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Y1 and Y2 transposases, mechanisms of transposition, biological function.
Zahradník, Jiří ; Lichá, Irena (advisor) ; Schierová, Michaela (referee)
Transposases are enzymes that catalyse cleavage, transmission and re-inserting of mobile genetic element into the DNA. Tyrosine transposase take between these enzymes completely independend status. Their uniqueness is determined by their structure and different mechanism of the transposition reaction, in which the covalent phosphotyrosine intermediate plays major role. Mandatory presence of the catalytic tyrosine gives name to these enzymes and it enables their further classification into a group that carries only a single catalytic tyrosine - Y1 transposases and a group carrying two tyrosines - Y2 transposases. This thesis summarizes the current knowledge about tyrosine transposases. It covers their occurrence, structure, reaction mechanism and biological function. The reaction mechanism of the most studied Y1 transposase, associated with IS608 element, is described in detail. The work also focuses on other members of the tyrosin transposases family which carry the characteristic HUH motive. These include transposases associated with the insertion sequence of IS200/IS605 family (Y1), transposases associated with REP elements (so called RAYT proteins), transposases associated with IS91 family (Y2), transposases of ISCRs family (Y1) and unusual eukaryotic transposases of the Helitron family (Y2)....
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Y1 and Y2 transposases, mechanisms of transposition, biological function.
Zahradník, Jiří ; Lichá, Irena (advisor) ; Schierová, Michaela (referee)
Transposases are enzymes that catalyse cleavage, transmission and re-inserting of mobile genetic element into the DNA. Tyrosine transposase take between these enzymes completely independend status. Their uniqueness is determined by their structure and different mechanism of the transposition reaction, in which the covalent phosphotyrosine intermediate plays major role. Mandatory presence of the catalytic tyrosine gives name to these enzymes and it enables their further classification into a group that carries only a single catalytic tyrosine - Y1 transposases and a group carrying two tyrosines - Y2 transposases. This thesis summarizes the current knowledge about tyrosine transposases. It covers their occurrence, structure, reaction mechanism and biological function. The reaction mechanism of the most studied Y1 transposase, associated with IS608 element, is described in detail. The work also focuses on other members of the tyrosin transposases family which carry the characteristic HUH motive. These include transposases associated with the insertion sequence of IS200/IS605 family (Y1), transposases associated with REP elements (so called RAYT proteins), transposases associated with IS91 family (Y2), transposases of ISCRs family (Y1) and unusual eukaryotic transposases of the Helitron family (Y2)....
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