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Mobile DNA Sequences and Their Possible Role in Evolution
Published in S. K. Dutta, DNA Systematics, 2019
Georgii P. Georgiev, Yurii V. Ilyin, Alexei P. Ryskov, Tatiana I. Gerasimova
One can conclude from this section that many different elements can play the role of passive transposons, mobilized either by transposase or by reverse transcriptase. For the first type of transposition, the inverted repeats are important. For the second type, the transcription of the element (existence of promoter) and the presence of a sequence appropriate for reverse transcriptase primer binding are required.
Epigenetic Reprogramming in Early Embryo Development
Published in Cristina Camprubí, Joan Blanco, Epigenetics and Assisted Reproduction, 2018
In eukaryotes, two main types of TEs have been described, retrotransposons and DNA transposons. DNA transposons or class II TEs move by a simple “cut and paste” mechanism: A DNA transposon sequence is removed from one genomic location and inserted in a new genomic site, using a specialized protein termed transposase (67). Its proportion in the human and mouse genome is lower than 5%, and no active DNA-transposons are present in these genomes at present. On the other hand, retrotransposons, or class I TEs, move by a “copy and paste” mechanism of mobilization that requires reverse transcription of an intermediate TEs RNA. In the human and mouse, more than 95% of TEs belong to this class (66) and represent more than 35% of the genome (68).
Porphyromonas gingivalis and its CRISPR-Cas system
Published in Journal of Oral Microbiology, 2019
Transposase is an enzyme that binds to the two ends of a transposon and bring them together to form a loop. It then catalyzes movement of the transposon to another part of the genome by a cut and paste mechanism or replicative transposition. In the study by Chen et al. [23] who did comparative genomics of 19 P. gingivalis strains, a high prevalence of transposase proteins was found encoded in P. gingivalis (Table 2); actually as much as 149 copies in strain A7436. In another study transposases were found in all of the 35 genomes of P. gingivalis examined, varying in number from 8 (strains Ando, F0185, SDJ5) to 103 (A7436) [28]. The lower number of transposases detected in the original genomes that were not completely sequenced in this study was most likely due to the in-between-contig sequence gaps that may contain highly repeated sequences such as transposases and IS elements. The completed genome with the lowest number of mobility-related genes was that of strain A7A1-28, where 68 transposases were detected.
Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool
Published in Gut Microbes, 2022
Vita Rozman, Petra Mohar Lorbeg, Primož Treven, Tomaž Accetto, Majda Golob, Irena Zdovc, Bojana Bogovič Matijašić
Annotation of the MGE genes allowed the classification of elements into groups based on their signature genes. A putative MGE was annotated as an ICE if it encoded an integrase, a relaxase, and a type IV secretion system, whereas an IME did not contain type IV secretion system genes. MGEs containing an integrase or a relaxase were classified as IME-like elements and elements containing a replicase (Rep) as plasmids. MGEs carrying a transposase were annotated as insertion sequences. Two insertion sequences of the same group were typical of a composite transposon. Prophages contained phage gene homologs, while a phage-inducible chromosomal island lacked structural and lytic genes.
Effects of ionizing radiation at Drosophila melanogaster with differently active hobo transposons
Published in International Journal of Radiation Biology, 2019
Transposable elements (TEs) are mobile DNA fragments of genome. The classification of TEs is based on differences in their structure and mechanisms of movement in the genome. Currently, there are three classes of TEs (Kim 2014). The first class includes retrotransposons — long terminal repeat (LTR)-retrotransposons (gypsy, copia et al.), non-LTR-retrotransposons and retroviruses (I, jockey, LINEs, SINEs et al.), and retroelements (PLEs). Mechanism (DNA-RNA-DNA displacement) of their movement is associated with the synthesis of DNA chain through the formation of RNA mediator with the participation of the enzyme reverse transcriptase (Finnegan 1989). The second class of TEs is represented by DNA transposons (P, hobo, mariner et al.) encoding a transposase. A transposase is able to recognize the ends of ‘its’ element, cut it out of the chromosome and/or embed it into the chromosome of the host genome (Bazin et al. 1999). Such a mechanism of transposition (DNA-DNA displacement) leads to DNA integrity disruption and the formation of double-stranded breaks (Kaufman and Rio 1992; Khromykh et al. 2004). The third class includes helitrons and polintons which move along the genome on the rolling circle replication (Jurka et al. 2007). In some papers, passive elements of the foldback (FB) type are considered as a separate class TEs. FBs found only in plants and in the genomes of the melanogaster subgroup flies (Macas et al. 2003; Badal et al. 2013). They are distinguished by the presence of large arrays of short terminally inverted repeat (TIRs), possibly representing nonhomologous recombination targets. Mechanism of their movement is still unknown. There is an opinion that when the FB moves, a so-called ‘complex with paired ends of the transposon’ is formed the transpososome (Kim 2014).