Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event

Abstract

All members of the IS1248 family residing in the genome of Paracoccus denitrificans have been isolated by using a set of insertion sequence entrapment vectors. The family consists of five closely related members that integrate the entrapment vectors at distinct sites. One of these, IS1248b, was sequenced and, except for a single base change, shown to be identical to the previously isolated IS1248a. Southern analysis of genomic DNA with labeled IS1248 revealed different hybridization patterns for different isolates of P. denitrificans and Thiosphaera pantotropha. No hybridization was observed with DNA from Thiobacillus versutus and more distantly related species. From a comparison of the fingerprints it was shown that one of the members of the IS1248 family found in P. denitrificans DSM413 is absent in strain NCIB8944, although they are catalogued in international strain catalogues as identical strains. Furthermore, strains Pd1222 and Pd1235, both derivatives of P. denitrificans DSM413, were shown to have different patterns of IS1248 hybridizing restriction fragments. In 14 of 18 strains, the entrapment vectors used in this study were incorporated into the genome via IS1248-mediated cointegrate formation. In the other four strains, the entrapment vectors were shown to be integrated through a different mechanism not involving IS1248.

Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

“…Size markers (kilobases) are indicated on the left. be identified in this species and in the entire genus Paracoccus (with the exception of IS1248 of P. denitrificans) (53). All of the elements have been identified by their integration into a selective cartridge of a novel vector, pMEC1, which proves that they are functional in transposition.…”

“…Since ISPpa2 and IS1248 cross-hybridize, we were unable to distinguish these elements by hybridization (they are 87% identical at the nucleotide sequence level). It has been previously shown that IS1248 is present in multiple copies in all strains of P. denitrificans tested (53). The presence of ISPpa2-like sequences in plasmids of DSM 65 (pHG16-a) and DSM 11073 (pKLW1) suggests the possibility of their dissemination by lateral transfer.…”

Bacterial Species and Speciation

“…This may occur as a side effect of homologous recombination, whereby a heterologous gene from a donor is integrated along with closely anking homologous DNA (Hamilton et al, 1989;Majewski and Cohan, 1999a). Alternatively, heterologous genes may be integrated along with a transposable element introduced into the recipient cell on a plasmid or phage (Van Spanning et al, 1995). I next consider the consequences of rare, promiscuous, localized recombination, both homologous and heterologous, on the properties of species and speciation in bacteria.…”

What are Bacterial Species?

“…This may occur as a side effect of homologous recombination, whereby a heterologous gene from a donor is integrated along with flanking homologous DNA (34,52). Alternatively, heterologous genes may be integrated along with a transposable element brought into the recipient on a plasmid or phage (97). Genomic analyses have recently shown that a sizeable fraction of bacterial species' genomes (frequently 5%-15%) has typically been acquired from other species (65).…”