Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa247 ◽

2020 ◽

Author(s):

Max Mergeay ◽

Rob Van Houdt

Keyword(s):

Type Strain ◽

Historical Perspective ◽

Bacterial Resistance ◽

Metal Resistance ◽

Early Research ◽

Molecular Techniques ◽

Ecological Niches ◽

Cupriavidus Metallidurans Ch34 ◽

Resistance Determinants ◽

Cupriavidus Metallidurans

Abstract Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.

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Crystal Structure and Metal-Binding Specificity of ZneB, the Periplasmic Adaptor Protein of A Heavy Metal Resistance System from Cupriavidus Metallidurans CH34

Biophysical Journal ◽

10.1016/j.bpj.2009.12.1347 ◽

2010 ◽

Vol 98 (3) ◽

pp. 248a

Author(s):

Fabien De Angelis ◽

John K. Lee ◽

Joseph D. O'Connell ◽

Larry J.W. Miercke ◽

Koen H. Verschueren ◽

...

Keyword(s):

Crystal Structure ◽

Heavy Metal ◽

Metal Binding ◽

Adaptor Protein ◽

Binding Specificity ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Cupriavidus Metallidurans Ch34 ◽

Cupriavidus Metallidurans ◽

Resistance System

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The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Genes ◽

10.3390/genes11091049 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1049

Author(s):

Laurens Maertens ◽

Natalie Leys ◽

Jean-Yves Matroule ◽

Rob Van Houdt

Keyword(s):

Sulfur Metabolism ◽

Model Organism ◽

Gene Clusters ◽

Resistance Mechanisms ◽

Metal Resistance ◽

Copper Resistance ◽

Messenger Rnas ◽

Antisense Transcripts ◽

Cupriavidus Metallidurans Ch34 ◽

Cupriavidus Metallidurans

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5′ end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

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The Response of Cupriavidus Metallidurans CH34 to Cadmium Involves a Decrease in Intracellular Levels of C-Di-GMP Probably Mediated by a Novel Metal Regulated Phosphodiesterase That Inhibits the Biofilm Lifestyle

10.20944/preprints201807.0520.v1 ◽

2018 ◽

Author(s):

Pablo Alviz ◽

Sebastian Fuentes ◽

Luis Rojas ◽

Raymond Turner ◽

Michael Seeger ◽

...

Keyword(s):

Heavy Metal ◽

Biofilm Formation ◽

Bioinformatic Analysis ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Cadmium Resistance ◽

Toxic Heavy Metal ◽

Transcription Analysis ◽

Cupriavidus Metallidurans Ch34 ◽

Cupriavidus Metallidurans

Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain for heavy metal resistance and bioremediation. The aim of this study was to determine the role of the c-di-GMP pathway in the C. metallidurans CH34 response to cadmium in both planktonic and biofilm cells. Increasing cadmium concentrations correlates with an inhibition of biofilm formation and EPS production in C. metallidurans cells. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium induced in planktonic cells and strongly induced in biofilm cells the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and null mutant complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated phosphodiesterase. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD* correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 involves a decrease in c-di-GMP content that inhibits the biofilm lifestyle.

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

BioMetals ◽

10.1007/s10534-011-9473-y ◽

2011 ◽

Vol 24 (6) ◽

pp. 1133-1151 ◽

Cited By ~ 72

Author(s):

Pieter Monsieurs ◽

Hugo Moors ◽

Rob Van Houdt ◽

Paul J. Janssen ◽

Ann Janssen ◽

...

Keyword(s):

Heavy Metal ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Transcriptional Network ◽

Cupriavidus Metallidurans Ch34 ◽

Cupriavidus Metallidurans

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Loss of mobile genomic islands in metal resistant, hydrogen-oxidizing Cupriavidus metallidurans

Applied and Environmental Microbiology ◽

10.1128/aem.02048-21 ◽

2021 ◽

Author(s):

Cornelia Große ◽

Thomas A. Kohl ◽

Stefan Niemann ◽

Martin Herzberg ◽

Dietrich H. Nies

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Metal Binding ◽

Selection Pressure ◽

Gene Array ◽

Metal Resistance ◽

Current Data ◽

Genomic Islands ◽

Resistance Determinants ◽

Cupriavidus Metallidurans

The genome of the metal resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans strain CH34 contains horizontally acquired plasmids and genomic islands. Metal-resistance determinants on the two plasmids may exert genetic dominance over other related determinants. To investigate whether these recessive determinants can be activated in the absence of the dominant ones, the transcriptome of the highly zinc-sensitive deletion mutant Δe4 (Δ cadA ΔzntA ΔdmeF ΔfieF ) of the plasmid-free parent AE104 was characterized using gene arrays. As a consequence of some unexpected results, close examination by PCR and genomic re-resequencing of strains CH34, AE104, Δe4 and others revealed that the genomic islands CMGIs 2, 3, 4, D, E, but no other islands or recessive determinants, were deleted in some of these strains. Provided CH34 wild type was kept under alternating zinc and nickel selection pressure, no comparable deletions occurred. All current data suggest that genes were actually deleted and were not, as previously surmised, simply absent from the respective strain. As a consequence, a cured database was compiled from the newly generated and previously published gene array data. Analysis of data from this database indicated that some genes of recessive, no longer needed determinants were nevertheless expressed and up-regulated. Their products may interact with those of the dominant determinants to mediate a mosaic phenotype. The ability to contribute to such a mosaic phenotype may prevent deletion of the recessive determinant. The data suggest that the bacterium actively modifies its genome to deal with metal stress and the same time ensures metal homeostasis. Significance In their natural environment, bacteria continually acquire genes by horizontal gene transfer and newly acquired determinants may become dominant over related ones already present in the host genome. When a bacterium is taken into laboratory culture, it is isolated from the horizontal gene transfer network. It can no longer gain genes, but instead may lose them. This was indeed observed in Cupriavidus metallidurans for loss key metal-resistance determinants when no selection pressure was continuously kept. However, some recessive metal-resistance determinants were maintained in the genome. It is proposed that they might contribute some accessory genes to related dominant resistance determinants, for instance periplasmic metal-binding proteins or two-component regulatory systems. Alternatively, they may only remain in the genome because their DNA serves as a scaffold for the nucleoid. Using C. metallidurans as an example, this study sheds light on the fate and function of horizontally acquired genes in bacteria.

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Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter

Microorganisms ◽

10.3390/microorganisms9020309 ◽

2021 ◽

Vol 9 (2) ◽

pp. 309

Author(s):

Rob Van Houdt ◽

Joachim Vandecraen ◽

Natalie Leys ◽

Pieter Monsieurs ◽

Abram Aertsen

Keyword(s):

Abc Transporter ◽

Rhizobium Leguminosarum ◽

Constitutive Expression ◽

Metal Resistance ◽

Cadmium Resistance ◽

Gene Encoding ◽

Cupriavidus Metallidurans Ch34 ◽

Cupriavidus Metallidurans ◽

High Zinc ◽

Zinc Concentrations

Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterization of CH34ZnR revealed that it was also more resistant to cadmium, and that it incurred seven insertion sequence-mediated mutations. Among these, an IS1088 disruption of the glpR gene (encoding a DeoR-type transcriptional repressor) resulted in the constitutive expression of the neighboring ATP-binding cassette (ABC)-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34ZnR with the parental glpR gene further demonstrated that loss of GlpR function and concomitant derepression of the adjacent ABC transporter is pivotal for the observed resistance phenotype. Importantly, addition of glycerol, presumably by glycerol-mediated attenuation of GlpR activity, also promoted increased zinc and cadmium resistance in the parental CH34 strain. Upregulation of this ABC-type transporter is therefore proposed as a new adaptation route towards metal resistance.

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CopK from Cupriavidus metallidurans CH34 Binds Cu(I) in a Tetrathioether Site: Characterization by X-ray Absorption and NMR Spectroscopy

Journal of the American Chemical Society ◽

10.1021/ja9083896 ◽

2010 ◽

Vol 132 (11) ◽

pp. 3770-3777 ◽

Cited By ~ 22

Author(s):

Géraldine Sarret ◽

Adrien Favier ◽

Jacques Covès ◽

Jean-Louis Hazemann ◽

Max Mergeay ◽

...

Keyword(s):

Nmr Spectroscopy ◽

Site Characterization ◽

Cupriavidus Metallidurans Ch34 ◽

X Ray ◽

Cupriavidus Metallidurans ◽

X Ray Absorption

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Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms

Microorganisms ◽

10.3390/microorganisms9030651 ◽

2021 ◽

Vol 9 (3) ◽

pp. 651

Author(s):

Alice Roedel ◽

Szilvia Vincze ◽

Michaela Projahn ◽

Uwe Roesler ◽

Caroline Robé ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Acquired Resistance ◽

Antibiotic Resistance Genes ◽

Animal Husbandry ◽

Metal Resistance ◽

Resistant Bacteria ◽

Virulence Determinants ◽

Phylogenetic Distribution ◽

Resistance Determinants

Biocides are frequently applied as disinfectants in animal husbandry to prevent the transmission of drug-resistant bacteria and to control zoonotic diseases. Concerns have been raised, that their use may contribute to the selection and persistence of antimicrobial-resistant bacteria. Especially, extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli have become a global health threat. In our study, 29 ESBL-/AmpC-producing and 64 NON-ESBL-/AmpC-producing E.coli isolates from three German broiler fattening farms collected in 2016 following regular cleaning and disinfection were phylogenetically characterized by whole genome sequencing, analyzed for phylogenetic distribution of virulence-associated genes, and screened for determinants of and associations between biocide tolerance and antibiotic resistance. Of the 30 known and two unknown sequence types detected, ST117 and ST297 were the most common genotypes. These STs are recognized worldwide as pandemic lineages causing disease in humans and poultry. Virulence determinants associated with extraintestinal pathogenic E.coli showed variable phylogenetic distribution patterns. Isolates with reduced biocide susceptibility were rarely found on the tested farms. Nine isolates displayed elevated MICs and/or MBCs of formaldehyde, chlorocresol, peroxyacetic acid, or benzalkonium chloride. Antibiotic resistance to ampicillin, trimethoprim, and sulfamethoxazole was most prevalent. The majority of ESBL-/AmpC-producing isolates carried blaCTX-M (55%) or blaCMY-2 (24%) genes. Phenotypic biocide tolerance and antibiotic resistance were not interlinked. However, biocide and metal resistance determinants were found on mobile genetic elements together with antibiotic resistance genes raising concerns that biocides used in the food industry may lead to selection pressure for strains carrying acquired resistance determinants to different antimicrobials.

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Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes

Genes ◽

10.3390/genes9100507 ◽

2018 ◽

Vol 9 (10) ◽

pp. 507 ◽

Cited By ~ 5

Author(s):

Rob Van Houdt ◽

Ann Provoost ◽

Ado Van Assche ◽

Natalie Leys ◽

Bart Lievens ◽

...

Keyword(s):

Genomic Island ◽

Space Station ◽

Nutrient Utilization ◽

Metal Resistance ◽

Human Infection ◽

Abietane Diterpenoids ◽

Cupriavidus Metallidurans ◽

Mobile Gene ◽

Phenotype Microarrays ◽

The Impact

Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.

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