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 IS621) 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 IS621 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 IS621 as the query revealed that the protein also has partial homology to transposases encoded by the IS110/IS492 family elements, which were known to have partial homology to PIV. This indicates that IS621 belongs to the IS110/IS492 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 IS621 belongs to the piv gene group, which is distinct from the IS110/IS492 family elements, which form several groups. PIV proteins and transposases encoded by the IS110/IS492 family elements, including IS621, 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, IS621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS621 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 IS110/IS492 family that also transpose to specific sites in the repeated sequences, as does IS621. IS621 does not have terminal inverted repeats like most of the IS110/IS492 family elements. The terminal sequences of IS621 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 IS621 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.

Site-specific recombination by the DDE family member mobile element IS30transposase

“…Even though the output of their activity can be simplified to insertion, deletion, or inversion of DNA segments, transposition and site-specific recombination are generally regarded as distinct phenomena (1). Classification according to the protein-sequence motifs revealed that some transposases (Tpases) and site-specific recombinases (Recases) with entirely different functions fall within the same family (2)(3)(4)(5)(6). This finding supports that mechanistically dissimilar enzymes can perform similar biological functions and suggests that transposition and site-specific recombination may be closer to each other in some respect than was supposed earlier.…”

Insertion of group II intron retroelements after intrinsic transcriptional terminators

“…There are notable exceptions, however, such as Tn7, which targets the attTn7 sequence found in many bacterial genomes, and IS231, IS21, and IS911, which each insert into sequences of other transposable elements (4). Some IS elements, such as IS1397 (28) and IS621 (29), target extragenic, palindromic repeats that are not terminators, a specificity similar to class C introns. The targeting of terminator motifs by class C introns provides an additional mechanism to avoid gene disruptions in bacteria: the element elegantly locates the end of a transcription unit and inserts after it.…”

Everyman's Guide to Bacterial Insertion Sequences

“…A similar type of Tpase, known as a DEDD Tpase, is related to the Holliday junction resolvase, RuvC (39,40). These possess a similar predicted structural topology in their catalytic site and presumably have similar chemistry to the DDE enzymes.…”

“…They encode a single Tpase gene that spans the entire length of the IS. One characteristic which distinguishes IS110 family members from all other elements whose Tpases exhibit a predicted RNase fold is that the predicted catalytic domain of their DEDD Tpases is located N-terminal to the DNA-binding domain (39,228). In the DDE Tpases it is generally located upstream.…”

“…The Tpase is closely related to the Piv and MooV invertases from Moraxella lacunata/Moraxella bovis (224,225) and Neisseria gonorrhoeae (39,226). Piv catalyzes inversion of a DNA segment permitting expression of a type IV pilin.…”