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Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: During the last two and a half decades a large body of research has accumulated indicating the presence of various natural and synthetic chemical compounds within the environment capable of inducing hormone-like responses in humans and animals. Such compounds, termed endocrine disruptors, have been implicated in a variety of developmental, reproductive and physiological abnormalities which have been shown to converge on the endocrine system. Given that endocrine disrupters are comprised of a diverse group of molecules with dissimilar chemical structures, general screening techniques are not feasible for effective environmental monitoring. A primary method of action by which these exogenous molecules affect the homeostatic regulation of the endocrine system is believed to be via the modulation of gene transcription. It is now well established that many endocrine disrupting compounds act upon a principal group of transcription factors, the nuclear receptors, by chance interaction with the ligand binding domains of these proteins. With a view to ultimately design a portable kit for the detection of endocrine disrupting compounds in water based on the bio-specific immobilisation of nuclear receptor ligand binding domains to a stationary membrane matrix, this study specifically describes: 1. The effects on recombinant protein expression by the addition of small molecules to the cultivation media of bacteria. 2. The optimisation of conditions for the lysis of bacterial cells to increase the solubility of heterologously expressed proteins. 3. The purification of recombinant proteins from bacterial cell lysates by means of a two-step chromatographic methodology. 4. The cloning of the genes for the human androgen and estrogen receptors’ ligand binding domains into baculovirus transfer plasmids. 5. Transfer of genetic material from the created baculovirus transfer plasmids to a linearised baculovirus genome for the generation of recombinant viruses. 6. The cultivation, and baculoviral infection, of Spodoptera frugiperda and Trichoplusia ni cell lines. 7. Expression and purification of N-terminal hexahistidine-tagged human nuclear receptor LBDs from insect cell lysates by means of immobilised metal affinity chromatography. / AFRIKAANSE OPSOMMING: Die teenwoordigheid van natuurlike en sintetiese chemiese middels wat oor die vermoë beskik om die aksies van hormone in die mens en dier na te boots het toenemend aftrek gekry in navorsing gedurende die laaste twee en ’n halwe dekades. 'n Verskeidenheid van ontwikkelings-, reproduktiewe- en fisiologiese abnormaliteite ontstaan as gevolg van die aksies van hierdie molekule, genaamd endokriene-ontwrigters, op die natuurlike funksionering van die endokriene-sisteem. Gegewe dat die groep chemiese middels waaruit endokriene-ontwrigters bestaan van diverse oorsprong afkomstig is lei dit daartoe dat algemene analitiese tegnieke nie in alle gevalle geskik is vir effektiewe omgewingsmonitering is nie. Die modulasie van geentranskripsie is een van die metodes wat voorgestel word as ’n metode waarop hierdie eksogene molekule die homeostatiese regulering deur die endokriene-sisteem omverwerp. ’n Algemene metode waarop vele endokrien-ontwrigtende stowwe geentranskripsie beïnvloed, is deur interaksie met die hormoon-bindende gedeeltes van ’n belangrike groep transkripsiefaktore, die nukluêre reseptore. Hierdie studie, met die uiteindelike ontwikkeling van ’n draagbare toetsstelsel vir die opsporing van endokrien-ontwrigtende-stowwe in water, gebasseer op die bio-spesifieke immobilisering van nukluêre reseptor ligand bindingsdomeins op ’n stasionêre membraanmatriks, het ten doel om die volgende te beskryf: 1. Die effek wat die byvoeging van klein molekule tot die groeimedium van bakteriëe het op die uitdrukking van rekombinante proteïene. 2. Die optimisering van bakteriese sel-lisering in terme van verhoging in die oplosbaarheid van heteroloë proteïene. 3. Die suiwering van rekombinante proteïen vanuit bakteriese sellisate deur middel van ’n twee-stap chromatografiese sisteem. 4. Die klonering van die gene vir die menslike androgeen en estrogeen reseptore se ligand bindingsdomeine in bakulovirus oordragplasmiede. 5. Die oordrag van genetiese materiaal vanaf hierdie bakulovirus oordragplasmiede na ’n gelineariseerde bakulovirus genoom deur middel van homoloë rekombinasie vir die produksie van rekombinante virusse. 6. Die groei en infeksie van Spodoptera frugiperda en Trichoplusia ni sellyne wat lei tot die uitdrukking van menssoortgelyke nukluêre reseptor ligandbindingsdomains. 7. Suiwering van N-terminaal heksahistidien-etiket-gekoppelde menslike nukluêre reseptor ligandbindingsdomeins vanuit inseksellisate deur middel van geïmmobiliseerde metaal affiniteitschromatografie.

The keratinase gene (kerA) of Bacillus licheniformis ATCC®53757 was PCR amplified and subsequently cloned into Bacillus megaterium expression vector; pHIS1525.SPlipA and transformed in Bacillus megaterium ATCC®14945. The kerA gene carrying the recombinant plasmid pKERHIS1525.SPlipA was expressed in Bacillus megaterium under xylose inducible promoter, purified using Ni-NTA affinity column chromatography and consequently produced an extracellular keratinase activity of 29 U ml-1 after 18 h of incubation. The recombinant strain was further examined for feather degradation of intact chicken feathers. The chopped chicken feathers were partially degraded by the recombinant strain after 3days and the total macroscopic digestion was ultimately observed after seven days resulting in a yellowish peptide rich fermentation broth.

The coat protein of satellite panicum mosaic virus (SPMV) was used to stabilize viral vector gene inserts in planta. A Potato virus X (PVX) vector carrying the SPMV capsid protein (CP) gene was successfully stabilized through three serial passages in Nicotiana benthamiana from the upper non-inoculated leaves following rub inoculation. The presence of SPMV CP expression from the PVX vector was confirmed by necrotic lesions that occur only when SPMV CP is present and by western blot and reversetranscription PCR analyses. In addition, PVX-SPCP was co-inoculated onto N. benthamiana with a Tomato bushy stunt virus vector carrying a green fluorescent protein gene, which normally does not yield GFP expression in upper tissue due to loss of the insert. However, upon co-inoculation with PVX-SPCP, upper non-inoculated leaves exhibited GFP accumulation based on green fluorescence by UV illumination at 488 nm and western blot analysis. GFP expression was more abundant in upper non-inoculated N. benthamiana leaves as well as systemic tissues when the co-inoculation experiments were performed at 20°C compared to 25°C. These results suggest that SPMV CP is a viable molecular tool for stabilizing viral vector gene inserts in planta.

In this study, the expression of HA, a key immunogenic protein of influenza viruses, in insect cells was compared using three baculovirus expression strategies: protein over-expression, surface (GP64) display, and capsid (VP39) display. Further, a recombinant virus expressing NA, another immunogenic influenza virus protein, was generated and fused to an HA epitope-tag. Western immunoblot using various antibodies, including those against HA, demonstrated the expression of HA and NA for all recombinant viruses. HA showed stronger expression when fused to the C-terminus of VP39 than the N-terminus, but unlike other expression methods, there was no observable cleavage of HA in VP39-displayed viruses. Cells infected with only over-expressed and surfaced-displayed HA were biologically active, and capable of hemadsorption and hemagglutination of chicken red blood cells. These results suggest that GP64 display or over-expression are the most efficacious modes of HA-expression for use as antigen to detect anti-HA antibodies in poultry. / NSERC, OGS, OMAFRA, CPRC

Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages over other expression systems such as lower production costs, rapid scale up of production, similar post-translational modification as animals and the low likelihood of contamination with animal pathogens, microbial toxins or oncogenic sequences. However, improving recombinant protein yield remains one of the greatest challenges to molecular farming. In-Plant Activation (InPAct) is a newly developed technology that offers activatable and high-level expression of heterologous proteins in plants. InPAct vectors contain the geminivirus cis elements essential for rolling circle replication (RCR) and are arranged such that the gene of interest is only expressed in the presence of the cognate viral replication-associated protein (Rep). The expression of Rep in planta may be controlled by a tissue-specific, developmentally regulated or chemically inducible promoter such that heterologous protein accumulation can be spatially and temporally controlled. One of the challenges for the successful exploitation of InPAct technology is the control of Rep expression as even very low levels of this protein can reduce transformation efficiency, cause abnormal phenotypes and premature activation of the InPAct vector in regenerated plants. Tight regulation over transgene expression is also essential if expressing cytotoxic products. Unfortunately, many tissue-specific and inducible promoters are unsuitable for controlling expression of Rep due to low basal activity in the absence of inducer or in tissues other than the target tissue. This PhD aimed to control Rep activity through the production of single chain variable fragments (scFvs) specific to the motif III of Tobacco yellow dwarf virus (TbYDV) Rep. Due to the important role played by the conserved motif III in the RCR, it was postulated that such scFvs can be used to neutralise the activity of the low amount of Rep expressed from a “leaky” inducible promoter, thus preventing activation of the TbYDV-based InPAct vector until intentional induction. Such scFvs could also offer the potential to confer partial or complete resistance to TbYDV, and possibly heterologous viruses as motif III is conserved between geminiviruses. Studies were first undertaken to determine the levels of TbYDV Rep and TbYDV replication-associated protein A (RepA) required for optimal transgene expression from a TbYDV-based InPAct vector. Transient assays in a non-regenerable Nicotiana tabacum (NT-1) cell line were undertaken using a TbYDV-based InPAct vector containing the uidA reporter gene (encoding GUS) in combination with TbYDV Rep and RepA under the control of promoters with high (CaMV 35S) or low (Banana bunchy top virus DNA-R, BT1) activity. The replication enhancer protein of Tomato leaf curl begomovirus (ToLCV), REn, was also used in some co-bombardment experiments to examine whether RepA could be substituted by a replication enhancer from another geminivirus genus. GUS expression was observed both quantitatively and qualitatively by fluorometric and histochemical assays, respectively. GUS expression from the TbYDV-based InPAct vector was found to be greater when Rep was expected to be expressed at low levels (BT1 promoter) rather than high levels (35S promoter). GUS expression was further enhanced when Rep and RepA were co-bombarded with a low ratio of Rep to RepA. Substituting TbYDV RepA with ToLCV REn also enhanced GUS expression but more importantly highest GUS expression was observed when cells were co-transformed with expression vectors directing low levels of Rep and high levels of RepA irrespective of the level of REn. In this case, GUS expression was approximately 74-fold higher than that from a non-replicating vector. The use of different terminators, namely CaMV 35S and Nos terminators, in InPAct vectors was found to influence GUS expression. In the presence of Rep, GUS expression was greater using pInPActGUS-Nos rather than pInPActGUS-35S. The only instance of GUS expression being greater from vectors containing the 35S terminator was when comparing expression from cells transformed with Rep, RepA and REnexpressing vectors and either non-replicating vectors, p35SGS-Nos or p35SGS-35S. This difference was most likely caused by an interaction of viral replication proteins with each other and the terminators. These results indicated that (i) the level of replication associated proteins is critical to high transgene expression, (ii) the choice of terminator within the InPAct vector may affect expression levels and (iii) very low levels of Rep can activate InPAct vectors hence controlling its activity is critical. Prior to generating recombinant scFvs, a recombinant TbYDV Rep was produced in E. coli to act as a control to enable the screening for Rep-specific antibodies. A bacterial expression vector was constructed to express recombinant TbYDV Rep with an Nterminal His-tag (N-His-Rep). Despite investigating several purification techniques including Ni-NTA, anion exchange, hydrophobic interaction and size exclusion chromatography, N-His-Rep could only be partially purified using a Ni-NTA column under native conditions. Although it was not certain that this recombinant N-His-Rep had the same conformation as the native TbYDV Rep and was functional, results from an electromobility shift assay (EMSA) showed that N-His-Rep was able to interact with the TbYDV LIR and was, therefore, possibly functional. Two hybridoma cell lines from mice, immunised with a synthetic peptide containing the TbYDV Rep motif III amino acid sequence, were generated by GenScript (USA). Monoclonal antibodies secreted by the two hybridoma cell lines were first screened against denatured N-His-Rep in Western analysis. After demonstrating their ability to bind N-His-Rep, two scFvs (scFv1 and scFv2) were generated using a PCR-based approach. Whereas the variable heavy chain (VH) from both cell lines could be amplified, only the variable light chain (VL) from cell line 2 was amplified. As a result, scFv1 contained VH and VL from cell line 1, whereas scFv2 contained VH from cell line 2 and VL from cell line 1. Both scFvs were first expressed in E. coli in order to evaluate their affinity to the recombinant TbYDV N-His-Rep. The preliminary results demonstrated that both scFvs were able to bind to the denatured N-His-Rep. However, EMSAs revealed that only scFv2 was able to bind to native N-His-Rep and prevent it from interacting with the TbYDV LIR. Each scFv was cloned into plant expression vectors and co-bombarded into NT-1 cells with the TbYDV-based InPAct GUS expression vector and pBT1-Rep to examine whether the scFvs could prevent Rep from mediating RCR. Although it was expected that the addition of the scFvs would result in decreased GUS expression, GUS expression was found to slightly increase. This increase was even more pronounced when the scFvs were targeted to the cell nucleus by the inclusion of the Simian virus 40 large T antigen (SV40) nuclear localisation signal (NLS). It was postulated that the scFvs were binding to a proportion of Rep, leaving a small amount available to mediate RCR. The outcomes of this project provide evidence that very high levels of recombinant protein can theoretically be expressed using InPAct vectors with judicious selection and control of viral replication proteins. However, the question of whether the scFvs generated in this project have sufficient affinity for TbYDV Rep to prevent its activity in a stably transformed plant remains unknown. It may be that other scFvs with different combinations of VH and VL may have greater affinity for TbYDV Rep. Such scFvs, when expressed at high levels in planta, might also confer resistance to TbYDV and possibly heterologous geminiviruses.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第13305号 / 論農博第2880号 / 新制||農||1074(附属図書館) / 学位論文||R2||N5242(農学部図書室) / 富山大学大学院理工学研究科生命環境科学専攻 / (主査)教授 小川 順, 教授 阪井 康能, 教授 栗原 達夫 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-04-04T18:15:33Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) 2010-Dissertação-MarceloCordeiro.pdf: 2495604 bytes, checksum: 2d51566d7f95818c5bd7b1860032afdc (MD5) / Made available in DSpace on 2017-04-04T18:15:33Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) 2010-Dissertação-MarceloCordeiro.pdf: 2495604 bytes, checksum: 2d51566d7f95818c5bd7b1860032afdc (MD5) Previous issue date: 2010-09-27 / Os papilomavírus são um grupo de pequenos vírus DNA dupla fita caracterizado por induzir a formação de lesões que, normalmente, são benignas e podem regredir naturalmente, mas também apresentam opotencial para se tornarem tumores malignos. O papilomavírus humano (HPV) está fortemente relacionado às doenças sexualmente transmissíveis (DST) e é uma das principais causas de câncer cervical. O papilomavírus bovino (BPV), por sua vez, representa um grave problema econômico em termos de pecuária. Em bovinos, são mais comuns as papilomatosescutânease mucosas nas regiões genital e orofaríngea. Existem bem caracterizados seis tipos diferentes de BPV (BPV 1 ao 6) e, recentemente, quatro novos tipos (BPVs 7 ao 10) foram seqüenciados. No Nordeste, especialmente no estado de Pernambuco (Zona da Mata), a incidência da papilomatose bovina é muito alta, causando grandes perdas econômicas para os criadores. Não há tratamento com eficácia comprovada. Proteção contra a infecção é conferida por anticorpos neutralizantes dirigidos contra osepítopos conformacionais de proteínas estruturais L1. Esses anticorpos podem ser eficientemente induzidos pela imunização com virus-like particles(VLP) que se formam espontaneamente, após a expressão de L1 em sistemas heterólogos. Nos últimos anos, a levedura metilotrófica Pichia pastoris emergiu como um sistema eficaz e barato para produzir altos níveis deproteínarecombinante. O foco deste trabalho foi construir e avaliar dois plasmídeos (pPICZAαL1B2 e pPICZAL1B2), como vetores para expressão do geneL1BPV-2 em células de P. pastoris. Um deles (pPICZAαL1B2) insere na proteína recombinante um sinal de secreção (α-mating). Assim, esperou-se comparar a eficiência da expressão heteróloga através das viasintra e extracelulares. O gene L1 foi amplificado por PCR do genoma completo BPV-2, foi clonado em vetor pGEM-T(Promega ®) e, posteriormente, foi subclonado nos vetores de expressão pPICZA e pPICZAα (Invitrogen ®). PCR e análise de restrição indicarama inserção correta do gene L1 em ambos os vetores, bem como o seqüenciamento. Por eletroporação, P. pastoris (cepa de levedura X-33) foi transformada com a construção pPICZAL1B2 ou pPICZAαL1B2, cuja integração no genoma de levedura pode ser identificada por PCR da colônia. As leveduras transformadas foram selecionadas para experimentos de cultura com indução com metanol. A expressão de L1 foi indicada por RT-PCR e análise de proteínas. A proteína recombinante L1foi detectada em células de levedura, que sofreram tratamento com solução de lise (via intracelular) e em meio de cultura submetido a precipitação com acetona (via extracelular). Este estudo fornece um caminho para uma estratégia de vacina com VLP contra papilomaviroses bovina e apresenta um modelo experimental para estudos de papilomatosessimilares, além de mostrar um modelo experimental interessante para futuras aplicações em seres humanos. / Papillomaviruses are a group ofsmall double-stranded DNA viruses characterized by inducingthe formation of lesions that are usually benign and may regress naturally, but also havethe potential to become malignant tumors. The human papillomavirus (HPV) is strongly related to sexually transmitted diseases (STDs) and is a major cause of cervical cancer. The bovine papillomavirus (BPV), in turn, represents a serious economic problem in terms of livestock. In cattle,cutaneous and mucosal papillomatosis at genital and oropharyngeal regionsare the most common. There are six different types of BPV (BPV 1-6) well characterized and, recently, four new types (BPVs 7-10) havebeen sequenced.In theNortheast, especially inthe state of Pernambuco (Zona da Mata), the incidence of bovine papillomatosis isveryhigh,causing great economic losses for breeders. There isno treatment with proven efficacy. Protection against infection is conferred by neutralizing antibodies directed against structural L1proteinconformational epitopes. These antibodies can be efficiently induced by immunization with virus-like particles (VLP) that are formed spontaneously after L1 expression in heterologous systems. In recent years, the methylotrophic yeast Pichia pastorishas emerged as an efficient and inexpensive heterologous system to produce high protein levels. The focus of this paper is to construct andevaluate two plasmids (pPICZAαL1B2 and pPICZAL1B2), as vectors to gene expression of L1BPV-2 in cells of P. pastoris. One of them (pPICZAαL1B2) inserts a secretion signal (α-matting)on recombinant protein. Thus, it had been expected to compare the heterologous expression via intracellular and extracellular pathway efficiency. L1 gene has been amplified by PCR from the complete BPV-2 genome, has been cloned into pGEM-T vector (Promega®) and, subsequently, has been sub cloned into pPICZA and pPICZAαexpression vectors (Invitrogen®). PCR and restriction analysis haveindicated the correct insertion of the L1 gene in both vectors, as well as sequencing. By electroporation, P. pastoris(strain X-33 yeast) has been transformed with pPICZAL1B2 orpPICZAαL1B2 constructions, whose integration into yeast genome could be identified by colony PCR. Transformed yeast has been selected to culture experiments withmethanol induction. L1 expression has been indicated by RT-PCR and protein analysis. L1 recombinant protein has been detected in yeast cells that has undergonelysis solution treatment (intracellular pathway) and from the culture medium acetone precipitation submitted (extracellularpathway). This study provides a way for a VLP-vaccine strategyagainst bovine papillomaviroses and exhibits an experimental model for similar papillomatosis studies, whileshowingan interesting experimental model for future applications in humans.

The bacterium Escherichia coli (E. coli) is in many situations an ideal host for production of recombinant proteins, since it generally provides a rapid and economical means to achieve sufficiently high product quantities. However, there are several factors that may limit this host’s ability to produce large amounts of heterologous proteins in a soluble and native form. For many applications a high purity of the recombinant protein is demanded, which implies a purification strategy where the product efficiently can be isolated from the complex milieu of host cell contaminants. In this thesis, different strategies based on both rational and combinatorial genetic engineering principles have been investigated, aiming at improving and facilitating recombinant E. coli protein production and purification. One objective was to improve the PEG/salt aqueous two-phase system (ATPS) purification process of the lipase cutinase, by increasing the selectivity of the protein for the system top-phase. Peptide tags, with varying properties, were designed and genetically fused to the C-terminal end of ZZ-cutinase. Greatly increased partitioning values were observed for purified protein variants fused to tryptophan containing peptide tags, particularly a (WP)4 peptide. The partitioning properties of the ZZ-cutinase-(WP)4 protein were also retained when added to the ATPS directly from an E. coli total cell disintegrate, emphasizing the applicability of this genetic engineering strategy for primary protein purification in ATPSs. Further on, a combinatorial library approach using phage display technology was investigated as a tool for identification of peptide tags capable of improving partitioning properties of ZZ-cutinase in an ATPS. Repeated ATPS-based partitioning-selection cycles of a large phagemid (pVIII) peptide library, resulted in isolation of phage particles preferentially decorated with peptides rich in tyrosine and proline residues. Both a peptide corresponding to a phage library derived peptide sequence as well as peptides designed based on information of amino acid appearance frequencies in later selection rounds, were shown to improve partitioning several-fold when genetically fused to the C-terminal end of ZZ-cutinase. From the two- to four–fold increased production yields observed for these fusion proteins compared to ZZ-cutinase-(WP)4, it was concluded that the selection system used allowed for selection of desired peptide properties related to both partitioning and E. coli protein production parameters. Bacterial protein production is affected by several different mRNA and protein sequence-related features. Attempts to address single parameters in this respect are difficult due to the inter-dependence of many features, for example between codon optimization and mRNA secondary structure effects. Two combinatorial expression vector libraries (ExLib1 and ExLib2) were constructed using a randomization strategy that potentially could lead to variations in many of these sequence-related features and which would allow a pragmatic search of vector variants showing positive net effects on the level of soluble protein production. ExLib1 was constructed to encode all possible synonymous codons of an eight amino acid N-terminal extension of protein Z, fused to the N-terminal of an enhanced green fluorescent reporter protein (EGFP). In ExLib2, the same eight positions were randomized using an (NNG/T) degeneracy code, which could lead to various effects on both the nucleotide and protein level, through the introduction of nucleotide sequences functional as e.g. alternative ribosome binding or translation initiation sites or as translated codons for an Nterminal extension of the target protein by a peptide sequence. Flow cytometric analyses and sorting of library cell cultures resulted in isolation of clones displaying several-fold increases in whole cell fluorescence compared to a reference clone. SDS-PAGE and western blot analyses verified that this was a result of increases (up to 24-fold) in soluble intracellular ZEGFP product protein content. Both position specific codon bias effects and the appearance of new ribosomal binding sites in the library sequences were concluded to have influenced the protein production. To explore the possibility of applying the same combinatorial library strategy for improving soluble intracellular production of heterologous proteins proven difficult to express in E. coli, three proteins with either bacterial (a transcriptional regulator (DntR)) or human (progesterone receptor ligand binding domain (PRLBD) and 11-β Hydroxysteroid dehydrogenase type I (11-β)) origin, were cloned into the ExLib2 library. Flow cytometric sorting of libraries resulted in isolation of DntR library clones showing increased soluble protein production levels and PR-LBD library clones with up to ten-fold increases in whole cell fluorescence, although the product under these conditions co-separated with the insoluble cell material. / QC 20100623