|
|
Evolution of RAYT/REP system in Stenotrophomonas
Staněk, Tadeáš ; Nunvář, Jaroslav (advisor) ; Zahradník, Jiří (referee)
REP (repetitive extragenic palindromes) are short DNA motifs found in the intergenic regions of many bacteria, typically in the hundreds of copies per genome. Unable to mobilize on their own, REP are propagated by RAYT (REP-associated tyrosine transposase). Stenotrophomonas are G- bacteria with a broad ecological niche, belonging to the Gammaproteobacteria. RAYT/REP systems are widespread in them, with over 132,000 REP found in 102 strains. Several classes of REP coexist in the genomes, the presence of associated RAYT is essential for high REP abundance. REP are localised in "REP loci", a series of intergenic regions with high evolutionary dynamics - the number, sequence, and orientation of REP vary at a given locus. In addition to genomic islands, REP are absent from the replication termination site, a region showing non-standard evolutionary dynamics (variable number and order of genes), probably related to chromosome segregation. Stenotrophomonas are insertion sequences (IS) rich. 35 unique IS were identified and their insertion target was verified. Ten IS insert into REP, and four other target YPAL (Yersinia palindromic elements), DNA motifs so far known only in the genus Yersinia. A total of 14 out of 35 IS in Stenotrophomonas target intergenic motifs, while their copy number accounts for 75%...
|
|
|
Bacterial REP elements
Staněk, Tadeáš ; Nunvář, Jaroslav (advisor) ; Zahradník, Jiří (referee)
Insertion sequences are the smallest type of mobile genetic element. They are formed from specific repetitive elements, between which gene for transposition is placed. That is an enzyme used for their genome propagation. REP elements are short repetitive sequences abundantly represented in many bacterial classes. They are placed in noncoding regions of genome. They have a palindromic structure, thanks to that their sides are complementary. ssRNA and ssDNA forms of REP can form a stem-loop structure. In the host genome, there are hundreds of these elements. REPs are usually grouped in higher structural units: REPIN, which has structure REP-spacer-REP, or BIME with iREP-spacer-iREP structure. These structures are associated with RAYT, tyrosine nuclease related to IS200/IS605 transposase family. The RAYT is a domesticated enzyme propagating REP elements through the genome. The presence of REP elements has an influence on transcription and translation of neighbouring genes. In addition, REPs interact with proteins important for cell physiology. This thesis is focused on the dissemination of REP elements, their characteristics, function in cells, and cooperation with RAYT nucleases. This thesis also summarizes the findings of RAYT and their similarities and differences from other families of...
|
guest ::
RSS feed.