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Methylation of viral RNA
Šimonová, Anna ; Macíčková Cahová, Hana (advisor) ; Sýkora, David (referee) ; Elleder, Daniel (referee)
Viruses are the major force that shapes the evolution of both pro- and eukaryotic organisms. They have a simple inner organization and contain only a few, usually well-described RNAs. In the case of +(ss)RNA viruses, their genomic RNA serves also as mRNA. This makes them a perfect model system for searching for new mRNA modifications as well as for understanding the role of already known modifications. In this work, Human Immunodeficiency Virus type 1 (HIV-1) from the Retroviridae family was used as a model system. In the following study, four representatives from the Picornaviridae family were tested for RNA methylation profile. To get the information, a combination of two techniques was developed, liquid chromatography- mass spectrometry (LC-MS) and sequencing techniques. Results of LC-MS reveal a surprisingly high amount of 1-methyladenosine (m1 A) in RNA isolated from HIV-1. Nevertheless, the m1 A mapping sequencing technique confirm m1 A position only in co-packed tRNA. This led to the recalculation of HIV-1 virion RNA composition. In the case of Picornaviridae, LC-MS revealed m1 A and 5-methylcytidine (m5 C) in two insect viruses (Sacbrood virus, SBV and Deformed wing virus, DWV). RNA seq techniques (m1 A mapping and bisulfite sequencing) confirmed the presence of m1 A and m5 C only in tRNA....
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tsRNA - biogenesis, regulation and function in gene expression
Ramanava, Marharyta ; Mašek, Tomáš (advisor) ; Fryaufová, Petra (referee)
Transfer RNA (tRNA) accounts for approximately 10% of total cellular RNA pool and plays a crucial role in translation. Here I focus on the alternative function of tRNA, which can serve as a precursor for the formation of so-called "small RNAs derived from tRNA" (tsRNAs). These small non-coding RNAs are primarily generated by the cleavage of tRNAs by the ribonucleases Angiogenin and Dicer. tRFs (tRNA-derived fragments) and tiRNAs (stress- induced RNA-derived RNAs) are two major classes that differ fundamentally in the position of the cleavage site in the parent tRNA and the length of the molecule. Some tsRNAs act as regulators of posttranscriptional gene expression, often affecting mRNA stability and translation initiation. tsRNAs are implicated in regulation of stress response, cell differentiation, development, and apoptosis. Further, there is strong evidence that they have a role in epigenetic processes, communication between organs or even between organisms. In addition, in humans, their profile is often cell-specific and its change in pathophysiological conditions makes tsRNAs a suitable diagnostic marker. This work summarizes current knowledge about tsRNAs and their biological function and significance. Kaywords: small RNAs derived from tRNA; tRNA; tiRNA; tRF; gene expression regulation
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Synthesis of proteins containing non-canonical amino acids
Knetl, Adam ; Vopálenský, Václav (advisor) ; Plocek, Vítězslav (referee)
0 Abstract: Non-canonical amino acids allow the introduction of new chemical properties into proteins, which is useful both for studying proteins, and designing proteins. However, the synthesis of proteins containing non-canonical amino acids faces problems with decreased effectivity of translation. This thesis examines the role of genetic code for coding non-canonical amino acids, proteosynthesis and aminoacilation of tRNA and finally the non-canonical amino acids and their application in proteins while including examples.
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RNA biology of symbiotic bacteria in insects
MACHOVÁ, Kamila
Non-coding RNAs (ncRNAs) represent an important part of bacterial genomes. However, only few studies RNAs with limited sampling were done concerning ncRNAs of insect endosymbiontic bacteria. This study provides a broad in silico genome sampling of insect endosymbionts (63 lineages of 27 genera) for ncRNAs and their modifications. Most strikingly it was found out that i) genes encoding modification enzymes conserved in particular genomes differ to high extent, ii) most of tRNA and rRNA modifications sites are conserved regardless whether the gene encoding the corresponding modification enzyme is conserved, iii) multiple endosymbiont lineages do not encode a full set of tRNAs. Our data imply that translation of endosymbionts is much less efficient compared to phylogenetically related free-living bacteria and that some of symbionts possibly need to cooperate with their cosymbionts or maybe even with their host to maintain translation.
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Molecular analysis of the mitochondrial genom of \kur{Diuraphis noxia} (Aphididae)
CHUNDELOVÁ, Daniela
The complete sequence of mitochondrial DNA from Diuraphis noxia was obtained and characterized. The mitogenome contains a standard set of 13 protein-coding genes, 19 tRNA genes, 2 ribosomal RNA genes. A+T-rich and ?repets? regions in the same order as those of the other analyzed aphids. Comparison to mtDNAs from other Sternorrhyncha species obtained from GenBank revealed possible markers for studies on population differentiation. Phylogenetic analysis using parsimony and maximum likelihood confirmed the classification of Diuraphis noxia into the Aphididae.
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