tnpA

tnpA is a gene that encodes the transposase enzyme responsible for the movement of certain bacterial DNA elements, most notably transposons of the Tn3 family and related insertion sequences. In many Tn3-like elements, tnpA lies adjacent to tnpR, which encodes a resolvase, and both are bordered by terminal inverted repeats that define the element. The tnpA-tnpR module is a hallmark of replicative transposons, where transposition relies on the coordinated actions of the transposase and the resolvase.

The transposase produced by tnpA is typically a DNA-cutting and -joining enzyme of the DDE family. It binds to the ends of the transposon, introduces DNA breaks and strand transfer during a replicative transposition cycle, and produces a cointegrate intermediate in which the donor and target molecules are joined. Resolution of this cointegrate and regulation of transposition are mediated by the adjacent tnpR gene, which encodes a site-specific recombinase that acts on the res site and modulates transposition frequency.

Distribution and significance of tnpA elements reflect their role in genome plasticity and horizontal gene transfer. TnpA homologs are found across various bacteria and on plasmids carrying transposons, and they have been implicated in the mobilization of antibiotic resistance determinants and other adaptive traits. As routine elements in genome annotation, tnpA is often described with its associated tnpR and the characteristic inverted repeats that define the transposon.

In comparative genomics, tnpA annotations aid in identifying mobile genetic elements and understanding mechanisms of transposition, regulation, and their impact on genome evolution.