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The ability of bacteria to maintain homeostasis of the essential-but-toxic “Janus”-faced element copper is important for their survival in many natural environments but also in case of pathogenic bacteria in their respective host. The most important contributors to copper homeostasis have been identified in the last decades and comprise P IB1 -type ATPases, periplasmic copper- and oxygen-dependent copper oxidases, transenvelope efflux systems, and glutathione; however, it is not known how all these players interact.

Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP.

Two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR) are often associated with transenvelope efflux systems, which export transition metal cations from the periplasm directly out of the cell. Although much work has been done in this field, more evidence is needed for the hypothesis that the respective two-component regulatory systems are indeed sensing periplasmic ions. If so, a regulatory circuit between the concentration of periplasmic metal cations, sensing of these metals, and control of expression of the genes for transenvelope efflux systems that remove periplasmic cations can be assumed. Escherichia coli possesses only one transenvelope efflux system for metal cations, the Cus system for export of Cu(I) and Ag(I). It is composed of the transenvelope efflux system CusCBA, the periplasmic copper chaperone CusF, and the two-component regulatory system CusS (HK) and CusR (RR). Using phoA- and lacZ-reporter gene fusions, it was verified that an assumed periplasmic part of CusS is located in the periplasm. CusS was more important for copper resistance in E. coli under anaerobic conditions than under aerobic conditions and in complex medium more than in mineral salts medium. Predicted copper-binding sites in the periplasmic part of CusS were identified that, individually, were not essential for copper resistance but were in combination. In summary, evidence was obtained that the two-component regulatory system CusSR that controls expression of cusF and cusCBA does indeed sense periplasmic copper ions.

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 (ΔcadA 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 resequencing of strains CH34, AE104, Δe4, and others revealed that the genomic islands CMGI2, 3, 4, D, and E, but no other islands or recessive determinants, were deleted in some of these strains. Provided that wild-type CH34 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 surmised previously, silenced in the respective strain. As a consequence, a cured database was compiled from the newly generated and previously published gene array data. An analysis of data from this database indicated that some genes of recessive, no longer needed determinants were nevertheless expressed and upregulated. 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 at the same time ensures metal homeostasis. IMPORTANCE 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 phenomenon was indeed observed in Cupriavidus metallidurans for the loss key metal resistance determinants when no selection pressure was kept continuously. 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 remain in the genome only 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.

The Zur regulon is central to zinc homeostasis in the zinc-resistant bacterium Cupriavidus metallidurans. It comprises the transcription regulator Zur, the zinc importer ZupT, and three members of the COG0523 family of metal-chaperoning G3E-type GTPases, annotated as CobW1, CobW2, and CobW3. The operon structures of the zur and cobW1 loci were determined. To analyze the interplay between the Zur regulon components and metal resistance, deletion mutants were constructed from the wild-type strain CH34 and various other strains. The Zur regulon components interacted with the plasmid-encoded and chromosomally encoded metal resistance factors to acquire metals from complexes of EDTA and for homeostasis of and resistance to zinc, nickel, cobalt, and cadmium. The three G3E-type GTPases were characterized in more detail. CobW1 bound only 1 Zn atom per mol of protein with a stability constant slightly above that of 2-carboxy-2′-hydroxy-5′-sulfoformazylbenzene (Zincon) and an additional 0.5 Zn with low affinity. The CobW1 system was necessary to obtain metals from EDTA complexes. The GTPase CobW2 is a zinc storage compound and bound 0.5 to 1.5 Zn atoms tightly and up to 6 more with lower affinity. The presence of MgGTP unfolded the protein partially. CobW3 had no GTPase activity and equilibrated metal import by ZupT with that of the other metal transport systems. It sequestered 8 Zn atoms per mol with decreasing affinity. The three CobWs bound to the metal-dependent protein FolE IB2 , which is encoded directly downstream of cobW1 . This demonstrated an important contribution of the Zur regulon components to metal homeostasis in C. metallidurans. IMPORTANCE Zinc is an important transition metal cation and is present as an essential component in many enzymes, such as RNA polymerase. As with other transition metals, zinc is also toxic at higher concentrations so that living cells have to maintain strict control of their zinc homeostasis. Members of the COG0523 family of metal-chaperoning GE3-type GTPases exist in archaea, bacteria, and eucaryotes, including humans, and they may be involved in delivery of zinc to thousands of different proteins. We used a combination of molecular, physiological, and biochemical methods to demonstrate the important but diverse functions of COG0523 proteins in C. metallidurans, which are produced as part of the Zur-controlled zinc starvation response in this bacterium.

The role of extracytoplasmic function (ECF) sigma factors in multiple metal homeostasis of the metallophilic bacterium Cupriavidus metallidurans was studied. RNA sequencing was used to predict 3084 operons in the genome of this bacterium, including 11 for ECF sigma factors, and to measure transcript abundances. Mutants carrying multiple deletions in genes for ECF sigma factors were constructed and characterized. Mutants and parent were challenged with a metal mix, changes in the global gene expression profile and the overall metal content determined. All 11 ECF sigma factors were involved in metal homeostasis. The three ECF sigma factors RpoI, RpoJ and RpoK synchronized iron homeostasis with that of other divalent metal cations, RpoO, RpoL and RpoM magnesium and phosphorous homeostasis with that of zinc and with cadmium resistance. Factors RpoE, CnrH and RpoP controlled the response to nickel and cobalt, RpoQ and RpoR may be assigned to the thiol and sulfide metabolism. All 11 ECF sigma factors overlap in their function and control gene expression involved in metal homeostasis, however, except CnrH, no other ECF sigma factor was needed for up-regulation of 63 predicted operons responding to metal shock, 48 of these encoding metal efflux pumps. Moreover, disturbance of the cellular metal content resulting from missing sigma factors also affected silencing and un-silencing of genomic islands. Together, these data demonstrate on a global and systemic level how a robust network of ECF sigma factors and other regulators allow C. metallidurans to handle a mixture of toxic transition metal cations, which are conditions the bacterium faces in its natural environment. Iron homeostasis is to be maintained at any cost, followed by the necessity for magnesium, phosphorous and zinc homeostasis on the second level, and cobalt plus nickel coming last.

Bacteria are rapidly killed on solid copper surfaces, so this material could be useful to limit the spread of multiple-drug-resistant bacteria in hospitals. In Escherichia coli , the DNA-protecting Dps protein and the NADH:ubiquinone oxidoreductase II Ndh were not involved in tolerance to copper ions or survival on solid copper surfaces. Decreased copper tolerance under anaerobic growth conditions in the presence of ascorbate and with melibiose as the carbon source indicated that sodium-dependent symport systems may provide an import route for Cu I into the cytoplasm. Glutathione-free Δ copA Δ gshA double mutants of E. coli were more rapidly inactivated on solid copper surfaces than glutathione-containing wild-type cells. Therefore, while DNA protection by Dps was not required, glutathione was needed to protect the cytoplasm and the DNA against damage mediated by solid copper surfaces, which may explain the differences in the molecular mechanisms of killing between glutathione-containing Gram-negative and glutathione-free Gram-positive bacteria.

Zinc is an essential trace element, yet it is toxic at high concentrations. In the betaproteobacterium Cupriavidus metallidurans , the highly efficient removal of surplus zinc from the periplasm is responsible for the outstanding metal resistance of the organism. Rather than having a typical Zur-dependent, high-affinity ATP-binding cassette transporter of the ABC protein superfamily for zinc uptake at low concentrations, C. metallidurans has the secondary zinc importer ZupT of the zinc-regulated transporter, iron-regulated transporter (ZRT/IRT)-like protein (ZIP) family. It is important to understand, therefore, how this zinc-resistant bacterium copes with exposure to low zinc concentrations. Members of the Zur regulon in C. metallidurans were identified by comparing the transcriptomes of a Δ zur mutant and its parent strain. The consensus sequence of the Zur-binding box was derived for the zupTp promoter-regulatory region by use of a truncation assay. The motif was used to predict possible Zur boxes upstream of Zur regulon members. The binding of Zur to these boxes was confirmed. Two Zur boxes upstream of the cobW 1 gene, encoding a putative zinc chaperone, proved to be required for complete repression of cobW 1 and its downstream genes in cells cultivated in mineral salts medium. A Zur box upstream of each of zur-cobW 2 , cobW 3 , and zupT permitted both low expression levels of these genes and their upregulation under conditions of zinc starvation. This demonstrates a compartmentalization of zinc homeostasis in C. metallidurans , where the periplasm is responsible for the removal of surplus zinc, cytoplasmic components are responsible for the management of zinc as an essential cofactor, and the two compartments are connected by ZupT. IMPORTANCE Elucidating zinc homeostasis is necessary for understanding both host-pathogen interactions and the performance of free-living bacteria in their natural environments. Escherichia coli acquires zinc under conditions of low zinc concentrations via the Zur-controlled ZnuABC importer of the ABC superfamily, and this was also the paradigm for other bacteria. In contrast, the heavy-metal-resistant bacterium C. metallidurans achieves high tolerance to zinc through sophisticated zinc handling and efflux systems operating on periplasmic zinc ions, so that removal of surplus zinc is a periplasmic feature in this bacterium. It is shown here that this process is augmented by the management of zinc by cytoplasmic zinc chaperones, whose synthesis is controlled by the Zur regulator. This demonstrates a new mechanism, involving compartmentalization, for organizing zinc homeostasis.

The zinc importer ZupT is required for the efficient allocation of zinc to zinc-dependent proteins in the metal-resistant bacterium Cupriavidus metallidurans but not for zinc import per se . The expression of zupT is upregulated under conditions of zinc starvation. C. metallidurans contains three members of the Fur family of regulators that qualify as candidates for the zupT regulator. The expression of a zupT-lacZ reporter gene fusion was strongly upregulated in a Δ furC mutant but not in a Δ furA or Δ furB mutant. Expression of the genes for transition-metal importers ( pitA , corA1 , corA2 , and corA3 ) was not changed in this pattern in all three Δ fur mutants, but they were still downregulated under conditions of elevated zinc concentrations, indicating the presence of another zinc-dependent regulator. FurA was a central regulator of the iron metabolism in C. metallidurans , and furA was constitutively expressed under the conditions tested. Expression of furB was upregulated under conditions of iron starvation, and FurB could be an iron starvation Fur connecting general metal and iron homeostasis, as indicated by the phenotype of a Δ furB Δ furC double mutant. FurC was purified as a Strep-tagged protein and retarded the electrophoretic mobility of a DNA fragment upstream of zupT . Binding of FurC to this operator region was influenced by the presence of zinc ions and EDTA. Thus, FurC is the main zinc uptake regulator (Zur) of C. metallidurans and represses synthesis of the central zinc importer ZupT when sufficient zinc is present.

International audience; When CnrX, the periplasmic sensor protein in the CnrYXH transmembrane signal transduction complex of Cupriavidus metallidurans CH34, binds the cognate metal ions Ni(II) or Co(II), the ECF-type sigma factor CnrH is made available in the cytoplasm for the RNA-polymerase to initiate transcription at the cnrYp and cnrCp promoters. Ni(II) or Co(II) are sensed by a metal-binding site with a N3O2S coordination sphere with octahedral geometry, where S stands for the thioether sulfur of the only methionine (Met123) residue of CnrX. The M123A-CnrX derivative has dramatically reduced signal propagation in response to metal sensing while the X-ray structure of Ni-bound M123A-CnrXs showed that the metal-binding site was not affected by the mutation. Ni(II) remained six-coordinate in M123A-CnrXs, with a water molecule replacing the sulfur as the sixth ligand. H32A-CnrXs, the soluble model of the wild-type membrane-anchored CnrX, was compared to the double mutants H32A-M123A-CnrXs and H32A-M123C-CnrXs to spectroscopically evaluate the role of this unique ligand in the binding site of Ni or Co. The Co- and Ni-bound forms of the protein display unusually blue-shifted visible spectra. TD-DFT calculations using structure-based models allowed identification and assignment of the electronic transitions of Co-bound form of the protein and its M123A derivative. Among them, the signature of the S-Co transition is distinguishable in the shoulder at 530 nm. In vitro affinity measurements point out the crucial role of Met123 in the selectivity for Ni or Co, and in vivo data support the conclusion that Met123 is a trigger of the signal transduction.

The β-Proteobacterium Cupriavidus metallidurans CH34, which dominates biofilm communities on natural gold (Au) grains, is a key species involved in their (trans)formation. Gold(III)-chloride complexes, with toxicity levels similar to those of Hg- and Ag-ions, are rapidly sorbed by C. metallidurans cells and detoxified by active reductive precipitation to metallic Au nanoparticles. In this study, we exposed C. metallidurans CH34 to a range of environmentally-relevant Au(I)- and Pt(II/IV)-complexes with differing toxicity levels, i.e., Au(I)-thiosulfate > Au(I)-cyanide, and cisplatin > Pt(IV)-chloride > Pt(II)-cyanide. The aim was to investigate how Au/Pt-complex toxicity, in combination with the metabolic state of cells, affects Au/Pt accumulation, speciation and biomineralization. Overall, more Au(I)- than Pt-complexes were accumulated. Significantly more Au(I)-thiosulfate was taken up by metabolically active vs. inactive or dead cells. Toxicity of Au(I)-complexes was ‘managed’ via the formation of intermediate species, e.g., Au(I)-C mixed ligand complexes. Over time Au(I) associated with active cells was reduced to metallic particles, with higher rates of transformation being observed in experiments amended with Au(I)-thiosulfate- compared to Au(I)-cyanide complexes. In contrast, Pt uptake did not differ with respect to metabolic state. Pt(IV)-complexes were reduced to Pt(II) within 1 min of amendment; further reduction of the Pt(II) was not observed. In conclusion, toxicity of Au/Pt-complexes is linked to the ability of cells to take up and actively detoxify the complexes. Gold uptake was linked to the detoxification of the Au(I)-complexes via active reductive precipitation to Au(0). In contrast, metabolic activity/toxicity did not influence Pt accumulation and/or transformation. This indicates that the ability of bacteria to cycle Au via mobilization, accumulation and biomineralization provides a selective advantage for organisms able to detoxify highly mobile Au-complexes. Because Pt-complexes are not taken up as readily and are hence less toxic, they do not provide a similar selective advantage, and hence Pt is less readily cycled. This may explain the substantially higher environmental mobility of Au compared to Pt., The authors acknowledge: the Australian Research Council (LP100200102 and DP1903238 to F.R.), Barrick Gold and Newmont Gold (LP100200102), and the International Synchrotron Access Program (AS_IA094_ESRFSC-2954).

Cupriavidus metallidurans is associated with gold grains and may be involved in their formation. Gold(III) complexes influence the transcriptome of C. metallidurans (F. Reith et al., Proc. Natl. Acad. Sci. U. S. A. 106:17757–17762, 2009), leading to the upregulation of genes involved in the detoxification of reactive oxygen species and metal ions. In a systematic study, the involvement of these systems in gold transformation was investigated. Treatment of C. metallidurans cells with Au(I) complexes, which occur in this organism's natural environment, led to the upregulation of genes similar to those observed for treatment with Au(III) complexes. The two indigenous plasmids of C. metallidurans , which harbor several transition metal resistance determinants, were not involved in resistance to Au(I/III) complexes nor in their transformation to metallic nanoparticles. Upregulation of a cupA-lacZ fusion by the MerR-type regulator CupR with increasing Au(III) concentrations indicated the presence of gold ions in the cytoplasm. A hypothesis stating that the Gig system detoxifies gold complexes by the uptake and reduction of Au(III) to Au(I) or Au(0) reminiscent to detoxification of Hg(II) was disproven. ZupT and other secondary uptake systems for transition metal cations influenced Au(III) resistance but not the upregulation of the cupA-lacZ fusion. The two copper-exporting P-type ATPases CupA and CopF were also not essential for gold resistance. The copABCD determinant on chromosome 2, which encodes periplasmic proteins involved in copper resistance, was required for full gold resistance in C. metallidurans . In conclusion, biomineralization of gold particles via the reduction of mobile Au(I/III) complexes in C. metallidurans appears to primarily occur in the periplasmic space via copper-handling systems.

In spite of the similar chemical properties of gold (Au) and platinum (Pt), Au is highly mobile in surface environments, whereas Pt appears to be far less so. In this study we assess if geomicrobial processes are likely to cause these differences, as the mobility of Pt and Au should differ little based on thermodynamic solubility alone. To achieve an accurate comparison it is important that both metals occur in the same environment. Mineral- and groundwater samples were obtained from the Fifield Pt–Au field in New South Wales, Australia, where Pt and Au nuggets occur in a series of Tertiary eluvial and alluvial paleo-placers. In particular, we studied the μm-scale dispersion of Au and Pt within an extraordinary 10 mm-sized fragment of ferruginous paleochannel material, which contained abundant native Au- and isoferroplatinum grains. Gold grains displayed complex secondary morphologies indicative of biogeochemical transformations, whereas isoferroplatinum grains appeared smooth and well-rounded and showed no signs of supergene transformation. Gold grains were surrounded by a dusting of highly pure metallic Au particles ( 10 μm in diameter), whereas no metallic Pt particles were detected. A search for ionic Pt was also unsuccessful. A series of biotic and abiotic incubation experiments was conducted to investigate the hypothesis that these differences in mobility are driven by interactions with microbiota. Biofilms consisting of metallophilic bacteria formed on ultraflat Au surfaces and caused significant surface transformations. In contrast, only subtle changes were observed on Pt surfaces incubated under similar conditions. Minimal inhibitory concentrations for Au complexes are more than an order of magnitude lower than those measured for Pt complexes in Cupriavidus metallidurans cells. This higher cell-toxicity of mobile Au- compared to Pt-complexes can lead to toxic levels of mobile Au in the vicinity of Au grain surfaces. The elevated toxicity drives the formation of Au-detoxifying biofilms that catalyze the biomineralization of spheroidal nano-particulate and bacteriomorphic Au. In contrast, this does not occur on isoferroplatinum grains due to the lower toxicity of Pt. In conclusion, these results are consistent with microbial adaptation to element toxicity driving the cycling of precious metals in surface environments.

Central to the ability of Cupriavidus metallidurans to maintain its metal homoeostasis is the metal transportome, composed of uptake and efflux systems. Seven secondary metal import systems, ZupT, PitA, CorA1, CorA2, CorA3, ZntB, and HoxN, interact and are at the core of the metal uptake transportome. The 7-fold deletion mutant Δ7 (ΔzupT ΔpitA ΔcorA1ΔcorA2ΔcorA3ΔzntB ΔhoxN) of parent strain AE104 is still able to maintain its cellular metal content, although at the cost of reduced fitness (M. Herzberg, L. Bauer, A. Kirsten, and D. H. Nies, Metallomics, in press, http://dx.doi.org/10.1039/C5MT00295H ). Strain Δ7 does not express genes for backup importers, and so Δ7 should use metal uptake systems also produced in the AE104 parent cells. These systems should be activated in Δ7 by posttranscriptional regulatory processes. The decreased fitness of Δ7 correlated with a zinc-dependent downregulation of the overall metabolic backbone of the cells even at nontoxic external zinc concentrations. Responsible for this decreased fitness of Δ7 was a negative interference of the activity of two P-type ATPases, MgtA and MgtB, which, on the other hand, kept Δ7 at a fitness level higher than that of the Δ9 (Δ7 ΔmgtA::kan ΔmgtB) mutant strain. This revealed a complicated interplay of the metal uptake transportome of C. metallidurans, which is composed of the seven secondary uptake systems, MgtA, MgtB, and yet-unknown components, with cytoplasmic transition metal pools and posttranscriptional regulatory processes. IMPORTANCE Bacteria, including pathogenic strains, need to make use of the metal composition and speciation of their environment to fulfill the requirement of the cytoplasmic metal content and composition. This task is performed by the bacterial metal transportome, composed of uptake and efflux systems. Seven interacting secondary metal uptake systems are at the core of the metal transportome in C. metallidurans. This publication verifies that posttranscriptional events are responsible for activation of even more, yet-unknown, metal import systems in the 7-fold deletion mutant Δ7. Two P-type ATPases were identified as new members of the metal uptake transportome. This publication demonstrates the complexity of the metal transportome and the regulatory processes involved.

The effect of different metal ions on the intestinal transport and the antibacterial activity of cefadroxil [(6R,7R)-7-{[(2R)-2-amino-2-(4-hydroxyphenyl)acetyl]amino}-3-methyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid] was investigated. The [14C]Gly-Sar uptake via PEPT1 was inhibited by Zn2+ and Cu2+ treatment in a concentration-dependent manner (Ki values 107 ± 23 and 19 ± 5 μM, respectively). Kinetic analysis showed that the Kt of Gly-Sar uptake was increased 2-fold in the presence of zinc sulphate (150 μM) whereas the Vmax value were not affected suggesting that zinc ions inhibited Gly-Sar uptake by PEPT1 in a competitively manner. Ni2+ exhibited moderate inhibitory effect, whereas Co2+, Mg2+, Al3+ ions showed no inhibitory effect on Gly-Sar uptake via PEPT1. Subsequently, we examined the effect of Zn2+ and Al3+ ions on the transepithelial transport of cefadroxil across Caco-2 cells cultured on permeable supports. The results showed that zinc ions inhibited the transepithelial flux of cefadroxil at Caco-2 cell monolayers while Al3+ ions had no effect. The interaction of cephalosporins with the metal ions could suggest negative effects of some metal ions on the clinical aspects of small intestinal peptide and drug transport. Finally, the effect of Zn2+, Cu2+ and Al3+ ions on the antibacterial activity of cefadroxil was tested. It was found that there is no significant difference between the activity of cefadroxil and the cefadroxil metal ion complexes studied against the investigated sensitive bacterial species.

While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans , which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au 0 . Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools.

The higher affinity of Cd 2+ for sulfur compounds than for nitrogen and oxygen led to the theoretical consideration that cadmium toxicity should result mainly from the binding of Cd 2+ to sulfide, thiol groups, and sulfur-rich complex compounds rather than from Cd 2+ replacement of transition-metal cations from nitrogen- or oxygen-rich biological compounds. This hypothesis was tested by using Escherichia coli for a global transcriptome analysis of cells synthesizing glutathione (GSH; wild type), γ-glutamylcysteine (Δ gshB mutant), or neither of the two cellular thiols (Δ gshA mutant). The resulting data, some of which were validated by quantitative reverse transcription-PCR, were sorted using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system, which groups genes hierarchically with respect to the cellular functions of their respective products. The main difference among the three strains concerned tryptophan biosynthesis, which was up-regulated in wild-type cells upon cadmium shock and strongly up-regulated in Δ gshA cells but repressed in Δ gshB cells containing γ-glutamylcysteine instead of GSH. Overall, however, all three E. coli strains responded to cadmium shock similarly, with the up-regulation of genes involved in protein, disulfide bond, and oxidative damage repair; cysteine and iron-sulfur cluster biosynthesis; the production of proteins containing sensitive iron-sulfur clusters; the storage of iron; and the detoxification of Cd 2+ by efflux. General energy conservation pathways and iron uptake were down-regulated. These findings indicated that the toxic action of Cd 2+ indeed results from the binding of the metal cation to sulfur, lending support to the hypothesis tested.

Cupriavidus metallidurans strain CH34 is a highly metal-resistant bacterium that contains 11 sigma factors of the extracytoplasmic function (ECF) protein family, which can be subgrouped into the ECF:FecI 1, ECF:FecI 2, ECF:RpoE and ‘(ECF)’ clusters. To analyze the contribution of these 11 sigma factors to metal resistance, upregulation of the respective genes was measured by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR). As determined by RT-PCR, the ECF sigma factor genes were part of two- to tetra-cistronic operons, each containing genes for the sigma factor plus one or two antisigma factors. The three sigma factors RpoJ, RpoK and RpoI (ECF:FecI 1 cluster) were upregulated by Cu(II) and Ni(II), and under conditions of iron depletion. The other 8 ECF sigma factor genes were not induced by iron depletion. Strong upregulation of rpoJ and rpoK under iron depletion in a ΔrpoI mutant strain and close vicinity of rpoI to genes involved in iron siderophore metabolism marked RpoI as the primary ECF sigma factor for siderophore-mediated iron uptake. Genes for RpoO, RpoL and RpoM (ECF:FecI 2 cluster) were not upregulated by transition metal cations and influenced metal resistance only weakly. Concerning the two ‘(ECF)’ group proteins, rpoQ was strongly upregulated by Cu(II) and deletion of rpoR led to a small decrease in copper resistance. Of the three ECF:RpoE-encoding genes, rpoP was not transcribed under the conditions tested, cnrH was upregulated by Ni(II) and essential for nickel resistance as known before. RpoE was required for full metal resistance of C. metallidurans. None of these 11 sigma factors was essential for metal resistance mediated by the cobalt, zinc and cadmium resistance determinant czc, or for its expression. However, RpoI was essential for siderophore production in C. metallidurans, and, in addition to the known role of CnrH in nickel resistance, RpoE, RpoI, RpoJ, RpoK and maybe also RpoQ are required for the outstanding transition metal resistance of this bacterium.

Cupriavidus metallidurans CH34 is able to grow autotrophically as a hydrogen-oxidizing bacterium and produces nickel-dependent hydrogenases, even under heterotrophic conditions. Loss of its two native plasmids resulted in inability of the resulting strain AE104 to synthesize the hydrogenases and to grow autotrophically in phosphate-poor, Tris-buffered mineral salts medium (TMM). Three of eleven previously identified catabolic genomic islands (CMGIs; Van Houdt et al., 2009), two of which harbor the genes for the membrane-bound (CMGI-2) and the soluble hydrogenase (CMGI-3), were silenced in strain AE104 when cultivated in phosphate-poor TMM, explaining its inability to produce hydrogenases. Production of the soluble hydrogenase from the aut region 1 of CMGI-3, and concomitant autotrophic growth, was recovered when the gene for the zinc importer ZupT was deleted in strain AE104. The transcriptome of the ΔzupT mutant exhibited two up-regulated gene regions compared to its parent strain AE104. Expression of the genes in the aut region 1 increased independently of the presence of added zinc. A second gene region was expressed only under metal starvation conditions. This region encoded a TonB-dependent outer membrane protein, a putative metal chaperone plus paralogs of essential zinc-dependent proteins, indicating the presence of a zinc allocation pathway in C. metallidurans. Thus, expression of the genes for the soluble hydrogenase and the Calvin cycle enzymes on aut region 1 of CMGI-3 of C. metallidurans is under global control and needs efficient ZupT-dependent zinc allocation for a regulatory role, which might be discrimination of nickel.

International audience; Resistance to high concentration of nickel ions is mediated in Cupriavidus metallidurans by the CnrCBA transenvelope efflux complex. Expression of the cnrCBA genes is regulated by the transmembrane signal transduction complex CnrYXH. Together, the metal sensor CnrX and the transmembrane antisigma factor CnrY control the availability of the extracytoplasmic function sigma factor CnrH. Release of CnrH from sequestration by CnrY at the cytoplasmic side of the membrane depends essentially on the binding of the agonist metal ion Ni(ii) to the periplasmic metal sensor domain of CnrX. CnrH availability leads to transcription initiation at the promoters cnrYp and cnrCp and to the expression of the genes in the cnrYXHCBA nickel resistance determinant. The first steps of signal propagation by CnrX rely on subtle metal-dependent allosteric modifications. To study the nickel-mediated triggering process by CnrX, we have altered selected residues, F66, M123, and Y135, and explored the physiological consequences of these changes with respect to metal resistance, expression of a cnrCBA-lacZ reporter fusion and protein production. M123C- and Y135F-CnrXs have been further characterized in vitro by metal affinity measurements and crystallographic structure analysis. Atomic-resolution structures of metal-bound M123C- and Y135F-CnrXs showed that Ni(ii) binds two of the three canonical conformations identified and that Ni(ii) sensing likely proceeds by conformation selection.

Cupriavidus (Wautersia, Ralstonia, Alcaligenes) metallidurans strain CH34is a well-studied example of a metal-resistant proteobacterium. Genome sequence analysis revealed the presence of a variety of paralogs of proteins that were previously shown to be involved in heavy metal resistance. Which advantage has C. metallidurans in maintaining all these paralogs during evolution? Paralogs investigated belong to the families RND (resistance nodulation cell division) or CHR (chromate resistance). The respective genes were localized by PCR either on one of the two native megaplasmids pMOL28 and pMOL30 of strain CH34, or on its chromosomal DNA. Gene expression was studied by real-time reverse transcriptase PCR and by reporter gene constructs. Genes found to be inducible were disrupted and their contribution to metal resistance measured. When two or three highly related genes were present, usually one was inducible by heavy metals while the other one or two were silent or constitutively expressed. This suggests that C. metallidurans CH34 carries a variety of no longer or not yet used genes that might serve as surplus material for further developments, an advantage that may compensate for the costs of maintaining these genes during evolution.

RpoE of Escherichia coli is a sigma factor of the extracytoplasmic function protein family and is required for the expression of proteins involved in maintaining the integrity of periplasmic and outer membrane components. RpoE of E. coli was needed for full resistance to Zn(II), Cd(II), and Cu(II). Promoter gene fusion and quantitative real time reverse transcription (RT)-PCR (qRT-PCR) assays demonstrated that expression of RpoE was induced by metals. Global gene expression profiles upon metal treatment of a Δ rpoE mutant strain and its wild-type strain were analyzed with microarrays, and selected genes were confirmed by qRT-PCR. The absolute number of genes that were changed in their expression upon metal stress was similar in both strains, but the increase or decrease in transcript levels upon metal treatment was smaller in the Δ rpoE mutant strain than in the wild type. Genes showing increased expression in the Δ rpoE mutant strain encoded proteins that belong to general defense systems against protein-denaturing agents. Genes showing decreased expression were part of the RpoE modulon itself plus the ompC gene, encoding a major outer membrane protein. A Δ ompC deletion strain was as sensitive to Cu(II) and Cd(II) as the Δ rpoE mutant or a Δ rpoE Δ ompC double mutant strain. In the case of Zn(II), the double mutant was more sensitive than either single mutant. This indicates that increased expression of OmpC contributes to the RpoE modulon-mediated response to metals.

The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB 2 A cation-proton antiporter. The CzcD protein is involved in the regulation of the Czc system. It is a membrane-bound protein with at least four transmembrane α-helices and is a member of a subfamily of the cation diffusion facilitator (CDF) protein family, which occurs in all three domains of life. The deletion of czcD in a Ralstonia sp. led to partially constitutive expression of the Czc system due to an increased transcription of the structural czcCBA genes, both in the absence and presence of inducers. The czcD deletion could be fully complemented in trans by CzcD and two other CDF proteins from Saccharomyces cerevisiae , ZRC1p and COT1p. All three proteins mediated a small but significant resistance to cobalt, zinc, and cadmium in Ralstonia , and this resistance was based on a reduced accumulation of the cations. Thus, CzcD appeared to repress the Czc system by an export of the inducing cations.

Cupriavidus metallidurans strain CH34 is a highly metal-resistant bacterium that contains 11 sigma factors of the extracytoplasmic function (ECF) protein family, which can be subgrouped into the ECF:FecI 1, ECF:FecI 2, ECF:RpoE and '(ECF)' clusters. To analyze the contribution of these 11 sigma factors to metal resistance, upregulation of the respective genes was measured by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR). As determined by RT-PCR, the ECF sigma factor genes were part of two- to tetra-cistronic operons, each containing genes for the sigma factor plus one or two antisigma factors. The three sigma factors RpoJ, RpoK and RpoI (ECF:FecI 1 cluster) were upregulated by Cu(II) and Ni(II), and under conditions of iron depletion. The other 8 ECF sigma factor genes were not induced by iron depletion. Strong upregulation of rpoJ and rpoK under iron depletion in a DeltarpoI mutant strain and close vicinity of rpoI to genes involved in iron siderophore metabolism marked RpoI as the primary ECF sigma factor for siderophore-mediated iron uptake. Genes for RpoO, RpoL and RpoM (ECF:FecI 2 cluster) were not upregulated by transition metal cations and influenced metal resistance only weakly. Concerning the two '(ECF)' group proteins, rpoQ was strongly upregulated by Cu(II) and deletion of rpoR led to a small decrease in copper resistance. Of the three ECF:RpoE-encoding genes, rpoP was not transcribed under the conditions tested, cnrH was upregulated by Ni(II) and essential for nickel resistance as known before. RpoE was required for full metal resistance of C. metallidurans. None of these 11 sigma factors was essential for metal resistance mediated by the cobalt, zinc and cadmium resistance determinant czc, or for its expression. However, RpoI was essential for siderophore production in C. metallidurans, and, in addition to the known role of CnrH in nickel resistance, RpoE, RpoI, RpoJ, RpoK and maybe also RpoQ are required for the outstanding transition metal resistance of this bacterium.

Escherichia coli possesses multiple routes for iron uptake. Here we present EfeU (YcdN), a novel iron acquisition system of E. coli strain Nissle 1917. Laboratory strains of E. coli such as K12 lack a functional (efeU) ycdN gene caused by a frameshift mutation. EfeU, a member of the oxidase-dependent iron transporters (OFeT), is a homologue of the iron permease Ftr1p from yeast. The ycdN gene is part of the ycdNOB tricistronic operon which is expressed in response to iron deprivation in a Fur-dependent manner. Expression of efeU resulted in improved growth of an E. coli mutant lacking all known iron-uptake systems and mediated increased iron uptake into cells. Furthermore, the presence of other divalent metal cations did not impair growth of strains expressing efeU. The EfeU protein functioned as ferrous iron permease in proteoliposomes in vitro. Topology analysis indicated that EfeU is an integral cytoplasmic membrane protein exhibiting seven transmembrane helices. Two REXXE motifs within transmembrane helices of OFeT family members are implicated in iron translocation. Site-directed mutagenesis of each REGLE motif of EfeU diminished iron uptake in vivo and growth yield. In vitro the EfeU variant protein with an altered first REGLE motif was impaired in iron permeation, whereas activity of the EfeU variant with a mutation in the second motif was similar to the wild-type protein.

Cupriavidus (Wautersia, Ralstonia, Alcaligenes) metallidurans strain CH34is a well-studied example of a metal-resistant proteobacterium. Genome sequence analysis revealed the presence of a variety of paralogs of proteins that were previously shown to be involved in heavy metal resistance. Which advantage has C. metallidurans in maintaining all these paralogs during evolution? Paralogs investigated belong to the families RND (resistance nodulation cell division) or CHR (chromate resistance). The respective genes were localized by PCR either on one of the two native megaplasmids pMOL28 and pMOL30 of strain CH34, or on its chromosomal DNA. Gene expression was studied by real-time reverse transcriptase PCR and by reporter gene constructs. Genes found to be inducible were disrupted and their contribution to metal resistance measured. When two or three highly related genes were present, usually one was inducible by heavy metals while the other one or two were silent or constitutively expressed. This suggests that C. metallidurans CH34 carries a variety of no longer or not yet used genes that might serve as surplus material for further developments, an advantage that may compensate for the costs of maintaining these genes during evolution.

Escherichia coli excretes the catecholate siderophore enterobactin in response to iron deprivation. While the mechanisms underlying enterobactin biosynthesis and ferric enterobactin uptake and utilization are widely understood, nearly nothing is known about how enterobactin is exported from the cell. Mutant and high-performance liquid chromatography analyses demonstrated that the outer membrane channel tunnel protein TolC but none of the respective seven resistance nodulation cell division (RND) proteins CusA, AcrB, AcrD, AcrF, MdtF (YhiV), or the twin RND MdtBC (YegNO) was essential for enterobactin export across the outer membrane. Mutant E. coli strains with additional deletion of tolC or the major facilitator entS were growth deficient in iron-depleted medium. Strains with deletion of tolC or entS , but not with deletion of genes encoding RND transporters, excreted very little enterobactin into the growth medium. Enterobactin excretion in E. coli is thus probably a two-step process involving the major facilitator EntS and the outer membrane channel tunnel protein TolC. Quantitative reverse transcription-PCR analysis of gene-specific transcripts showed no significant changes in tolC expression upon iron depletion. However, iron starvation led to increased expression of the RND gene mdtF and a decrease in acrD .

The CzcCBA cation-proton-antiporter is the most complicated and efficient heavy-metal resistance system known today and is essential for survival of Ralstonia metallidurans at high cobalt, zinc, or cadmium concentrations. Expression of Czc is tightly controlled by the complex interaction of several regulators. Double- and multiple-deletion studies demonstrated that four regulators encoded downstream of the czcCBA operon, CzcD, CzcS, CzcR and the newly identified CzcE, are involved in, but not essential for metal-dependent induction of czc. These proteins control expression of the czcNICBA region from the promoter czcNp. Northern analysis showed that czcDRS was transcribed as czcDR-specific and czcDRS-specific mRNAs. Transcription of czcE occurred independently of czcDRS transcription and was induced by zinc. CzcE is a periplasmic protein as indicated by phoA fusions. CzcE was purified and identified as a metal-binding protein. These data demonstrate that the transport protein CzcD, the two-component regulatory system CzcR, CzcS, and the periplasmic metal-binding protein CzcE exert metal-dependent control of czcNICBA expression via regulation of czcNp activity.

Chromate resistance inRalstonia metallidurans CH34 is based on chromate efflux catalyzed by ChrA efflux pumps. The bacterium harbors two chromate resistance determinants, the previously knownchr 1 on plasmid pMOL28 (geneschrI, chrB 1,chrA 1,chrC, chrE, chrF 1) andchr 2 on the chromosome (geneschrB 2,chrA 2,chrF 2). Deletion of the geneschrl, chrC, chrA 2,chrB 2 andchrF 2 influenced chromate resistance and transcription from achrBp 1::lacZ fusion. Deletion of the plasmid-encoded genechrBx did not change chromate resistance orchrBp 1 regulation. Northern hybridization and primer-extension experiments were used to study transcription of the plasmid-encodedchr 1 determinant. Transcription ofchrB 1,chrA 1 andchrC was induced by chromate. The presence of sulfate influenced transcription positively. ThechrBp 1,chrAp 1 andchrCp promoters showed some similarity to heat-shock promoters. Transcription of the generpoH encoding a putative heat-shock sigma factor was also induced by chromate, butrpoH was not essential for chromate resistance. The ChrC protein was purified as a homotetramer and exerted superoxide dismutase activity. Thus, possible regulators for chromate resistance (Chrl, ChrB1, ChrB2, ChrF1, and ChrF2) and an additional detoxification system (ChrC) were newly identified as parts of chromate resistance inR. metallidurans. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-002-0492-5.

Ralstonia sp. strain CH34 (formerly Alcaligenes eutrophus strain CH34 [3]) contains at least seven determinants encoding resistances to toxic heavy metals, located either on the bacterial chromosome or on one of the two indigenous plasmids pMOL28 (180 kb [37]) and pMOL30 (238 kb [7, 20]). The cnr determinant of plasmid pMOL28 mediates inducible resistance to Co2+ and Ni2+ in Ralstonia sp. strain CH34 (15). The cnr determinant is similar to ncc (nickel-cobalt-cadmium resistance) of Alcaligenes xylosoxidans 31A (34) and czc (cobalt-zinc-cadmium resistance) on plasmid pMOL30 of Ralstonia sp. strain CH34 (28). All three resistances are based on cation efflux, which is best characterized for Czc (13, 24, 29). In analogy to Czc (9, 25, 28, 32), the products of the genes cnrA, cnrB, and cnrC are likely to form a membrane-bound protein complex catalyzing an energy-dependent efflux of Ni2+ and Co2+, and the mechanism of action of the CnrCBA complex may be that of a proton/cation antiporter. Three regulators seem to control Cnr, an extracellular function (ECF) sigma factor (CnrH) and the products of two additional genes with unknown precise functions (CnrX and CnrY products, respectively) (15, 16). The genes cnrYXH are located upstream of cnrCBA and have the same direction of transcription. Transposon Tn5 insertion upstream of cnrH led to a constitutive expression of nickel resistance and to low zinc resistance as well (4, 15). However, this may be a polar effect and, additionally, a readthrough from a transposon promoter. As shown with Tn5-lacZ fusions (31), cnr is best induced by 128 μM Ni2+. Other metals serve as less efficient inducers; however, this experiment was done with nickel-sensitive cnr-lacZ transposon-insertion mutants. In this study an improved cnrCBA-lacZ operon fusion was constructed, which mediates full nickel resistance and which was used to evaluate the physiology of cnr regulation.

The Czc system of Alcaligenes eutrophus mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB 2 A cation-proton antiporter. DNA sequencing of the region upstream of the czcNICBADRS determinant located on megaplasmid pMOL30 revealed the 5′ end of czcN and a gene for a MgtC-like protein which is transcribed in the orientation opposite that of czc . Additional open reading frames upstream of czc had no homologs in the current databases. Using oligonucleotide-probed Northern blotting experiments, a 500-nucleotide czcN message and a 400-nucleotide czcI message were found, and the presence of 6,200-nucleotide czcCBA message (D. Van der Lelie et al., Mol. Microbiol. 23:493–503, 1997) was confirmed. Induction of czcN , czcI , czcCBA , and czcDRS followed a similar pattern: transcription was induced best by 300 μM zinc, less by 300 μM cobalt, and only slightly by 300 μM cadmium. Reverse transcription-PCR gave evidence for additional continuous transcription from czcN to czcC and from czcD to czcS , but not between czcA and czcD nor between czcS and a 131-amino-acid open reading frame following czcS . The CzcR putative response regulator was purified and shown to bind in the 5′ region of czcN . A reporter strain carrying a czcNIC-lacZ-czcBADRS determinant on plasmid pMOL30 was constructed, as were Δ czcR and Δ czcS mutants of this strain and of AE128(pMOL30) wild type. Experiments on (i) growth of these strains in liquid culture containing 5 mM Zn 2+ , (ii) induction of the β-galactosidase in the reporter strains by zinc, cobalt, and cadmium, and (iii) cDNA analysis of czcCBA mRNA synthesis under inducing and noninducing conditions showed that the CzcRS two-component regulatory system is involved in Czc regulation.