Molecular study of cell degeneration and evolution induced by mRNA mistranslation

As proteínas existentes nas células são produzidas pelo mecanismo de tradução do mRNA, no qual a informação genética contida nos genes é descodificada em cadeias polipeptídicas. O código genético, que define as regras de descodificação do genoma, minimiza os erros de tradução do mRNA, garantindo a síntese de proteínas com elevada fidelidade. Esta é essencial para a estabilidade do proteoma e para a manutenção e funcionamento dos processos celulares. Em condições fisiológicas normais, os erros da tradução do mRNA ocorrem com frequências que variam de 10-3 a 10-5 erros por codão descodificado. Situações que aumentam este erro basal geralmente estão associadas ao envelhecimento, stresse e a doenças; no entanto, em certos organismos o código genético é traduzido naturalmente com elevado erro, indicando que a síntese de proteínas aberrantes pode de algum modo ser vantajosa. A fim de estudar a resposta celular aos erros de tradução do mRNA, construímos leveduras que incorporam serina no proteoma em resposta a um codão de leucina, usando a expressão constitutiva de um tRNASer mutante. Este fenómeno genético artificial provocou uma forte diminuição da esporulação, da viabilidade e da eficiência de mating, afectando imensamente a reprodução sexual da levedura. Observou-se também uma grande heterogeneidade no tamanho e na forma das células e elevada instabilidade genómica, com o aparecimento de populações poliplóides e aneuplóides. No sentido de clarificar as bases celulares e moleculares daqueles fenótipos e compreender melhor a biologia do erro de tradução do mRNA, construímos também células de levedura que inserem serina em resposta a um codão de leucina de modo indutível e controlado. Utilizaram-se perfis de mRNA total e de mRNA associado a polissomas para elucidar a resposta celular ao erro de tradução do mRNA. Observou-se a indução de genes envolvidos na resposta ao stresse geral, stresse oxidativo e na unfolded protein response (UPR). Um aumento significativo de espécies reactivas de oxigénio (ROS) e um forte impacto negativo na capacidade das células pós-mitóticas re-iniciarem o crescimento foram também observados. Este fenótipo de perda de viabilidade celular foi resgatado por scavangers de ROS, indicando que o stresse oxidativo é a principal causa de morte celular causada pelos erros de tradução. Este estudo levanta a hipótese de que o stresse oxidativo e a acumulação de ROS, ao invés do colapso súbito do proteoma, são as principais causas da degeneração celular e das doenças humanas associadas aos erros de tradução do genoma. ABSTRACT: Proteins are synthesized through the mechanism of translation, which uses the genetic code to transform the nucleic acids based information of the genome into the amino acids based information of the proteome. The genetic code evolved in such a manner that translational errors are kept to a minimum and even when they occur their impact is minimized by similar chemical properties of the amino acids. Protein synthesis fidelity is essential for proteome stability and for functional maintenance of cellular processes. Indeed, under normal physiological conditions, mistranslation occurs at frequencies that range from 10-3 to 10-5 errors per codon decoded. Situations where this basal error frequency increases are usually associated to aging and disease. However, there are some organisms where genetic code errors occur naturally at high level, suggesting that mRNA mistranslation can somehow be beneficial. In order to study the cellular response to mRNA mistranslation, we have engineered single codon mistranslation in yeast cells, using constitutive expression of mutant tRNASer genes. These mistranslating strains inserted serines at leucine-CUG sites on a proteome wide scale due to competition between the wild type tRNALeu with the mutant tRNASer. Such mistranslation event decreased yeast sporulation, viability and mating efficiencies sharply and affected sexual reproduction strongly. High heterogeneity in cell size and shape and high instability in the genome were also observed, with the appearance of some polyploid or aneuploid cell populations. To further study the cellular and molecular basis of those phenotypes and the biology of mRNA mistranslation, we have also engineered inducible mRNA misreading in yeast and used total mRNA and polysome associated mRNA profiling to determine whether codon misreading affects gene expression. Induced mistranslation up-regulated genes involved in the general stress response, oxidative stress and in the unfolded protein response (UPR). A significant increase in reactive oxygen species (ROS) and a strong negative impact on the capacity of post-mitotic cells to re-initiate growth in fresh media were also observed. This cell viability phenotype was rescued by scavengers of ROS, indicating that oxidative stress is the main cause of cell death caused by mRNA mistranslation. This study provides strong support for the hypothesis that oxidative stress and ROS accumulation, rather than sudden proteome collapse or major proteome disruption, are the main cause of the cellular degeneration observed in human diseases associated mRNA mistranslation.

Photodynamic inactivation of bacteria by cationic porphyrins : their cellular targets and potential environmental applications

Photodynamic inactivation (PDI) is defined as the process of cell destruction by oxidative stress resulting from the interaction between light and a photosensitizer (PS), in the presence of molecular oxygen. PDI of bacteria has been extensively studied in recent years, proving to be a promising alternative to conventional antimicrobial agents for the treatment of superficial and localized infections. Moreover, the applicability of PDI goes far beyond the clinical field, as its potential use in water disinfection, using PS immobilized on solid supports, is currently under study. The aim of the first part of this work was to study the oxidative modifications in phospholipids, nucleic acids and proteins of Escherichia coli and Staphylococcus warneri, subjected to photodynamic treatment with cationic porphyrins. The aims of the second part of the work were to study the efficiency of PDI in aquaculture water and the influence of different physicalchemical parameters in this process, using the Gram-negative bioluminescent bacterium Vibrio fischeri, and to evaluate the possibility of recycling cationic PS immobilized on magnetic nanoparticles. To study the oxidative changes in membrane phospholipids, a lipidomic approach has been used, combining chromatographic techniques and mass spectrometry. The FOX2 assay was used to determine the concentration of lipid hydroperoxides generated after treatment. The oxidative modifications in the proteins were analyzed by one-dimensional polyacrylamide gel electrophoresis (SDS-PAGE). Changes in the intracellular nucleic acids were analyzed by agarose gel electrophoresis and the concentration of doublestranded DNA was determined by fluorimetry. The oxidative changes of bacterial PDI at the molecular level were analyzed by infrared spectroscopy. In laboratory tests, bacteria (108 CFU mL-1) were irradiated with white light (4.0 mW cm-2) after incubation with the PS (Tri-Py+-Me-PF or Tetra-Py+-Me) at concentrations of 0.5 and 5.0 μM for S. warneri and E. coli, respectively. Bacteria were irradiated with different light doses (up to 9.6 J cm-2 for S. warneri and up to 64.8 J cm-2 for E. coli) and the changes were evaluated throughout the irradiation time. In the study of phospholipids, only the porphyrin Tri-Py+-Me-PF and a light dose of 64.8 J cm-2 were tested. The efficiency of PDI in aquaculture has been evaluated in two different conditions: in buffer solution, varying temperature, pH, salinity and oxygen concentration, and in aquaculture water samples, to reproduce the conditions of PDI in situ. The kinetics of the process was determined in realtime during the experiments by measuring the bioluminescence of V. fischeri (107 CFU mL-1, corresponding to a level of bioluminescence of 105 relative light units). A concentration of 5.0 μM of Tri-Py+-Me-PF was used in the experiments with buffer solution, and 10 to 50 μM in the experiments with aquaculture water. Artificial white light (4.0 mW cm-2) and solar irradiation (40 mW cm-2) were used as light sources.

Nanocomposites as probes for biodetection by SERS

The present work aimed to explore the potential of new nanocomposites based on carbon nanostructures and metal nanoparticles for the detection of biomolecules through surface enhanced Raman scattering (SERS). In a first step, polyvinyl alcohol composites were prepared incorporating silver nanoparticles by two different reduction procedures. At first without introduction of carbon nanostructures. These composites showed good results for the SERS identification of nucleic acids. Next, the synthesis and characterization of graphene oxide was studied to be used in the preparation of silver and gold nanocomposites. The reduction of this nanomaterial with different chemical agents was explored, since its reduction degree may be a determinant factor for the application envisaged (biomolecules interaction). The preparation of the nanocomposites with silver and gold was performed with different reducing agents. The SERS activity of these new nanocomposites was then explored in the presence of different analytes, varying the experimental conditions for Raman spectra acquisition. It was interesting to verify that the silver containing nanocomposites presented the particularity to intensify the graphene D and G bands. It is also important to highlight that a new eco-friendly reducing agent was tested for the synthesis of the graphene oxide composites, an Eucalyptus Globulus extract. Other variable introduced was the preparation of gold nanostars synthesized with hydroxylamine in the presence of graphene oxide, which allowed the preparation of a new nanocomposite with SERS potential. Fibrous membranes were also prepared by electrospinning with the aim to prepare SERS supports with adequate topography and porosity for the formation of nanoparticles agglomerates for the creation of the so-called hot-spots and also to allow the penetration of the analyte molecules. The polymers polyvinyl alcohol and polyacrylonitrile were selected for electrospinning. Using this technique, electrospun mantles with silver and gold nanoparticles and nanocomposites were prepared. Several variables were studied, such as the introduction of the nano-fillers during the electrospinning process, later deposition of the nano-fillers on the simple electrospun polymeric fibres and surface functionalization of the simple polymeric membranes to link the nano-fillers. At last, the potentialities of using carbon nanotubes forests, produced by chemical vapor deposition and coated with gold film by sputtering, as new SERS substrates were explored. It was found that the SERS detection of DNA bases and ADN itself is possible using these substrates.

Development of infrared spectroscopy for assessing bacterial quality in foods

Rapid and specific detection of foodborne bacteria that can cause food spoilage or illness associated to its consumption is an increasingly important task in food industry. Bacterial detection, identification, and classification are generally performed using traditional methods based on biochemical or serological tests and the molecular methods based on DNA or RNA fingerprints. However, these methodologies are expensive, time consuming and laborious. Infrared spectroscopy is a reliable, rapid, and economic technique which could be explored as a tool for bacterial analysis in the food industry. In this thesis it was evaluated the potential of IR spectroscopy to study the bacterial quality of foods. In Chapter 2, it was developed a calibration model that successfully allowed to predict the bacterial concentration of naturally contaminated cooked ham samples kept at refrigeration temperature during 8 days. In this part, it was developed the methodology that allowed the best reproducibility of spectra from bacteria colonies with minimal sample preparation, which was used in the subsequent work. Several attempts trying different resolutions and number of scans in the IR were made. A spectral resolution of 4 cm-1, with 32 scans were the settings that allowed the best results. Subsequently, in Chapter 3, it was made an attempt to identify 22 different foodborne bacterial genera/species using IR spectroscopy coupled with multivariate analysis. The principal component analysis, used as an exploratory technique, allowed to form distinct groups, each one corresponding to a different genus, in most of the cases. Then, a hierarchical cluster analysis was performed to further analyse the group formation and the possibility of distinction between species of the same bacterial genus. It was observed that IR spectroscopy not only is suitable to the distinction of the different genera, but also to differentiate species of the same genus, with the simultaneous use of principal component analysis and cluster analysis techniques. The utilization of IR spectroscopy and multivariate statistical analysis were also investigated in Chapter 4, in order to confirm the presence of Listeria monocytogenes and Salmonella spp. isolated from contaminated foods, after growth in selective medium. This would allow to substitute the traditional biochemical and serological methods that are used to confirm these pathogens and that delay the obtainment of the results up to 2 days. The obtained results allowed the distinction of 3 different Listeria species and the distinction of Salmonella spp. from other bacteria that can be mistaken with them. Finally, in chapter 5, high pressure processing, an emerging methodology that permits to produce microbiologically safe foods and extend their shelf-life, was applied to 12 foodborne bacteria to determine their resistance and the effects of pressure in cells. A treatment of 300 MPa, during 15 minutes at room temperature was applied. Gram-negative bacteria were inactivated to undetectable levels and Gram-positive showed different resistances. Bacillus cereus and Staphylococcus aureus decreased only 2 logs and Listeria innocua decreased about 5 logs. IR spectroscopy was performed in bacterial colonies before and after HPP in order to investigate the alterations of the cellular compounds. It was found that high pressure alters bands assigned to some cellular components as proteins, lipids, oligopolysaccharides, phosphate groups from the cell wall and nucleic acids, suggesting disruption of the cell envelopes. In this work, bacterial quantification and classification, as well as assessment of cellular compounds modification with high pressure processing were successfully performed. Taking this into account, it was showed that IR spectroscopy is a very promising technique to analyse bacteria in a simple and inexpensive manner.

FTIR, a potential tool to dementia diagnosis trough analysis of plasma

Nowadays it is still difficult to perform an early and accurate diagnosis of dementia, therefore many research focus on the finding of new dementia biomarkers that can aid in that purpose. So scientists try to find a noninvasive, rapid, and relatively inexpensive procedures for early diagnosis purpose. Several studies demonstrated that the utilization of spectroscopic techniques, such as Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopy could be an useful and accurate procedure to diagnose dementia. As several biochemical mechanisms related to neurodegeneration and dementia can lead to changes in plasma components and others peripheral body fluids, blood-based samples and spectroscopic analyses can be used as a more simple and less invasive technique. This work is intended to confirm some of the hypotheses of previous studies in which FTIR was used in the study of plasma samples of possible patient with AD and respective controls and verify the reproducibility of this spectroscopic technique in the analysis of such samples. Through the spectroscopic analysis combined with multivariate analysis it is possible to discriminate controls and demented samples and identify key spectroscopic differences between these two groups of samples which allows the identification of metabolites altered in this disease. It can be concluded that there are three spectral regions, 3500-2700 cm -1, 1800-1400 cm-1 and 1200-900 cm-1 where it can be extracted relevant spectroscopic information. In the first region, the main conclusion that is possible to take is that there is an unbalance between the content of saturated and unsaturated lipids. In the 1800-1400 cm-1 region it is possible to see the presence of protein aggregates and the change in protein conformation for highly stable parallel β-sheet. The last region showed the presence of products of lipid peroxidation related to impairment of membranes, and nucleic acids oxidative damage. FTIR technique and the information gathered in this work can be used in the construction of classification models that may be used for the diagnosis of cognitive dysfunction.