A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites

Abstract

IS1202, originally isolated from Streptococcus pneumonia in the mid-1990s had been previously tagged as an emerging IS family in ISfinder. While searching for plasmid-associated Xer recombinase recombination sites (xrs) in Acinetobacter baumannii, we observed that some insertion sequences related to IS1202 were repeatedly found abutting these sites in a number of plasmids. The plasmids often carried repeated xrs thought to form a new type of mobile genetic element (MGE) which uses the chromosomally-encoded XerCD recombinase for mobility. The MGE (xrs cassette) consist of xrs flanking one or a small number of genes often including different clinically important carbapenemase-encoding bla-OXA. The IS1202- related IS are inserted with their left, transposase proximal extremity, IRL, five base pairs from xrs and include a characteristic 5bp flanking target duplication. Further searches revealed that many different plasmid- and chromosome-borne xrs can be targeted and that IS1202-xrs combinations are not limited to Acinetobacter baumannii but occur in other bacteria. In addition to 28 IS1202 group ISs in ISfinder and a number which had been subsequently submitted, we undertook a survey of the NCBI (February 2020) and identified 138 additional IS1202-related IS. These could be divided into 3 principal subgroups based on their transposase sequences and on the length of the DR generated on insertion: subgroup IS1202 27-28bp DR); ISTde1 (15-17bp); and ISAba32 (5-6bp). Members of each group which lacked DR were also found. But since other examples of most of these were subsequently identified having DR, those lacking DR may have been generated by intra-replicon recombination. Only members of the group which generate 5bp DR were found to target xrs. These were not only identified in plasmids but also occurred at some individual xrs sites, dif, located at the chromosome replication terminus and involved in post-replication chromosome segregation. Further analysis showed the presence of subgroup-specific indels in their transposases which may be responsible for the differences in their behavior. We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of at three subfamilies, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.