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

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Abstract

Cupriavidus metallidurans strain CH34 is a β-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 β-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.

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Acknowledgments

This work was supported by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the MISSEX project (PRODEX agreements C90254) and by the collaboration agreement between SCK•CEN and Université Libre of Bruxelles. SM was supported by a SCK•CEN Ph.D. grant. Thanks are due to Claudine Médigue, Zoé Rouy, David Vallenet from the MAGE Genoscope platform of annotation for their availability and their kind pedagogy, to the SCK•CEN annotation team and especially Paul Janssen, Pieter Monsieurs, Hugo Moors and Nicolas Morin, to Niels van der Lelie and Safieh Taghavi for 20 years collaboration about the genetics of C. metallidurans CH34, to Ariane Toussaint and Jacques Mahillon for comments and suggestions about the mobile genetic elements and the introduction to the ACLAME and ISfinder databases, and to Simon Silver for patience and comprehension.

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  1. Unit for Microbiology, SCK•CEN, Boeretang 200, 2400, Mol, Belgium

    Rob Van Houdt, Sébastien Monchy, Natalie Leys & Max Mergeay

  2. Biology Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA

    Sébastien Monchy

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  1. Rob Van Houdt
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  2. Sébastien Monchy
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Correspondence to Max Mergeay.

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Van Houdt, R., Monchy, S., Leys, N. et al. New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria. Antonie van Leeuwenhoek 96, 205–226 (2009). https://doi.org/10.1007/s10482-009-9345-4

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