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Role of Ccr4 deadenylase in cell cycle regulation in yeast colonies
Daumová, Lenka ; Čáp, Michal (advisor) ; Převorovský, Martin (referee)
Regulation of cellular processes is of key importance for survival of cells. Many regulations are mediated by the CCR4-Not complex, a highly conserved protein complex, which is present in eucaryotic cells, from yeast to mammals. In this work I study mostly the role of the Ccr4 subunit on yeast survival in the aging colony of Saccharomyces cerevisiae, mainly during cell cycle progression. Ccr4 si a deadenylase, and its main function is cleavage of poly(A) tail of mRNA molecules, and by doing so, shortening the mRNA life-time. It is very important during strictly regulated cellular processes, because it is essential that gene expression of specific genes happens only at specific time. Saccharomyces cerevisiae BY 4742 is a haploid yeast strain, which can easily be used for making deletion mutants in specific genes. In this diploma thesis I focus on studying a deletion mutant of CCR4, along with deletion of other genes, which influence yeast cell cycle. By comparing the phenotype of these mutants with wild type, it is possible to identify changes in phenotype, caused by these deletions, and their influence on yeast cell survival. Key words: cell processes regulation, CCR4-Not complex, Ccr4 subunit, cell cycle, yeast, Saccharomyces cerevisiae, gene deletion
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Codon usage and isoacceptor tRNA expression as a mechanism to control gene expression
Daumová, Lenka ; Čáp, Michal (advisor) ; Štěpánek, Luděk (referee)
Genetic code is defined as a set of rules, which encode aminoacid sequences in proteins, according to codon usage. It is widely known, that there are multiple codons for most aminoacids, thanks to the degeneracy of the genetic code. There was a hypothesis, that silent mutations, which result in a synonymous codon and not in incorporating of a different aminoacid into the peptide chain, don't affect the gene expression. Later however, it was found through more detailed research on molecular level, that codon usage bias is in fact one of the factors, that regulate translation effectivity and rate, mRNA stability or even protein folding and gene expression. There has been many studies published on these topics. This bachelor thesis is a review of these studies. First, I summarize basic information on tRNA, its structure and modifications in anticodon loop. Next I write about base pairing between codon and anticodon, including the non-canonical wobble base pairing. Then I emphasize on codon bias, its causes, its relationship with genome GC content. I also include some author's conjectures about how to approach this phenomenon, which codons are optimal and what is the impact of codon usage bias on translation efficiency. I cite many studies on this topis, which was researched on many model organisms,...
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