Cytochrome b5 is a small heme protein. There are three isoforms present in human organism, one is located in the membrane of endoplasmic reticulum (microsomal cyt b5), second in the outer mitochondrial membrane and the third (soluble form) was found in cytoplasm of matured erythrocytes. The main role of cytochrome b5 is to transport single electron in various reactions including cytochrome P450-dependent reactions. First aim of the thesis was to prepare and to isolate the soluble form of rabbit microsomal cytochrome b5, using heterologous expression in Escherichia coli strain BL-21 Gold. The plasmid pET22b containing synthetic gene for rabbit microsomal cytochrome b5, lacking the sequence encoding the membrane associated C-terminal domain, was used as an expression vector. The second aim was to synthesize the expression vectors carrying genes for human microsomal and erythrocytic cytochromes b5. These genes were prepared by gene synthesis, ligated to cloning vector pUC19, amplified in E. coli DH5α competent cells and their sequences were verified by DNA sequencing. Consequently the pET22b expression vectors containing genes for human microsomal and erythrocytic cytochrome b5 were constructed and finally their suitability for heterologous expression was evaluated. Keywords: Heterologous expression,...

RNA polymerase (RNAP) transcribes DNA into RNA and is the only transcriptional enzyme in bacteria. This key enzyme responds to external and internal signals from the cell, resolves the intensity of transcription of individual genes and thus regulates gene expression. RNAP is not only affected by its own subunits, but also protein factors, small molecules or small RNAs (sRNAs). The aim of this Thesis was to contribute to the understanding of the regulation of the RNAP and to add missing fragments to this broad topic. The first part of this Thesis is focused on the influence of selected proteins (δ, YdeB, GreA) on the sensitivity of RNAP to the concentration of the initiating nucleoside triphosphate ([iNTP]) during transcription initiation in Bacillus subtilis. We showed that δ affects the sensitivity of RNAP to [iNTP] at [iNTP]-sensitive promoters, but not at [iNTP]-insensitive promoters neither in vitro nor in vivo. The δ subunit is essential for cell survival during competition with other strains, because it enables the cell to react immediately to changing conditions. Further we showed that YdeB protein does not bind to RNAP in B. subtilis, and has not shown any effect on transcription in vitro. We found that both, GreA and YdeB proteins (unlike δ subunit) were unable to affect RNAP by [iNTP] at...

Bacterial DNA-dependent RNA polymerase (RNAP) is a key enzyme of bacterial transcription. Its activity must be tightly regulated. This could be done on the level of promoter DNA topology recognition, by changing the intracellular levels of metabolites, or by binding proteins, known as transcription factors. Even though the RNAP regulatory network has been intensively studied for decades, new regulators are still being described. The main focus of this Thesis is to characterize some of them: i) HelD, a novel RNAP interacting factor, with so far unknown protein 3D structure; ii) RNase J1, an enzyme with a unique mechanism of functioning; iii) Spx, a major regulator of gene expression in Bacillus subtilis, with still new roles to be defined and iv) the effect of the topological state of promoters on transcription. We identified HelD as an interacting protein of RNAP in Bacillus subtilis and described its biochemical properties. It stimulates transcription in an ATP-dependent manner, by enhancing recycling of RNAP molecules (Publication I). We published the first insight into the HelD structure by SAXS (small angle X-ray scattering) and deepened the understanding of HelD domain composition (Publication III). And finally, we were able to solve the cryo-EM structure of HelD:RNAP complexes from...

Polyoma BK virus is associated with graft dysfunction leading to BK viral nephropathy (BKVN) in 1-10% of kidney transplant recipients, moreover 30-80% of kidney transplant recipients experience asymptomatic reactivation of the virus that does not result in BKV associated damage of the renal allograft. The first aim of this study was to introduce monitoring of BK virus replication in the blood and urine of patients within first year after transplantation. Risk factors were evaluated and limit values for viremia and viruria for BKVN development was established. Positive BK viruria >107 copies/ml and positive BK viremia >104 copies/ml occurred in 25.8% and 5%; respectively. 3 patients out of monitoring study developed BKVN. Using ROC analysis, limit values for the development of BKVN were set at 103 copies/ml serum for BK viremia and 6.7x107 copies/ml BK viruria. The second objective was to determine the expression profile of the immune genes in kidney biopsies in three groups of patients with varying degrees of reactivation of the BK virus (without virus reactivation, with asymptomatic viruria, BKVN). 90 genes of immune response were measured by the TaqMan® low density array RT-qPCR. The analysis of biopsies from patients with non-signalling viruses led to the identification of 5 differentially...

Introduction: Inherited retinal diseases (IRDs) are one of the most common causes of incurable blindness in children and young adults. In the Czech Republic, prior to the start of our work, these disorders had not been the subject of a systematic research. The aim of the study was to identify, clinically characterize and molecular genetically analyse Czech patients with monogenic IRDs and based on the knowledge gained subsequently implement preventive and therapeutic measures to clinical practice. Material and methods: We have performed a comprehensive clinical examination, genealogical analysis and molecular genetic investigation in patients with IRDs and their family members. Detailed ocular examination included spectral domain optical coherence tomography, high-resolution fundus photography and autofluorescence imaging. DNA was isolated from venous blood samples or buccal cells. Causal variants were searched for using Sanger and massively parallel sequencing, and their pathogenicity was evaluated in the context of previously published data, bioinformatical analysis and segregation in available family members. Results: In total, 103 individuals from 76 Czech families diagnosed with IRDs were characterized and their data published. Specifically, we have described clinical and molecular genetic...

Bacterial DNA-dependent RNA polymerase (RNAP) is a key enzyme of bacterial transcription. Its activity must be tightly regulated. This could be done on the level of promoter DNA topology recognition, by changing the intracellular levels of metabolites, or by binding proteins, known as transcription factors. Even though the RNAP regulatory network has been intensively studied for decades, new regulators are still being described. The main focus of this Thesis is to characterize some of them: i) HelD, a novel RNAP interacting factor, with so far unknown protein 3D structure; ii) RNase J1, an enzyme with a unique mechanism of functioning; iii) Spx, a major regulator of gene expression in Bacillus subtilis, with still new roles to be defined and iv) the effect of the topological state of promoters on transcription. We identified HelD as an interacting protein of RNAP in Bacillus subtilis and described its biochemical properties. It stimulates transcription in an ATP-dependent manner, by enhancing recycling of RNAP molecules (Publication I). We published the first insight into the HelD structure by SAXS (small angle X-ray scattering) and deepened the understanding of HelD domain composition (Publication III). And finally, we were able to solve the cryo-EM structure of HelD:RNAP complexes from...

The TCF/LEF transcriptional factors regulate the target genes of the Wnt signalling pathway - one of the key signalling mechanisms involved in development of multicellular organisms. The TCF/LEF genes produce a number of various protein isoforms, which consequently leads to a great functional diversity of the TCF/LEF proteins. In this diploma project we focused on the Caenorhabditis elegans gene pop-1, the ortholog of the TCF/LEF genes, whose isoforms have not been studied yet. Using the Northern blot analysis we tried to identify alternative isoforms of the pop-1 mRNA in C. elegans. Using quantitative RT-PCR we also analyzed the pop-1 mRNA levels during seven developmental stages of C. elegans. Further, we also determined the expression profile of two important partners of pop-1, the bar-1 and sys-1 genes, whose protein products function as transcriptional co-activators. Key words: canonical Wnt signaling pathway, TCF/LEF transcription factors, Caenorhabditis elegans, pop-1

Colorectal cancer is one of the most common type of malignity. Despite of the existence of numerous studies focused on this carcinoma, there are still many unknown features regarding its diagnosis, treatment or prognosis. In the thesis we focused on the identification of novel prognostics markers that could be useful for the stratification of patients based on the disease outcomes. In the first study we immunohistochemically assessed expression of two proteins associated with cancer stem cells in the samples of primary colorectal cancer and matched liver metastasis. Goal of the study was to evaluate relation among expression of CD44 and CD133 and overall survival and disease free interval in our set of patients. We observed that increased ratio of CD133 positive compared to CD133 negative tumor glands resulted in longer disease free interval, finding which is opposite to the general view on the CD133 role in the cancer development. Our hypothesis is that we analyzed confined group of patients and followed a bit different goal, where we measured ratio between positive and negative glands in the view-field and not the intensity of staining as the previous studies did. Our second study was focused on the transcriptional analysis of the selected set of twelve genes using frozen samples from colorectal...

Cutaneous wound healing could be distinguished into two main types: embryonic and adult. Embryonic healing in contrast to adult is faster, scar-less and consists of early, middle, and late phases. Actin ring is formed during the early phase and its cables pull the edges of the wound towards apposite sites during the following middle phase. De novo expression of healing specific genes is initiated also during middle phase. However, process of the wound healing continues under the closed wound in the late phase which has been poorly described. Adult wound healing is more complex, longer, and is divided into 4 phases: haemostasis, inflammation, proliferation, and remodelling phase. Adult wound healing might end with the scar. Pivotal role in the wound healing is given to matrix metalloproteinases (MMPs). These remodelling enzymes are important for releasing cytokines, inducing apoptosis, and degradation of extracellular matrix. Our laboratory performed temporal RNA-sequencing of the healing tissue using tailbud stage and swimming tadpole embryos. Results showed predominant expression of four mmps: mmp1.L, mmp7.S, mmp8.S, and mmp9.L. Injury or amputation caused the upregulation and their expression level peaked at 3-6 hours post injury which corresponds with late phase of healing. Thus, I focused on...

Adaptive evolution of Toll-like receptors in birds Hana Velová, PhD thesis 6 Abstract Toll-like receptors (TLRs) are one of the key and presumably also evolutionary most original components of animal immune system. As Pattern recognition receptors they form the first line of innate immune defence against various pathogens. The proper receptor binding of pathogenic ligands is crucial for their correct recognition and for subsequent triggering of an appropriate immune response. Because there exists a direct interaction between the receptor surface and the pathogenic ligand, host-pathogen coevolution on molecular level can be predicted. Thus, through variability of their ligands, TLRs are exposed to extensive selective pressures that may be detected on both genetic and protein levels. Surprisingly, the variability we revealed in birds is even higher than previously expected based on the reports from other vertebrates, mainly mammals. In my doctoral thesis I summarise the results of my contribution to the avian TLR research. We were the first who experimentally verify the absence of functional TLR5 in several avian species and duplication of TLR7 in others. We finally resolved the origin of duplication in TLR1 and in TLR2 family. An important part of my research project focused on the prediction of potentially...