DNA Transposition at Work

Abstract

DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.

A single active site in the mariner transposase cleaves DNA strands of opposite polarity

“…In common with many nucleases and polymerases, the IS4 family and mariner use the two-metal-ion mechanism for catalysis (45–47). Yang et al.…”

A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici

“…The transposon insertion site was located 368 bp upstream of the ZtSDHC3 start codon and at 195 bp upstream of the other transposon insertion site in the 06STD024 strain. In both cases, a 9 bp sequence of the ZtSDHC3 promoter was duplicated at the border of each transposon, suggesting the recent insertion of these transposons at these loci (target site duplication, Fig 8B) [39]. Overall the insertion of transposons in the promoter of ZtSDHC3 was only observed in the two highly resistant isolates 07STGB009 and 06STD024.…”

Unlocking Tn3-family transposase activity in vitro unveils an asymetric pathway for transposome assembly

“…The primary cleavage activity of TnpA is to introduce a nick at the 3′ end of the IR, as expected from classical models for copy-in replicative transposition (1,2). However, TnpA also can catalyze specific DSBs, a property that is normally associated with transposases that mediate nonreplicative cut-and-paste transposition.…”

“…DDE/D transposase | DNA transposition | target immunity | Tn3 | transpososome D NA transposition generically refers to the movement of a broad diversity of genetic elements from one location to another within and between genomes. This movement is mediated by specialized recombination enzymes termed "transposases" that catalyze the required DNA cleavage and joining reactions (1,2). Transposase-encoding genes are by far the most abundant and most ubiquitous genes in nature, reflecting the importance of transposable elements in shaping and organizing genetic material in all domains of life (3,4).…”

“…Transposase TnpA of Tn4430 belongs to a large family of proteins, the DDE/D transposase superfamily, that share a motif of three conserved acidic residues intimately involved in catalysis (2,15). The active site is included in an RNaseH fold structural domain that is characteristic of a variety of polynucleotide hydrolases and transferases ( Fig.…”