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Regulation of protein expression non-specific immunity in Caenorhabditis elegans
Kaštánková, Iva ; Kostrouch, Zdeněk (advisor) ; Cmarko, Dušan (referee)
6 Abstract Lipopolysaccharides are composed of covalently bound saccharides. They are a characteristic component of the cell wall of gram-negative bacteria. They are the cause of severe sepsis in humans and complications in human medicine. Lipopolysaccharides are a constant part of the infections of gram-negative bacteria. We expect an evolutionarily conserved non-specific immune response and protection. The question is whether there is an immune response in the model organism Caenorhabditis elegans. If so, what mechanism is controlled and regulated. We submitted lipopolysaccharides from the bacteria Pseudomona aeruginosa with the bacteria Escherichia coli OP50 and observed the influence of lipopolysaccharides on the expression of selected genes. We examined metabolism and development. We have shown the influence of lipopolysaccharides on gene expression of C-type lectine clec-60 a clec-71, nextna lys-5, hsp-60 a F44G.3.2.1 genes. We incubated Caenorhabditis elegans on some components of lipopolysaccharide. We found regulation of these selected genes with hydrophobic components of lipopolysacharide, lipid A. We did not observe regulation with saccharide components of lipopolysaccharide, glucose and galatose. The metabolism of lipids had changed. We demonstrated a reduction of neutral lipids and changes in...
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Gene expression regulation by nuclear receptors in a specific metabolic context - evolutionary perspective
Kaššák, Filip ; Kostrouch, Zdeněk (advisor) ; Macůrková, Marie (referee) ; Leontovyč, Ivan (referee)
In animals, some of the most critical regulators of gene expression are nuclear hormone receptors (NRs) and their coregulators, specifically the Mediator complex. Of particular interest are the NRs implicated in metabolic and developmental regulation and in carcinogenesis: thyroid hormone receptors (TRs) and retinoid X receptors (RXRs). In this work, I venture to elucidate some aspects of gene expression regulation by these NRs: the degree of evolutionary conservation of signalling based on NRs and their coregulators; the mechanisms of negative regulation by NRs; and possible implications of these findings for clinical medicine. State-of-the-art bioinformatical, genome editing and microscopic techniques are applied at three levels of animal evolution to study NRs and Mediator. Reverse genomics in human patients suffering from the syndrome of resistance to thyroid hormones β are used to infer the structure and function of TRβ subdomains. Alignments, binding studies and in vivo experiments in Trichoplax adhaerens allow identification of a close orthologue of human RXR at the basis of metazoan evolution. Employing database queries, genome editing and microscopy, we describe a correct orthologue of the Mediator subunit 28 in Caenorhabditis elegans, indicating a complete homology of the Mediator complex...
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The role of phosphatidylinositol-4-phosphate 5-kinase PPK-1 in Wnt signalling regulation in Caenorhabditis elegans
Zavadilová, Kristýna ; Macůrková, Marie (advisor) ; Kostrouch, Zdeněk (referee)
The Wnt signalling pathway is highly conserved signalling among Eukaryotes that regulates many cellular processes. In particular, it plays a role during invidual's development, but it is also important at later stage of life, when it is involved in maintaining homeostasis in the body. Recent studies have shown that phosphatidylinositol-4-phospahte 5-kinase (PIP5K), which is key to the production of phosphatidylinositol (4,5)-bisphosphate in the cell, is also involved in regulation of the canonical Wnt signalling cascade. In mammalian cells, a model has been described in which PIP5K is involved in signal transduction in a Wnt receiving cell. We decided to verify the involvement of PIP5K in the regulation of Wnt signalling also in Caenorhabditis elegans, an excellent model organism for study of signalling pathways, and thus contribute to a better understanding of this evolutionarily conserved pathway. In this work, we found that decreased expression of PPK-1/PIP5K in wild type animals does not result in Wnt signalling disruption. Nevertheless, in conditions, where the activity of Wnt signalling is already reduced, decrease in PPK-1 levels leads to defective migration of the QL neuroblast daughter cell. By analyzing the migration of QL progeny, which is controlled by EGL-20/Wnt dependent Wnt...
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The role of evolutionarily conserved proteins BIR-1/Survivin and SKP-1 in the regulation of gene expression
Kostrouch, David ; Kostrouch, Zdeněk (advisor) ; Dráber, Pavel (referee) ; Pacák, Karel (referee)
SKIP and BIR/Survivin are evolutionarily conserved proteins. SKIP is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Loss of function of C. elegans SKIP (SKP-1) and BIR-1 induces overlapping developmental phenotypes. In order to uncover the possible interactions of SKP-1 and BIR-1 on the protein level, we screened the complete C. elegans mRNA library using the yeast two-hybrid system. These experiments identified partially overlapping categories of proteins as SKP-1 and BIR-1 interactors. The interacting proteins included ribosomal proteins, transcription factors, translation factors and cytoskeletal and motor proteins suggesting involvement of the two studied proteins in multiple protein complexes. To visualize the effect of BIR-1 on the proteome of C. elegans we induced a short time pulse BIR-1 overexpression in synchronized L1 larvae. This led to a dramatic alteration of the whole proteome pattern indicating that BIR-1 alone has the capacity to alter the chromatographic profile of many target proteins including proteins found to be interactors in yeast two hybrid screens. The results were validated for ribosomal proteins RPS-3, RPL-5, non-muscle myosin and TAC-1, a transcription cofactor and a centrosome associated...
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Orphan Nuclear Receptor TLX (NR2E1) in Regulation of Cell Reproduction and Differentiation
Raška, Otakar ; Kostrouch, Zdeněk (advisor) ; Otová, Berta (referee) ; Nedvídková, Jara (referee)
Nuclear receptors constitute a large family of transcription factors that are powerful regulators of animal tissue metabolism, homeostasis, tissue maintenance and development. They are particularly attractive for their ability to respond to the binding of hormones, metabolites, xenobiotics and artificially prepared molecules and transmit the interaction with these small lipophylic molecules to specific regulatory potential. In search for nuclear receptors that are likely to be critical for neural tissues in invertebrates and conserved during the evolution of animals, we have identified a close homologue of vertebrate TLX in a planarian Schmidtea mediterranea. Planaria represent very promising biological model systems for studies on tissue maintenance and regeneration. Planaria are able to resorb their tissues and use them as sources of energy during fasting and they re-build their bodies from neoblasts when food is plentiful. Our search in Schmidtea mediterranea's publicly accessible genome sequencing data indicated that planarian genome contains at least one gene with a high degree of similarity to vertebrate TLX. We cloned full length CDS (coding DNA sequence of cDNA) and characterized the gene functionally. This showed that the planarian and vertebrate NR2E1 are highly similar...
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Nuclear receptors in regulation of gene expression, development and metabolism in Celegans elegans.
Yilma, Petr ; Kostrouch, Zdeněk (advisor) ; Pompach, Petr (referee) ; Vaněk, Ondřej (referee)
5 Abstract Genetic mechanisms of regulation of gene expression form the basis for proper development, function of organisms and their responses to variable life conditions. However, they are relatively slow. Life processes that require a fast response to the changing environmental and metabolic conditions are mostly executed on the level of proteins especially their posttranslational modifications and protein- protein interactions.The goal of the experimental work that led to the presented thesis consisted in exploitation of the model organism Caenorhabditis elegans for analysis of regulation of gene expression by transcription factors from the protein family of nuclear receptors. The model system C. elegans enables very efficient experimental procedures in the field of genetics, genomics and functional analysis of phenotypes. In the experimental work connected with this thesis, I studied the regulation of gene expression under specific experimental conditions from the perspective of advanced functional proteomics and I focused on the employment of separation methods and methods of advanced proteomics, especially by mass spectrometry.In the first part of the work, I characterized the nuclear receptor NHR-60 on the protein level. This nuclear receptor is expressed as two protein forms with a mass of 50 kDa...
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Evolutionarily conserved mechanisms of gene expression regulation by nuclear receptors.
Chughtai, Ahmed Ali ; Kostrouch, Zdeněk (advisor) ; Malínský, Jan (referee) ; Brábek, Jan (referee)
Transcriptional regulation of gene expression in eukaryotes has evolved over millions of years. The regulatory pathways of nuclear receptors represent an evolutionarily ancient, but conserved mechanism with associated accessory proteins, many of them forming a functional nexus known as the Mediator complex involved in transcription. Despite the versatility of the pathway, e.g. through the adoption of new regulatory functions in phylogenetically more recent Metazoa, we hypothesise that the intrinsic potential of the NR-Mediator axis to directly translate a stimulus to a biological response is conserved across species, and additional regulation could also be achieved through secondary functions of its essential members. To support the hypothesis, we assessed the ligand-binding capability of retinoic X receptor in Trichoplax adhaerens and provided evidence to support the concept that this capability was already present at the base of metazoan evolution. With regards to the potential secondary functions, we took inspiration from previous research and identified the Mediator subunit 28 (MED28) as the only known member having documented nuclear and cytoplasmic dual roles, and thus possessing the potential to transmit signals from the cellular structural states to the nucleus. Due to the lack of...
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Regulation of gene expression at posttranscriptional levels.
Kollárová, Johana ; Kostrouch, Zdeněk (advisor) ; Macůrková, Marie (referee) ; Jindra, Marek (referee)
Regulation of gene expression in response to cellular and organismal needs is essential for sustaining organisms' survival and successful competition in the evolution of life forms. This regulation is executed at multiple levels starting with regulation of gene transcription, followed by regulation at multiple posttranscriptional levels. In this thesis, I focused on posttranscriptional mechanisms that contribute to gene expression regulation in the model organism Caenorhabditis elegans which enables powerful genetic and genomic techniques and allows the visualization of experimental genetic manipulations in toto, on the level of the complete organism during its life span. For this, we analysed the function of the orthologue of mammalian transcriptional corepressor NCOR, GEI-8. We used a functionally defective mutant gei-8(ok1671). I analysed the whole genome expression of homozygous gei- 8(ok1671) mutant and its link with observed mutant phenotype that includes defective gonad development and sterility and performed experiments leading to the proposition that disbalances in 21-U RNAs of piRNA class present in the most derepressed gene, the predicted mitochondrial sulfide:quinine reductase encoded by Y9C9A.16, are associated with the gonadal phenotype. In the second part of the thesis, I focused on...
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Conserved Mechanisms of Gene Expression Regulation by Nuclear Receptors.
Novotný, Jan Philipp ; Kostrouch, Zdeněk (advisor) ; Stopka, Pavel (referee) ; Lazar, Jozef (referee)
7 Abstract With the first appearance of life on Earth, organisms had to adapt to an ever-changing surrounding environment in order to survive. Since the emergence of metazoan multi- cellularity, subsets of cells could adapt to perform specific biological tasks beneficial to the whole organism, necessitating not only spatiotemporal regulation of gene expression during development, but also integration of tissue specific needs with overall organis- mal status. Within the set of evolutionary conserved regulatory systems, the family of nuclear receptor (NR) transcription factors stands out due to its high degree of evolu- tionary conservation, plasticity and uniqueness to the metazoan kingdom, regulating gene expression in response to, or in the absence of a ligand by genomic and non- genomic actions. With an increasing number of different compounds being recognized as ligands to NRs, it is now thought that ancient NRs were probably characterized by low ligand binding specificity, eventually serving as environmental sensors, integrating nutrient availability and gene expression at the base of metazoan evolution. Characteri- zation of the NR network in one of the simplest metazoan organisms, Trichoplax ad- haerens, revealed not only a functional network and sub-specialization of NR dependent gene regulation, but...
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Nuclear architecture and gene expression in Caenorhabditis elegans
Bolková, Jitka ; Lanctôt, Christian (advisor) ; Macůrková, Marie (referee) ; Kostrouch, Zdeněk (referee)
Nuclear architecture and gene expression in Caenorhabditis elegans Mgr. Jitka Bolková ABSTRACT The parental genomes are initially separated in each pronucleus after fertilization. During the first mitosis this spatial distribution is being disintegrated. In my thesis we used green-to-red phoroconversion of Dendra2-H2B-labeled pronuclei to distinguish maternal and paternal chromatin domains and to track their distribution in space in living Caenorhabditis elegans embryos starting shortly after fertilization. Both of the parental chromatin domains within the nucleus are separated in the zygote and at the 2-cell stage. Intermingling occurs first after chromatin decondensation at the beginning of the cell cycle at the 4-cell stage. To our knowledge, we report to the first live observation of the separation and subsequent mixing of parental chromatin during embryogenesis. Following of the photoconverted chromatin also allowed us to detect a reproducible 180ř rotation of the nuclei during cytokinesis of the zygote. Tracking of fluorescently-labelled P granules and polar bodies showed that the entire embryo rotates during the first cell division. In the second part of the thesis we used the C. elegans model to investigate relationship between nuclear architecture and gene expression. We focused on localization of...
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