ISAfe1, an ISL3 family insertion sequence from Acidithiobacillus ferrooxidans ATCC 19859

A 1.3-kb insertion sequence, termed ISAfe1 (U66426), from Acidithiobacillus ferrooxidans ATCC 19859 is described. ISAfel exhibits the features of a ty pical bacterial insertion sequence. It has 26-bp, imperfectly matched, term inal inverted repeats and an open reading frame (ORF) that potentially enco des a transposase (TPase) of 404 amino acids (AAB07489) with significant si milarity to members of the ISL3 family of insertion sequences; A potential ribosome-binding site and potential -10 and -35 promoter sites for the TPas e ORF were identified, and a +1 transcriptional start site was detected exp erimentally. A potential outwardly directed -35 site was identified in the right inverted repeat of ISAfe1. A second ORF (ORF B), of unknown function, was found on the complementary strand with significant similarity to ORF 2 of ISAe1 from Ralstonia eutropha. Southern blot analyses demonstrated that ISAfe1-like elements can be found in multiple copies in a variety of A. fe rrooxidans strains and that they exhibit transposition. A codon adaptation index (CAI) analysis of the TPase of ISAfe1 indicates that is has a CAI of 0.726 and can be considered well adapted to its host, suggesting that ISAfe 1 might be an ancient resident of A. ferrooxidans. Analysis of six of its t arget sites of insertion in the genome of A. ferrooxidans ATCC 19859 indica tes a preference for 8-bp pseudopalindromic sequences, one of which resembl es the termini of its inverted repeats. Evidence is presented here that is consistent with the possibility that ISAfe1 can promote both plasmid cointe grate formation and resolution in E. coli.