Acinetobacter Insertion Sequence IS Aba11 Belongs to a Novel Family That Encodes Transposases with a Signature HHEK Motif

Abstract

Experimental and in silico PCR analysis targeting ISAba11 and TnAbaR islands in 196 epidemiologically unrelatedAcinetobacter strains representative of >19 species were performed. The first two Acinetobacter baumannii ISAba11 elements identified had been found to map to the same site on TnAbaR transposons. However, no further evidence of physical linkage between the two elements was demonstrated. Indeed, examination of 25 definite or putative insertion sites suggested limited sequence specificity. Importantly, an aacC1-tagged version of ISAba11 was shown to actively transpose in A. baumannii. Similarity searches identified nine iso-ISAba11 elements in Acinetobacter and one in Enhydrobacter and single representatives of four distant homologs in bacteria belonging to the phyla "Cyanobacteria" and Proteobacteria. Phylogenetic, sequence, and structural analyses of ISAba11 and/or its associated transposase (Tnp ISAba11 ) suggested that these elements be assigned to a new family. All five homologs encode transposases with a shared extended signature comprising 16 invariant residues within the N2, N3, and C1 regions, four of which constituted the cardinal ISAba11 family HHEK motif that is substituted for the YREK DNA binding motif conserved in the IS4 family. Additionally, ISAba11 family members were associated with either no flanking direct repeat (DR) or an ISAba11-typical 5-bp DR and possessed variable-length terminal inverted repeats that exhibited extensive intrafamily sequence identity. Given the limited pairwise identity among Tnp ISAba11 homologs and the observed restricted distribution of ISAba11, we propose that substantial gaps persist in the evolutionary record of ISAba11 and that this element represents a recent though potentially highly significant entrant into the A. baumannii gene pool.

Dissemination and characterization of NDM-1-producing Acinetobacter pittii in an intensive care unit in China

“…It was recently shown that the ISAba11 elements belong to a novel family that encodes transposases with a signature HHEK motif and had been found in many kinds of Acinetobacter spp. [36]. The ISAba11 in the pAP-D499 was associated with typical 5-bp DR and possessed 13-bp TIR as previously reported [36].…”

“…[36]. The ISAba11 in the pAP-D499 was associated with typical 5-bp DR and possessed 13-bp TIR as previously reported [36]. ISAba11 movement can result in inactivation of the A. baumannii lipid A biosynthesis genes lpxA and lpxC, resulting in the loss of lipopolysaccharide production and high-level colistin resistance.…”

“…The bla NDM‐1 region in the pAP‐D499 plasmid was flanked by two insertion sequence (IS) elements (IS Aba125 and IS Aba11 ), a finding that differed from those of earlier reports of A. lwoffii , A. pittii and A. baumannii [14,15,26]. The insertion sequence element IS Aba11 , which had a length of 1101 bp, represents an emerging insertion sequence family that encodes transposases [36]. IS Aba11 was bracketed by identical 5‐bp direct repeats (attta), indicating target site duplication, and contained matching 13‐bp terminal inverted repeat (TIR).…”

“…IS Aba11 was bracketed by identical 5‐bp direct repeats (attta), indicating target site duplication, and contained matching 13‐bp terminal inverted repeat (TIR). It shared 99% sequence identity with that identified in A. baumannii strain ATCC 19606 and 98% sequence identity with a hypothetical protein encoded by A. baumannii ATCC 17978 [36,37].…”

Everyman's Guide to Bacterial Insertion Sequences

“…There are several clades within this family. A new clade, ISAba11, was proposed as a new family based on five IS (156). Members of this group generate 5 bp target duplications (instead of 4 bp), exhibit conserved IR and include HHEK instead of YREK.…”