IS4 is still found at its chromosomal site after transposition to galT

Variable expression of extracellular polysaccharide in the marine bacterium Pseudomonas atlantica is controlled by genome rearrangement

Production of extracellular polysaccharide by the marine bacterium Pseudomonas atlantica is a variable trait. Strains that produce extracellular polysaccharide (EPS(+)) have a mucoid colony phenotype, but during cultivation in the laboratory nonmucoid, EPS(-) variants arise that have a crenated colony morphology. This change is reversible since crenated variants rapidly switch to the original mucoid phenotype. We have cloned the locus (eps) controlling variable expression of EPS production by screening a recombinant cosmid library for clones that restore EPS production in the crenated variant. By using eps as a probe of genomic structure in variant strains, expression of EPS production was found to be controlled by a specific DNA rearrangement. Insertion of a 1.2-kilobase-pair DNA sequence in the eps locus results in EPS(-), whereas excision of the sequence restores the EPS(+) phenotype. Properties of the rearrangement suggest the involvement of a mobile genetic element. The possible significance of this DNA rearrangement to the survival of P. atlantica in the ocean is discussed.

IS6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains

In recent years, various polymorphic loci and multicopy insertion elements have been discovered in the Mycobacterium tuberculosis genome, such as the direct repeat (DR) locus, the major polymorphic tandem repeats, the polymorphic GC-rich repetitive sequence, IS6110, and IS1081. These, especially IS6110 and the DR locus, have been widely used as genetic markers to differentiate M. tuberculosis isolates and will continue to be so used, due to the conserved nature of the genome of M. tuberculosis. However, little is known about the processes involved in generating these or of their relative rates of change. Without an understanding of the biological characteristics of these genetic markers, it is difficult to use them to their full extent for understanding the population genetics and epidemiology of M. tuberculosis. To address these points, we identified a cluster of 7 isolates in a collection of 101 clinical isolates and investigated them with various polymorphic genetic markers, which indicated that they were highly related to each other. This cluster provided a model system for the study of IS6110 transposition, evolution at the DR locus, and the effects of these on the determination of evolutionary relationships among M. tuberculosis strains. Our results suggest that IS6110 restriction fragment length polymorphism patterns are useful in grouping closely related isolates together; however, they can be misleading if used for making inferences about the evolutionary relationships between closely related isolates. DNA sequence analysis of the DR loci of these isolates revealed an evolutionary scenario, which, complemented with the information from IS6110, allowed a reconstruction of the evolutionary steps and relationships among these closely related isolates. Loss of the IS6110 copy in the DR locus was noted, and the mechanisms of this loss are discussed.

Bidirectional deletions associated with IS4

A new type of chromosomal rearrangements associated with a transposable element has been described for IS4. These rearrangements are deletions, in which the transposable element IS4 and DNA adjacent to it on either side is lost. These deletions are at least ten times more frequent in the presence of IS4, than when the element is absent from that region. The formation of bidirectional deletions is more than 1,000 times more frequent than precise excision of IS4.

The requirement for both DNA polymerase and 5' to 3' exonuclease activities of DNA polymerase I during Tn5 transposition

By assaying transposition of Tn5 from lambda b221 cI857 rex::Tn5 (Berg 1977) in polA-proficient and deficient cells, both the polymerase activity and 5' to 3' exonuclease activity of DNA polymerase I have been shown to be required for transposition. This requirement could not be observed in three other systems in which the transposon donor replicon had existed in the PolA-proficient and deficient cells before the transposition event to be assayed occurred. By analogy to Tn3, this may indicate that the repressor encoded by Tn5 has already been expressed and hence become rate-limiting in the overall transposition process, even PolA-deficient cells still possessing a residual activity. One PolA mutant was found among more than 50 transposition deficient (tnp) mutants isolated by the use of lambda b221 cI857 rex::Tn5.

IS4 at its chromosomal site in E. coli K12

IS4 DNA has been isolated in pure form. Hybridization of this DNA against restricted DNA of several E. coli K12 strains by Southern's blotting technique has shown that, in most strains, only one copy of IS4 is present. Though the restriction fragments around this site differ in size, IS4 can be shown always to be located at the same site. In one strain, one additional copy has been found in a new location. In this strain, IS4 in its original location has been retained.