Isolation and characterization of the IS3-like element from Thermus aquaticus

A novel insertion sequence transposed to thermophilic bacteriophage {phi}IN93

The nucleotide sequence of IStaqTZ2 are available in the DDBJ/EMBL/GenBank databases under the accession number AB063392. A novel insertion sequence (IStaqTZ2) was transposed from the genome of Thermus thermophilus TZ2 to that of the thermophilic bacteriophage IN93. The complete nucleotide sequence of IStaqTZ2 was determined and was found to be 1,258 bp in length and to contain an open reading frame (ORF1179), which is predicted to encode a transposase. IStaqTZ2 was also found to contain two terminal inverted repeats with 48 and 52 bp, respectively. Based on homology analysis, IStaqTZ2 was classified as a member of the IS256 family.

Transposition of an insertion sequence, ISTth7, in the genome of the extreme thermophile Thermus thermophilus HB8

We have identified an active insertion sequence (IS) in the genome of Thermus thermophilus HB8. Transposition was detected as insertional inactivation of a 16S rRNA methyltransferase gene, rsmG, resulting in streptomycin resistance. The IS element, ISTth7, is 1029 bp in length, encodes an imperfect 12 bp inverted repeat, and produces a 9 bp direct repeat of the target sequence. The sequence of a putative transposase encoded by ISTth7 indicates that it is a member of the IS427 group within the IS5 family of ISs. Nine intact copies and several partial copies were identified throughout the chromosome and the megaplasmid pTT27. ISTth7 was also detected in T. thermophilus strain IB-21 and Thermus igniterrae but not Thermus antranikianii, suggesting a widespread occurrence of ISTth7 among Thermus spp.

IS911 transposition is regulated by protein-protein interactions via a leucine zipper motif

Efficient intermolecular transposition of bacterial insertion sequence IS911 involves the activities of two element-encoded proteins: the transposase, OrfAB, and a regulatory factor, OrfA. OrfA shares the majority of its amino acid sequence with the N-terminal part of OrfAB. This includes a putative helix-turn-helix and three of four heptads of a leucine zipper motif. OrfA strongly stimulates OrfAB-mediated intermolecular transposition both in vivo and in vitro. The present results support the notion that this is accomplished by direct interaction between these two proteins via the leucine zipper. We used both a genetic approach, based on gene fusions with phage lambda repressor, and a physical approach, involving co-immunoprecipitation, to show that OrfA not only undergoes oligomerisation but is capable of engaging with OrfAB to form heteromultimers, and that the leucine zipper is necessary for both types of interaction. Furthermore, mutation of the leucine zipper in OrfA inactivated its regulatory function. Previous observations demonstrated that the integrity of the leucine zipper motif was also important for OrfAB binding to the IS911 terminal inverted repeats. Here, we show, in gel shift experiments, using a derivative of OrfAB deleted for the C-terminal catalytic domain, OrfAB[1-149], that the protein is capable of pairing two inverted repeats to generate a species resembling a "synaptic complex". Preincubation of OrfAB[1-149] with OrfA dramatically reduced formation of this complex and favored formation of an alternative complex devoid of OrfA. Together these results suggest that OrfA exerts its regulatory effect by interacting transiently with OrfAB via the leucine zipper and modifying OrfAB binding to the inverted repeats.

Insertion sequences

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.