The maize Ac transposable element is only one of several types found in Nature. Transposable elements can be divided into two major classes based on method of transposition:
· Retrotransposons (class 1)
Ø Use reverse transposase to make RNA intermediate for transposition.
Ø Encode an integrase and reverse transcriptase for transposition.
Ø Found in viruses.
· Transposons (class 2)
Ø DNA fragments transpose directly from DNA segment to DNA segment:
· Producing a DNA copy that transposes (replicative transposition)
· Or, cut/paste into a new locus (conservative transposition).
Ø Encode a transposase for transposition.
Ø Can carry additional genes.
Ø Found in eukaryotes and prokaryotes.
Transposase and integrase proteins carry a ribonuclease-like catalytic domain and can use the same target site to catalyse both DNA cleavage and DNA strand transfer. However, transposases and integrases are only active when assembled into a synaptic complex (transpososome) on the DNA. The transpososome provides a scaffold to support the transposition reactions, changing its conformation to accommodate the different steps in transposition.
At least five families have been classified, although this number will most likely grow as new transposases are characterised. These families use distinct catalytic mechanisms for break/rejoining of DNA. For example, some transposases cut/transfer/paste original DNA, while others copy DNA into the target site. These families are listed below:
These transposases carry a triad of conserved amino acids: aspartate (D), aspartate (D) and glutamate (E), which are required for the coordination of a metal ion required for catalysis, although the DDE chemistry can be integrated into the transposition cycle in differing ways. These employ a cut-and-paste mechanism of the original transposon. This family includes the maize Ac transposon, as well as the Drosophila P element, bacteriophage Mu, Tn5 and Tn10, Mariner, IS10, and IS50.
These also use a cut-and-paste mechanism of transposition, but employ a site-specific tyrosine residue. The transposon is excised from its original site (which is repaired); the transposon then forms a closed circle of DNA, which is integrated into a new site by a reversal of the original excision step. These transposons are usually found only in bacteria, and include Kangaroo, Tn916, and DIRS1.
These transposases use a cut-and-paste (cut-out/paste-in) mechanism of transposition involving a circular DNA intermediate, which is similar to that of tyrosine transposases, only they employ a site-specific serine residue. These transposons are usually found only in bacteria, and include Tn5397 and IS607.
These employ either a copy-in mechanism, where they copy a single strand directly into the target site by DNA replication, so that the old (template) and new (copied) transposons both have one newly synthesized strand. These transposons usually employ host DNA replication enzymes. Examples include IS91 and helitrons.
Retrotransposons can vary in their mechanism of transposition. Some use the RT/En method, employing an endonuclease to nick the target site DNA, the nick serving as a primer for reverse transcription of an RNA copy by the reverse transcriptase enzyme. Examples include LINE-1 and TP-retrotransposons.