TheclcElement ofPseudomonassp. Strain B13, a Genomic Island with Various Catabolic Properties

Abstract

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3-and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties.

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa

“…PAPI-1, along with pKLC102, represents the cluster of GIs that encode XerCD type integrases and use tRNA Lys for integration. The clc element is more closely related to PAGI-2 and -3, the two tRNA Gly -associated GIs in P. aeruginosa (27). To date, only PAPI-1 and the clc element are known to be transferable in Pseudomonas bacteria, thus providing two good models to elucidate the molecular mechanism of horizontal gene transfer in a natural environment and in infected hosts.…”

“…Like PAPI-1, the clc element is normally integrated into the bacterial chromosome, and it can excise at low frequency and self-transfer to a new strain in which it reintegrates (26). The clc element also carries an integrase gene, and the gene encoding a chromosome partitioning-related protein, located at the opposite ends of the island (27). The P4 integrase of the clc element is known to be responsible for mobilization of the island (28).…”

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

“…It has been estimated that conjugative systems of ICEs are more abundant among bacteria than those of plasmids (7), yet we know far less about ICE behavior because they are difficult to follow and isolate. ICEs have attracted interest because they can transmit antibiotic resistance genes (8) and suspected virulence factors (9)(10)(11), but also genes for toxic compound degradation (12,13) and heavy metal resistance (14). Several evolutionary distinct families of ICEs have been described, which have a mechanistically similar lifestyle (4,6,15).…”

“…1B). We showed for the model ICEclc (named for carrying the clc genes for chlorocatechol metabolism) in the bacterium Pseudomonas knackmussii B13 (13,24) that conjugative transfer necessitates development of the host bacterial cell into a "transfer competence" state (25). Development of transfer competence is orchestrated by ICEclc and results in a bistable differentiation of transfer competent (tc) cells and non-tc cells (in which ICEclc remains silent; Fig.…”

Phosphorothioation: An Unusual Post-Replicative Modification on the DNA Backbone

“…Moreover, ICEclc of Pseudomonas sp. strain B13 can self-transfer to P. putida, Cupriviadus necator or P. aeruginosa at similar frequencies [25]. He et al demonstrated that the 93 kb genomic island in S. lividans was capable of spontaneous excision from the chromosome at a level of 0.016%-0.027%.…”