgz). Aquesta tesi resumeix la feina feta per desenvolupar un sistema d'expressió utilitzant dos microorganismes recombinants, Escherichia coli (E. coli) i Pichia pastoris (P. pastoris) per produir i caracteritzar l'enzim transglutaminasa (TGZ). Treballs anteriors en E. coli van mostrar que la proteïna recombinant era present principalment en forma de cossos d'inclusió (IBs). Per tal d'obtenir la proteïna en forma activa i soluble, es van optimitzar les condicions d'expressió en E. coli. Es va assajar la coexpressió de xaperones i es va desenvolupar un sistema no clàssic de solubilització de IBs. A més, es va transformar P. pastoris per estudiar la seva expressió i comparar ambdós sistemes. Les metodologies de Taguchi i de la superfície de resposta es van utilitzar per formular un medi de cultiu que, juntament amb el desenvolupament d’una aplicació informàtica per modelar i simular el procés, va permetre establir un cultiu d'alta densitat d'E coli. Els resultats van mostrar que les condicions òptimes per a expressar TGZ en E. coli van ser d’una concentració de IPTG de 100μmol IPTG / g de biomassa seca i un temps d'inducció de 5 h. Aquestes condicions van permetre obtenir un rendiment TGZ de 160 mg / L amb una activitat específica de 450 putrescina pmol / mg TGZ resolubilitzada · h. Es va realitzar una caracterització bioquímica completa de la TGZ obtinguda mitjançant E. coli. Es va posar a punt un sistema de cultiu d'alta densitat cel·lular en P. pastoris i es va expressar TGZ amb èxit. La reacció de reticulació de TGZ a la caseïna es va estudiar, i el resultat va ser igual que la reacció de la caseïna per TGZ expressada en E. coli. Es va obtenir una producció de 480 mg / L de proteïna total amb una activitat de 4000 pmol putrescina / mg de proteïna total · h. Aquests resultats indiquen que també es va establir un procediment eficaç per expressar TGZ en P. pastoris.
La transglutaminasa (TGasa) es una enzima que cataliza modificaciones postraduccionales de proteínas mediante enlaces ε- (γ-glutamil) y puentes covalentes de amida. En plantas, esta enzima está poco estudiada, y sólo ha sido clonado el gen TGasa de Zea mays (tgz). Esta tesis resume el trabajo realizado para desarrollar un sistema de expresión utilizando dos microorganismos recombinantes, Escherichia coli (E. coli) y Pichia pastoris (P. pastoris) para producir y caracterizar la enzima transglutaminasa (TGZ). Trabajos anteriores en E. coli mostraron que la proteína recombinante estaba presente principalmente en forma de cuerpos de inclusión (IBs). Con el fin de obtener la proteína en forma activa y soluble, se optimizaron las condiciones de expresión en E. coli. Se ensayó la coexpresión de chaperonas y se desarrolló un sistema no clásico de solubilización de IBs. Además, se transformó P. pastoris para estudiar su expresión y comparar ambos sistemas. Se utilizaron las metodologías de Taguchi y de la superficie de respuesta para formular un medio de cultivo que, junto con el desarrollo de una aplicación informática para modelar y simular el proceso, permitieron establecer un cultivo de alta densidad de E. coli. Los resultados mostraron que las condiciones óptimas para expresar TGZ en E. coli fueron de una concentración de IPTG de 100μmol IPTG / g de biomasa seca y un tiempo de inducción de 5 h. Estas condiciones permitieron obtener un rendimiento TGZ de 160 mg / L con una actividad específica de 450 putrescina pmol / mg TGZ resolubilizada · h. Se realizó una caracterización bioquímica completa de la TGZ obtenida mediante E. coli. Se puso a punto un sistema de cultivo de alta densidad celular en P. pastoris y se expresó TGZ con éxito. La reacción de reticulación de TGZ en la caseína se estudió, y el resultado fue igual que la reacción de la caseína por TGZ expresada en E. coli. Se obtuvo una producción de 480 mg / L de proteína total con una actividad de 4000 pmol putrescina / mg de proteína total · h. Estos resultados indican que también se estableció un procedimiento eficaz para expresar TGZ en P. pastoris.
Transglutaminase (TGase) is an enzyme that catalyzes post-translational protein modifications by ε-(γ-glutamyl) links and covalent amide bonds. In plant, this enzyme is poorly studied and only the Zea mays TGase gene (tgz) has been cloned. This thesis summarizes the work done to develop an expression system using two recombinant microorganisms, Escherichia coli (E. coli) and Pichia pastoris (P. pastoris) to produce and characterize the enzyme transglutaminase (TGZ). Previous works expressing TGZ in E. coli showed that the recombinant protein was mainly present as inclusion bodies (IBs). In order to obtain active, soluble protein, expression conditions were optimized in E. coli, coexpression of chaperones was tested and a non-classic IBs resolubilizing system was developed. Additionally, the gene was also inserted in P. pastoris to study its expression, being able to compare both systems. Taguchi and response surface methodologies were used to develop a culture media that, together with the implementation of a computer application to model and simulate the process, allowed to develop a high-density culture of E. coli. Results showed that the optimal conditions to express TGZ in E. coli were an IPTG concentration of 100µmol IPTG/ g dry biomass and an induction time of 5h. These conditions allowed to obtain a TGZ yield of 160 mg/L with a specific activity of 450 pmol putrescine/mg resolubilized TGZ·h. A full biochemical characterization of the TGZ obtained using E. coli was performed. A P. pastoris high cell density cultivation system was implemented and TGZ was successfully expressed. The cross-linking reaction of TGZ to the casein was also studied, and the result was same as the reaction of casein by TGZ expressed in E. coli. A production of 480mg/L of total protein with an activity of 4000 pmol putrescine/mg total protein·h was obtained. These results indicated that an effective procedure for expressing TGZ in P. pastoris was also established.

Enzimas são biocatalisadores específicos que são utilizadas em vários campos de atuação, desde a indústria de alimentos, até na formulação de detergentes. As proteases são biocatalisadores de grande interesse comercial na indústria, movimentando bilhões de dólares com produção de toneladas de detergentes para diferentes aplicações. A demana de proteases no mercado brasileiro promove pesquisas como também o empreendorismo nesse segmento embora mais investimentos por parte das agências do governo devem ser necessárias. A potencialidade da matéria prima renovável e o aumento do desenvolviemnto de tecnologias para enzimas, como o conhecimento sobre a conformação protéica e estabilidade com atividades catalítica são as bases que podem promover a exportação de enzimas. Ligações de hidrogênio, forças iônicas e de van der Walls, como também as interações hodrofóbicas precisam ser matindas entre os amimoácidos para gerenciar a conformação espacial das enzimas, evitando desnaturação protéica. No processo de formulação, é necessário investigar a interrrelação de parâmetros físicos e aditivos químicos cujas variáveis são importantes para manter a estabilidade da conformação espacial, adicionando elementos como conservantes, sais, polímeros, surfactantes, solventes, detergentes e outros elementos para manter a estrutura da enzima. Nesse trabalho foram analizadas as composições de três bioprodutos dispostos no mercado brasileiro para lavagem de roupa. A presença de agentes ativos entre eles: enzimas e tensioativos e, a interação entre esses aditivos durante o armazenamento e as condições operacionais promovem as respectivas diferenças e características que impulsionam a competitividade desses produtos.
Enzymes are specific biocatalysts that work in wide field of applications as food industry as detergent formulation. The proteases represents an important commercial bioproduct used in industry, managing billion of dollars year by year, producing tons of detergents for different applications. Enzymatic reactions are processed under mild temperature and pressure with great commercial interest, being these catalysts biodegradable. The proteases demand in the brazilian market promoves the researches, as the entrepreneurship in this area althought more investments from government agencies must be necessary. The potenciality in renewable raw material and the increase of development of enzyme technologies are the bases that can promove the enzymes exportation. Hydrogen and disulfide bonds, van der Waals and ionic powers, as well as hydrophobic interactions need to be keeped among these amino acids to manage the spacial conformation of the enzymes, avoiding the inactivation or the protein desnaturation. The formulation process need of physical and chemical managements to promove the stability of the protein chains to try to protect the catalytic site and the spacial structure, adding elements like preservatives, salts, polymers, surfactantes, solvents, detergents and others elements to manage the structure of the enzyme in this process of formulation is necessary. In this work was analyzed the chemical composition of three bioprocts sold in the brazilian market used for domestic laundry, the presence of the main active agents among them like: enzymes, tensioactives and others, and the interaction these additives during the formulation process that could promove the respective differences and characteristics that make these products competitive.

Conselho Nacional de Desenvolvimento Científico e Tecnológico
As refinarias de petróleo, assim como outros processos industriais em grande escala, são fontes potenciais de poluição ambiental. Os acidentes ocorridos com derramamento de petróleo e seus derivados no Brasil, no período de 1975 a 2012, somam milhões de litros de poluentes que promoveram a contaminação de solos, rios e mar. Os processos fisíco-químicos tais como, a centrifugação, ultrafiltração e flotação por ar dissolvido (FAD), podem ser eficazes quando usados para separar óleos emulsionados. Nesse sentido, o processo de FAD continua sendo amplamente utilizado nas indústrias, tanto para águas de abastecimento como para águas residuárias. A FAD pode ser considerada como uma tecnologia limpa, uma vez que utiliza pequenas quantidades de coagulantes e ar para promover a separação. A utilização de coletores/coagulantes é essencial para melhorar a eficiência do processo, tendo em vista suas características específicas que facilitam a adesão das partículas e, consequentemente, a separação dos poluentes. Por outro lado, esses coletores químicos são tóxicos, fator que representa um agravante no sentido da geração de outros poluentes ambientais. Assim, os surfactantes microbianos ou biossurfactantes, biomoléculas anfipáticas produzidas por bactérias e leveduras, em detrimento dos coagulantes sintéticos, apresentam-se como uma tecnologia sustentável e promissora no aumento de eficiência da flotação. Essas biomoéculas, além de serem muito eficientes, são biodegradáveis e atóxicas, motivando as pesquisas no sentido de produzir e utilizar cada vez mais esses agentes tensoativos. Dessa forma, o presente trabalho foi desenvolvido na busca de uma estratégia para comparar as eficiências de separação água/derivado de petróleo por FAD, em escala piloto, com e sem a adição de um biossurfactante. De acordo com os resultados obtidos, o biossurfactante produzido por Candida sphaerica cultivada em residuos industriais foi considerado adequado como coletor do processo de separação. A utilização da biomolécula elevou a eficiência do processo de FAD de 80,0% para 98,0%, proporcionando a determinação das melhores condições operacionais. Dessa forma, concluiu-se que o uso de biossurfactantes como auxiliares na flotação constitui uma alternativa promissora na mitigação da poluição provocada pelo derramamento de petróleo e derivados em ambientes marinhos.
Oil refineries, as well as other large-scale industrial processes, are potential sources of environmental pollution. Accidents involving spills of oil and oil products in Brazil, in the period 1975-2012, add infective million liters of soil, rivers and sea. In this sense, the process of dissolved air flotation (DAF) is still widely used in industry, both for water supply and for wastewater. The physico-chemical processes such as centrifugation, ultrafiltration and dissolved air flotation (DAF), can be effective when used to separate emulsified oils. The effluent from the oily water type cause many environmental problems, particularly in thermal power plants (TPPs). Thus the aim of the study was to propose the separation water/oil by FAD in pilot scale and to compare the efficiency of the pilot prototype of FAD with and without addition of biosurfactant separation of oily waste waters. According the results, the biosurfactant produced by Candida sphaerica was selected, this being cultivated in using low cost industrial waste. Use of this bioproduct increased the efficiency of the flotation 80.0% to 98.0 %, to provide better determination of the operating conditions. Thus, it is suggested that the use of biosurfactants as auxiliary flotation is a promising alternative for the mitigation of pollution caused by the accumulation of synthetic surfactants in the environment.

Spider silk is renowned for its extraordinary mechanical properties, having a balance of high tensile strength and extensibility. To date, the majority of studies have focused on the production of dragline silks from synthetic spider silk gene products. Here we report the first mechanical analysis of synthetic egg case silk fibers spun from the Latrodectus hesperus tubuliform silk proteins, TuSp1 and ECP-2. We provide evidence that recombinant ECP-2 proteins can be spun into fibers that display mechanical properties similar to other synthetic spider silks. We also demonstrate that silks spun from recombinant thioredoxin-TuSp 1 fusion proteins that contain the conserved C-terminal domain exhibit increased extensibility and toughness when compared to the identical fibers spun from fusion proteins lacking the C-terminus. Mechanical analyses reveal that the properties of synthetic tubuliform silks can be modulated by altering the post-spin draw ratios of the fibers . Fibers subject to increased draw ratios showed elevated tensile strength and decreased extensibility, but maintained constant toughness. Wide-angle X-ray diffraction studies indicate that post-drawn fibers containing the Cterminal domain of TuSp 1 have more amorphous content when compared to fibers lacking the C-terminus. Taken together, these studies demonstrate that recombinant tubuliform spidroins that contain the conserved C-terminal domain with embedded protein tags can be effectively spun into fibers, resulting in similar tensile strength but increased extensibility relative to non-tagged recombinant dragline silk proteins spun from equivalently sized proteins.

O sequenciamento genômico da L. interrogans sorovar Copenhageni e ferramentas de bioinformática nos permitiram selecionar 15 genes que codificam proteínas hipotéticas conservadas preditas de superfície. A conservação foi confirmada por PCR em seis dos sorovares mais predominantes de L. interrogans. As proteínas recombinantes foram clonadas em vetor de expressão de E. coli em fusão com seis resíduos de histidina, que permite a purificação por cromatografia de afinidade a metal. Seis proteínas apresentaram reatividade com anticorpos presentes em soros de pacientes com leptospirose. Através de um ensaio de adesão por ELISA, identificamos uma nova adesina de leptospira, Lsa21, que interage fortemente com laminina, colágeno IV e fibronectina plasmática. Usando a metodologia de Western blotting, identificamos mais nove possíveis adesinas. Nossos ensaios de desafio demonstraram que as proteínas rLIC12730 conferiu proteção contra infecção letal de L. interrogans em hamsters. Nossos dados sugerem que seja um promissor candidato na prevenção da leptospirose.
The whole-genome sequences of L. interrogans serovar Copenhageni and the bioinformatic tools allow us to choose fifteen genes encoding for conserved hypothetical proteins predicted to be exported to the membrane. The chosen genes were amplified by PCR from six predominant pathogenic serovars, the DNA cloned in an E. coli vector, the recombinant proteins expressed in fusion with 6xHis-tag at N-terminus and purified by metal affinity chromatography. Six proteins were recognized by antibodies present in sera from human patients diagnosed with leptospirosis. By ELISA-attachment assay, we have identified a novel adhesion, named Lsa21, that binds strongly to laminin, collagen IV, and plasma fibronectin. By western blotting assay, we have further identified nine novel probable adhesions. The immunization/challenge assays showed that the recombinant protein rLIC12730 afforded protection against lethal leptospiral inoculation in hamsters. Our data suggest that it is a promising candidate for prevention of leptospirosis.

Uma característica associada à capacidade de Pseudomonas aeruginosa sobreviver e disseminar-se frente a situações adversas encontradas no ambiente e no organismo de hospedeiros é a regulação de genes de resposta a condições de estresse celular, que incluem o evento de choque térmico. A exposição do microrganismo a um ambiente de alta temperatura resulta na indução da síntese de proteínas específicas, representadas por chaperonas e proteases, que conferem um aumento da viabilidade celular microbiana em condições consideradas letais. Presume- se que o gene PA 0657 de P. aeruginosa O1 possa estar associado à indução ou supressão do processo transcricional de genes envolvidos na resposta ao choque térmico. Neste contexto, o objetivo deste trabalho foi caracterizar a função do gene PA0657 de P. aeruginosa O1. Para isso, análises bioinformáticas foram realizadas e o gene foi clonado e expresso em sistema bacteriano, produzindo uma proteína recombinante que foi purificada e caracterizada enzimaticamente. Além disso, uma linhagem de P. aeruginosa O1 com o gene PA0657 rompido por recombinação homóloga foi construída, sendo submetida, juntamente com a linhagem selvagem, a uma condição de estresse térmico, permitindo que a expressão de diversos genes associados ao evento de choque térmico pudessem ser avaliadas por qRT-PCR. Os resultados mostraram que a proteína recombinante PA0657 foi capaz de degradar adenosina trifosfato (ATP), dependente do íon Zn2+. Foi possível verificar também que a linhagem rompida perdeu a capacidade de produzir o pigmento piocianina quando crescida em meio cetrimida e não apresentou seu fenótipo mucóide. Em análise in silico observou-se que a região promotora do gene PA0657 é dependente de σ32 e a análise de expressão gênica evidenciou uma diminuição de expressão do gene rpoH na linhagem selvagem de PAO1 após choque térmico, sendo este gene significativamente expresso na linhagem rompida. Observou-se também um acentuado aumento na expressão do gene algU, nestas mesmas condições, na linhagem selvagem PAO1, com ausência de expressão na linhagem rompida. É possível concluir, dessa forma, que o gene PA0657 exerce participação importante no processo de regulação de resposta ao choque térmico e está relacionado com a conversão do fenótipo mucóide.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES
A feature associated with the ability of Pseudomonas aeruginosa survive and dissemination in adverse conditions found in the environment and in hosts‘ organisms is a specific genes regulation of stress response, including heat shock event. The exposure of microorganisms to a high temperature environment results in the induction of synthesis os specific proteins, represent by chaperones and proteases, conferring an increase og the microbial cell viability under conditions considered lethal. . It is presumed that the PA0657 gene of P. aeruginosa O1 can be related to the induction or suppression of transcriptional process of genes that are involved in a response to heat shock. In this context, the aim of this work was to characterize the function of the PA0657 gene of P. aeruginosa O1. In this way, bioinformatic analyzes were performed and the gene was cloned and expressed in bacterial system, producing recombinant protein which was purified and enzymatically characterized. Moreover, the PA0657 gene of P. aeruginosa O1 strain was disrupted by homologous recombination. The wild type strain and the disrupted strain were submitted to a thermal stress and the expression of various genes associated with heat shock event could be evaluated by qRT -PCR. The results showed that the PA0657 recombinant protein was capable of degrading adenosine triphosphate (ATP) of Zn2+ dependent manner. It was also verified that the ruptured strain lost its ability to produce pyocyanin pigment when grown on cetrimide means and its mucoid phenotype. It was possible to find in computational analysis that the promoter region of the PA0657 gene is dependent on σ32. The gene expression analysis showed a decrease in expression of the rpoH gene in the wild type strain after heat shock, this gene is significantly expressed in the disrupted strain. A significant increase in expression of the algU gene was observed, on the wild type strain with absence of expression in the disrupted strain. Therefore, it was possible to conclude that the PA0657 gene cts in the regulatory process of thermal shock response and is related to the conversion of the mucoid phenotype.

Our increasing understanding of disease mechanisms coupled with technological advances has facilitated the generation of pharmaceutical proteins, which are able to address yet unmet medical needs. Diseases that were fatal in the past can now be treated with novel biological medications improving and prolonging life for many patients. Pharmaceutical protein production is, however, a complex undertaking, which is by no means problem-free. The demand for more complex proteins and the realization of the importance of post-translational modifications have led to an increasing use of mammalian cells for protein expression. Despite improvements in design and production, the costs required for the development of pharmaceutical proteins still are far greater than those for conventional, small molecule drugs. To render such treatments affordable for healthcare suppliers and assist in the implementation of precision medicine, further progress is needed. In five papers this thesis describes strategies and methods that can help to advance the development and manufacturing of pharmaceutical proteins. Two platforms for antibody engineering have been developed and evaluated, one of which allows for efficient screening of antibody libraries whilst the second enables the straightforward generation of bispecific antibodies. Moreover, a method for epitope mapping has been devised and applied to map the therapeutic antibody eculizumab’s epitope on its target protein. In a second step it was shown how this epitope information can be used to stratify patients and, thus, contribute to the realization of precision medicine. The fourth project focuses on the cell line development process during pharmaceutical protein production. A platform is described combining split-GFP and fluorescence-activated droplet sorting, which allows for the efficient selection of highly secreting cells from a heterogeneous cell pool. In an accompanying study, the split-GFP probe was improved to enable shorter assay times and increased sensitivity, desirable characteristics for high-throughput screening of cell pools. In summary, this thesis provides tools to improve design, development and production of future pharmaceutical proteins and as a result, it makes a contribution to the goal of implementing precision medicine through the generation of more cost-effective biopharmaceuticals for well-characterized patient groups.

QC 20170828

Orientador: Maria Helena Andrade Santana
Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica
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Resumo: Neste trabalho foi feito o estudo da preparação de microesferas de hialuronato de sódio pelo método de emulsificação e evaporação de solvente, utilizando temperatura como agente de retificação física. O assunto foi abordado com ênfase na influência das condições operacionais do processo nas propriedades físico-químicas das microesferas e na sua capacidade de incorporação de proteínas, visando atender os requisitos da administração nasal. Inicialmente, a albumina de soro bovino foi usada como proteína modelo e, na segunda etapa, a ovoalbumina foi incorporada nas melhores condições do processo. Para conferir maior resistência mecânica às partículas e prolongar o tempo de liberação da proteína encapsulada, foi utilizado um segundo método de preparação, também por emulsificação, porem com reticulação química feita pela ligação cruzada (crosslinking), com dihidrazida adípica (ADH) em meio aquosos. As microesferas foram caracterizadas pelo seu diâmetro médio e distribuição de tamanhos, morfololgia, cristalinidade, mucoadesividade, intumescimento, eficiência de encapsulação e perfil de liberação das proteínas encapsuladas, eficiência de encapsulação e perfil de liberação das proteínas encapsuladas. Para as partículas reticuladas com ADH, o grau de reticulação foi correlacionado com a sua capacidade de intumescimento e com a cinética de liberação da proteína. Esses efeitos foram caracterizados através do coeficiente de difusão da ovoalbumina nas partículas com diferentes graus de reticulação... Observação: O resumo, na íntegra, poderá ser visualizado no texto completo da tese digital
Abstract: This work describes the study of sodium hyaluronate microspheres preparation through the emulsification and solvent evaporation technique, using temperature as the physical crosslinking agent. The subject was analyzed with emphasis on the influence of the process operations conditions on the physical and chemical properties of the microspheres and on its protein encapsulation capacity, willing to attend the nasal administration requirements. Initially, bovine serum albumin (BSA) was used as model protein, and in the second step, ovoalbumin (OVA) was incorporated using the best process conditions. In order to improve the mechanical resistance of the particles and extend the release time of the encapsulated protein, a second preparation method, also based on an emulsification but involving a chemical crosslinking reaction using adipic dihidrazide (ADH) in an aqueous solution, was evaluated. The microspheres were characterized by the mean diameter and size distribution, morphology, cristallinity, mucoadhesiveness, swelling capacity, encapsulation efficiency and release profile of the encapsulated proteins. For the particles crosslinked with ADH, the degree of crosslinking was correlated to the swelling capacity and with the protein release kinetics. These effects were characterized by the diffusion coefficient of ovoalbumin from the particles with different crosslinking degrees. The results showed the feasubillity of the sodium hyaluronate microspheres production, its protein encapsulation capability and the flexibility to modulate its properties according to the process conditions... Note: The complete abstract is available with the full electronic digital thesis or dissertations
Mestrado
Desenvolvimento de Processos Biotecnologicos
Mestre em Engenharia Química

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior
Calotropis procera à uma planta laticÃfera, pertencente à famÃlia Apocynaceae. ProteÃnas de defesa foram descritas no lÃtex com atividade contra insetos fitÃfagos e fungos fitopatogÃnicos. A fraÃÃo proteica do lÃtex tambÃm apresenta atividades farmacolÃgicas, dentre tais efeito citotÃxico seletivo em cÃlulas carcinogÃnicas. A partir da fraÃÃo proteica efetiva sobre cÃlulas neoplÃsicas, o trabalho teve por meta central identificar proteÃna(s) citotÃxica(s) e proceder a sua caracterizaÃÃo bioquÃmica, biolÃgica e suas perspectivas biotecnolÃgicas. As proteÃnas solÃveis do lÃtex (PL) foram fracionadas em matriz de troca iÃnica e a fraÃÃo proteica detentora da citotoxicidade foi refracionada em outra matriz de troca iÃnica (Mono-Q) acoplada a sistema de mÃdia pressÃo. P4 foi identificado como a fraÃÃo citotÃxica, apresentando uma IC50 de 2,2, 1,2 e 2,9 Âg/mL para as linhagens celulares HCT-116, Ovcar-8 e SF-295, respectivamente. A anÃlise proteÃmica da fraÃÃo citotÃxica por eletroforese bidimensional permitiu identificar 15 spots, contendo proteÃnas Ãcidas (pI entre 4 e 6) e com massa molecular aparente de 30 kDa. Quando avaliados por espectrometria de massas todos esses spots foram identificados como quitinases e apresentaram massa intacta de 27,4 kDa. A amostra reagiu positivamente ao reagente de Schiff, sugerindo glicosilaÃÃes. O teor de carboidratos foi estimado em 12,8%. A sequÃncia amino terminal obtida (1QPVMNLEYPRYLNDINDYRDDNNYD28) revelou 50% de similaridade com quitinases de Solanum lycopersicum, Oryza sativa, Nicotiana tomentosiformes dentre outras. As enzimas apresentaram forte atividade quitinolÃtica, com pH Ãtimo variando entre 5-6 e temperatura Ãtima de 25 ÂC. A atividade quitinolÃtica foi reduzida quando tratada com concentraÃÃes crescentes de DTT (3, 10 e 30 mM) o que sugere a presenÃa de pontes dissulfeto estabilizadoras da enzima. AnÃlises por dicroÃsmo circular indicam a presenÃa majoritÃria de alfa-hÃlices na estrutura e que as isoformas se mostraram pouco resistentes a variaÃÃes de temperatura e pH. Imagens de alta resoluÃÃo geradas por microscopia de forÃa atÃmica sugeriram homogeneidade na amostra e um arranjo hexamÃrico foi evidenciado. As quitinases nÃo inibiram o crescimento micelial dos fungos fitopatogÃnicos Fusarium oxysporum e Colletotrichum gloeosporioides, mas reduziram a germinaÃÃo de esporos de C. gloeosporioides. Em consonÃncia as quitinases nÃo induziram estresse oxidativo nos esporos, mas causaram leves alteraÃÃes na permeabilidade membranar dos esporos avaliados. As quitinases laticÃferas (0,1 % m/m) apresentaram forte efeito deletÃrio sobre o inseto fitÃfago Callosobruchus maculatus. Os efeitos produziram 57% de reduÃÃo na sobrevivÃncia larval, reduÃÃo do peso de larvas (7,8 mg  0,2 /4,0  0,8) e emergÃncia de insetos adultos (50%), alÃm de prolongar de 28 para 33 dias o tempo mÃdio de desenvolvimento de insetos adultos. As quitinases (2 mg/Kg, e.v.) apresentaram forte atividade anti-inflamatÃria, reduzindo em 95% a infiltraÃÃo de neutrÃfilos na cavidade peritoneal em ensaio de inflamaÃÃo induzido por carragenina em camundongos. Este efeito foi revertido por L-NAME e Aminoguanidina, dois inibidores da enzima Ãxido nÃtrico sintase, indicando o possÃvel envolvimento do Ãxido nÃtrico no efeito observado. Esta aÃÃo foi associada à reduÃÃo dos nÃveis das citocinas prÃ-inflamatÃrias TNF-α e IL-1 na cavidade peritoneal e do aumento dos nÃveis sÃricos das citocinas prÃ-inflamatÃrias TNF-α, IL-6 e IL-1. à concluÃdo que vÃrias isoformas de quitinases coexistem no lÃtex de C. procera. Estas proteÃnas atuam possivelmente na defesa contra insetos, mas tÃm pouca aÃÃo contra fungos. As quitinases laticÃferas foram identificadas como as proteÃnas citotÃxicas do lÃtex sobre cÃlulas neoplÃsicas e ainda foram capazes de modular os nÃveis de citocinas prÃ-inflamatÃrias e sÃntese de Ãxido nÃtrico em modelo de inflamaÃÃo aguda. As quitinases do lÃtex de C. procera representam interessantes molÃculas para prospecÃÃo biotecnolÃgica em defesa vegetal e farmacologia.
Calotropis procera is a latificer plant in the Apocynaceae family. Defensive proteins with activity against phytophagous insects and phytopathogenic fungi in latex have been described. Latexâs proteic fraction also performs pharmacological activities, such as selective cytotoxic effect in carcinogenic cells. From the proteic fraction effective against neoplastic cells, this work had the goal to identify and further characterize cytotoxic protein(s) biochemically, biologically, and evaluate their biotechnological prospects. Soluble proteins in latex (LP) have been fractioned in ion-exchange matrix, and the fraction capable of cytotoxicity was further fractioned in another ion-exchange matrix (Mono-Q) coupled to a medium-pressure system. P4 was identified as cytotoxic fraction, showing an IC50 of 2.2, 1.2 and 2.9 mg/mL for the cell lines HCT-116, Ovcar-8 and SF-295, respectively. Proteomic analysis of the cytotoxic fraction by two-dimensional electrophoresis allowed 15 spots to be identified, comprising acid proteins (pI among 4 and 6) with 30 kDa apparent molecular weight. All spots were identified as chitinases when evaluated by mass spectrometry, and showed intact mass of 27.4 kDa. The sample reacted positively to the Schiff reagent, suggesting glycosilations. The carbohydrate content was estimated at 12.8%. The amino-terminal sequence obtained (1QPVMNLEYPRYLNDINDYRDDNNYD28) revealed 50% similarity with Solanum lycopersicum, Oryza sativa and Nicotiana tomentosiformes chitinases, among others. The enzymes showed strong chitinolytic activity, with optimal pH varying between 5-6 and optimal temperature of 25 ÂC. The chitinolytic activity was diminished when treated with increasing concentrations of DTT (3, 10 and 30 mM), which suggests the presence of disulfide bonds stabilizing the enzyme. Circular dichroism analyses indicate a larger presence of alpha helices in the structure and that the isoforms has low resistance to pH and temperature variation. High-resolution images generated through atomic force microscopy suggested sample homogeneity and a hexameric configuration. The chitinases did not inhibit mycelial growth of phytopathogenic fungi Fusarium oxysporum and Colletotrichum gloeosporioides, however reduced the germination C. gloeosporioides spores. In consonancy the chitinases did not induce spore oxidative stress, but caused a slight change in membrane permeability of the evaluated spores. Laticifer chitinases (0.1% w/w) showed a strong deleterious effect on the phytophagous insect Callosobruchus maculatus. Effects produced a 57% survival reduction, larval weight reduction (7.8 mg  0.2 / 4.0  0.8), adult insets emergence reduction (50%), in addition to prolonging the mean maturation time from 28 to 33 days. The chitinases (2 mg/Kg, i.v.) showed a strong anti-inflammatory activity, reducing 95% of neutrophil infiltration into the peritoneal cavity in mouse in an inflammation induced by carrageenan assay. L-NAME and Aminoguanidine, two inhibitors of nitric oxide synthase, reversed this effect, possibly indicating involvement of nitric oxide in the effects observed. This action was associated to a reduction of pro-inflammatory cytokines TNF-α and IL-1 levels within the peritoneal cavity and increased serum levels of pro-inflammatory cytokines TNF-α, IL-6 and IL-1. The conclusion is reached that many isoforms of chitinases coexist in C. procera latex. These proteins act possibly in defense against insects, though low action against fungi is shown. Laticifer chitinases were identified as latex proteins cytotoxic on neoplastic cells and they have even been able to modulate pro-inflammatory cytokines levels and nitric oxide in an acute inflammation model. C. procera laticifer chitinases represent interesting molecules for biotechnology prospection in plant defense and pharmacology.

Cette thèse se place dans le cadre de l'étude in silico, c'est-à-dire assistée par ordinateur, des liens qui unissent la séquence d'une protéine à la (ou aux) structure(s) tri-dimensionnelle(s) qu'elle adopte. Le décryptage de ces liens présente de nombreuses applications dans divers domaines et constitue sans doute l'une des problématiques les plus fascinantes de la recherche en biologie moléculaire.

Le premier aspect de notre travail concerne le développement de potentiels statistiques dérivés de bases de données de protéines dont les structures sont connues. Ces potentiels présentent plusieurs avantages: ils peuvent être aisément adaptés à des représentations structurales simplifiées, et permettent de définir un nombre limité de fonctions énergétiques qui incarnent l'ensemble complexe d'interactions gouvernant la structure et la stabilité des protéines, et qui incluent également certaines contributions entropiques. Cependant, leur signification physique reste assez nébuleuse, car l'impact des diverses hypothèses nécessaires à leur dérivation est loin d'être clairement établi. Nous nous sommes attachés à l'étude de certaines limitations des ces potentiels: leur dépendance en la taille des protéines incluses dans la base de données, la non-additivité des termes de potentiels, et l'importance souvent négligée de l'environnement protéique spécifique ressenti par chaque résidu. Nous avons ainsi mis en évidence que l'influence de la taille des protéines de la base de données sur les potentiels de distance entre résidus est spécifique à chaque paire d'acides aminés, peut être relativement importante, et résulte essentiellement de la répartition inhomogène des résidus hydrophobes et hydrophiles entre le coeur et la surface des protéines. Ces résultats ont guidé la mise au point de fonctions correctives qui permettent de tenir compte de cette influence lors de la dérivation des potentiels. Par ailleurs, la définition d'une procédure générale de dérivation de potentiels et de termes de couplage a rendu possible la création d'une fonction énergétique qui tient compte simultanément de plusieurs descripteurs de séquence et de structure (la nature des résidus, leurs conformations, leurs accessibilités au solvant, ainsi que les distances qui les séparent dans l'espace et le long de la séquence). Cette fonction énergétique présente des performances nettement améliorées par rapport aux potentiels originaux, et par rapport à d'autres potentiels décrits dans la littérature.

Le deuxième aspect de notre travail concerne l'application de programmes basés sur des potentiels statistiques à l'étude de protéines qui adoptent des structures alternatives. La permutation de domaines est un phénomène qui affecte diverses protéines et qui implique la génération d'un oligomère suite à l'échange de fragments structuraux entre monomères identiques. Nos résultats suggèrent que la présence de "faiblesses structurales", c'est-à-dire de régions qui ne sont pas optimales vis-à-vis de la stabilité de la structure native ou qui présentent une préférence marquée pour une conformation non-native en absence d'interactions tertiaires, est intimement liée aux mécanismes de permutation. Nous avons également mis en évidence l'importance des interactions de type cation-{pi}, qui sont fréquemment observées dans certaines zones clés de la permutation. Finalement, nous avons sélectionné un ensemble de mutations susceptibles de modifier sensiblement la propension de diverses protéines à permuter. L'étude expérimentale de ces mutations devrait permettre de valider, ou de raffiner, les hypothèses que nous avons proposées quant au rôle joué par les faiblesses structurales et les interactions de type cation-{pi}. Nous avons également analysé une autre protéine soumise à d'importants réarrangements conformationnels: l'{alpha}1-antitrypsine. Dans le cas de cette protéine, les modifications structurales sont indispensables à l'exécution de l'activité biologique normale, mais peuvent sous certaines conditions mener à la formation de polymères insolubles et au développement de maladies. Afin de contribuer à une meilleure compréhension des mécanismes responsables de la polymérisation, nous avons cherché à concevoir rationnellement des protéines mutantes qui présentent une propension à polymériser contrôlée. Des tests expérimentaux ont été réalisés par le groupe australien du Professeur S.P. Bottomley, et ont permis de valider nos prédictions de manière assez remarquable.

The work presented in this thesis concerns the computational study of the relationships between the sequence of a protein and its three-dimensional structure(s). The unravelling of these relationships has many applications in different domains and is probably one of the most fascinating issues in molecular biology.

The first part of our work is devoted to the development of statistical potentials derived from databases of known protein structures. These potentials allow to define a limited number of energetic functions embodying the complex ensemble of interactions that rule protein folding and stability (including some entropic contributions), and can be easily adapted to simplified representations of protein structures. However, their physical meaning remains unclear since several hypotheses and approximations are necessary, whose impact is far from clearly understood. We studied some of the limitations of these potentials: their dependence on the size of the proteins included in the database, the non-additivity of the different potential terms, and the importance of the specific environment of each residue. Our results show that residue-based distance potentials are affected by the size of the database proteins, and that this effect can be quite strong, is residue-specific, and seems to result mostly from the inhomogeneous partition of hydrophobic and hydrophilic residues between the surface and the core of proteins. On the basis of these observations, we defined a set of corrective functions in order to take protein size into account while deriving the potentials. On the other hand, we developed a general procedure of derivation of potentials and coupling terms and consequently created an energetic function describing the correlations between several sequence and structure descriptors (the nature of each residue, the conformation of its main chain, its solvent accessibility, and the distances that separate it from other residues, in space and along the sequence). This energetic function presents a strongly improved predictive power, in comparison with the original potentials and with other potentials described in the literature.

The second part describes the application of different programs, based on statistical potentials, to the study of proteins that adopt alternative structures. Domain swapping involves the exchange of a structural element between identical proteins, and leads to the generation of an oligomeric unit. We showed that the presence of “structural weaknesses”, regions that are not optimal with respect to the folding mechanisms or to the stability of the native structure, seems to be intimately linked with the swapping mechanisms. In addition, cation-{pi} interactions were frequently detected in some key locations and might also play an important role. Finally, we designed a set of mutations that are likely to affect the swapping propensities of different proteins. The experimental study of these mutations should allow to validate, or refine, our hypotheses concerning the importance of structural weaknesses and cation-{pi} interactions. We also analysed another protein that undergoes large conformational changes: {alpha}1-antitrypsin. In this case, the structural modifications are necessary to the proper execution of the biological activity. However, under certain circumstances, they lead to the formation of insoluble polymers and the development of diseases. With the aim of reaching a better understanding of the mechanisms that are responsible for this polymerisation, we tried to design mutant proteins that display a controlled polymerisation propensity. An experimental study of these mutants was conducted by the group of Prof. S.P. Bottomley, and remarkably confirmed our predictions.

Doctorat en sciences appliquées
info:eu-repo/semantics/nonPublished

Dissertation (PhD)--University of Stellenbosch, 2007.
ENGLISH ABSTRACT: Plants have developed sophisticated means of combating plant diseases. The events that prepare the plant for, and follow plant-pathogenic interactions, are extremely complex and have been the topic of intensive investigation in recent years. These interactions involve a plethora of genes and proteins, and intricate regulation thereof; from the host and pathogen alike. Studying the contribution of single genes and their encoded proteins to the molecular dialogue between plant and pathogen has been a focus of plant molecular biologists. To this end, a gene encoding a polygalacturonase-inhibiting protein (PGIP) was recently cloned from Vitis vinifera. These proteins have the ability to inhibit fungal endopolygalacturonases (ePGs), enzymes which have been shown to be required for the full virulence of several fungi on their respective plant hosts. The activity of PGIP in inhibiting fungal macerating enzymes is particularly attractive for the improvement of disease tolerance of crop species. The VvPGIP-encoding gene was subsequently transferred to Nicotiana tabacum for high-level expression of VvPGIP. These transgenic plants were found to be less susceptible to infection by Botrytis cinerea in an initial detached leaf assay. Also, it was shown that ePG inhibition by protein extracts from these lines correlated to the observed decrease in susceptibility to B. cinerea. This study expands on previous findings by corroborating the antifungal nature of the introduced PGIP by whole-plant, timecourse infection assays. Six transgenic tobacco lines and an untransformed wildtype (WT) were infected and the lesions measured daily from day three to seven, and again at day 15. The transgenic lines exhibited smaller lesions sizes from three to seven days post-inoculation, although these differences only became statistically significant following seven days of incubation. At this point, four of the six lines exhibited significantly smaller lesions than the WT, with reductions in disease susceptibility ranging between 46 and 69% as compared to the WT. Two of the lines exhibited disease susceptibility comparable to the WT. In these resistant plant lines, a correlation could be drawn between Vvpgip1 expression, PGIP activity and ePG inhibition. These lines were therefore considered to be PGIP-specific resistant lines, and provided ideal resources to further study the possible in planta roles of PGIP in plant defense. The current hypothesis regarding the role(s) of PGIP in plant defense is twofold. Firstly, PGIPs have the ability to specifically and effectively inhibit fungal ePGs. This direct inhibition results in reduced fungal pathogenicity. Alternatively, unhindered action of these enzymes results in maceration of plant tissue and ultimately, tissue necrosis. Subsequently, it could be shown that, in vitro, the inhibition of ePGs prolongs the existence of oligogalacturonides, molecules with the ability to activate plant defense responses. Thus, PGIPs limit tissue damage by inhibition of ePG; this inhibition results in activation of plant defense responses aimed at limiting pathogen ingress. Several publications reported reduced susceptibility to Botrytis in transgenic plant lines overexpressing PGIP-encoding genes. However, none of these publications could expand on the current hypotheses regarding the possible in planta roles of PGIP in plant defense. In this study we used transgenic tobacco lines overexpressing Vvpgip1 as resources to study the in planta roles for PGIP. Transcriptomic and hormonal analyses were performed on these lines and a WT line, both before and following inoculation with Botrytis cinerea. Transcriptomic analysis was performed on uninfected as well as infected tobacco leaf material utilizing a Solanum tuberosum microarray. From the analysis with healthy, uninfected plant material, it became clear that genes involved in cell wall metabolism were differentially expressed between the transgenic lines and the WT. Under these conditions, it could be shown and confirmed that the gene encoding tobacco xyloglucan endotransglycosylase (XET/XTH) was downregulated in the transgenic lines. Additionally, genes involved in the lignin biosynthetic pathway were affected in the individual transgenic lines. Biochemical evidence corroborated the indication of increased lignin deposition in their cell walls. Additionally, phytohormone profiling revealed an increased indole-acetic acid content in the transgenic lines. These results show that constitutive levels of PGIP may affect cell wall metabolism in the Vvpgip1-transgenic lines which may have a positive impact on the observed reduced susceptibilities of these plants. An additional role for PGIP in the contribution to plant defenses is therefore proposed. PGIP may directly influence defense responses in the plant leading to the strengthening of cell walls. This might occur by virtue of its structural features or its integration in the cell wall. These reinforced cell walls are thus “primed” before pathogen ingress and contribute to the decrease in disease susceptibility observed in lines accumulating high levels of PGIP. Transcriptional and hormonal analyses, at the localized response, were performed on Botrytis-infected leaf tissue of the transgenic lines and a WT line. Several Botrytis responsive genes were found to be upregulated in both the WT and the transgenic lines. Although limited differential expression was observed between the two genotypes, the analyses identified a gene which was upregulated two-fold in the transgenic lines, as compared to WT. This was confirmed by quantitative Real-Time PCR. This gene is involved in the lipoxygenase pathway, specifically the 9-LOX branch, leading to the synthesis of the divinyl ether oxylipins colneleic and colnelenic acid, which show inhibitory effects on Botrytis spore germination. Phytohormone profiling revealed that the transgenic lines accumulated more of the defense-related hormone pool of jasmonates. These are formed via the 13-LOX pathway and have been shown to be important for the restriction of Botrytis growth at the site of infection. Collectively, the results from the infection analyses indicate that in these transgenic lines, both branches of the lipoxygenase pathway are differentially induced at the level of the localized response to Botrytis infection. Similarly, an increased induction of the synthesis of the defense-related hormone salicylic acid could be observed, although this hormone did not accumulate to significantly higher levels. These results are the first report of differential induction of a defense-related pathway in pgip-overexpressing lines and substantiate the proposal that following ePG inhibition by PGIP, signaling which activates plant defense responses, takes place. Taken together, these results significantly contribute to our understanding of the in planta role of PGIP in plant defense responses.
AFRIKAANSE OPSOMMING: Plante het deur evolusie gesofistikeerde meganismes teen die aanslag van plantsiektes ontwikkel. Die gebeure wat die plant voorberei, asook dié wat op plant-patogeen interaksies volg, is uiters kompleks en vorm die kern van verskeie navorsingstemas die afgelope paar jaar. Etlike plant- én patogeengene en proteïene is by hierdie interaksies betrokke en aan komplekse reguleringsprosesse onderworpe. Die bestudering van die bydrae van enkelgene en hul gekodeerde proteïene tot die molekulêre interaksie tussen ‘n plant en patogeen is ‘n sterk fokus van plant-molekulêre bioloë. Met hierdie doel as fokus, is ‘n geen wat vir ‘n poligalakturonaseinhiberende proteïen (PGIP) kodeer, van Vitis vinifera gekloneer. Hierdie proteïene beskik oor die vermoë om fungiese endopoligalakturonases (ePG's), ensieme wat benodig word vir die virulensie van verskeie fungi op hul gasheerplante, te inhibeer. Die inhibisie van ePG's deur PGIP en die gepaardgaande verminderde weefseldegradasie is ‘n baie belowende strategie vir die verbetering van verboude gewasse se patogeentoleransie. Die VvPGIPenkoderende geen is gevolglik na Nicotiana tabacum oorgedra vir hoëvlakuitdrukking van VvPGIP. Daar is gevind dat hierdie transgeniese plante minder vatbaar vir Botrytis cinerea-infeksies was in ‘n inisiële antifungiese toets wat gebruik gemaak het van blaarweefsel wat van die moederplant verwyder is. Daar is ook ‘n korrelasie gevind tussen B. cinerea-siekteweerstand en ePG-inhibisie deur proteïenekstrakte van die transgeniese populasie. Die huidige studie bou voort op en bevestig vorige bevindinge betreffende die antfungiese aard van die heteroloë PGIP in die heelplant en oor tyd. Ses transgeniese tabaklyne en 'n ongetransformeerde wilde-tipe (WT) is geïnfekteer en die lesies is vanaf dag drie tot sewe, en weer op dag 15, gemeet. Die transgeniese lyne het in die tydperk van drie tot sewe dae ná-inokulasie kleiner lesies as die WT getoon, alhoewel hierdie verskille slegs statisties beduidend geword het na sewe dae van inkubasie. Op daardie tydstip het vier van die ses lyne aansienlik kleiner lesies as die WT getoon, en verlagings in siektevatbaarheid het, in vergelyking met die WT, van 46% tot 69% gewissel. Twee van die lyne het siektevatbaarheid getoon wat vergelykbaar was met dié van die WT. In die siekteweerstandbiedende plantlyne was daar 'n verband tussen Vvpgip1-ekspressie, PGIP-aktiwiteit en ePG-inhibisie. Hierdie plantlyne is dus as PGIP-spesifieke siekteweerstandslyne beskou en dien dus as ideale eksperimentele bronne vir die ontleding van die moontlike in plantafunksies van PGIP in plantsiekteweerstandbiedendheid. Die huidige hipotese betreffende die funksie(s) van PGIP in plantsiekteweerstand is tweeledig. Eerstens het PGIP die vermoë om fungusePG's spesifiek en doeltreffend te inhibeer. Hierdie direkte inhibisie veroorsaak ‘n vermindering in patogenisiteit van die fungus op die gasheer. Indien ePG's egter hulle ensimatiese aksie onverstoord voortsit, sal weefseldegradasie en uiteindelik weefselnekrose die gevolg wees. Daar kon ook bewys word dat die in vitroinhibisie van ePG's deur PGIP die leeftyd van oligogalakturoniede, molekules wat die vermoë het om die plantweerstandsrespons aan te skakel, kan verleng. PGIP het dus nie net die vermoë om ePG's, en dus weefseldegradasie, te inhibeer nie; maar hierdie inhibisie lei ook daartoe dat plantweerstandsresponse aangeskakel word met die oog op die vermindering van patogeenindringing. Verskeie publikasies het reeds gerapporteer oor verminderde Botrytisvatbaarheid in PGIP transgeniese plantlyne. Geeneen van hierdie publikasies kon egter uitbrei op die huidige hipotese aangaande die moontlike in planta-funksie van PGIP in plantsiekteweerstand nie. In hierdie studie is transgeniese tabaklyne wat PGIP ooruitgedruk gebruik om hierdie moontlike in planta-funksies vir PGIP uit te klaar. Transkriptoom- en hormonale analises is op hierdie plantlyne en ‘n WT voor en ná inokulasie met die nekrotroof Botrytis cinerea uitgevoer,. Transkriptoomanalises is uitgevoer op ongeïnfekteerde, sowel as geïnfekteerde tabakblaarmateriaal deur gebruik te maak van ‘n Solanum tuberosum-mikroraster. Die analises met gesonde, ongeïnfekteerde plantmateriaal het daarop gewys dat gene betrokke by selwandmetabolisme tussen die transgeniese lyne en die WT verskillend uitgedruk was. Dit kon bewys word dat, sonder infeksiedruk, die geen wat xiloglukaan-endotransglikosilase (XET) kodeer, in die transgeniese lyne afgereguleer was. Gene wat betrokke is in die lignien-biosintetiese pad was ook in die individuele transgeniese lyne beïnvloed. Biochemiese toetse het ook die aanduiding van verhoogde ligniendeposisie in die transgeniese lyne se selwande bevestig. Addisionele fitohormoonprofiele het getoon dat hierdie lyne ook beskik oor verhoogde vlakke van indoolasynsuur (IAA). Hierdie resultate wys daarop dat konstitutiewe vlakke van PGIP selwandmetabolisme in die Vvpgip1-transgeniese lyne moontlik kan beïnvloed, wat plantsiekteweerstand in dié lyne positief kan beïnvloed. Dit wil dus voorkom asof PGIP 'n bykomende funksie in plantsiekteweerstand het. Plantweerstandsreponse kan direk deur PGIP beïnvloed word, wat tot die versterking van plantselwande kan lei; dit kan geskied by wyse van die strukturele eienskappe van die proteïen of die integrasie daarvan in die selwand. Hierdie selwande is dus “voorberei” alvorens patogeenindringing plaasvind en kon bydra tot die verminderde siektevatbaarheid wat waargeneem is in lyne wat hoë vlakke van PGIP akkumuleer. Transkriptoom- en hormonale analises is ook uitgevoer op Botrytisgeïnfekteerde blaarmateriaal van beide die transgeniese lyne en ‘n WT. Verskeie Botrytis-responsgene is in beide die transgeniese lyne en die WT opgereguleer. Differensïele geenekspressie tussen die twee genotipes was taamlik beperk, maar in die analises kon ‘n geen geïdentifiseer word wat tweevoudig in die transgeniese lyne opgereguleer was in vergelyking met die WT. Hierdie resultaat is ook bevestig met behulp van die “Real-Time” Polimerasekettingreaksie (PKR). Hierdie geen is betrokke in die lipoksigenase (LOX) -pad (spesifiek die 9-LOXarm), wat tot die sintese van die diviniel-eter oksilipiene “colneleic-” en “colnelenic”-suur lei. Daar is al bewys dat hierdie twee verbindings Botrytisspoorontkieming kan inhibeer. Fitohormoonprofiele van die geïnfekteerde plante het gewys dat die transgeniese lyne verhoogde vlakke van die poel van jasmonate wat plantsiekteweerstands-hormone is, ná inokulasie akkumuleer. Hierdie hormone word in die 13-LOX-arm van die lipoksigenase pad gevorm en is belangrik vir die beperking van Botrytis by die infeksiesetel. Die resultate van die analises wat op Botrytis-infeksie volg, dui daarop dat beide arms van die lipoksigenasepad in die transgeniese lyne verskillend by die lokale respons geïnduseer word. ‘n Verhoogde induksie van ‘n ander plantsiekteweerstandshormoon, salisielsuur, kon ook opgemerk word, alhoewel die totaal geakkumuleerde vlakke nie beduidend hoër was as dié van die WT nie. Hierdie resultate is die eerste wat onderskeidende induksie van ‘n siekteweerstandspad in enige van die pgip-ooruitgedrukte plantlyne rapporteer. Daarmee ondersteun dit ook die hipotese dat, seintransduksie wat plantweerstandsresponse aanskakel, ná inhibisie van ePG deur PGIP plaasvind. Die resultate wat met hierdie studie verkry is, dra dus beduidend by tot die huidige kennis van die in planta-funksie van PGIP in plantsiekteweerstandsresponse.