A Novel IS Element, IS 621 , of the IS 110 /IS 492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli

Abstract

An Escherichia coli strain, ECOR28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. This insertion sequence (named IS 621 ) has one large open reading frame encoding a putative protein that is 326 amino acids in length. A computer-aided homology search using the DNA sequence as the query revealed that IS 621 was homologous to the piv genes, encoding pilin gene invertase (PIV). A homology search using the amino acid sequence of the putative protein encoded by IS 621 as the query revealed that the protein also has partial homology to transposases encoded by the IS 110 /IS 492 family elements, which were known to have partial homology to PIV. This indicates that IS 621 belongs to the IS 110 /IS 492 family but is most closely related to the piv genes. In fact, a phylogenetic tree constructed on the basis of amino acid sequences of PIV proteins and transposases revealed that IS 621 belongs to the piv gene group, which is distinct from the IS 110 /IS 492 family elements, which form several groups. PIV proteins and transposases encoded by the IS 110 /IS 492 family elements, including IS 621 , have four acidic amino acid residues, which are conserved at positions in their N-terminal regions. These residues may constitute a tetrad D-E(or D)-D-D motif as the catalytic center. Interestingly, IS 621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS 621 may not recognize the entire REP sequence in transposition, but it recognizes a 15-bp sequence conserved in the REP sequences around the target site. There are several elements belonging to the IS 110 /IS 492 family that also transpose to specific sites in the repeated sequences, as does IS 621 . IS 621 does not have terminal inverted repeats like most of the IS 110 /IS 492 family elements. The terminal sequences of IS 621 have homology with the 26-bp inverted repeat sequences of pilin gene inversion sites that are recognized and used for inversion of pilin genes by PIV. This suggests that IS 621 initiates transposition through recognition of their terminal regions and cleavage at the ends by a mechanism similar to that used for PIV to promote inversion at the pilin gene inversion sites.