Dissertations / Theses: 'Sigma faktory'

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Fischer, Tim Steffen [Verfasser], and Matthias [Akademischer Betreuer] Herrmann. "Aktivität und Funktion des alternativen Sigma-Faktors δΗ in Staphylococcus aureus / Tim Steffen Fischer. Betreuer: Matthias Herrmann." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2016. http://d-nb.info/1101454725/34.

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Alcayaga, Christian Junior, and Ebba Adolfsson. "Implementering av strategi för kvalitetskontroll : Viktiga faktorer att beakta vid tillämpning av MSA & SPS." Thesis, Tekniska Högskolan, Jönköping University, JTH, Industriell organisation och produktion, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-49863.

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Černý, Zbyněk. "Vývoj rychlé metody cílené mutageneze bakterie Streptococcus zooepidemicus." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2016. http://www.nusl.cz/ntk/nusl-240515.

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This diploma thesis is focused on development of a fast method for site-directed gene mutagenesis in Streptococcus zooepidemicus based on the mechanism of natural competence. Several genes were selected based on experimental data which highly probably influence hyaluronic acid synthesis. The deletion of the selected genes from genomic DNA was performed as proof of concept, and the resulting recombinant strains were characterized regarding changes of hyaluronic acid precursor concentrations (glucuronic acid and N-acetylglucosamin) in time of cultivation and the end production of hyaluronic acid.

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Särnqvist, Linda, and Charlotte Bälter. "Kritiska faktorer i projektets tidiga faser -En studie av ABB Contracting, TietoEnator Processing&Network Support och Sigma Design&Development." Thesis, Linköping University, Department of Management and Economics, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-912.

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Att arbeta i projekt är historiskt ingen ny företeelse då idén om att strukturera upp arbetet i projektform är något vi burit med ossunder årtusenden. Trots att det med tiden vuxit fram nya bra idéer kring hur arbetet i projekt skall styras är det många av dagens företag som misslyckas med att uppnå de uppsatta målen. Hur kommer detta sig? Idag är många teoretiker inom projektområdet överens om att svaret många gånger ligger i projektets startfas. Förmågan att starta projekt anses vara alltför bristfällig i många företag. Att startfasens inverkan på projektets resultat blivit allt mer uppmärksammat kan bl.a. ses som ett resultat av pressen från marknaden. Den snabba tekniska utvecklingen har medfört ökade krav på allt mer tidspressade och komplexa projekt. Genom att lägga ned tid på förberedelserna under startfasen har företagen en bättre möjlighet att kunna minska projektets totala tid och därigenom skapa sig en bättre konkurrenssituation på marknaden. Trots insikten om startfasens inverkan på projektarbetet finns det få djupgående studier inom området "startfasen i projekt". Vårt mål med denna studie har därför varit att kartlägga startfasens roll i projektarbetet. I studien analyseras vidare vilka typer av problem som egentligen kan kopplas till ett projekts startfas, samt hur startfasens betydelse skiljer sig åt mellan olika typer av projekt. Vidare försöker vi klargöra om dagens krav på allt mer komplexa projekt ytterligare kommer förstärka startfasens påverkan på projektarbetet.För att kunna besvara dessa frågor har vi analyserat arbetet under startfasen i tre olika projekttyper i tre fallföretag, ABB Contracting, Sigma Design och Development samt TietoEnator Processing&Network Support

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Benda, Martin. "Regulace transkripce faktory sigma u Bacillus subtilis." Master's thesis, 2016. http://www.nusl.cz/ntk/nusl-351450.

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RNA polymerase (RNAP) is a key enzyme in regulation of bacterial gene expression. RNAP is multi-subunit enzyme and its σ subunits (factors) are used for DNA recognition. Regulation of RNAP complexed with the major σ factor has been thoroughly studied; in contrast, mechanisms of regulation of RNAP containing alternative σ factors are much less understood. This thesis is focused mainly on the model organism Bacillus subtilis and its alternative σ factors σF , σG , σI a σK . We studied the ability of RNAP in complex with these factors to recognize promoter sequences, to initiate transcription in dependence on the concentration of the initiating nucleoside triphosphate (iNTP), and to interact with selected proteins. For σF , a promoter regulated by the concentration of iNTP was discovered; for σI , to the contrary, this mechanism was not observed. In the case of σG -dependent transcription we were not able to examine regulation by the concentration of iNTP. Nevertheless, stimulation of σG -dependent transcription by a protein called YlyA, previously described in the literature, was confirmed. This stimulation was newly identified also for σF -dependent transcription. Further, we examined possible functional interaction between HelD and σK , but this link was not confirmed. Finally, this thesis...

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Blumenstein, Jan. "Hybridní faktory sigma RNA polymerasy u Corynebacterium glutamicum." Master's thesis, 2019. http://www.nusl.cz/ntk/nusl-404319.

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Corynebacterium glutamicum is a Gram-positive non-sporulating soil bacterium which is used in biotechnology as a producer of amino acids, nucleotides, biofuels and alcohols. The aim of this thesis was to create a hybrid σ factor of RNA polymerase which would be able to recognize a matching hybrid promoter without effect on expression of the host genes. Based on the σD and σH amino acid sequence, two types of hybrid factors, σDH and σHD , were designed by the sequence combination of sigD and sigH. As an alternative approach, based on the in silico homology modeling, mutations of wild-type σH in the region recognizing the -35 promoter element of the σH -dependent promoter were introduced. Hybrid promoters were constructed by combining the -35 and -10 promoter regions that were derived from the σD - and σH - dependent promoters. Promoter activity was determined by using gfpuv reporter gene under the control of hybrid promoter. The expression of gfpuv in strains with hybrid sigma factors σDH / σHD and hybrid promoters was rather low compared to strains that carried wild-type σ factor and the respective promoter. The aim of the thesis was achieved by using one of the mutant σH factor (σmutH_6A ) with alterations in the region recognizing the -35 element of the σH -dependent promoter. This mutant σ...

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Ramaniuk, Volha. "Faktory interagující s bakteriální RNA polymerázou a jejich vliv na regulaci iniciace transkripce." Doctoral thesis, 2019. http://www.nusl.cz/ntk/nusl-394901.

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(ENGLISH) The bacterial cell needs to regulate its gene expression in response to changing environmental conditions. RNA polymerase (RNAP) is the pivotal enzyme of this process and its activity is controlled by a number of auxiliary factors. Here I focus on RNAP-associating factors involved in regulation of transcription in G+ bacteria:  factors, initiating nucleoside triphosphates (iNTPs), HelD, δ and small RNA Ms1. The main emphasis is on σ factors from Bacillus subtilis. σ factors allow RNAP to specifically recognize promoter DNA. In my first project I set up in vitro transcription systems with purified alternative σ factors, σB , σD , σH , σI from B. subtilis. Using these systems, I studied the effect of initiating NTP concentration ([iNTP]) on transcription initiation. I showed that promoters of alternative  factors are often regulated by [iNTP]. In the next project I comprehensively characterized one of the least explored alternative  factors from B. subtilis, I . I identified ~130 genes affected by I , though only 16 of them were directly affected. Moreover, I discovered that I is involved in iron metabolism. Finally, I showed that I binding requires not only the conserved -35 and -10 hexamers, but also extended -35 and -10 elements located in the spacer region. In collaboration with...

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Straková, Eva. "Identifikace a modelování regulačních sítí genové exprese v průběhu germinace streptomycet." Doctoral thesis, 2013. http://www.nusl.cz/ntk/nusl-326738.

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Streptomycetes have been studied mostly as producers of antibiotics and for fundamentals of complex bacterial cell development. Here, transcriptomic and proteomic approaches were applied to systems study of Streptomyces coelicolor germination as a developmental transition from dormancy to the vegetative stage. The time dynamics of the gene expression levels represented by mRNA and intracellular protein accumulation and synthesis were measured throughout 5.5 h of germination at 13 time points by employing both DNA microarray and two-dimensional gel electrophoresis techniques. Using a numerical model of gene expression, genetic networks were reconstructed and functional groups of genes controlled by the sigma factors were identified. Modeling of the regulatory interactions provided a set of parameters allowing simulate kinetics of gene expression control among the sigma factors and their target genes. Particularly regulons of two sigma factors, SigR and HrdD, were identified. The analysis assigned their key role during the germination process. Analysis of global trends in the gene/protein expression revealed that the full capability of regulatory mechanisms responding to the environmental cues is reached within the first hour of germination, and identified the basic gene/protein functional groups...

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Šilar, Radoslav. "Účast alternativních sigma faktorů RNA polymerasy při regulaci exprese genů Corynebacterium glutamicum." Doctoral thesis, 2016. http://www.nusl.cz/ntk/nusl-353385.

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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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Kálalová, Debora. "Doména 1.1 primárního faktoru sigma a nový systém pro expresi RNA polymerázy z Bacillus subtilis." Master's thesis, 2019. http://www.nusl.cz/ntk/nusl-404169.

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RNA polymerase (RNAP) is a key multi-subunit enzyme of gene expression that, together with the σ factor, forms a holoenzyme and transcribes genetic information from DNA to RNA. RNAP from Bacillus subtilis and its primary factor σA were studied in this thesis. The σA factor determines the specificity for the promoters to which the holoenzyme binds. Part of its structure is domain 1.1, which is likely to prevent binding of σA to the promoter by itself (unless it is part of the holoenzyme) by binding to domains 2 and 4. The first part of the thesis verifies the hypothesis that domain 1.1 binds domains 2 and 4 and thus prevents binding of σA to the promoter. To this end, various domain constructs have been created and their interactions have been tested. Domain interaction was tested by Nitrocellulose Filter Binding Assay, EMSA, and in vitro transcription. The results did not show significant interaction between domains. The second part of the thesis deals with the creation of a tool for the study of the enzymatology of RNAP from B. subtilis - recombinant RNAP (rRNAP). First, a plasmid construct for expression of rRNAP in Escherichia coli was constructed by a series of cloning steps, followed by protein isolation and characterization. Isolation was achieved without contamination by σ factors (this...

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Dostálová, Hana. "Funkce alternativních sigma faktorů RNA polymerasy při stresové odpovědi u Corynebacterium glutamicum." Master's thesis, 2012. http://www.nusl.cz/ntk/nusl-309696.

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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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Pospíšil, Jiří. "Vnitrobuněčná a mezibuněčná regulace genové exprese u Gram-pozitivních bakterií." Doctoral thesis, 2021. http://www.nusl.cz/ntk/nusl-438094.

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Bacteria, the most dominant organisms on Earth, are an everyday presence in our lives. Symbiotic bacteria, which are present in the digestive tract of animals, usually have a beneficial effect on the body. On the opposite side of the spectrum are pathogenic species that cause more or less serious diseases around the world. In order to fight pathogens effectively, it is necessary to learn as much as possible about the molecular mechanisms by which bacteria respond to their environment, and also about the types of communication within bacterial populations that allow them to react to environmental changes as "multicellular" organisms. This Thesis consists of two main parts. In the first part, selected aspects of bacterial gene expression are characterized, using Bacillus subtilis and Mycobacterium smegmatis as model organisms. DNA-dependent RNA polymerase (RNAP) is the enzyme that is responsible for transcription of DNA into RNA, and thus plays a key role in gene expression. This Thesis deals with the structure of bacterial RNAP and important auxiliary factors (proteins and RNA) that associate with this enzyme and modulate its function. In the second part, the focus is on cell-to-cell communication, revealing which factors/mechanisms, including gene expression, affect this process in B. subtilis....

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Pospíšil, Jiří. "Charakterizace Ms1, nově identifikované malé RNA z Mycobacterium smegmatis." Master's thesis, 2014. http://www.nusl.cz/ntk/nusl-332209.

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Introduction: In recent years, there has been growing interest in regulation of gene expression by small non-coding RNA (sRNA). The first sRNA discovered in 1960s was 6S RNA from E. coli (length ~184 nt). It took ~ 30 years to obtain meaningful insights into its function. 6S RNA binds during stationary phase to RNA polymerase (RNAP) containing sigma factor 70 (primary sigma factor), thereby preventing transcription from σ70 - dependent promoters. In our laboratory we discovered a small RNA (length ~300 nt) in stationary phase of growht in Mycobacterium smegmatis. This sRNA was named Ms 1. The function of Ms 1 is uknown and preliminary experiments indicated that Ms 1may bind to RNAP that lacks σ factor (σA ). Goals: The aim of this Diploma project is to contribute to the characterization of Ms 1. Approaches: First, by molecular cloning, affinity chromatography and in vitro transcription I prepared the tools for subsequent experiments in vitro: RNAP, σA , Ms 1 and its mutated variants. Next, these tools were used for binding experiments on native gels and for transcription experiments. Results: RNAP, σA , Ms 1 and its variants were prepared. In vitro binding assays showed that wt Ms 1 but not a mutated variant of Ms 1 binds to RNAP. Using this assays were identified areas of Ms 1 that are important...

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Dvořáková, Pavla. "Vlastnosti expresních vektorů pro Corynebacterium glutamicum a jejich využití při studiu faktorů sigma RNA polymerasy." Master's thesis, 2017. http://www.nusl.cz/ntk/nusl-355666.

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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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Burýšková, Barbora. "Vliv 6S-like RNA molekul na fyziologickou diferenciaci Streptomyces coelicolor." Master's thesis, 2018. http://www.nusl.cz/ntk/nusl-373540.

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The variety of bacteria and their genomes sometimes causes conservation of homologue molecules to be displayed not in sequence but in secondary and tertiary structures. In the case of the regulatory 6S RNA, sequence homologues have been found in over 100 bacterial species so far. However, none were found in the genus Streptomyces. The unique genome of these soil- dwelling bacteria, known for their capacity to produce antibiotics, has a high G/C content and diverges substantially from distantly related bacteria. Yet in the non-coding 6S RNA it is the secondary structure that is crucial for its function. The 6S RNAs trap sigma factors by mimicking target promoter sequences in order to help with switching sets of expressed genes during developmental transitions. 6S-like RNA genes in Streptomyces coelicolor have been computationally predicted by comparison of in silico modelled secondary structures of known 6S RNAs. The aim of this thesis was the verification of these 6S-like RNA predictions. The experimental approach was based on RNA co-immunoprecipitation (RNA CoIP), as well as RT- PCR from RNA samples. The outcomes of this project are the detection of six novel ncRNA transcripts with possible 6S-like RNA functions, which also served as the wet-lab verification of the in silico prediction technique...

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Šmídová, Klára. "Analýza a mapování vazebných míst regulátorů genové exprese u streptomycet." Doctoral thesis, 2020. http://www.nusl.cz/ntk/nusl-437114.

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Streptomyces are medically important soil-living bacteria that undergo morphological changes from spores to aerial hyphae and are important producers of bioactive compounds including antibiotics. Their gene expression is tightly regulated at the early level of transcription and translation. In the transcriptional control, sigma factors play a central role; the model organism Streptomyces coelicolor possesses astonishing 65 sigma factors. The expression of sigma factors themselves is controlled on the post-transcriptional level through the action of sRNAs that modify their mRNA level. However, only several sigma factors in Streptomyces have known regulons and also their sRNAs-mediated regulation has not been studied so far. According to previously measured gene expression data, we selected several highly expressed sigma factors. Using mutant strains with HA-tagged sigma factors, regulons of two important sigma factors, SigQ and HrdB, were analyzed by ChIP-seq procedure. Other sigma factors were further studied to see if they possess asRNAs, using 5' and 3' RACE method and northern blotting. Our data confirm the essentiality of HrdB sigma factor during the vegetative phase of growth. The other sigma factor, SigQ, has been revealed to be an important regulator of nitrogen metabolism and osmotic...

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Dissertations / Theses on the topic 'Sigma faktory'

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