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Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network

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Abstract

The soil bacterium Cupriavidus metallidurans CH34 contains a high number of heavy metal resistance genes making it an interesting model organism to study microbial responses to heavy metals. In this study the transcriptional response of strain CH34 was measured when challenged to sub-lethal concentrations of various essential or toxic metals. Based on the global transcriptional responses for each challenge and the overlap in upregulated genes between different metal responses, the sixteen metals were clustered in three groups. In addition, the transcriptional response of already known metal resistance genes was assessed, and new metal response gene clusters were identified. The majority of the studied metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex interplay at transcriptional level between the different metal responses. The pronounced redundancy of these metal resistant regions—as illustrated by the large number of paralogous genes—combined with the phylogenetic distribution of these metal response regions within either evolutionary related or other metal resistant bacteria, provides important insights on the recent evolutionary forces shaping this naturally soil-dwelling bacterium into a highly metal-resistant strain well adapted to harsh and anthropogenic environments.

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Acknowledgments

This work is supported by internal funds of SCK·CEN and by the European Space Agency through the MESSAGE contracts (PRODEX agreements No. 90037 and 90094).

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  1. Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Boeretang 200, 2400 Mol, Belgium

    Pieter Monsieurs, Hugo Moors, Rob Van Houdt, Paul J. Janssen, Ann Janssen, Ilse Coninx, Max Mergeay & Natalie Leys

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  1. Pieter Monsieurs
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  2. Hugo Moors
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Correspondence to Pieter Monsieurs.

Electronic supplementary material

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10534_2011_9473_MOESM1_ESM.pdf

Supplementary File 1: Overview of the total number of upregulated genes and split up per replicon, after exposure of C. metallidurans CH34 to a given metal. obs.: the number of upregulated genes located on a specific replicon for a certain metal. exp: the number of expected genes relative to the total number of upregulated genes and the size of the replicon. fold: the fold-change of the number of observed over the number of expected genes. pval: the p-value for a significant enrichment of metal response genes on that replicon based on the hypergeometric distribution. Red colored fields indicate a statistically significant enrichment.(PDF 54 kb)

10534_2011_9473_MOESM2_ESM.pdf

Supplementary File 2: Detailed expression data for all upregulated genes upon metal exposure. Excel file containing all upregulated genes. Different columns are: (A) Probe ID: Probe Identifier, (B) Rmet: Gene number, (C) Genename: gene name, (D) Replicon: accession number of replicon, (E) Product: gene function, (F) cluster name: name of cluster where the gene belongs to, (G) COG: COG classes where the gene belongs to, (H) KEGG: KEGG pathway where the gene belongs to, (I-X) log2 fold changes after induction with one of the 16 metals (#N/A means no measurement). Color code represents: Red = more than 4-fold upregulated, Orange = between 2- and 4-fold upregulated, Green = more than 2-fold down-regulated.(PDF 1752 kb)

Supplementary File 3: Detailed discussion of metal response regions not discussed in manuscript. (PDF 199 kb)

10534_2011_9473_MOESM4_ESM.ppt

Supplementary File 4: Visual summary of the different metal response regions in C. metallidurans CH34. In the vertical axis the different regions are listed (replicon name + name or location of the region). In the horizontal axis, the different metals that were tested are shown. The number indicated on the figure indicates the percentage of genes belong to a certain region that is upregulated by a specific metal.(PPT 523 kb)

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Monsieurs, P., Moors, H., Van Houdt, R. et al. Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 24, 1133–1151 (2011). https://doi.org/10.1007/s10534-011-9473-y

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