Insertion sequences related to ISAjo2 target p dif and dif sites and belong to a new IS family, the IS 1202 family

• Published in: Microbial genomics Vol. 9; no. 3
• Main Authors: Harmer, Christopher J, Pong, Carol H, Hall, Ruth M
• Format: Journal Article
• Language: English
• Published: England 01.03.2023
• Subjects: Amino Acids; Binding Sites; DNA Transposable Elements - genetics; Protein Domains; Transposases - genetics; dif modules; antibiotic resistance; pdif; Acinetobacter; mobile genetic elements
• ISSN: 2057-5858

Several insertion sequences (IS) found in various species exhibit target specificity. They are found, in the same orientation, 5 bp from the XerC binding site of the p sites associated with modules in plasmids, and searches revealed they are also found near chromosomal sites of species. These IS are 1.5 kb long, bounded by 24-26 bp imperfect terminal inverted repeats (TIRs) and encode a large transposase of 441-457 aa. They generate 5 bp target site duplications (TSDs). Structural predictions of the ISAjo2 transposase, TnpAjo2, modelled on TnsB of Tn revealed two N-terminal HTH domains followed by an RNaseH fold (DDE domain), a β barrel and a C-terminal domain. Similar to Tn , the outer IS ends are 5'-TGT and ACA-3', and an additional Tnp binding site, corresponding to the internal portion of the IR, is found near each end. However, the IS do not encode further proteins related to those required by Tn for targeted transposition, and the transposase may interact directly with XerC bound to a -like site. We propose that these IS, currently in the IS group in the not characterized yet (NCY) category in ISFinder, are part of a distinct IS family. Other IS listed as in the IS group encode transposases related to TnpAjo2 (25-56 % amino acid identity) and have similar TIRs but fall into three groups based on the TSD length (3-5, >15, 0 bp). Those with 3-5 bp TSDs may also target -like sites but targets were not found for the other groups.