|
|
The presence and localization of local DNA structures in the genome of Schizosaccharomyces pombe
Kubínová, Michaela ; Šedrlová, Zuzana (referee) ; Brázda, Václav (advisor)
The thesis focuses on the study of local DNA structures (cruciforms and G quadruplexforming sequence) in the genome of Schizosaccharomyces pombe, a yeast used in the food industry. The analysed local structures are non-randomly distributed within the genome. Based on previous studies, it has been found that they often colocalize with regulatory regions of genes and that the role of these secondary structures in the regulation of basic cellular processes (e.g. replication or transcription) is significant. This analysis was performed using specialized bioinformatics tools (G4Hunter and Palindrome Analyser) that allowed me to identify and analyze these structures in terms of their presence and localization. Many times less IR was found in mtDNA compared to the occurrence of IR in chromosomes. The number and frequency of PQS in mtDNA was also found to be very low. It is very different from the yeast Saccharomyces cerevisiae in this respect. It was also found that the number of IRs found decreases with increasing IR length and about 17% of IRs do not have a loop. A large enrichment of IRs was observed in the repeat_region and rRNA, and in the case of PQS in the rRNA and mRNA regions, i.e. sequences important for cellular processes.
|
|
|
Vlastnosti DNA vazebných mutant proteinů CSL
Teska, Mikoláš ; Folk, Petr (advisor) ; Šťovíček, Vratislav (referee)
Notch pathway plays a critical role during the development and life of metazoan organisms. CSL proteins are the component of the Notch pathway that mediates the regulation of target genes. The discovery of CSL-like proteins in yeast raised the question of their function in unicellular organisms which did not utilize the canonical Notch pathway. CSL-homologues in yeast are conserved in parts that are important for DNA binding and for fission yeast proteins it was shown that they bind to CSL recognition elements in vitro. In fission yeast, CSL paralogues Cbf11 and Cbf12 play antagonistic roles in cell adhesion and the coordination of cell and nuclear division. Yeast CSL proteins have long and intrinsically unstructured N- terminal domains compared to metazoan CSL proteins. In this study, we investigated the functional significance of these extended N-termini of CSL proteins by their complete removal. For newly constructed truncated variants of proteins Cbf11 and Cbf12 in Schizosaccharomyces pombe we observed the lack of ability to bind CSL recognition RBP probe. The removal of N-terminal parts of CSL proteins in fission yeast led to the change in their cellular localization. Once strongly preferred nuclear localization changed by the removal of N-terminal domains to cytoplasmic localization with a...
|
|
|
Transcription factors CSL and their role in the yeast Schizosaccharomyces pombe
Oravcová, Martina ; Převorovský, Martin (advisor) ; Heidingsfeld, Olga (referee) ; Krásný, Libor (referee)
Proteins of the CSL family (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) act as effectors of the Notch signalling pathway in metazoan organisms. They function as repressors or activators of gene transcription in the framework of this pathway and influence many developmental processes. Metazoan CSL proteins can regulate gene expression Notch-independently as well. Notch-independent functions of CSL proteins might be evolutionarily ancestral and in cells and organisms may be important equally as Notch-dependent functions. Presence of CSL proteins was identified in several fungal species, organisms lacking the Notch signalling pathway components and most of known metazoan interacting partners of CSL proteins. CSL paralogs of the fission yeast Schizosaccharomyces pombe, cbf11 and cbf12, are non-essential genes encoding proteins localized in the nucleus of the cell. They exert antagonistic effects on regulation of processes like coordination of nuclear and cellular division and cell cycle progression, ploidy maintenance, cell adhesion and other. In this study, we have proved that both CSL paralogs are able to sequence-specifically bind the CSL-response element DNA in vitro and Cbf11 in vivo as well. Both proteins could activate gene expression in vivo and perform the function of transcription factors....
|
|
|
Transcription factors CSL and their role in the yeast Schizosaccharomyces pombe
Oravcová, Martina
Proteins of the CSL family (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) act as effectors of the Notch signalling pathway in metazoan organisms. They function as repressors or activators of gene transcription in the framework of this pathway and influence many developmental processes. Metazoan CSL proteins can regulate gene expression Notch-independently as well. Notch-independent functions of CSL proteins might be evolutionarily ancestral and in cells and organisms may be important equally as Notch-dependent functions. Presence of CSL proteins was identified in several fungal species, organisms lacking the Notch signalling pathway components and most of known metazoan interacting partners of CSL proteins. CSL paralogs of the fission yeast Schizosaccharomyces pombe, cbf11 and cbf12, are non-essential genes encoding proteins localized in the nucleus of the cell. They exert antagonistic effects on regulation of processes like coordination of nuclear and cellular division and cell cycle progression, ploidy maintenance, cell adhesion and other. In this study, we have proved that both CSL paralogs are able to sequence-specifically bind the CSL-response element DNA in vitro and Cbf11 in vivo as well. Both proteins could activate gene expression in vivo and perform the function of transcription factors....
|
|
|
Counterbalances: antagonistic regulation of fission yeast growth and proliferation under favourable conditions and stress
Hohoš, Patrik ; Převorovský, Martin (advisor) ; Groušl, Tomáš (referee)
Microorganisms come across dramatically changing conditions in the environment. It is important for them to be agile for a quick and effective response. Signal transduction pathways are essential for this ability. They can sense a broad spectrum of extracellular and intracellular stimuli and regulate a great number of processes in the cell. For unicellular microorganisms, the most essential ability is to sense environmental conditions for proliferation or abnormal stress conditions. One of the most popular model microorganisms, the fission yeast Schizosaccharomyces pombe, is used for the signal transduction pathways research. Findings obtained by research on the fission yeast are applicable to other eukaryotic organisms, thanks to the high conservation of the signal transduction pathways between the fission yeast and other eukaryotic organisms. Proliferation-promoting signal transduction pathways promote cell proliferation, growth and mitotic cell cycle in fission yeast. The stress-response signal transduction pathways play an opposite role. They promote cellular defence against stress stimuli and promote the sexual differentiation process alongside meiotic cell cycle. At first sight, the whole machinery may look like a switch mechanism. There is, however, a more complex crosstalk mechanism...
|
|
|
Characterization of DNA binding of CSL transcription factors in fission yeast
Jordáková, Anna ; Převorovský, Martin (advisor) ; Čáp, Michal (referee)
Cbf11 and Cbf12 proteins, the members of the CSL transcription factors family, are involved in a wide range of cellular processes in the fission yeast Schizosaccharomyces pombe - among other things they regulate cell adhesion and they have also been implicated in maintenance of genome integrity. At the level of the whole genome we previously identified target loci bound by CSL proteins in vivo. Many of them do not contain any consensus CSL-binding element. There are probably different DNA binding modes of the Cbf11/12 proteins and it has not been known what specific biological function is associated with the particular way of DNA binding. For the purpose of studying CSL DNA binding modes we have worked in this project on the implementation of the DNA binding mutation (DBM), which prevents direct DNA binding of CSL proteins to canonical motif in vitro, into the chromosomal locus of the cbf11 and cbf12 genes. Using the "ura4 selection system" we have successfully constructed the scar-less Cbf12-TAP and Cbf12DBM-TAP knock-ins, i.e. the strains without/with DBM in the open reading frame of Cbf12 where Cbf12 is C- terminally TAP-tagged and contains the intact 3'UTR. In our laboratory we have established the CRISPR/Cas9 system by which we have been able to prepare the Cbf11- TAP strain. We have failed to...
|
|
|
Transcription factors CSL and their role in the yeast Schizosaccharomyces pombe
Oravcová, Martina ; Převorovský, Martin (advisor) ; Heidingsfeld, Olga (referee) ; Krásný, Libor (referee)
Proteins of the CSL family (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) act as effectors of the Notch signalling pathway in metazoan organisms. They function as repressors or activators of gene transcription in the framework of this pathway and influence many developmental processes. Metazoan CSL proteins can regulate gene expression Notch-independently as well. Notch-independent functions of CSL proteins might be evolutionarily ancestral and in cells and organisms may be important equally as Notch-dependent functions. Presence of CSL proteins was identified in several fungal species, organisms lacking the Notch signalling pathway components and most of known metazoan interacting partners of CSL proteins. CSL paralogs of the fission yeast Schizosaccharomyces pombe, cbf11 and cbf12, are non-essential genes encoding proteins localized in the nucleus of the cell. They exert antagonistic effects on regulation of processes like coordination of nuclear and cellular division and cell cycle progression, ploidy maintenance, cell adhesion and other. In this study, we have proved that both CSL paralogs are able to sequence-specifically bind the CSL-response element DNA in vitro and Cbf11 in vivo as well. Both proteins could activate gene expression in vivo and perform the function of transcription factors....
|
|
|
Transcription factors driving periodic gene expression during the fission yeast cell cycle
Jordáková, Anna ; Převorovský, Martin (advisor) ; Paleček, Jan (referee)
The fission yeast Schizosaccharomyces pombe plays an important role in elucidation of the mechanisms of cell cycle regulation and characterization of the relevant effector molecules involved. The cell cycle of S. pombe consists of a prolonged period of growth (G2 phase), which is followed by a nuclear division (M phase), a very short G1 phase and DNA replication (S phase). Already during S phase formation of division septum occurs. Cell cycle progression is regulated at multiple levels. Although the yeast S. pombe is an extensively studied model organism, knowledge of the transcriptional network regulating progression through the cell cycle is still incomplete. Transcription factors are very important regulators of gene expression and therefore their characterization is the subject of research. At the transcriptional level, several key transcription factors have been identified that regulate periodically oscillating and interdependent waves of gene expression during the cell cycle. This study summarizes the current state of knowledge in the field of the transcriptional regulation of periodic gene expression in the fission yeast cell cycle.
|
|
|
Transcription factors CSL and their role in the yeast Schizosaccharomyces pombe
Oravcová, Martina
Proteins of the CSL family (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) act as effectors of the Notch signalling pathway in metazoan organisms. They function as repressors or activators of gene transcription in the framework of this pathway and influence many developmental processes. Metazoan CSL proteins can regulate gene expression Notch-independently as well. Notch-independent functions of CSL proteins might be evolutionarily ancestral and in cells and organisms may be important equally as Notch-dependent functions. Presence of CSL proteins was identified in several fungal species, organisms lacking the Notch signalling pathway components and most of known metazoan interacting partners of CSL proteins. CSL paralogs of the fission yeast Schizosaccharomyces pombe, cbf11 and cbf12, are non-essential genes encoding proteins localized in the nucleus of the cell. They exert antagonistic effects on regulation of processes like coordination of nuclear and cellular division and cell cycle progression, ploidy maintenance, cell adhesion and other. In this study, we have proved that both CSL paralogs are able to sequence-specifically bind the CSL-response element DNA in vitro and Cbf11 in vivo as well. Both proteins could activate gene expression in vivo and perform the function of transcription factors....
|
|
|
The role of CSL proteins in oxidative stress response of Schizosaccharomyces pombe
Tvarůžková, Jarmila ; Převorovský, Martin (advisor) ; Rallis, Charalampos (referee)
Oxidative stress represents a complex and intensely studied phenomenon tightly linked to a range of human diseases, and to aging in many organisms. A plethora of key cellular regulators, including the Notch signaling pathway, have been recently described to respond to the cellular redox status. We have characterized the role of CSL (CBF1/Su(H)/LAG-1) proteins, the effectors of Notch signaling pathway in metazoa, in oxidative stress response in fission yeast. Schizosaccharomyces pombe contains two CSL paralogs, Cbf11 and Cbf12, that have antagonistic functions in the regulation of cell cycle and cellular adhesion. Both proteins are able to bind the canonical CSL motif and activate transcription and, thus, function as genuine CSL transcription factors. We have determined that the strain lacking cbf11 is resistant to hydrogen peroxide but not to menadione, a source of superoxide anion radical. Using double knock-outs to assess genetic interactions we have revealed that the resistance of cbf11 knock-out is dependent on the antioxidants catalase and sulfiredoxin. Genes encoding these antioxidants are under transcriptional control of the Sty1 MAP kinase pathway and the Pap1 transcription factor which are also required for the resistance of Δcbf11 cells. Cbf12 is believed to play only a minor role in...
|
guest ::
