DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

A platform for anti-biofilm assays combining viability, biomass and matrix quantifications in susceptibility assessments of antimicrobials against Staphylococcus aureus biofilms

Bacteria can exist as planktonic, the lifestyle in which single cells exist in suspension, and as biofilms, which are surface-attached bacterial communities embedded in a selfproduced matrix. Most of the antibiotics and the methods for antimicrobial work have been developed for planktonic bacteria. However, the majority of the bacteria in natural habitats live as biofilms. Biofilms develop dauntingly fast high resistance towards conventional antibacterial treatments and thus, there is a great need to meet the demands of effective anti-biofilm therapy. In this thesis project it was attempted to fill the void of anti-biofilm screening methods by developing a platform of assays that evaluate the effect that screened compounds have on the total biomass, viability and the extracellular polysaccharide (EPS) layer of the biofilms. Additionally, a new method for studying biofilms and their interactions with compounds in a continuous flow system was developed using capillary electrochromatography (CEC). The screening platform was utilized with a screening campaign using a small library of cinchona alkaloids. The assays were optimized to be statistically robust enough for screening. The first assay, based on crystal violet staining, measures total biofilm biomass, and it was automated using a liquid handling workstation to decrease the manual workload and signal variation. The second assay, based on resazurin staining, measures viability of the biofilm, and it was thoroughly optimized for the strain used, but was then a very simple and fast method to be used for primary screening. The fluorescent resazurin probe is not toxic to the biofilms. In fact, it was also shown in this project that staining the biofilms with resazurin prior to staining with crystal violet had no effect on the latter and they can be used in sequence on the same screening plate. This sequential addition step was indeed a major improvement on the use of reagents and consumables and also shortened the work time. As a third assay in the platform a wheat germ agglutinin based assay was added to evaluate the effect a compound has on the EPS layer. Using this assay it was found that even if compounds might have clear effect on both biomass and viability, the EPS layer can be left untouched or even be increased. This is a clear implication of the importance of using several assays to be able to find “true hits” in a screening setting. In the pilot study of screening for antimicrobial and anti-biofilm effects using a cinchona alkaloid library, one compound was found to have antimicrobial effect against planktonic bacteria and prevent biofilm formation at low micromolar concentration. To eradicate biofilms, a higher concentration was needed. It was also shown that the chemical space occupied by the active compound was slightly different than the rest of the cinchona alkaloids as well as the rest of the compounds used for validatory screening during the optimization processes of the separate assays.

Parenteral administration of vitamins A, D and E on the oxidative metabolism and function of polymorphonuclear leukocytes in swine

The weaning period of piglets is characterized by physiological alterations, such as decreased weight gain, increased reactive oxygen species (ROS) and increased serum cortisol levels with possible effects on the immune response. The effect of parenteral administration of vitamins A, D and E on production performance, oxidative metabolism, and the function of polymorphonuclear leukocytes (PMNLs) was assessed in piglets during the weaning period. The sample was comprised of 20 male piglets that were given an injectable ADE vitamin combination (135,000 IU vitamin A, 40,000 IU vitamin D and 40mg vitamin E/ animal) at 20 and 40 days of age. Weight gain, concentration of reduced glutathione (GSH), malondialdehyde (MDA), superoxide dismutase (SOD) and the microbicidal and phagocytic activity of PMNLs were assessed. No difference was observed in the average piglet weight during the study; however, a greater percentage of weight gain was observed after weaning in the treated group. The concentrations of GSH and SOD did not differ between groups, although lipid peroxidation was greater in the control group at 60 days of age. The investigated variables of oxidative metabolism were correlated as follows: -0.41 for GSH and MDA, -0.54 for GSH and SOD and 0.34 for MDA and SOD. The intensity of intracellular ROS production, the percentage of ROS-producing PMNLs and the intensity of phagocytosis by PMNLs did not differ between treatment groups. Administration of the injectable ADE combination improved the percentage of weight gain between 20 and 40 days of age, decreased oxidative stress at 60 days of age and did not influence the function of PMNLs in piglets.

Oxidative metabolism and muscle biochemical profile of polo horses supplemented with an ADE vitamin complex

Horses used for the game of polo experience abrupt and frequent changes in exercise intensity. To meet this variable energy demand, the horses use both aerobic and anaerobic pathways in varying proportions and intensities. In this context, there must be a balance between the formation of reactive oxygen species (ROS) and the action of antioxidants to prevent oxidative stress and its consequences. The effect of supplementation with an ADE vitamin complex on oxidative metabolism was evaluated in 18 crossbred horses randomly divided between a treated group (TG) and a control group (CG). The TG animals received the ADE vitamin complex (1mL/50 kg of body weight) by deep intramuscular injection at 30 and 15 days before the game. The CG horses received 10ml of saline by the same administration route and schedule. During the polo match, the animals played for a total of 7.5 min. Blood samples were collected on the same days as the treatments were administered, and immediately before and at 15, 90 and 180 minutes after the game. The concentrations of creatine phosphokinase (CK), lactate dehydrogenase (LDH), lactate, glucose, aspartate aminotransferase (AST), glutathione (GSH), superoxide dismutase (SOD) and malondialdehyde (MDA) were measured in the blood samples. After the game, the TG demonstrated higher levels of AST, lactate and glucose than the CG, suggesting more efficient energy use by the treated animals. The higher GSH and lower lactate levels in the TG before the game suggest the presence of a greater antioxidant supply in the treated animals. The maintenance of the MDA levels indicates that neither of the groups exhibited oxidative stress.

Regulation of photosynthetic electron transfer in plant chloroplasts

This thesis focuses on the molecular mechanisms regulating the photosynthetic electron transfer reactions upon changes in light intensity. To investigate these mechanisms, I used mutants of the model plant Arabidopsis thaliana impaired in various aspects of regulation of the photosynthetic light reactions. These included mutants of photosystem II (PSII) and light harvesting complex II (LHCII) phosphorylation (stn7 and stn8), mutants of energy-dependent non-photochemical quenching (NPQ) (npq1 and npq4) and of regulation of photosynthetic electron transfer (pgr5). All of these processes have been extensively investigated during the past decades, mainly on plants growing under steady-state conditions, and therefore many aspects of acclimation processes may have been neglected. In this study, plants were grown under fluctuating light, i.e. the alternation of low and high intensities of light, in order to maximally challenge the photosynthetic regulatory mechanisms. In pgr5 and stn7 mutants, the growth in fluctuating light condition mainly damaged PSI while PSII was rather unaffected. It is shown that the PGR5 protein regulates the linear electron transfer: it is essential for the induction of transthylakoid ΔpH that, in turn, activates energy-dependent NPQ and downregulates the activity of cytochrome b6f. This regulation was shown to be essential for the photoprotection of PSI under fluctuations in light intensity. The stn7 mutants were able to acclimate under constant growth light conditions by modulating the PSII/PSI ratio, while under fluctuating growth light they failed in implementing this acclimation strategy. LHCII phosphorylation ensures the balance of the excitation energy distribution between PSII and PSI by increasing the probability for excitons to be trapped by PSI. LHCII can be phosphorylated over all of the thylakoid membrane (grana cores as well as stroma lamellae) and when phosphorylated it constitutes a common antenna for PSII and PSI. Moreover, LHCII was shown to work as a functional bridge that allows the energy transfer between PSII units in grana cores and between PSII and PSI centers in grana margins. Consequently, PSI can function as a quencher of excitation energy. Eventually, the LHCII phosphorylation, NPQ and the photosynthetic control of linear electron transfer via cytochrome b6f work in concert to maintain the redox poise of the electron transfer chain. This is a prerequisite for successful plant growth upon changing natural light conditions, both in short- and long-term.

Toxic action of aqueous wheat straw extract on horse e purslane

The toxic action of aqueous wheat (Triticum aestivum) straw extracts was investigated on germination, early seedling growth, some biochemical attributes and the antioxidant enzymes of horse purslane (Trianthemaportulacastrum). Aqueous extracts of wheat straw were prepared by soaking the wheat straw in distilled water in 1:10 w/v ratio and diluted to obtain the concentrations of 0, 25, 50, 75 and 100%. These were used as pre and post emergence in laboratory and screen house trials. Wheat aqueous extracts exhibited phytotoxicity to horse purslane by inhibiting and delaying its germination and suppressing seedling growth. Wheat phytotoxins in its aqueous extracts suppressed the chlorophyll content and soluble protein, and enhanced soluble phenolics and the activity of antioxidant enzymes as catalase, peroxidase and superoxide dismutase in the seedlings of horse purslane compared with the control. Such inhibitory activity is believed to originate from exposure to wheat phytotoxins that are present in its aqueous straw extract. The suppressive effects of wheat straw need to be investigated further under field conditions.

Network connectance and autonomy analyses of the photosynthetic apparatus in tropical tree species from different successional groups under contrasting irradiance conditions

Biological systems are complex dynamical systems whose relationships with environment have strong implications on their regulation and survival. From the interactions between plant and environment can emerge a quite complex network of plant responses rarely observed through classical analytical approaches. The objective of this current study was to test the hypothesis that photosynthetic responses of different tree species to increasing irradiance are related to changes in network connectances of gas exchange and photochemical apparatus, and alterations in plant autonomy in relation to the environment. The heat dissipative capacity through daily changes in leaf temperature was also evaluated. It indicated that the early successional species (Citharexylum myrianthum Cham. and Rhamnidium elaeocarpum Reiss.) were more efficient as dissipative structures than the late successional one (Cariniana legalis (Mart.) Kuntze), suggesting that the parameter deltaT (T ºCair - T ºCleaf) could be a simple tool in order to help the classification of successional classes of tropical trees. Our results indicated a pattern of network responses and autonomy changes under high irradiance. Considering the maintenance of daily CO2 assimilation, the tolerant species (C. myrianthum and R. elaeocarpum) to high irradiance trended to maintain stable the level of gas exchange network connectance and to increase the autonomy in relation to the environment. On the other hand, the late successional species (C. legalis) trended to lose autonomy, decreasing the network connectance of gas exchange. All species showed lower autonomy and higher network connectance of the photochemical apparatus under high irradiance.

Photosynthetic responses of tropical tree species from different successional groups under contrasting irradiance conditions

This study evaluated the photosynthetic responses of seven tropical trees of different successional groups under contrasting irradiance conditions, taking into account changes in gas exchange and chlorophyll a fluorescence. Although early successional species have shown higher values of CO2 assimilation (A) and transpiration (E), there was not a defined pattern of the daily gas exchange responses to high irradiance (FSL) among evaluated species. Cariniana legalis (Mart.) Kuntze (late secondary) and Astronium graveolens Jacq. (early secondary) exhibited larger reductions in daily-integrated CO2 assimilation (DIA) when transferred from medium light (ML) to FSL. On the other hand, the pioneer species Guazuma ulmifolia Lam. had significant DIA increase when exposed to FSL. The pioneers Croton spp. trended to show a DIA decrease around 19%, while Cytharexyllum myrianthum Cham. (pioneer) and Rhamnidium elaeocarpum Reiss. (early secondary) trended to increase DIA when transferred to FSL. Under this condition, all species showed dynamic photoinhibition, except for C. legalis that presented chronic photoinhibition of photosynthesis. Considering daily photosynthetic processes, our results supported the hypothesis of more flexible responses of early successional species (pioneer and early secondary species). The principal component analysis indicated that the photochemical parameters effective quantum efficiency of photosystem II and apparent electron transport rate were more suitable to separate the successional groups under ML condition, whereas A and E play a major role to this task under FSL condition.

Talousvesilaitoksen saostusvaiheen tehostaminen esihapetuksella – Case Suomen Sokeri Oy:n vedenkäsittely

Diplomityö tehtiin Suomen Sokeri Oy:n vesilaitokselle Vihreän Kemian laboratoriossa. Prosessia tarkasteltiin saostuksen osalta ja tavoitteena oli sen kehittäminen esihapetusmenetelmän tai saostuskemikaalin vaihdon avulla. Tarkastelu tehtiin orgaanisen, kiintoaineksen ja metallien poiston, desinfiointitehon sekä ympäristöystävällisyyden osalta. Potentiaalisia esihapetusmenetelmiä (kaliumpermanganaatti, vetyperoksidi, valokemiallinen, H2O2/UV, valokatalyyttinen, TiO2/UV, H2O2/ultraääni sekä esihapetus peretikkahapolla) tarkasteltiin eri pitoisuuksilla ja tehoilla laboratoriomittakaavassa jar-testin avulla. Saostustehoa testattiin alumiinikloridilla ja ferrisulfaatilla. Raakaveden laadun muutoksia eri vaiheissa seurattiin laboratorioanalyysein. Hapetusmenetelmien desinfiointiteho, vaikutukset syanobakteereihin ja -toksiineihin sekä reaktioissa syntyvät sivutuotteet kartoitettiin teorian perusteella. Työn tuloksien perusteella kaliumpermanganatti, vetyperoksidi erityisesti kehittyneenä hapetustekniikkana sekä valokatalyyttinen menetelmä tehostivat vedenkäsittelyä, mutta koska TiO2/UV- tai ultraäänihapetukselle ei ole vielä olemassa kaupallista sovellusta laitosmittakaavassa niin suositeltavat menetelmät ovat KMnO4- ja H2O2(/UV)-hapetukset jatkotutkimussuositukset huomioiden. Peretikkahappo ei tämän tutkimuksen perusteella vaikuttanut suositeltavalta hapetusmenetelmältä, mutta sen sijaan teorian perusteella potentiaaliselta desinfektioaineelta myös talousvedenpuhdistukseen. Opinnäytetyötä eri hapetusmenetelmien osalta talousvedelle ei ole aiemmin tehty eikä peretikkahappohapetuksesta ole laajalti aiempaa tutkimustietoa. Kokeellisen osuuden tulokset antavat uutta tietoa menetelmien soveltuvuudesta vastaaville laitoksille.

Molecular Mechanisms and Interactions in Regulation of Photosynthetic Reactions

In photosynthesis, light energy is converted to chemical energy, which is consumed for carbon assimilation in the Calvin-Benson-Bassham (CBB) cycle. Intensive research has significantly advanced the understanding of how photosynthesis can survive in the ever-changing light conditions. However, precise details concerning the dynamic regulation of photosynthetic processes have remained elusive. The aim of my thesis was to specify some molecular mechanisms and interactions behind the regulation of photosynthetic reactions under environmental fluctuations. A genetic approach was employed, whereby Arabidopsis thaliana mutants deficient in specific photosynthetic protein components were subjected to adverse light conditions and assessed for functional deficiencies in the photosynthetic machinery. I examined three interconnected mechanisms: (i) auxiliary functions of PsbO1 and PsbO2 isoforms in the oxygen evolving complex of photosystem II (PSII), (ii) the regulatory function of PGR5 in photosynthetic electron transfer and (iii) the involvement of the Calcium Sensing Receptor CaS in photosynthetic performance. Analysis of photosynthetic properties in psbo1 and psbo2 mutants demonstrated that PSII is sensitive to light induced damage when PsbO2, rather than PsbO1, is present in the oxygen evolving complex. PsbO1 stabilizes PSII more efficiently compared to PsbO2 under light stress. However, PsbO2 shows a higher GTPase activity compared to PsbO1, and plants may partially compensate the lack of PsbO1 by increasing the rate of the PSII repair cycle. PGR5 proved vital in the protection of photosystem I (PSI) under fluctuating light conditions. Biophysical characterization of photosynthetic electron transfer reactions revealed that PGR5 regulates linear electron transfer by controlling proton motive force, which is crucial for the induction of the photoprotective non-photochemical quenching and the control of electron flow from PSII to PSI. I conclude that PGR5 controls linear electron transfer to protect PSI against light induced oxidative damage. I also found that PGR5 physically interacts with CaS, which is not needed for photoprotection of PSII or PSI in higher plants. Rather, transcript profiling and quantitative proteomic analysis suggested that CaS is functionally connected with the CBB cycle. This conclusion was supported by lowered amounts of specific calciumregulated CBB enzymes in cas mutant chloroplasts and by slow electron flow to PSI electron acceptors when leaves were reilluminated after an extended dark period. I propose that CaS is required for calcium regulation of the CBB cycle during periods of darkness. Moreover, CaS may also have a regulatory role in the activation of chloroplast ATPase. Through their diverse interactions, components of the photosynthetic machinery ensure optimization of light-driven electron transport and efficient basic production, while minimizing the harm caused by light induced photodamage.

Photosynthetic properties of three Brazilian seaweeds

Photosynthetic performance of distinct marine macroalgae, Ulva fasciata Delile (green alga), Lobophora variegata (J. V. Lamouroux) Womersley ex E. C. Oliveira (brown alga), and Plocamium brasiliensis (Greville) M. A. Howe & W. R. Taylor (red alga), were compared using a pulse amplitude-modulated fluorometer. The maximum quantum yield (Fv/Fm) ranged from 0.80 to 0.51, and the lowest value was found in P. brasiliensis. Under 400 µmol photons m-2 s-1 irradiance, the highest value of photochemical quenching (qP = 0.92 ± 0.13) was observed for U. fasciata. The red alga P. brasiliensis dissipated high amounts of excitation energy (qN = 0.56 ± 0.09), resulting in relatively low values for the effective quantum yield of PS-II (0.23 ± 0.04), as well as for the relative electron transport rate (3.3 ± 0.7). The high photosynthetic potential found for U. fasciata partially explains the species ability for rapid growth and high productivity.

Photosynthetic responses of four tropical tree species grown under gap and understorey conditions in a semi-deciduous forest

Leaf CO2 assimilation (A) as a function of photosynthetic photon flux density (Q) or intercellular CO2 concentration (Ci) and chlorophyll fluorescence measurements were carried out on four tropical woody species growing in forest gap and understorey (Bauhinia forficata Link. and Guazuma ulmifolia Lam. as pioneers, and Hymenaea courbaril L. and Esenbeckia leiocarpa Engl. as non-pioneers). Chlorophyll fluorescence indicated similar acclimation capacities of photochemical apparatus to contrasting light environments irrespective to plant species. Maximum CO2 assimilation and quantum yield derived from A/Q curves indicated higher photosynthetic capacity in pioneer than in non-pioneer species in forest gap. However, the differences among species did not show a straightforward relation with their successional status regarding data derived from A/Q curves under understorey conditions. Both successional groups are able to sustain positive carbon balance under contrasting natural light availabilities, modifying photochemical and biochemical photosynthetic traits with similar phenotypic plasticity capacity.

Effects of host resistance on the isozymatic patterns of Bipolaris sorokiniana (Dematiaceae, Moniliales)

Nine isolates of Bipolaris sorokiniana were inoculated on three cultivars of wheat plants (susceptible, moderately resistant, resistant). Eight days after the inoculation, the isolates were recovered (27 isolates) and the following isozymatic patterns were analyzed: esterase, alkaline phosphatase, acid phosphatase, malate dehydrogenase, and superoxide dismutase. The esterase system was the most polymorphic, and the isolates recovered from the susceptible cultivar showed the highest variability. This is evidence that this cultivar exerts low selection pressure on the pathogen

Effects of ouabain on vascular reactivity

Ouabain is an endogenous substance occurring in the plasma in the nanomolar range, that has been proposed to increase vascular resistance and induce hypertension. This substance acts on the a-subunit of Na+,K+-ATPase inhibiting the Na+-pump activity. In the vascular smooth muscle this effect leads to intracellular Na+ accumulation that reduces the activity of the Na+/Ca2+ exchanger and to an increased vascular tone. It was also suggested that circulating ouabain, even in the nanomolar range, sensitizes the vascular smooth muscle to vasopressor substances. We tested the latter hypothesis by studying the effects of ouabain in the micromolar and nanomolar range on phenylephrine (PE)-evoked pressor responses. The experiments were performed in normotensive and hypertensive rats in vivo, under anesthesia, and in perfused rat tail vascular beds. The results showed that ouabain pretreatment increased the vasopressor responses to PE in vitro and in vivo. This sensitization after ouabain treatment was also observed in hypertensive animals which presented an enhanced vasopressor response to PE in comparison to normotensive animals. It is suggested that ouabain at nanomolar concentrations can sensitize vascular smooth muscle to vasopressor stimuli possibly contributing to increased tone in hypertension

Application of various antioxidants in the treatment of influenza

We determined the effect of the antioxidants superoxide dismutase, desferrioxamine and allopurinol on the survival of male CBA mice infected intranasally with 2-5 LD50 lung influenza virus A/Aichi/2/68. Survival for at least 20 days was observed for 45% of the mice that received 1000 U/day superoxide dismutase prepared from red blood cells on days 5, 6, 7 and 8 after infection, and 75% survival was observed for mice that received the same dose on days 4, 5, 6, 7 and 8. Desferrioxamine, 25 mg/kg per day and 100 mg/kg per day injected subcutaneously, resulted in survival rates of 5 and 0%, respectively, compared to 10% survival observed for saline-injected controls. Allopurinol at doses of 5 to 50 mg/kg per day had no effect on mouse survival. These data demonstrate the efficacy of superoxide dismutase for the protection of mice against hemorrhagic lung edema. The ineffectiveness of allopurinol suggests that the xanthine oxidase system does not play a major role in hemorrhage or lung edema and that caution is necessary when desferrioxamine is administered during an acute inflammatory process accompanied by erythrocyte lysis