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Characteristics of expression vectors for Corynebacterium glutamicum and their use for studies of sigma factors of RNA polymerase
Dvořáková, Pavla ; Pátek, Miroslav (advisor) ; Konopásek, Ivo (referee)
The aim of the thesis was to characterize chosen expression vectors used in biotechnologically important bacterial species, Corynebacterium glutamicum, and to test their use in studies of promoter activity control by sigma factors of RNA polymerase. Different properties of these vectors (level of expression of the cloned gene, leaky expression without inducer, dependence of expression level on inducer concentration and cell population homogeneity) were found by determination of expression level of the model gfpuv gene by fluorescence intensity assay of the produced protein and by gfpuv-expressing C. glutamicum cell population analysis using flow cytometry. The vector pEC-XT99A was chosen for testing the bi-plasmid system for assignment of a sigma factor to the chosen promoter. Although the level of expression provided by pEC-XT99A was not high, the vector showed no leaky expression, expression from the vector was comparable for a wide range of IPTG concentrations and the cell population was homogenous concerning the gene expression. Using pEC-XT99A from which individual stress sig genes were expressed, the σD factor was clearly assigned to the up-to-now unknown Pcg0420 promoter. Another vector for isolation and purification of C. glutamicum proteins was used to express the C. glutamicum sigM gene and to...
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Membrane interactions studied by advanced fluorescent techniques: From ions to macromolecules
Pokorná, Šárka ; Hudeček, Jiří (advisor) ; Konopásek, Ivo (referee) ; Benda, Aleš (referee)
Advanced fluorescence techniques were used to explore tree distinct topics concerning biological membrane and their interactions. Following thesis is according to the topic divided into three parts: 1) Ionic effects were studied employing time dependent fluorescence shift experiments and molecular dynamic simulations. Combination of these two approaches are suitable to reveal characteristic like mobility and hydration of particular bilayer segment, lipid packing or ion binding sites. Halide anions were reported to adsorb to the cationic lipid bilayer specifically, altering membrane mobility and organization. Changes in observed parameters follows Hofmeister order. Their effect is mediated either by direct ionic interaction (soft, polarizable ions) as well as via alteration of water structure (hard, non-polarizable ions) in proximity of ion molecule. Further, divalent calcium was shown to bind strongly to neutral and negatively charged lipid bilayers. Several types of binding sites depending on calcium concentration were identified. 2) Two complementary lipopeptides, CPK and CPE, incorporated into distinct lipid bilayers serve as a minimal model inducing membrane fusion. Effectiveness of fusion event might be influenced by lipopeptide-membrane and lipopeptide-lipopeptide interaction. To reveal...
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Study of the interaction between fungus Pleurotus ostreatus and bacterial cultures on the abiotic surfaces - morphological, biochemical and proteomic analysis
Kozická, Barbora ; Petráčková, Denisa (advisor) ; Konopásek, Ivo (referee)
Ligninolytic fungi are well known for their ability to degrade a wide range of xenobiotics contaminating the environment, including synthetic industrial dyes. In this work Pleurotus ostreatus was used for decolorization of a synthetic textile dye Remazol Brilliant Blue R (RBBR). To set up a model fungal "fixed-bed" bioreactor the fungus was immobilized on a polyurethane foam and artificially contaminated with a model bacterium Rhodococcus erythropolis. The development of bacterial contamination can be expected during a real application of fungal bio filters in wastewater treatment. The main aim of the work was to study interspecies interactions in the model bioreactors during the dye decolorization. Ligninolytic enzyme activities were followed in the bioreactor cultures as markers of fungal biodegradation ability. In contrast to the controls, no bacterial growth was observed in the P. ostreatus bioreactor culture liquid. The results showed that fungal laccase, pH of the culture liquid, and glucose consumption by the fungus had no effect on the bacterial growth. However, 4*105 - 1,3*106 CFU/ml of R. erythropolis was detected to be associated with the fungal solid support. The presence of these bacteria had no effect on the decolorization performance of the bioreactors. Dye decolorization efficiency...
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Pore-forming properties of Bordetella pertussis CyaA toxin and composition of the lipid bilayer.
Rädisch, Robert ; Konopásek, Ivo (advisor) ; Krůšek, Jan (referee)
Bordetella pertussis produces many virulent factors including adenylate cyclase toxin (CyaA) This toxin preferentially invades cells of immune system with integrin receptor CD11b/CD18 and weakens the immune system of the host. CyaA affects invaded cells in two ways. First, CyaA creates a cation-selective pores in the membrane of invaded cell and causes colloidal osmotic lysis. Second, CyaA converts cytosolic ATP into signal molecule cAMP, which causes a loss of physiological function of invaded cell and also leads to cellular death. The aim of my thesis was to test a suitability of a new model system composed from synthetic lipids - diphytanoyls, for a characterization of pore-forming properties of adenylate cyclase toxin. In the past, asolectin model system comprising many different lipid was used for characterization but it was found to be too complex for defining the role of individual lipids in CyaA activity. Further the effect of cholesterol for activity of CyaA was studied in a new model system because it was found recently that translocation of adenylate cyclase domain takes place at lipids rafts with high concentration of cholesterol. The last aim of my thesis was to characterize a newly discovered type of channel with the two conductance levels. Key words: Bordetella pertussis, adenylate...
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The role of RTX domain in the activity of adenylate cyclase toxin from Bordetella pertussis
Klímová, Nela ; Bumba, Ladislav (advisor) ; Konopásek, Ivo (referee)
The adenylate cyclase toxin (CyaA) of Bordetella pertussis is a 1706-residue protein comprising an amino-terminal adenylate cyclase (AC) domain and a carboxy-terminal Repeat-in-Toxin (RTX) domain. The RTX domain is a hallmark of the family of RTX proteins, which are secreted from the cytosol of Gram-negative bacteria to the cell environment through the Type I Secretion System (T1SS). The RTX domain of CyaA consists of five blocks of RTX nonapetide repeats with a consensus sequence X-(L/I/V)-X-G-G-X-G- X-D. The aim of this work was to determine the role of the RTX domain in biological activities of CyaA and its role in the secretion of the toxin molecule from Bordetella pertussis. Systematic deletion analysis revealed that none of the prepared CyaA constructs was able to translocate its AC domain across the cytoplasmic membrane of host cells and make pores in target membranes. Moreover, deletion of individual RTX repeat blocks resulted in a very low efficacy of secretion of CyaA mutants into cell exterior. These data suggested that structural integrity of the RTX domain of CyaA is essential not only for cytotoxic activities of the toxin molecule but also for its secretion through the T1SS.
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Analysis of Memrane Proteins of Pathogenic Bacterim Francisella Tularensis
Schmidt, Monika ; Szotáková, Barbora (advisor) ; Černý, Jan (referee) ; Konopásek, Ivo (referee)
Charles University in Prague, Faculty of Pharmacy in Hradec Králové Department of Biochemical Sciences Candidate Mgr. Monika Schmidt Supervisor Doc. Ing. Barbora Szotáková, Ph.D. Title of Doctoral Thesis Analysis of membrane proteins of pathogenic bacterium Francisella tularensis Bacterium Francisella tularensis is highly infectious pathogen causing disease tularaemia. Due to the lack of standardization and little protection against highly virulent strains, the only vaccine developed against this pathogen is not allowed for clinical usage. Conserved hypothetical lipoprotein homological to thiol/disulfide oxidoreductase (DsbA) was recently described as essential virulence factor of Francisella tularensis. The dsbA gene deletion led to attenuation of the strain and development of immunoprotection. The DsbA protein sequence revealed the presence of carboxy-terminal DsbA_Com1-like domain harbouring the catalytic active site C-X-X-C and cis-proline and domain amino-terminal to FKBP type peptidyl-prolyl isomerase. This work was focused on functional a substrate characterization of DsbA protein. The functional analysis of this protein showed both the importance of the active site, cis-proline and the FKBP_N domain for the thiol/disulphide oxidoreductase activity. Further, this work also revealed the in...
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Simulation of the interaction of steroid allosteric modulators of NMDA receptors with membrane
Riedlová, Kamila ; Konopásek, Ivo (advisor) ; Novák, Josef (referee)
Molecular dynamics (MD) method allows the real-time monitoring of the system composed of molecules and atoms, such as phospholipid bilayer or biomolecule. Applications of MD are very common in drug design where the real experimental procedures could be much more financially- and time-consuming or even impossible. The aim of this project is to explain the applications and advantages of MD method in case of studies of lipid membranes, with a special emphasis on a study od neurosteriod behaviour in lipid bilayer. Properly designed and synthesized neurosteroids could be used for the treatment of the serious neurological diseases. This work also included the experimental data obtained by MD simulations for two neurosteroids - pregnanolone glutamate and pregnanolone sulphate. Behaviour of this molecules in model membranes was observed and analyzed by MD simulations. Key words: molecular dynamics simulation, model membrane, lipid bilayer, NMDA receptor, neurosteroids, pregnanolone glutamate, pregnanolone sulfate
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Intracellular life of pathogenic bacterium Francisella tularensis in the host.
Rädisch, Robert ; Konopásek, Ivo (advisor) ; Vopálenská, Irena (referee)
Francisella tularensis is a facultative intracellular pathogenic bacterium, which causes disease named tularemia. For the entrance to the host cells Francisella uses host's cell mechanisms by which it is incorporated into cell phagosome. Subsequently, it escapes from phagosome to cytosole where bacterial growth takes place. Some of bacteria are cleared from cytosol by autophagy, from another ones dsDNA is released. This DNA is recognized by cytosolic receptors, which form inflammasome complex. Inflammasome sets off pathway leading to the death of infected cell. Since the penetration to the cell Francisella modulates cell signallization in its own benefit to ensure enough time and nutrients for its growth. Francisella do not act only in the infected cells, where it reduces recognition of itself and clearance from cytosol, but it also induces secretion of factors, which moderate activation of adaptive immunity of the host. Key words: Francisella, tularemia, fagosome, inflammasome, autophagy, adaptive immunity
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Development and validation of methods for GMO detection
Hodek, Jan ; Ovesná, Jaroslava (advisor) ; Konopásek, Ivo (referee) ; Pazlarová, Jarmila (referee)
The present work is focused on the issue of genetically modified organisms (GMOs) detection in the plants and derived products. Existing legislation in the European Union regulates monitoring of GMO and lays down rules for their labeling and traceability. The aim was to contribute to solving certain issues of critical points in GMO detection. The first point was DNA extraction. The problem was adressed to the example of DNA extraction from the fruit of papaya and candied papaya. For both food products the suitability of the selected extraction methods was verified and confirmed by amplification of a specific DNA sequence by PCR. The second critical point was related to PCR inhibitors. We observed the effect of real-time PCR inhibition due to the influence of the residual EDTA and the residual amount of heavy metal ions, which were present in laboratory plastic. In both examples, the inhibition affects the PCR efficiency. Another critical point in the GMO detection is use of screening elements. That work was focused on false positive results. Development of new methods for GMO detection was another goal of this work. We have developed the method for garden pea taxon-specific gene quantification by real-time PCR. The method was tested on 13 cultivars of garden pea and several related plants of...
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Ecology of deadwood-associated fungi in the ecosystems of nature-like forests
Zrůstová, Petra ; Baldrian, Petr (advisor) ; Konopásek, Ivo (referee)
Dead wood plays an important role in forest ecosystems in the context of C dynamics, nutrient cycling, forest regeneration and biodiversity. Decaying wood sustains biodiversity by providing habitats and energy for fungi, bacteria, invertebrates, and many other organisms. Dead wood is resistant to decomposition and its decay is driven mainly by filamentous fungi. Community structure of wood- inhabiting fungi changes during decomposition, but the relationship between substrate quality and decomposer community is still poorly understood. This work studied fungal community composition with respect to tree species, stage of decay, volume and physico-chemical properties (such as pH, carbon and nitrogen content) of dead wood. Fungi were identified using next generation sequencing approaches - 454-pyrosequencing and Illumina MiSeq sequencing. Tree species, volume of dead wood (branches x logs) and stage of decay were the main variables affecting fungal community composition. Higher enzyme activities and content of fungal biomass indicate faster colonization of small branches than tree trunks by fungi. Fungal community composition, wood chemical properties and enzyme activities changed during decomposition. Both content of nitrogen and fungal biomass increased during decomposition. Enzyme activites peaked...
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