abstract: Over the past decade, several high-value proteins have been produced using plant-based transient expression systems. However, these studies exposed some limitations that must be overcome to allow plant expression systems to reach their full potential. These limitations are the low level of recombinant protein accumulation achieved in some cases, and lack of efficient co-expression vectors for the production of multi-protein complexes. This study report that tobacco Extensin (Ext) gene 3' untranslated region (UTR) can be broadly used to enhance recombinant protein expression in plants. Extensin is the hydroxyproline-rich glycoprotein that constitutes the major protein component of cell walls. Using transient expression, it was found that the Ext 3' UTR increases recombinant protein expression up to 13.5- and 6-fold in non-replicating and replicating vector systems, respectively, compared to previously established terminators. Enhanced protein accumulation was correlated with increased mRNA levels associated with reduction in read-through transcription. Regions of Ext 3' UTR essential for maximum gene expression included a poly-purine sequence used as a major poly-adenylation site. Furthermore, modified bean yellow dwarf virus (BeYDV)-based vectors designed to allow co-expression of multiple recombinant genes were constructed and tested for their performance in driving transient expression in plants. Robust co-expression and assembly of heavy and light chains of the anti-Ebola virus monoclonal antibody 6D8, as well as E. coli heat-labile toxin (LT) were achieved with the modified vectors. The simultaneous co-expression of three fluoroproteins using the single replicon, triple cassette is demonstrated by confocal microscopy. In conclusion, this study provides an excellent tool for rapid, cost-effective, large-scale manufacturing of recombinant proteins for use in medicine and industry. / Dissertation/Thesis / Ph.D. Plant Biology 2012

Magister Scientiae - MSc (Medical BioSciences) / Despite attempts to develop new drugs to reduce the worldwide mortality rate attributable to tuberculosis (TB), the illness remains a threat. Isoniazid (INH) has been used as a frontline drug for decades. However, several resistant strains of the organism - Mycobacterium tuberculosis (M. tuberculosis) - still emerge. The drug is mainly metabolised by a family of enzymes, arylamine N-acetyltransferases (NAT). The three human NAT genes - NAT1, NAT2 and the pseudogene, NATP - are found on chromosome 18p22. NAT1 and NAT2 are isoenzymes which differ at certain amino acid positions. Subsequently, the differences affect substrate specificity. NAT1 shows specificity to p-aminobenzoic acid (PABA) and paminosalicylate (PAS). Previously, computer algorithms were used to predict the efficacy of the enzyme with regard to the acetylation phenotype it confers. The two which were focused on, Sorting Intolerant From Tolerant (SIFT) program and Polymorphism phenotyping version 2 program (PolyPhen-2), showed conflicting results for the effect of SNPs on the acetylation rate and subsequent enzyme function. Further structural prediction methods were used to test the effect of V231G on the structure and consequent function of the native protein, NAT1.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2013-11-06T19:57:37Z No. of bitstreams: 1 Leonardo Vicitini Arruda Desenvolvido de plasmídio para expressão proteíca....pdf: 2125843 bytes, checksum: cf2e5fe050fd36b4ebba0206f40d6e3a (MD5) / Made available in DSpace on 2013-11-06T19:57:37Z (GMT). No. of bitstreams: 1 Leonardo Vicitini Arruda Desenvolvido de plasmídio para expressão proteíca....pdf: 2125843 bytes, checksum: cf2e5fe050fd36b4ebba0206f40d6e3a (MD5) Previous issue date: 2013 / Universidade Federal da Bahia. Faculdade de Medicina da Bahia. Salvador, BA, Brasil / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil. / Protozoários do gênero Leishmania provocam uma ampla gama de doenças, e passam por um processo de diferenciação entre o inseto vetor e a forma intracelular no hospedeiro mamífero. Apesar das diferenças entre as formas do ciclo de vida, não estava descrita ferramenta para expressar proteínas de modo estágio específico. Neste trabalho apresentamos um plasmídio para Leishmania que expressa proteína recombinante de forma estágio específica. Testamos uma possível construção que usava as região 3’ UTR do gene amastina para controlar a expressão de uma proteína fluorescente e a expressar exclusivamente na fase amastigota. Também utilizamos a região 3’ UTR de uma tubulina para obter uma fluorescência homogênea em todos os estágios do ciclo de vida do parasita. Assim como esperado, obtivemos uma fluorescência exclusiva para a fase amastigota quando utilizamos a região 3’ UTR da amastina, e uma fluorescência constitutiva quando a expressão foi regulada pela região 3’ UTR da tubulina. O plasmídio descrito neste trabalho é versátil, pois a droga de seleção ou a proteína a ser expressa podem ser substituídas com grande facilidade. Adicionalmente, como o plasmídio pFL expressou um gene repórter exclusivamente no estágio amastigota ou constitutivamente, acreditamos que este plasmídio pode também ser utilizado para expressar proteínas de forma restrita aos estágios promastigota metacíclico e procíclico. Alguns possíveis usos desta nova ferramenta também são discutidos nesta tese / The parasitic protozoan Leishmania causes a wide spectrum of diseases and passes through differentiation between the sand fly and the intracellular form. Despite distinction between life-cycle forms of the parasite, there is no described tool to express a protein in a specific stage. Here, we present a plasmid for Leishmania that can express recombinant proteins in a specific life-cycle stage. We tested one possible construction that used the 3’ UTR region of the amastin gene to control the expression of a fluorescent protein exclusively in the amastigote stage. We also used the 3’ UTR of a tubulin to obtain a homogeneous fluorescence in all stages of the parasite life cycle. As expected, was observed a fluorescence exclusive to the amastigote phase with the 3’ UTR amastin construction, and a constitutive fluorescence when the expression were regulated by the 3’ UTR of a tubulin. The plasmid described here is versatile since the drug that will be used for selection or the protein that will be expressed can be easily changed. Moreover, plasmid pFL have expressed a reporter gene exclusively in the amastigote stage or constitutively, we believe that this plasmid can also be used to express proteins in metacyclic and procyclic promastigote stages only. Some possible uses of this new tool are also discussed.

abstract: Viral protein U (Vpu) is a type-III integral membrane protein encoded by the Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays vital roles in down-regulation of CD4 receptors in T cells and also in the budding of virions. But, there remain key structure/function questions regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis and thus, it makes for an attractive target to study the structural attributes of this protein by elucidating a structural model with X-ray crystallography. This study describes a multi-pronged approach of heterologous over-expression of Vpu. The strategies of purification and biophysical/ biochemical characterization of the different versions of the protein to evaluate their potential for crystallization are also detailed. Furthermore, various strategies employed for the crystallization of Vpu by both in surfo and in cubo techniques, and the challenges faced towards the structural studies of this membrane protein by characterization with solution Nuclear magnetic resonance (NMR) spectroscopy are also described. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2016

Os hantavírus, membros da família Bunyaviridae, são os agentes infecciosos responsáveis pela Febre Hemorrágica com Síndrome Renal e pela Síndrome Cardiopulmonar por Hantavírus. São vírus com genoma constituído por três segmentos de RNA fita simples, de polaridade negativa, designados como S, M e L, que codificam, respectivamente, a nucleoproteína, as glicoproteínas G1 e G2 e a RNA polimerase dependente de RNA. Com o objetivo de estudar a montagem de pseudopartículas quiméricas de hantavírus, a proteína N do vírus Araraquara e as glicoproteínas G1 e G2 do vírus Andes foram expressas em sistema baculovírus. A microscopia confocal mostrou a colocalização das proteínas G1 e G2 com a proteína N. Pelos ensaios de imunoprecipitação e de centrifugação em gradiente de sacarose, foi observada a interação entre as proteínas N, G1 e G2. Nas análises por microscopia eletrônica de transmissão foi observada a montagem do pseudo-hantavírus quimera, com morfologia semelhante ao do vírion. O pseudo-hantavírus quimera obtido neste estudo poderá, no futuro, ser utilizado em estudos imunológicos, estruturais e morfológicos. / Hantaviruses, members of the Bunyaviridae family, are the infectious agents responsible for Hemorrhagic Fever with Renal Syndrome and the Hantavirus Cardiopulmonary Syndrome. The viral genome is composed by three segments of single-stranded negative-sense RNA, designated as S, M and L, which encode, respectively, the nucleoprotein, the G1 and G2 glycoproteins, and the RNA-dependent RNA polymerase. In order to study the assembly of a chimeric hantavirus-like particle, the Araraquara nucleoprotein and the Andes glycoproteins were expressed in a baculovirus system. Confocal microscopy showed the colocalization of G1 and G2 proteins with the N protein. Immunoprecipitation assay and sucrose density gradient showed the interaction among N, G1 and G2 proteins. The transmission electron microscopy showed the hantavirus-like particle with the same morphology of the virion. The chimeric hantavirus-like particle produced in this study could be used, in the future, in immunological, structural and morphological studies.

Made available in DSpace on 2014-08-20T14:31:33Z (GMT). No. of bitstreams: 1 dissertacao_fernanda_antunes_brum.pdf: 139752 bytes, checksum: 989f0c94f1c779f13cc72237d9ab8552 (MD5) Previous issue date: 2010-12-23 / The Ehrlichia canis is a canine monocytic ehrlichiosis responsible for (EMC). The incubation period of EMC is 8 to 20 days, the disease has three phases: acute, subclinical and chronic. The species E. canis is transmitted to the dog and the man by the tick Rhipicephalus sanguineus. It is diagnosed by blood smear, serological or polymerase chain reaction (PCR), with the immunofluorescence method used. Recently E. canis was described as being capable of causing severe disease in humans, with death cases, mainly children and elderly. The gp 19 protein is an important immunodominant antigen, it induces rapid immune response in dogs. The similarity between the geographically distinct samples suggests that the gp19 protein can be used for testing the diagnostic immunoassays, as well as vaccination programs, because this protein is specific for E. canis and thus not have cross reactions with other genera of Ehrlichia.Este study aimed to clone and express the glycoprotein 19 of Ehrlichia canis in Escherichia coli for use as immunobiological, rapid and accurate detection of this disease. The gp 19 gene was amplified by polymerase chain reaction (PCR) using specific primers containing sites for restriction enzymes. The PCR product after digestion, was purified and cloned into a vector and inserted into E. pAE coli TOP 10 competent by electroporation. Of the identified clones was extracted plasmid, which was digested with restriction enzymes to confirm the presence of the insert. After selection of recombinant clones containing the gene linked to the vector, this was purified by heat shock and inserted in expression strain E. coli Star, cultured and induced to express the protein gp19. / A Ehrlichia canis é a responsável pela erliquiose monocitica canina (EMC). O período de incubação da EMC é de 8 a 20 dias; a doença apresenta três fases: aguda, subclínica e crônica. As espécies de E. canis são transmitidas para o cão e para o homem pelo carrapato da espécie Rhipicephalus sanguineus. O diagnóstico é realizado através de esfregaços sanguíneos, métodos sorológicos ou reação em cadeia da polimerase (PCR), sendo a imunofluorescencia o método mais utilizado. Recentemente E. canis, foi descrita como sendo capaz de causar doença grave em humanos, com casos de óbito principalmente em crianças e idosos. A proteína gp 19 é um importante antígeno imunodominante, pois induz rápida resposta imunológica nos cães. A similaridade entre as amostras geograficamente distintas sugere que a proteína gp19 possa ser usada para ensaios de imunoenzimáticos de diagnóstico, bem como em programas vacinais, pois esta proteína é especifica para E. canis não tendo assim reações cruzadas com outros gêneros de Ehrlichia. O gene gp 19 foi amplificado pela reação da polimerase em cadeia (PCR) utilizando oligonucleotídeos iniciadores específicos contendo sítios para enzimas de restrição. O produto da PCR, após digestão, foi purificado e clonado no vetor pAE e inserido em E. coli TOP 10 competente por eletroporação. Dos clones identificados extraiu-se o plasmídio, o qual foi digerido com as enzimas de restrição para comprovar a presença do inserto. Após seleção dos clones recombinantes contendo o gene ligado ao vetor, este foi purificado e inserido por choque térmico na cepa de expressão E. coli Star cultivado e induzido para expressar a proteína gp19. Esta expressão foi verificada por gel de SDS-Page 12% e confirmada por Dot-Blot.

Bacteria are one of the largest causes of human disease, with millions of deaths every year attributed to bacterial infections, and they have become more difficult to tackle with the widespread emergence of antibiotic resistance. In this thesis, I describe my studies that pursued two approaches: one focus was on using antimicrobial histones as an alternative to treatment for antibiotic resistant bacteria; in another approach the recombinant version of an eggshell cuticle protein was expressed and purified for testing against food-safety pathogens. One major pathogen that is contributing to this challenge of antibiotic resistance is Staphylococcus aureus. The methicillin-resistant strain of S. aureus leads to increased hospital stays and increased mortality in patients. The impact of such pathogens is worsened when bacteria form surface-attached aggregates known as biofilms. Development of new approaches to eradicate antibiotic- resistant biofilms will benefit human health. This study looked at an alternative method to eradicate bacteria compared to traditional antibiotics. Histones with antimicrobial activity were extracted from chicken blood and tested against methicillin-sensitive and methicillin-resistant strains of Staphylococcus aureus biofilm (MSSA and MRSA). The histone mixture completely eradicated both strains in biofilm form at relatively low concentrations. In addition, the histone mixture also displayed fast kill kinetics against planktonic forms of the two strains. Finally, the interaction of the histone mixture with the bacterial membrane in MRSA biofilms was observed by scanning electron microscopy (SEM). Bacteria treated with the histone mixture showed clear morphological changes, including pore formation and cell collapse. Therefore, the histone mixture purified from chicken red blood cells could prove to be a good alternative to traditional antibiotics for protection against antibiotic-resistant strains of bacteria in their planktonic and biofilm forms. Reduction of food-borne illness is another important aspect in the promotion of human health. A significant contributor to food-borne illness is contaminated table eggs. The unfertilized egg can be contaminated by a variety of pathogens including Salmonella spp. and Bacillus spp. The egg is protected by the eggshell which is traversed by respiratory pores that are normally covered by a cuticle plug to restrict pathogen entry. This cuticle consists of several proteins including ovocaxlyin-32 (OCX-32). OCX-32 has a large number of naturally occurring haplotypes due non-synonymous single nucleotide polymorphisms (SNPs). In this study, the goal was to express five of the most common haplotypes of OCX-32 in Escherichia coli and purify the recombinant protein for assay of its antimicrobial activity. Five constructs that contain the cDNA of common OCX-32 haplotypes (A, B, C, D, and O) with a histidine tag at the C-terminus were generated. The constructs were subcloned into pGEX4T-1 vector which encodes Glutathione-S-transferase (GST) upstream of the multiple cloning site. My study developed methods to optimize the expression conditions, and to increase the solubility of the recombinant protein. Various expression strains of E. coli and solubility buffers were tested. In addition, the construct was subcloned into a plasmid containing the small ubiquitin-like modifier (SUMO) fusion tag; the solubility of the new SUMO-OCX-32 haplotype A recombinant fusion protein was evaluated. The best results were obtained by slow dialysis refolding of denatured SUMO-OCX-32 fusion protein. This recombinant protein showed almost complete solubility with minimal precipitation and was tested against the egg-related pathogen, Bacillus cereus. Unfortunately, the SUMO-OCX-32 recombinant protein did not inhibit growth of B. cereus. In my studies reported in this thesis, two very different approaches were taken. A histone mixture was isolated from an abundant starting material, which proved to be highly effective and promising in the eradication of S. aureus biofilms at relatively low concentrations. Alternatively, expression of a soluble recombinant protein for functional activity assay was very challenging and required the optimization of a number of methods to prepare soluble protein for testing. One of the methods tested proved effective in obtaining large amounts of soluble protein. However, further developmental work will be essential to determine if this approach is a viable strategy in acquiring functional protein.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / Coronaviridae family is composed of a number of ribonucleic acid (RNA)-containing viruses currently classified into two genera, the coronavirus and torovirus. The family is classified together with the Arteviridae in the order Nidovirales. Coronaviruses are enveloped single stranded positive sense RNA viruses about 80-160 nm in diameter. The coronavirus is, as in the case of all positive sense RNA virus, a messenger, and the naked RNA is infectious. The 5′-two thirds of the genome encodes for a polyprotein that contains all the enzymes necessary for replication, whereas the 3′-one third encodes for all the structural proteins that mediate viral entry into the host cell. The structural proteins include spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins.Nucleocapsid protein is one of the most crucial structural components of coronaviruses;hence major attention has been focused on characterization of this protein. Some laboratories have demonstrated that this protein interferes with different cellular pathways, thus implying it to be a key regulatory component of the virus (Zakhartchouk, Viswanathan et al. 2005). Furthermore, it has been shown that severe acute respiratory syndrome (SARS)-N protein interacts with cellular proteins, including cyclophilin A (CypA), heterogenous nuclear ribonucleoprotein (hnRNP) A1, human ubiquitin-conjugating enzyme, cyclin dependent kinase (CDK)-cyclin complex protein, Ikappaßalpha (IkBα), cytochrome (Cyt) P450 etc. For the purpose of this study, the focus is based on CypA interaction with human coronavirus (HCoV) NL63-N protein. These interactions might play a role in the pathology of HCoV-NL63. Using glutathione-S-transferase (GST), the interaction of CypA with the nucleocapsid protein can be clearly demonstrated to be direct and specific. Since the N protein is involved in viral RNA packaging to form a helical core, it is suffice to say that both NL63-N and CypA are possibly within the HCoV-NL63 replication/transcription complex and NL63-N/human CypA interaction might function in the regulation of HCoV-NL63 RNA synthesis. In addition, the results will demonstrate that HCoV-NL63-N has only a specific domain for interacting with CypA.

The cytochrome P450 system plays an important role in metabolism of endogenous compounds and xenobiotics. This system consists of cytochrome P450, NADPH:cytochrome P450 oxidoreductase (CPR), cytochrome b5 and NADH:cytochrome b5 reductase (CYB5R3). Explanation of protein-protein interactions among these reaction partners is essential for understanding the function of the entire system. Covalent cross-linking is a favorable method for studying these interactions. In this work a photo-activatable analogue of amino acid L-methionine (L-photo-methionine) was used as a cross-linking agent. This work is focused on the organic synthesis of L-photo-methionine, expression and isolation of CPR and CYB5R3 as photoactivable proteins containing incorporated L-photo-methionine. Auxotrophic strain of E.coli B834 (DE3) and minimal media were used for the expression. CYB5R3 with incorporated L-photo-methionine was successfully expressed and isolated. The extent of L-photo-methionine incorporation was verified by mass spectrometry. Furthermore, the photo-initiated cross-linking of CYB5R3 with cytochrome b5 was tested. Key words: photolabile amino acid, protein expression, synthesis

Abstract Collagen prolyl 4-hydroxylase (C-P4H) plays a central role in the biosynthesis of collagens by hydroxylating proline residues. The enzyme has been a subject of intense interest as a target enzyme for drug development. The recombinant expression of human C-P4H in prokaryotes has not yet been described. This work reports on the development of an expression system for human C-P4H in E. coli. The vertebrate C-P4H enzymes are α2β2 tetramers, consisting of two β subunits which are identical to protein disulphide isomerase (PDI), aside from the two α subunits which have the catalytic activity. The function of PDI is to keep the α subunit in a soluble and active state. Therefore, the expression system should assure the expression of the β subunit in the cell before the α subunit by using two different promoters. An active C-P4H tetramer was obtained in the periplasm of E. coli. However, further optimization for production by stepwise regulated coexpression of its subunits in the cytoplasm of a thioredoxin reductase and glutathione reductase mutant E. coli strain resulted in large amounts of human C-P4H tetramer. The exchange of four rare E. coli codons of the pdi gene and the optimized distance between ribosome binding site and translation initiation, resulted in 50-fold P4H-activity and 25 mg/l purified enzyme. Comparison of the expression level of mRNA from the α and β subunits by Sandwich hybridization identified single induction with anhydrotetracycline in fed-batch fermentations as a limiting parameter. This caused an insufficient expression level of mRNA and thereby a low yield of C-P4H. A maximum yield was obtained by repeated addition of anhydrotetracycline that led to higher mRNA levels and increased productivity. A newly developed stochastic simulation model of translational ribosome traffic in bacteria assesses the effect of codon usage to ribosome traffic and to the overall translation rate and mRNA stability. Using human PDI, it was shown that substitution of four 5' codons of the human PDI sequence that are rare in E. coli sequences, by synonymous codons preferred in E. coli led to a 2-fold increase of total PDI amount and even to a 10-fold increase of soluble PDI amount.