Rapid diagnostic tests for COVID-19, influenza, and blood analytes currently have many drawbacks. They vary greatly in accuracy, are expensive to manufacture, and can be insufficiently sensitive to small antigen loads. Leucine lock is designed to rectify these issues that exist in current rapid diagnostics by creating a rapid antigen test with minimal background activity, tunable sensitivity, and low manufacturing cost. Leucine lock consists of a novel leucine zipper containing an intramolecular hairpin, an ScFv antigen binding domain, and a fluorophore reporter in a FRET combination. By altering the number of hydrophobic and electrostatic mismatches in the intramolecular hairpin, as well as utilizing either a three or four heptad repeat in the hairpin, our results show that the rate of recombination can be controlled. We chose a construct with an appropriate rate of recombination and designed a rapid test for insulin. We show that the test can determine the presence or absence of insulin, and with further optimization can be used to directly quantify insulin levels.

Les lésions hépatiques observées au cours de l'obésité (NAFLD, stéatopathie non alcoolique) s'étendent de la stéatose isolée à la stéatohépatite (NASH, stéatohépatitie non alcoolique), la fibrose, la cirrhose et au carcinome hépatocellulaire. L'identification des mécanismes de recrutement des cellules immunitaires par le foie stéatosique est une étape clé dans la compréhension du déclenchement de l'inflammation hépatique et la recherche de nouvelles cibles thérapeutiques. Au cours de l’obésité, la stéatose sensibilise le foie au lipopolysaccharide (LPS), qui active la voie pro-inflammatoire NFκB. Nous avons récemment montré que: 1) la stéatose induisait une augmentation du recrutement lymphocytaire (TCD4+, TCD8+ et B) vers le foie mais également une augmentation de la réponse des lymphocytes TCD4+ à la chimiokine CXCL12 (SDF-1α), dont le récepteur est CXCR4 ; 2) GILZ (Glucocorticoid-Induced Leucine Zipper), une protéine induite par les glucocorticoïdes (GCs), inhibait la voie NFkB et jouait un rôle clé dans l’inflammation hépatique au cours de la consommation excessive d’alcool.Le but de ce travail était d’étudier les mécanismes de l’inflammation hépatique liée à l’obésité. Au cours de mon travail, nous avons montré que le chimiotactisme des lymphocytes TCD4+ à la chimiokine CXCL12 était augmenté non seulement chez les souris obèses mais également chez des patients ayant une NASH. L’augmentation de l’effet chimiotactique de CXCL12 était due à une augmentation de l’affinité de CXCL12 à son récepteur CXCR4. La migration anormale des lymphocytes T CD4+ vers le foie stéatosique était réversible pharmacologiquement en inhibant la liaison de CXCL12 à CXCR4 par AMD3100 (antagoniste deCXCR4). Le déficit d’expression et l’altération de l’induction du facteur anti-inflammatoire GILZ dans les cellules des Kupffer des souris obèses étaient responsables de la sensibilisation de ces cellules au LPS. Cette altération était liée à la diminution de l’expression du récepteur aux glucocorticoïdes (GR) dans les cellules de Kupffer des souris obèses. La surexpression de GILZ dans l’obésité en utilisant des souris trangéniques restaurait la tolérance hépatique au LPS. Ces anomalies des lymphocytes TCD4+ et de l’expression de GILZ dans les cellules de Kupffer participent au déclenchement d’une inflammation hépatique sur un foie stéatosique et pourraient représenter de nouvelles cibles thérapeutiques / Non alcoholic fatty liver disease (NAFLD) includes a spectrum ranging from simple steatosis to nonalcoholic steatohepatitis (NASH), fibrosis, cirrhosis, and hepatocellular carcinoma. The identification of the mechanisms involved in the recruitment of immunity cells by the fatty liver is a key in the comprehension of the onset of liver and the finding of new therapeutic targets. In obesity, steatosis sensitizes the liver to the lipopolysaccharide (LPS) from the gastrointestinal tract and the NFkB pro-inflammatory pathway is activated. We recently showed that: 1) the steatosis led to an increase recruitment of lymphocytes (TCD4+, TCD8+ and B) by the liver but also an hyperresponsive of CD4+T cells to CXCL12 (SDF-1"), the ligand of CXCR4; 2) GILZ(Glucocorticoid-Induced Leucine Zipper), a protein induced by glucocorticoids (GCs), inhibits the nuclear factor kB pathway and plays a key role in alcoholic hepatitis.This aim of my work was to study the mechanisms involved in obesity-related liver inflammation.I demonstrated that the chemotaxis of CD4+T cells to CXCL12 was increased not only in obese mice but also in patients with NASH. This increased chemotactisme of CXCL12 was due to an increase of the affinity ofCXCL12 to its receptor. The abnormal migration of CD4+T lymphocytes to the fatty liver was reversible by pharmacologically inhibiting the binding of CXCL12 to CXCR4 using AMD3100.The decreased expression and the impairment of the induction of the anti-inflammatory factor GILZ in Kupffer cells from obese mice was responsible for a sensitization of these cells to LPS. This impairment was due to a decrease of the glucocorticoid receptor (GR) expression in Kupffer cells from obese mice. The overexpression of GILZ level in obese transgenic mice restored the liver tolerance to LPS. These abnormalities of CD4+T lymphocytes and the GILZ expression in Kupffer cells contribute to the onset of liver inflammation in obesity and may represent new therapeutic targets.

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Orientador: Michel Georges Albert Vincentz / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T14:21:25Z (GMT). No. of bitstreams: 1 Viana_AmericoJoseCarvalho_D.pdf: 5804951 bytes, checksum: a3c65fa34ad298641a9b177952050af3 (MD5) Previous issue date: 2014 / Resumo: O fator de transcrição do tipo basic leucine leucine zipper (bZIP) de Arabidopsis thaliana AtbZIP63 faz parte da via de resposta a carência energética coordenada pelas quinases KIN10/11, integradoras centrais dos sinais relacionados ao estado de privação de energia. O mutante de inserção de T-DNA atbzip63-2 apresenta uma redução do crescimento e desenvolvimento das folhas assim como um atraso do florescimento em comparação ao tipo selvagem (TS, acesso Ws) quando cultivado em fotoperíodo de dia curto (10 h/14 h). Condições de fotoperíodo de dia longo ou luz contínua promoveram uma reversão parcial ou completa, respectivamente, do fenótipo mutante para o tipo selvagem, levantando a possibilidade de que este fenótipo seja o resultado de uma carência energética. Plantas silenciadas para expressão de AtbZIP63 por RNAi apresentaram características similares a do mutante atbzip63-2 confirmando o envolvimento deste fator de transcrição no crescimento. O perfil de expressão gênica e os níveis de alguns metabólitos do mutante atbzip63-2 indicaram que AtbZIP63 participa do controle da degradação do amido, pois a expressão de alguns genes centrais na degradação deste carboidrato de reserva está desregulada neste mutante. Mostramos que as oscilações no nível do transcrito AtbZIP63 são reguladas pelo relógio circadiano e a fase da oscilação do AtbZIP63 é aparentemente influenciada pela disponibilidade de carboidratos na célula. Além de estar sob o controle do relógio, AtbZIP63 também atua como um ativador direto da expressão de PRR7, que codifica um dos componentes chave do oscilador central do relógio. Portanto, evidenciamos uma interação recíproca entre o relógio e AtbZIP63 que possivelmente está impactando o processo de degradação do amido à noite. Este conjunto de evidências revela novos aspectos do ajuste do relógio circadiano pelo status de açúcar na célula que estão de acordo com trabalhos recentes mostrando que os açúcares afetam diretamente o funcionamento do relógio. Nossa hipótese é que o AtbZIP63 está agindo como um mediador entre a disponibilidade de viii açúcar e o mecanismo oscilatório do relógio circadiano de A. thaliana. Adicionalmente, verificamos que o perfil de transcritos no final do dia no mutante atbzip63-2 é diferente do observado no final da noite, sugerindo a participação do AtbZIP63 na regulação de genes envolvidos em redes regulatórias distintas em função do período do dia. Dentre os genes desregulados no atbzip63-2 no final do dia, observamos um enriquecimento para genes relacionados com metabolismo secundário e síntese de trealose, o que sugere a participação do AtbZIP63 na regulação da síntese destes compostos durante o dia, e possivelmente reflete a ocorrência de stress no mutante / Abstract: he Arabidopsis thaliana basic leucine zipper domain (bZIP) AtbZIP63 transcription factor is part of the response pathway to energy shortage coordinated by kinases KIN10/11. The T-DNA insertion mutant atbzip63-2 shows a reduction in the growth and development of leaves, as well as a delay in flowering compared to wild type (WT; ecotype Ws), when grown in short-day conditions. Long day or continuous light conditions promoted a partial or complete reversion, respectively, of the mutant to wild-type phenotype, raising the possibility that this phenotype is the result of an energy shortage. Plants silenced for AtbZIP63 showed similar characteristics to the atbzip63-2 mutant, confirming the involvement of this transcription factor in the growth. The gene expression profile and the levels of some metabolites of the atbzip63-2 indicated that AtbZIP63 takes part in the control of starch degradation, regulating the expression of some key genes in starch degradation. Diurnal AtbZIP63 mRNA level fluctuation is regulated by the circadian clock, and the phase oscillation is influenced by the availability of carbohydrates. In addition, to be controlled by the circadian clock, AtbZIP63 directly regulates the expression of PRR7 which encodes one of the key regulators of the core clock. We have therefore identified a reciprocal interaction between the clock and AtbZIP63 which is probably affecting the starch degradation process. This set of evidence reveals new aspects of the entrainment of the circadian clock by sugars, and is consistent with recent studies showing that sugars directly regulate the circadian clock. Our hypothesis is that AtbZIP63 is acting as a mediator between the energy status (availability of sugar) and the oscillatory mechanism of the A. thaliana circadian clock. Additionally, we found that the profile of transcripts at the end of the day in atbzip63-2 mutant is different from that observed in the end of the night, suggesting the involvement of AtbZIP63 in the regulation of genes involved in distinct regulatory networks according to the period of day. Among the genes deregulated in atbzip63-2 at the end of the x day, an enrichment for genes related to secondary metabolism and trehalose biosynthesis was observed. Suggesting the involvement of AtbZIP63 in regulating the synthesis of these compounds during the day, and probably reflects the occurrence of stress in the mutant / Doutorado / Genetica Vegetal e Melhoramento / Doutor em Genetica e Biologia Molecular

Herewithin, two transcription factor (TF) regulatory complexes were investigated. A bHLH–MYB–WDR (BMW) DNA-binding complex from maize was the first complex to be studied. R, a maize bHLH involved in the activation of genes in the anthocyanin pathway, had been characterized to indirectly bind DNA despite the presence of a functional DNA-binding domain. Findings presented here reveal that this is only partially correct. Direct DNA-binding by R was found to be dependent upon two distinct dimerization domains that function as a switch. This switch-like mechanism allows R to be repurposed for the activation of promoters of differing cis-element structure. The second regulatory complex studied was of the Arabidopsis thaliana MIKC-MADS TF family. For many TFs, DNA-binding site recognition is relatively straightforward and very sequence specific, while others exhibit relaxed sequence specificity. MADS-domain TFs are one family of TFs with a wider range of cis-element sequences. Though consensus cis-element sequences have been determined for various MADS-domains, correctly predicting and identifying biologically functional cis-elements has been a challenge. In order to study the influence of nucleobase associations within the cis-element, a DNA-Protein Interaction (DPI)-ELISA method was modified and optimized to screen a panel of specific probes. Screening of the SEP3 homodimer against a panel of sequential, palindromic probes revealed that nucleobases in position -1:+1 of the CArG-box influence binding strength between the MADS-domain and DNA. Additionally, the specificity of AGL15 towards CT-W6-AG forms was discovered to be determined by the functional groups present in the minor groove at position -4:+4 using inosine:cytosine (I:C) base pairs. Finally, the FLC–SVP MADS-domain heterodimer, bound to a native cis-element, was modeled and binding simulated using molecular dynamics. In conjunction with simulations of AGL15 and SEP3 homodimers, a potential binding mechanism was identified for this unique heterodimer. DNA sequence recognition by the MADS-domain was found to occur asymmetrically. In the case of the FLC–SVP heterodimer, the direction of asymmetrical DNA-binding in heterodimers was found to be fixed. Furthermore, the molecular dynamics simulations provided insight towards understanding the results generated from previous DPI-ELISA experiments, which should provide an improved means for predicting biologically significant CArG-boxes around genes.

Transcription factors are proteins that regulate transcription of genes by binding to specific DNA sequences proximal to the gene. The specificity and affinity of protein-DNA recognition is critical for proper gene regulation. This thesis explores the mechanisms of binding to the sequence 5’CACGTG, a common recognition sequence both in plants where it is known as the G-box and in mammalian cells where it is termed the E-box. This sequence is of clinical interest because it is the target of the transcription factor Myc, an oncogene linked to many cancers. A number of alpha-helical proteins with different dimerization elements, from the basic region-leucine zipper (bZIP), basic region helix-loop-helix leucine zipper (bHLHZ) and basic region helix-loop-helix-PAS (bHLH-PAS) protein families, are capable of binding to this sequence. The basic regions of all these protein families contain residues that contact DNA and determine DNA sequence specificity while the other subdomains are responsible for dimerization specificity. First, the influence of protein-DNA contacts on sequence specificity of the plant bZIP protein EmBP-1 was probed by point mutations in the basic region. Residues that contact the DNA outside the core G-box sequence and residues that contact the phosphate backbone were found to be important for sequence specificity. Second, the impact of the dimerization subdomains of bHLHZ protein Max, the required heterodimerization partner of the Myc protein, and bHLH-PAS protein Arnt was probed by mutation, deletion and inter-family subdomain swapping studies. All studied protein families are intrinsically disordered, forming structure upon dimerization and DNA binding. The dimerization domains were found to indirectly influence DNA binding by affecting folding, dimerization ability or proper orientation of the basic regions relative to DNA. Lastly, a new strategy for selection of G-box binding proteins in the Yeast One-hybrid system is explored. Together, these studies broaden our understanding of the structure-function relationship of the DNA-binding activities of these closely related families of transcription factors. The creation and characterization of mutants with altered specificity, affinity and dimerization specificity may also be useful for biotechnology applications.

Transcription factors are proteins that regulate transcription of genes by binding to specific DNA sequences proximal to the gene. The specificity and affinity of protein-DNA recognition is critical for proper gene regulation. This thesis explores the mechanisms of binding to the sequence 5’CACGTG, a common recognition sequence both in plants where it is known as the G-box and in mammalian cells where it is termed the E-box. This sequence is of clinical interest because it is the target of the transcription factor Myc, an oncogene linked to many cancers. A number of alpha-helical proteins with different dimerization elements, from the basic region-leucine zipper (bZIP), basic region helix-loop-helix leucine zipper (bHLHZ) and basic region helix-loop-helix-PAS (bHLH-PAS) protein families, are capable of binding to this sequence. The basic regions of all these protein families contain residues that contact DNA and determine DNA sequence specificity while the other subdomains are responsible for dimerization specificity. First, the influence of protein-DNA contacts on sequence specificity of the plant bZIP protein EmBP-1 was probed by point mutations in the basic region. Residues that contact the DNA outside the core G-box sequence and residues that contact the phosphate backbone were found to be important for sequence specificity. Second, the impact of the dimerization subdomains of bHLHZ protein Max, the required heterodimerization partner of the Myc protein, and bHLH-PAS protein Arnt was probed by mutation, deletion and inter-family subdomain swapping studies. All studied protein families are intrinsically disordered, forming structure upon dimerization and DNA binding. The dimerization domains were found to indirectly influence DNA binding by affecting folding, dimerization ability or proper orientation of the basic regions relative to DNA. Lastly, a new strategy for selection of G-box binding proteins in the Yeast One-hybrid system is explored. Together, these studies broaden our understanding of the structure-function relationship of the DNA-binding activities of these closely related families of transcription factors. The creation and characterization of mutants with altered specificity, affinity and dimerization specificity may also be useful for biotechnology applications.

For all living systems, there is a requirement to recycle and regulate proteins. In eukaryotic organisms this is accomplished by the proteasome. The p97 ATPase is another highly conserved and essential complex present throughout the eukaryotic cell. In Paper I we utilized UFD fluorescent substrates to address the role of p97 and cofactors in soluble proteasome degradation. Results using RNAi and Drosophila p97 mutants propose p97 to function upstream of the proteasome on cytosolic proteasome targets as an important unfoldase together with its Ufd1/Npl4 cofactors. The results implicate p97 to be important for degradation of proteasome substrates lacking natural extended peptide regions. In Paper II we focused on identifying transcription factors essential for production of proteasomal subunits and associated proteins in Drosophila S2 cells. We utilized an RNA library targeting 993 known or candidate transcription factors and monitored RNAi depleted Drosophila S2 cells expressing the UFD reporter UbG76VGFP. We identified a range of potential candidates and focused on the bZIP transcription factor Cnc-C. RNAi and qrt-PCR experiments implicated Cnc-C to be involved in transcription of proteasomal subunits. In Paper III we applied our knowledge gained from Paper I about p97 dependent substrates and set up a high-throughput microscopy screening method to potentially find inhibitors specifically targeting the p97 proteasomal sub-pathway. Utilizing UFD substrates with and without C-terminal peptide tails we determined if compounds inhibited the core proteasomal machinery or the p97 pathway specifically. Through a primary and secondary round of screening we identified several new compounds inhibiting the ubiquitin-proteasome pathway though none from our initial screening had specificity for p97. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2008. / Härtill 3 uppsatser.