New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria

Abstract

Cupriavidus metallidurans strain CH34 is a beta-Proteobacterium that thrives in low concentrations of heavy metals. The genetic determinants of resistance to heavy metals are located on its two chromosomes, and are particularly abundant in the two megaplasmids, pMOL28 and pMOL30. We explored the involvement of mobile genetic elements in acquiring these and others traits that might be advantageous in this strain using genome comparison of Cupriavidus/Ralstonia strains and related beta-Proteobacteria. At least eleven genomic islands were identified on the main replicon, three on pMOL28 and two on pMOL30. Multiple islands contained genes for heavy metal resistance or other genetic determinants putatively responding to harsh environmental conditions. However, cryptic elements also were noted. New mobile genetic elements (or variations of known ones) were identified through synteny analysis, allowing the detection of mobile genetic elements outside the bias of a selectable marker. Tn4371-like conjugative transposons involved in chemolithotrophy and degradation of aromatic compounds were identified in strain CH34, while similar elements involved in heavy metal resistance were found in Delftia acidovorans SPH-1 and Bordetella petrii DSM12804. We defined new transposons, viz., Tn6048 putatively involved in the response to heavy metals and Tn6050 carrying accessory genes not classically associated with transposons. Syntenic analysis also revealed new transposons carrying metal response genes in Burkholderia xenovorans LB400, and other bacteria. Finally, other putative mobile elements, which were previously unnoticed but apparently common in several bacteria, were also revealed. This was the case for triads of tyrosine-based site-specific recombinases and for an int gene paired with a putative repressor and associated with chromate resistance.

Heavy Metal Resistance Strategies of Acidophilic Bacteria and Their Acquisition: Importance for Biomining and Bioremediation

“…Other non-acidophilic microorganisms able to grow in the presence of several toxic metals, such as C. metallidurans, tolerate CuSO 4 in a much lower range (1.5 to 12.5 mM) (Chen et al, 2008). Nevertheless, this property of C. metallidurans has also been attributed to the occurrence of a great variety of metal resistance determinants, many of them present in GIs (van Houdt et al, 2009). Although as already mentioned it is not possible to compare MIC values of microorganisms growing in entirely diff erent media, the presence of metal resistance genes in genomic islands may be a general strategy used by environmental microorganisms to tolerate high levels of toxic metals.…”

“…These DNA regions would have been previously transferred by other MGEs and they carry one or more genes that can increase the adaptability and versatility of the microorganism. They have been defi ned in general as clusters of genes having one or a set of the following properties (Dobrindt et al, 2004;van Houdt et al, 2009): a tyrosine-based site-specifi c recombinase gene and an adjacent tRNA gene at one extremity; flanking insertion sequence elements; a base composition and/or phylogeny diff ering from the bulk of the genome, indicating acquisition through HGT; higher content of hypothetical genes than neighboring regions; clustering of genes characteristic of MGEs such as recombinase genes and IS elements; conservation of the GI between different (unrelated) hosts; a high concentration of genes specialized for resistance, catabolism and unusual metabolism.…”

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

“…Many of the known efflux systems play a role in antibiotic resistance; therefore, their distribution and propagation in clinically relevant strains pose a major health concern (3). Although mostly located on the bacterial chromosome (1), genes for efflux systems can be transmitted via mobile genetic elements like plasmids or integrative and conjugative elements (ICE) (4)(5)(6). Recently, we described a class of widespread ICE among beta-and gammaproteobacteria, which, through a region permissive for gene insertions, can carry a wide range of auxiliary gene functions (7)(8)(9).…”

Structure Analysis of Genomic Islands Flanked by 5’ and 3’ End of the tRNAGly-CCC Gene in Delftia Acidovorans SPH-1

“…Genomic islands are products of horizontal gene transfer (HGT) that plays an important role for the evolution of prokaryote chromosomes. DAGI-1 and DAGI-2 were determined as the metal resistance genomic islands (GIs) in D. acidovorans SPH-1 through comparative genomics analysis with Cupriavidus metallidurans CH34, and their integration sites are not the tRNA Gly genes [5] . Accidentally, two integrases (Daci_4138 and Daci_4139) that exist nearby left and right flanking sequence of tRNA Gly-CCC gene (Daci_R0056) were found in D. acidovorans SPH-1, respectively.…”