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Expression, localisation, and interactome of the RefZ protein during sporulation in Bacillus subtilis.
Paliesková, Anna Mária ; Krásný, Libor (advisor) ; Nešvera, Jan (referee)
Bacillus subtilis is a gram-positive sporulating bacterium. Under unfavorable conditions, it initiates the sporulation process that results in a resistant spore. The transcription factor Spo0A is a master regulator of sporulation initiation. The hallmark of sporulation is the formation of an asymmetric septum near a cell pole, which divides the cell into the larger mother cell and smaller prespore. The asymmetric septum is localized at 1/6 of the cell length relative to the nearer pole. One of the players involved in this localization is the RefZ protein, referred to as the FtsZ regulatory protein, which forms the Z-ring. The Z-ring is important for the formation of both the vegetative (mid-cell) and asymmetric septa. RefZ facilitates the relocalization of the Z-ring from midcell to the poles at an early stage of sporulation. RefZ also binds DNA (RefZ binding motifs [RBMs]) near the ori site of the chromosome, thereby promoting precise positioning of the chromosome arms during sporulation. The entire sporulation process is controlled by a cascade of compartment-specific sporulation σ factors that recognize specific consensus sequences in the promoter regions of genes, thereby allowing RNA polymerase to initiate transcription of sporulation-specific genes. These σ factors ensure spatially and...
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The omega subunit of Bacillus subtilis RNA polymerase.
Mikesková, Klára ; Krásný, Libor (advisor) ; Nešvera, Jan (referee)
Transcription is catalysed by the enzyme RNA polymerase (RNAP). RNAP contains a core made up of two α subunits, one of each β, β'and ω. These subunits are conserved in all bacteria. The ω subunit is a small subunit with a molecular weight of 7.6 kDa that binds β'. ω is important for the folding and integrity of RNAP and promoter selection. This was shown by experiments performed with Gram-negative bacteria but the knowledge about in Gram-positive bacteria is minimal. In my Diploma Thesis, I characterized from the model Gram-positive bacterium from the phylum Firmicutes, Bacillus subtilis. First, I prepared various expression strains for isolation of Bacillus subtilis ω. Then, I successfully isolated the ω subunit, which was the main initial aim of this Diploma Thesis. Subsequently, I tested the influence of the ω subunit on in vitro transcription by RNAP associated with the primary σA factor and alternative σF and σE factors that regulate sporulation in Bacillus subtilis. I also evaluated the effect of , a small RNAP subunit found in Firmicutes, both alone and in combination with . The experiments revealed that ω stimulated transcription both from vegetative promoters and sporulation-related promoters. Moreover, this stimulation was synergistically amplified by the δ subunit. This nicely...
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Role of the yxkO gene of Bacillus subtilis in responce to environmental stress.
Petrovová, Miroslava ; Lichá, Irena (advisor) ; Nešvera, Jan (referee)
ROLE OF THE YXKO GENE OF BACILLUS SUBTILIS IN RESPONCE TO ENVIRONMENTAL STRESS Abstract Mutation of the yxkO gene, which encodes a putative ribokinase and belongs to the σB general stress response regulon, leads to reduced salt tolerance under potassium limitation in Bacillus subtilis. The biological function of the yxkO gene has not been determined yet, but it may be involved in the high affinity potassium uptake system, which has been described in Escherichia coli in contrast to Bacillus subtilis. Our goal was to describe another features of a mutant in the yxkO gene and to try to propose the role of this gene. Using the integration vector pMutin4, we prepared a Bacillus subtilis strain MP2 with a yxkO gene inactivation. The MP2 strain displays limited growth in a rich medium and it is a sensitive strain to tetracycline. Furthermore, this strain is unable to form endospores and the cells are longer, which indicates a septum formation defect. We accomplished a 2-D protein gel analysis to compare expression profiles of the MP2 strain and the 1A680 standard strain after salt and ethanol stress. The MP2 strain shows changes in productions of some energy metabolism enzymes and flagellin protein. We conclude that yxkO is a regulatory gene, whose product has a pleiotropic effect on many of cell functions.
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The role of alternative sigma factors of RNA polymerase in regulation of gene expression in Corynebacterium glutamicum
Šilar, Radoslav ; Nešvera, Jan (advisor) ; Branny, Pavel (referee) ; Lichá, Irena (referee)
Abstract Regulation of transcription by extracytoplasmic-function (ECF) sigma factors of RNA polymerase is an efficient way of cell adaptation to diverse environmental stresses. Amino acid-producing gram-positive bacterium Corynebacterium glutamicum codes for seven sigma factors: the primary sigma factor SigA, the primary-like sigma factor SigB and five ECF stress- responsive sigma factors (SigC, SigD, SigE, SigH and SigM). The sigH gene encoding SigH sigma factor is located in a gene cluster together with the rshA gene, encoding the anti-sigma factor of SigH. Anti-sigma factors bind to their cognate sigma factors and inhibit their transcriptional activity. Under the stress conditions the binding is released allowing the sigma factors to bind to the RNAP core enzyme. In this thesis, regulation of expression of genes encoding the most important ECF sigma factor SigH and its anti-sigma factor RshA as well as genes belonging to the SigH-regulon were mainly studied. The transcriptional analysis of the sigH-rshA operon revealed four housekeeping promoters of the sigH gene and one SigH-dependent promoter of the rshA gene. For testing the role of the complex SigH-RshA in gene expression, the C. glutamicum ΔrshA strain was used for genome-wide transcription profiling with DNA Microarrays technique under...
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SigN from Bacillus subtilis: Functional characterization.
Kambová, Milada ; Krásný, Libor (advisor) ; Nešvera, Jan (referee)
Bacillus subtilis strain 3610 is an ancestral undomesticated strain. It diers from the laboratory strain 168 in many aspects. One dierence in strain 3610 is the presence of plasmid pBS32 encoding the sigma factor N (σN). This σ factor is activated when DNA damage occurs and induces the bacteria's cell death. The aim of the Thesis was a systematic characterisation of σN-dependent transcription. First, I showed that plasmid-borne but not chromosome-borne predicted σN-dependent promoters were ac- tive in transcription in vitro. Next, the anities of RNAP with σN for DNA, initiating NTP (iNTP) were determined for both relaxed and supercoiled DNA templates. Sur- prisingly, the activity of RNAP on relaxed σN-dependent promoters was higher than on their supercoiled versions, an opposite trend than displayed by RNAP associated with other σ factors. This property of σN-dependent promoters was not encoded by the core promoter sequence. In summary, this Thesis contributed to our understanding of the bacterial transcription apparatus. 1
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The role of alternative sigma factors of RNA polymerase in regulation of gene expression in Corynebacterium glutamicum
Šilar, Radoslav ; Nešvera, Jan (advisor) ; Branny, Pavel (referee) ; Lichá, Irena (referee)
Abstract Regulation of transcription by extracytoplasmic-function (ECF) sigma factors of RNA polymerase is an efficient way of cell adaptation to diverse environmental stresses. Amino acid-producing gram-positive bacterium Corynebacterium glutamicum codes for seven sigma factors: the primary sigma factor SigA, the primary-like sigma factor SigB and five ECF stress- responsive sigma factors (SigC, SigD, SigE, SigH and SigM). The sigH gene encoding SigH sigma factor is located in a gene cluster together with the rshA gene, encoding the anti-sigma factor of SigH. Anti-sigma factors bind to their cognate sigma factors and inhibit their transcriptional activity. Under the stress conditions the binding is released allowing the sigma factors to bind to the RNAP core enzyme. In this thesis, regulation of expression of genes encoding the most important ECF sigma factor SigH and its anti-sigma factor RshA as well as genes belonging to the SigH-regulon were mainly studied. The transcriptional analysis of the sigH-rshA operon revealed four housekeeping promoters of the sigH gene and one SigH-dependent promoter of the rshA gene. For testing the role of the complex SigH-RshA in gene expression, the C. glutamicum ΔrshA strain was used for genome-wide transcription profiling with DNA Microarrays technique under...
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Analysis og gene expression in prokaryotic and eukaryotic model organisms by proteomic gel-based separation tools
Petráčková, Denisa ; Weiser, Jaroslav (advisor) ; Nešvera, Jan (referee) ; Stulík, Jiří (referee)
This PhD thesis showed the applicability of a gel-based proteomic separation tool, 2-D electrophoresis in three independent projects. Supplemented with results obtained using different techniques the proteomic studies enabled a global imaging of proteoms in the studied biological systems. Comparing total proteoms of E. coli 61 protein changes were identified and connected with the development of the bacterial population in the presence of an antibiotic compound, erythromycin. This classic proteomic approach included sample extraction, optimization of its 2D separation followed by 2D gel analysis and protein identification by MS methods. A disadvantage of this work was an enourmously large amount of data to be analyzed by computer analysis. For the study of membrane proteom of B. subtilis during a pH induced stress, on the other hand, a modification of isolation techniques for membrane and membrane associated proteins was required first to improve the subsequent protein separation by 2-D electrophoresis. The optimalization of protein extraction included changes in detergents used for protein solubilization and a prolongation of time periods in the protein solubilization protocol. 5 relevant protein changes were then described that play a role in the bacterial response to pH stress. The proteins were...
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Functional studies of Ser/Thr protein kinases and phosphatases of Pseudomonas aeruginosa
Goldová, Jana ; Branny, Pavel (advisor) ; Nešvera, Jan (referee) ; Španová, Alena (referee)
Reversible protein phosphorylation is considered the universal language for intracellular communication in all living organisms. This process, catalysed by protein kinases and phosphatases, enables the translation of extracellular signals into cellular responses and also allows for adaptation to a constantly changing environment. In recent years, a number of bacterial eukaryotic-type Ser/Thr protein kinases and phosphatases have been identified. However, their precise functions and substrates are not yet well defined. The genome of opportunistic human pathogen Pseudomonas aeruginosa contains at least five genes encoding putative eukaryotic-type Ser/Thr protein kinases and phosphatases. In the first part of this study, we have attempted to establish the role of Ser/Thr protein kinase PpkA and phosphatase PppA, which belong to type VI secretion system H1-T6SS. Double mutant strain ∆pppA-ppkA was prepared in P. aeruginosa PAO1 background. Phenotypic studies revealed that the mutant grew slower than the wild-type strain in minimal media and exhibited reduced secretion of pigment pyocyanin. In addition, the mutant had altered sensitivity to oxidative and hyperosmotic stress conditions. Consequently, mutant cells had an impaired ability to survive in murine macrophages and an attenuated virulence in the...
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Function of alternative sigma factors of RNA polymerase in stress response of Corynebacterium glutamicum
Dostálová, Hana ; Nešvera, Jan (advisor) ; Lichá, Irena (referee)
The aim of this thesis was to contribute to understanding of the functions of the alternative sigma factors of RNA polymerase, σH a σM , during stress response of C. glutamicum. The role of σH and σM in the transcription of the gene sigM encoding σM and the genes of the operon dnaK-grpE-dnaJ-hspR which encode proteins involved in heat-shock response of C. glutamicum was studied. The promoters of the tested genes were cloned into the "promoter-probe" vector pET2 and their activity was determined by the measuring of specific activity of the reporter enzyme chloramfenicol acetyltransferase. It was found, that the heat stress has a moderate positive effect on the activity of the promoter of the gene sigM (P-sigM), whereas no effect of the oxidative stress induced by diamide was found. It was proved, that deletion of the gene sigH or sigM itself does not lead to decrease of activity of the promoter P-sigM neither in standard conditions nor after heat-shock. On the other hand, complete abolition of the activity of the promoter P-sigM was observed in the strain C. glutamicum ∆sigH∆sigM. The promoter of the gene sigM is thus recognized in standard conditions and after heat stress is recognized by both sigma factors σH and σM , but not by the sigma factor σA . It was shown, that mutation in the -10 region...
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