Novel Tn4371-ICE like element in Ralstonia pickettiiand Genome mining for comparative elements

Abstract

BackgroundIntegrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements.A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element.ResultsComparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type.ConclusionAll elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

“…The mfsR-mfsABC genes in Acidovorax sp. strain JS42 are present on ICE(Tn4371)6039 from the Tn4371 family (39,40). Whether the mfsR-mfsABC genes in A. hydrophila SSU are also part of an ICE cannot be determined yet, since this genome has not been finished.…”

Life History Analysis of Integrative and Conjugative Element Activation in Growing Microcolonies of Pseudomonas

“…On the other hand, to avoid that the microcolony became multilayered and individual cells could no longer be traced accurately, we had to restrict the amount of carbon available to cells. As a consequence of this, only a limited number of generations (7,8) could be followed before the colony entered stationary phase. Therefore, there is a relatively low number of cells with "old" poles within the demographic distribution of the clonal population in the colony.…”

“…Interestingly, however, ICE carry not only the genes for their own lifestyle but also dozens of genes with adaptive benefit for the host cell. As such, ICE have been implicated in adaptation of bacteria to antimicrobial (5) and xenobiotic compounds (6)(7)(8), acquisition of suspected virulence factors (9,10), or plant symbiotic association (11). Recent evidence on a model ICE in the bacterium Pseudomonas knackmussii B13, named ICEclc for its propensity to bestow the host with the capacity to metabolize chlorocatechols, indicated that in order to transfer, the ICE induces a so-named "transfer-competent" (TC) state in host cells in stationary phase (4).…”

Conjugal Transfer of Polychlorinated Biphenyl/Biphenyl Degradation Genes in Acidovorax sp. Strain KKS102, Which Are Located on an Integrative and Conjugative Element

“…Van Houdt et al described two similar elements residing in the genome of Cupiriavidus metallidurans CH34 (33). Ryan et al described 18 related elements from beta-and gammaproteobacteria (27) and presented a list of genes conserved among the Tn4371-like elements in beta-and gammaproteobacteria. A recent study also added several other elements and described the conserved genes and their predicted functions (34).…”

“…However, none of the elements have so far been proven to transfer conjugally. Although Tn4371 has been considered an ICE on the basis of its gene contents and the detection of covalently linked Tn4371 ends, intercellular transfer of Tn4371 has not yet been observed, and only the intracellular transposition of Tn4371 has been proven (12,27,32). The right part of Tn4371, called Tn-bph, is capable of horizontal transfer, a process thought to rely on the host genes, and furthermore, the boundaries of the transferred entity have been only roughly characterized by Southern blot analysis (12,32).…”