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Nies DH, Schleuder G, Galea D, Herzberg M. A flow equilibrium of zinc in cells of Cupriavidus metallidurans. J Bacteriol 2024; 206:e0008024. [PMID: 38661374 PMCID: PMC11112998 DOI: 10.1128/jb.00080-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
The hypothesis was tested that a kinetical flow equilibrium of uptake and efflux reactions is responsible for balancing the cellular zinc content. The experiments were done with the metal-resistant bacterium Cupriavidus metallidurans. In pulse-chase experiments, the cells were loaded with radioactive 65Zn and chased with the 100-fold concentration of non-radioactive zinc chloride. In parallel, the cells were loaded with isotope-enriched stable 67Zn and chased with non-enriched zinc to differentiate between zinc pools in the cell. The experiments demonstrated the existence of a kinetical flow equilibrium, resulting in a constant turnover of cell-bound zinc ions. The absence of the metal-binding cytoplasmic components, polyphosphate and glutathione, metal uptake, and metal efflux systems influenced the flow equilibrium. The experiments also revealed that not all zinc uptake and efflux systems are known in C. metallidurans. Cultivation of the cells under zinc-replete, zinc-, and zinc-magnesium-starvation conditions influenced zinc import and export rates. Here, magnesium starvation had a stronger influence compared to zinc starvation. Other metal cations, especially cobalt, affected the cellular zinc pools and zinc export during the chase reaction. In summary, the experiments with 65Zn and 67Zn demonstrated a constant turnover of cell-bound zinc. This indicated that simultaneously occurring import and export reactions in combination with cytoplasmic metal-binding components resulted in a kinetical flow equilibrium that was responsible for the adjustment of the cellular zinc content. IMPORTANCE Understanding the biochemical action of a single enzyme or transport protein is the pre-requisite to obtain insight into its cellular function but this is only one half of the coin. The other side concerns the question of how central metabolic functions of a cell emerge from the interplay of different proteins and other macromolecules. This paper demonstrates that a flow equilibrium of zinc uptake and efflux reactions is at the core of cellular zinc homeostasis and identifies the most important contributors to this flow equilibrium: the uptake and efflux systems and metal-binding components of the cytoplasm.
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Affiliation(s)
- Dietrich H. Nies
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Grit Schleuder
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Diana Galea
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Halle (Saale), Germany
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Joshi S, Gangola S, Bhandari G, Bhandari NS, Nainwal D, Rani A, Malik S, Slama P. Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies. Front Microbiol 2023; 14:1229828. [PMID: 37555069 PMCID: PMC10405491 DOI: 10.3389/fmicb.2023.1229828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.
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Affiliation(s)
- Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Geeta Bhandari
- Department of Biosciences, Himalayan School of Bio Sciences, Swami Rama Himalayan University, Dehradun, India
| | | | - Deepa Nainwal
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | - Anju Rani
- Department of Life Sciences, Graphic Era (Deemed to be) University, Dehradun, Uttarakhand, India
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
- Guru Nanak College of Pharmaceutical Sciences, Dehradun, Uttarakhand, India
- Department of Applied Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
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Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes. J Bacteriol 2023; 205:e0034322. [PMID: 36892288 PMCID: PMC10127602 DOI: 10.1128/jb.00343-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
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. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.
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Fang L, Zhu H, Geng Y, Zhang G, Zhang H, Shi T, Wu X, Li QX, Hua R. Resistance properties and adaptation mechanism of cadmium in an enriched strain, Cupriavidus nantongensis X1 T. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128935. [PMID: 35461001 DOI: 10.1016/j.jhazmat.2022.128935] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Bacterial adaption to heavy metal stress is a complex and comprehensive process of multi-response regulation. However, the mechanism is largely unexplored. In this study, cadmium (Cd) resistance and adaptation mechanism in Cupriavidus nantongensis X1T were investigated. Strain X1T could resist the stress of 307 mg/L Cd2+ and remove 70% Cd2+ in 48 h. Spectroscopic analyses suggested interactions between Cd2+ with C-N, -COOH, and -NH ligands of extracellular polymeric substances. Whole-genome sequencing found that the resistance of Cd2+ in strain X1T was caused by the joint action of Czc and Cad systems. Cd2+ at 20 mg/L elicited differential expression of 1157 genes in strain X1T. In addition to the reported effects of uptake, adsorption, effluxion, and accumulation system, the oxidative stress system, Type-VI secretory protein system, Fe-S protein synthesis, and cysteine synthesis system in strain X1T were involved in the Cd2+ resistance and accumulation. The intracellular accumulation content of Cd2+ in strain X1T was higher than the extracellular adsorption content made strain X1T to be an important resource strain in the bioremediation of Cd-contaminated sewage. The results provide a theoretical network for understanding the complex regulatory system of bacterial resistance and adaptation of Cd against stressful environments.
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Affiliation(s)
- Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hao Zhu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Genrong Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Houpu Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China.
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Sun S, Zhang K, Wu Y, Zhu N, Wang Y, Chen J, Leng F. Transporter drives the biosorption of heavy metals by Stenotrophomonas rhizophila JC1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45380-45395. [PMID: 35143001 DOI: 10.1007/s11356-022-18900-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
To better understand the function of transporter in heavy metal detoxification of bacteria, the transporters associated with heavy metal detoxification in S. rhizophila JC1 were analyzed, among which four members were verified by RT-qPCR. In addition, the removal rates of four single metal ions (Cr6+, Cu2+, Zn2+, Pb2+) and polymetallic ions by strain JC1 were studied, respectively. We also researched the physiological response of strain JC1 to different metal stress via morphological observation, elemental composition, functional group and membrane permeability analysis. The results showed that in the single metal ion solution, removal capacities of Cu2+ (120 mg/L) and Cr6+ (80 mg/L) of S. rhizophila JC1 reached to 79.9% and 89.3%, respectively, while in polymetallic ions solution, the removal capacity of each metal ion all decreased, and in detail, the adsorption capacity was determined Cr6+>Cu2+>Zn2+>Pb2+ under the same condition. The physiological response analyses results showed that extracellular adsorption phenomena occurred, and the change of membrane permeability hindered the uptake of metal ions by bacteria. The analysis of transporters in strain JC1 genome illustrated that a total of 323 transporters were predicted. Among them, two, six and five proteins of the cation diffusion facilitator, resistance-nodulation-division efflux and P-type ATPase families were, respectively, predicted. The expression of corresponding genes showed that the synergistic action of correlative transporters played important roles in the process of adsorption. The comparative genomics analysis revealed that S. rhizophila JC1 has long-distance evolutionary relationships with other strains, but the efflux system of S. rhizophila JC1 contained the same types of metal transporters as other metal-resistant bacteria.
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Affiliation(s)
- Shangchen Sun
- School of Petrochemical Engineering, Lanzhou University of Technology, 730050, Lanzhou, China
| | - Kexin Zhang
- School of Life Science and Engineering, Lanzhou University of Technology, Langongping Road 287, Qilihe District, 730050, Lanzhou, China
| | - Yamiao Wu
- School of Life Science and Engineering, Lanzhou University of Technology, Langongping Road 287, Qilihe District, 730050, Lanzhou, China
| | - Ning Zhu
- School of Life Science and Engineering, Lanzhou University of Technology, Langongping Road 287, Qilihe District, 730050, Lanzhou, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Langongping Road 287, Qilihe District, 730050, Lanzhou, China.
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, 730050, Lanzhou, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Langongping Road 287, Qilihe District, 730050, Lanzhou, China
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Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans. Microbiol Spectr 2022; 10:e0012122. [PMID: 35311568 PMCID: PMC9045368 DOI: 10.1128/spectrum.00121-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans contains a large number of horizontally acquired plasmids and genomic islands that were integrated into its chromosome or chromid. For the C. metallidurans CH34 wild-type strain growing under nonchallenging conditions, 5,763 transcriptional starting sequences (TSSs) were determined. Using a custom-built motif discovery software based on hidden Markov models, patterns upstream of the TSSs were identified. The pattern TTGACA, −35.6 ± 1.6 bp upstream of the TSSs, in combination with a TATAAT sequence 15.8 ± 1.4 bp upstream occurred frequently, especially upstream of the TSSs for 48 housekeeping genes, and these were assigned to promoters used by RNA polymerase containing the main housekeeping sigma factor RpoD. From patterns upstream of the housekeeping genes, a score for RpoD-dependent promoters in C. metallidurans was derived and applied to all 5,763 TSSs. Among these, 2,572 TSSs could be associated with RpoD with high probability, 373 with low probability, and 2,818 with no probability. In a detailed analysis of horizontally acquired genes involved in metal resistance and not involved in this process, the TSSs responsible for the expression of these genes under nonchallenging conditions were assigned to RpoD- or non-RpoD-dependent promoters. RpoD-dependent promoters occurred frequently in horizontally acquired metal resistance and other determinants, which should allow their initial expression in a new host. However, other sigma factors and sense/antisense effects also contribute—maybe to mold in subsequent adaptation steps the assimilated gene into the regulatory network of the cell. IMPORTANCE In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed. We show here that the main housekeeping sigma factor RpoD plays an important role in the expression of horizontally acquired genes in the metal-resistant hydrogen-oxidizing bacterium C. metallidurans. By conservation of the RpoD recognition consensus sequence, a newly arriving gene has a high probability to be expressed in the new host cell. In addition to integrons and genes travelling together with that for their sigma factor, conservation of the RpoD consensus sequence may be an important contributor to the overall evolutionary success of horizontal gene transfer in bacteria. Using C. metallidurans as an example, this publication sheds some light on the fate and function of horizontally acquired genes in bacteria.
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Loss of mobile genomic islands in metal resistant, hydrogen-oxidizing Cupriavidus metallidurans. Appl Environ Microbiol 2021; 88:e0204821. [PMID: 34910578 DOI: 10.1128/aem.02048-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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 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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Ducret V, Abdou M, Goncalves Milho C, Leoni S, Martin-Pelaud O, Sandoz A, Segovia Campos I, Tercier-Waeber ML, Valentini M, Perron K. Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics. Front Microbiol 2021; 12:739988. [PMID: 34690984 PMCID: PMC8531726 DOI: 10.3389/fmicb.2021.739988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022] Open
Abstract
Zinc is one of the most important trace elements for life and its deficiency, like its excess, can be fatal. In the bacterial opportunistic pathogen Pseudomonas aeruginosa, Zn homeostasis is not only required for survival, but also for virulence and antibiotic resistance. Thus, the bacterium possesses multiple Zn import/export/storage systems. In this work, we determine the expression dynamics of the entire P. aeruginosa Zn homeostasis network at both transcript and protein levels. Precisely, we followed the switch from a Zn-deficient environment, mimicking the initial immune strategy to counteract bacterial infections, to a Zn-rich environment, representing the phagocyte metal boost used to eliminate an engulfed pathogen. Thanks to the use of the NanoString technology, we timed the global silencing of Zn import systems and the orchestrated induction of Zn export systems. We show that the induction of Zn export systems is hierarchically organized as a function of their impact on Zn homeostasis. Moreover, we identify PA2807 as a novel Zn resistance component in P. aeruginosa and highlight new regulatory links among Zn-homeostasis systems. Altogether, this work unveils a sophisticated and adaptive homeostasis network, which complexity is key in determining a pathogen spread in the environment and during host-colonization.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Melina Abdou
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Catarina Goncalves Milho
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Oriane Martin-Pelaud
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Antoine Sandoz
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Inés Segovia Campos
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | | | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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Behind the shield of Czc: ZntR controls expression of the gene for the zinc-exporting P-type ATPase ZntA in Cupriavidus metallidurans. J Bacteriol 2021; 203:JB.00052-21. [PMID: 33685972 PMCID: PMC8117531 DOI: 10.1128/jb.00052-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the metallophilic beta-proteobacterium Cupriavidus metallidurans, the plasmid-encoded Czc metal homeostasis system adjusts the periplasmic zinc, cobalt and cadmium concentration, which influences subsequent uptake of these metals into the cytoplasm. Behind this shield, the PIB2-type APTase ZntA is responsible for removal of surplus cytoplasmic zinc ions, thereby providing a second level of defense against toxic zinc concentrations. ZntA is the counterpart to the Zur-regulated zinc uptake system ZupT and other import systems; however, the regulator of zntA expression was unknown. The chromid-encoded zntA gene is adjacent to the genes czcI2C2B2', which are located on the complementary DNA strand and transcribed from a common promoter region. These genes encode homologs of plasmid pMOL30-encoded Czc components. Candidates for possible regulators of zntA were identified and subsequently tested: CzcI, CzcI2, and the MerR-type gene products of the locus tags Rmet_2302, Rmet_0102, Rmet_3456. This led to the identification of Rmet_3456 as ZntR, the main regulator of zntA expression. Moreover, both CzcIs decreased Czc-mediated metal resistance, possibly to avoid "over-excretion" of periplasmic zinc ions, which could result in zinc starvation due to diminished zinc uptake into the cytoplasm. Rmet_2302 was identified as CadR, the regulator of the cadA gene for an important cadmium-exporting PIB2-type ATPase, which provides another system for removal of cytoplasmic zinc and cadmium. Rmet_0102 was not involved in regulation of the metal resistance systems examined here. Thus, ZntR forms a complex regulatory network with CadR, Zur and the CzcIs. Moreover, these discriminating regulatory proteins assign the efflux systems to their particular function.ImportanceZinc is an essential metal for numerous organisms from humans to bacteria. The transportome of zinc uptake and efflux systems controls the overall cellular composition and zinc content in a double feed-back loop. Zinc starvation mediates, via the Zur regulator, an up-regulation of the zinc import capacity via the ZIP-type zinc importer ZupT and an amplification of zinc storage capacity, which together raise the cellular zinc content again. On the other hand, an increasing zinc content leads to ZntR-mediated up-regulation of the zinc efflux system ZntA, which decreases the zinc content. Together, the Zur regulon components and ZntR/ZntA balance the cellular zinc content under both high external zinc concentrations and zinc starvation conditions.
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11
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Kelley BR, Lu J, Haley KP, Gaddy JA, Johnson JG. Metal homeostasis in pathogenic Epsilonproteobacteria: mechanisms of acquisition, efflux, and regulation. Metallomics 2021; 13:mfaa002. [PMID: 33570133 PMCID: PMC8043183 DOI: 10.1093/mtomcs/mfaa002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
Epsilonproteobacteria are a diverse class of eubacteria within the Proteobacteria phylum that includes environmental sulfur-reducing bacteria and the human pathogens, Campylobacter jejuni and Helicobacter pylori. These pathogens infect and proliferate within the gastrointestinal tracts of multiple animal hosts, including humans, and cause a variety of disease outcomes. While infection of these hosts provides nutrients for the pathogenic Epsilonproteobacteria, many hosts have evolved a variety of strategies to either sequester metals from the invading pathogen or exploit the toxicity of metals and drive their accumulation as an antimicrobial strategy. As a result, C. jejuni and H. pylori have developed mechanisms to sense changes in metal availability and regulate their physiology in order to respond to either metal limitation or accumulation. In this review, we will discuss the challenges of metal availability at the host-pathogen interface during infection with C. jejuni and H. pylori and describe what is currently known about how these organisms alter their gene expression and/or deploy bacterial virulence factors in response to these environments.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Jacky Lu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
| | - Kathryn P Haley
- Department of Biology, Grand Valley State University, Grand Rapids, MI, USA
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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12
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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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13
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Sung HL, Nesbitt DJ. Sequential Folding of the Nickel/Cobalt Riboswitch Is Facilitated by a Conformational Intermediate: Insights from Single-Molecule Kinetics and Thermodynamics. J Phys Chem B 2020; 124:7348-7360. [DOI: 10.1021/acs.jpcb.0c05625] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States,
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J. Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States,
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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14
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Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area. PLoS One 2020; 15:e0234128. [PMID: 32497143 PMCID: PMC7272022 DOI: 10.1371/journal.pone.0234128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022] Open
Abstract
Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.
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15
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Große C, Poehlein A, Blank K, Schwarzenberger C, Schleuder G, Herzberg M, Nies DH. The third pillar of metal homeostasis inCupriavidus metalliduransCH34: preferences are controlled by extracytoplasmic function sigma factors. Metallomics 2019; 11:291-316. [DOI: 10.1039/c8mt00299a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
InC. metallidurans, a network of 11 extracytoplasmic function sigma factors forms the third pillar of metal homeostasis acting in addition to the metal transportome and metal repositories as the first and second pillar.
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Affiliation(s)
- Cornelia Große
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory
- Georg-August-University Göttingen, Grisebachstr. 8
- 37077 Göttingen
- Germany
| | - Kathrin Blank
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Claudia Schwarzenberger
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Grit Schleuder
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Martin Herzberg
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Dietrich H. Nies
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
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16
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Abstract
Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.
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17
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Peng J, Miao L, Chen X, Liu P. Comparative Transcriptome Analysis of Pseudomonas putida KT2440 Revealed Its Response Mechanisms to Elevated Levels of Zinc Stress. Front Microbiol 2018; 9:1669. [PMID: 30087671 PMCID: PMC6066579 DOI: 10.3389/fmicb.2018.01669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/04/2018] [Indexed: 01/03/2023] Open
Abstract
The whole-genome transcriptional response of Pseudomonas putida KT2440 to stress-inducing concentrations of zinc was analyzed in this study by RNA sequencing to thoroughly investigate the bacterial cell response to zinc toxicity. The data revealed that different levels of zinc stress strongly affected the transcription of genes from the following categories: metal transport genes, genes involved in membrane homeostasis, oxidative-stress-responding genes, and genes associated with basic cellular metabolism. At the lowest zinc dose, only several genes associated with metal transport and membrane homeostasis were strongly influenced. At the intermediate zinc dose, transcriptional changes of genes belonging to these two categories were highly pronounced. In addition, the intermediate zinc stress produced high levels of oxidative stress, and influenced amino acid metabolism and respiratory chains of P. putida. At the highest zinc dose, the induction of genes responsible for Fe–S cluster biogenesis was the most remarkable feature. Moreover, upregulation of glyoxylate cycle was observed. In summary, the adaptation of the cell envelope, the maintenance of metal homeostasis and intracellular redox status, and the transcriptional control of metabolism are the main elements of stress response, which facilitates the survival of P. putida KT2440 in zinc-polluted environments.
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Affiliation(s)
- Jun Peng
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Lihong Miao
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Pulin Liu
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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18
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Nies DH. The biological chemistry of the transition metal "transportome" of Cupriavidus metallidurans. Metallomics 2017; 8:481-507. [PMID: 27065183 DOI: 10.1039/c5mt00320b] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review tries to illuminate how the bacterium Cupriavidus metallidurans CH34 is able to allocate essential transition metal cations to their target proteins although these metals have similar charge-to-surface ratios and chemical features, exert toxic effects, compete with each other, and occur in the bacterial environment over a huge range of concentrations and speciations. Central to this ability is the "transportome", the totality of all interacting metal import and export systems, which, as an emergent feature, transforms the environmental metal content and speciation into the cellular metal mélange. In a kinetic flow equilibrium resulting from controlled uptake and efflux reactions, the periplasmic and cytoplasmic metal content is adjusted in a way that minimizes toxic effects. A central core function of the transportome is to shape the metal ion composition using high-rate and low-specificity reactions to avoid time and/or energy-requiring metal discrimination reactions. This core is augmented by metal-specific channels that may even deliver metals all the way from outside of the cell to the cytoplasm. This review begins with a description of the basic chemical features of transition metal cations and the biochemical consequences of these attributes, and which transition metals are available to C. metallidurans. It then illustrates how the environment influences the metal content and speciation, and how the transportome adjusts this metal content. It concludes with an outlook on the fate of metals in the cytoplasm. By generalization, insights coming from C. metallidurans shed light on multiple transition metal homoeostatic mechanisms in all kinds of bacteria including pathogenic species, where the "battle" for metals is an important part of the host-pathogen interaction.
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Affiliation(s)
- Dietrich H Nies
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Germany.
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19
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Romaniuk K, Dziewit L, Decewicz P, Mielnicki S, Radlinska M, Drewniak L. Molecular characterization of the pSinB plasmid of the arsenite oxidizing, metallotolerant Sinorhizobium sp. M14 - insight into the heavy metal resistome of sinorhizobial extrachromosomal replicons. FEMS Microbiol Ecol 2017; 93:fiw215. [PMID: 27797963 DOI: 10.1093/femsec/fiw215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
Sinorhizobium sp. M14 is an As(III)-oxidizing, psychrotolerant strain, capable of growth in the presence of extremely high concentrations of arsenic and many other heavy metals. Metallotolerant abilities of the M14 strain depend upon the presence of two extrachromosomal replicons: pSinA (∼ 109 kb) and pSinB (∼ 300 kb). The latter was subjected to complex analysis. The performed analysis demonstrated that the plasmid pSinB is a narrow-host-range repABC-type replicon, which is fully stabilized by the phd-vapC-like toxin-antitoxin stabilizing system. In silico analysis showed that among the phenotypic gene clusters of the plasmid pSinB, eight modules are potentially involved in heavy metals resistance (HMR). These modules carry genes encoding efflux pumps, permeases, transporters and copper oxidases, which provide resistance to arsenic, cadmium, cobalt, copper, iron, mercury, nickel, silver and zinc. The functional analysis revealed that the HMR modules are active and have an effect on the minimal inhibitory concentration (MIC) values observed for the heterological host cells. The phenotype was manifested by an increase or decrease of the MICs of heavy metals and it was strain specific. The analysis of distribution of the heavy metal resistance genes, i.e. resistome, in Sinorhizobium spp. plasmids, revealed that the HMR modules are common in these replicons.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sebastian Mielnicki
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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20
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Qin W, Liu X, Yu X, Chu X, Tian J, Wu N. Identification of cadmium resistance and adsorption gene from Escherichia coli BL21 (DE3). RSC Adv 2017. [DOI: 10.1039/c7ra10656d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cadmium resistance and adsorption genecapBfromEscherichia coliBL21 (DE3).
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Affiliation(s)
- Weitong Qin
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
| | - Xiaoqing Liu
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
| | - Xiaoxia Yu
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
| | - Xiaoyu Chu
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
| | - Jian Tian
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
| | - Ningfeng Wu
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 100081
- China
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21
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Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol Cell 2016; 57:1088-1098. [PMID: 25794617 DOI: 10.1016/j.molcel.2015.02.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022]
Abstract
Bacteria regularly encounter widely varying metal concentrations in their surrounding environment. As metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. A suite of metal-sensing regulatory ("metalloregulatory") proteins orchestrate these responses by allosterically coupling the selective binding of target metals to the activity of DNA-binding domains. However, we report here the discovery, validation, and structural details of a widespread class of riboswitch RNAs, whose members selectively and tightly bind the low-abundance transition metals, Ni(2+) and Co(2+). These riboswitches bind metal cooperatively, and with affinities in the low micromolar range. The structure of a Co(2+)-bound RNA reveals a network of molecular contacts that explains how it achieves cooperative binding between adjacent sites. These findings reveal that bacteria have evolved to utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins, for detecting and responding to toxic levels of heavy metals.
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Affiliation(s)
- Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Arati Ramesh
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhiyuan Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Howard Hughes Medical Institute, New Haven, CT 06520, USA
| | - Tenaya Vallery
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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22
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Liu P, Chen X, Huang Q, Chen W. The Role of CzcRS Two-Component Systems in the Heavy Metal Resistance of Pseudomonas putida X4. Int J Mol Sci 2015. [PMID: 26225958 PMCID: PMC4581181 DOI: 10.3390/ijms160817005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The role of different czcRS genes in metal resistance and the cross-link between czcRS and czcCBA in Pseudomonas putida X4 were studied to advance understanding of the mechanisms by which P. putida copes with metal stress. Similar to P. putida KT2440, two complete czcRS1 and czcRS2 two-component systems, as well as a czcR3 without the corresponding sensing component were amplified in P. putida X4. The histidine kinase genes czcS1 and czcS2 were inactivated and fused to lacZ by homologous recombination. The lacZ fusion assay revealed that Cd2+ and Zn2+ caused a decrease in the transcription of czcRS1, whereas Cd2+ treatment enhanced the transcription of czcRS2. The mutation of different czcRSs showed that all czcRSs are necessary to facilitate full metal resistance in P. putida X4. A putative gene just downstream of czcR3 is related to metal ion resistance, and its transcription was activated by Zn2+. Data from quantitative real-time polymerase chain reaction (qRT-PCR) strongly suggested that czcRSs regulate the expression of czcCBA, and a cross-link exists between different czcRSs.
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Affiliation(s)
- Pulin Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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23
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Herzberg M, Bauer L, Nies DH. Deletion of the zupT gene for a zinc importer influences zinc pools in Cupriavidus metallidurans CH34. Metallomics 2014; 6:421-36. [DOI: 10.1039/c3mt00267e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Valencia EY, Braz VS, Guzzo C, Marques MV. Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria. BMC Microbiol 2013; 13:79. [PMID: 23578014 PMCID: PMC3637150 DOI: 10.1186/1471-2180-13-79] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/21/2013] [Indexed: 11/15/2022] Open
Abstract
Background Heavy metal Resistance-Nodulation-Division (HME-RND) efflux systems help Gram-negative bacteria to keep the intracellular homeostasis under high metal concentrations. These proteins constitute the cytoplasmic membrane channel of the tripartite RND transport systems. Caulobacter crescentus NA1000 possess two HME-RND proteins, and the aim of this work was to determine their involvement in the response to cadmium, zinc, cobalt and nickel, and to analyze the phylogenetic distribution and characteristic signatures of orthologs of these two proteins. Results Expression assays of the czrCBA operon showed significant induction in the presence of cadmium and zinc, and moderate induction by cobalt and nickel. The nczCBA operon is highly induced in the presence of nickel and cobalt, moderately induced by zinc and not induced by cadmium. Analysis of the resistance phenotype of mutant strains showed that the ΔczrA strain is highly sensitive to cadmium, zinc and cobalt, but resistant to nickel. The ΔnczA strain and the double mutant strain showed reduced growth in the presence of all metals tested. Phylogenetic analysis of the C. crescentus HME-RND proteins showed that CzrA-like proteins, in contrast to those similar to NczA, are almost exclusively found in the Alphaproteobacteria group, and the characteristic protein signatures of each group were highlighted. Conclusions The czrCBA efflux system is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt. The nczCBA efflux system is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. CzrA belongs to the HME2 subfamily, which is almost exclusively found in the Alphaproteobacteria group, as shown by phylogenetic analysis. NczA belongs to the HME1 subfamily which is more widespread among diverse Proteobacteria groups. Each of these subfamilies present distinctive amino acid signatures.
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Affiliation(s)
- Estela Y Valencia
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av, Prof, Lineu Prestes 1374, São Paulo, SP, 05508-900, Brazil
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25
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Gutiérrez-Barranquero JA, de Vicente A, Carrión VJ, Sundin GW, Cazorla FM. Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae. Appl Environ Microbiol 2013; 79:1028-33. [PMID: 23183969 PMCID: PMC3568574 DOI: 10.1128/aem.02644-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/15/2012] [Indexed: 11/20/2022] Open
Abstract
We describe the genetic organization of a copper-resistant plasmid containing copG and cusCBA genes in the plant pathogen Pseudomonas syringae. Chromosomal variants of czcCBA and a plasmid variant of cusCBA were present in different P. syringae pathovar strains. Transformation of the copper-sensitive Pseudomonas syringae pv. syringae FF5 strain with copG or cusCBA conferred copper resistance, and quantitative real-time PCR (qRT-PCR) experiments confirmed their induction by copper.
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Affiliation(s)
- José A. Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - George W. Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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26
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Abstract
As a trace element copper has an important role in cellular function like many other transition metals. Its ability to undergo redox changes [Cu(I) ↔ Cu(II)] makes copper an ideal cofactor in enzymes catalyzing electron transfers. However, this redox change makes copper dangerous for a cell since it is able to be involved in Fenton-like reactions creating reactive oxygen species (ROS). Cu(I) also is a strong soft metal and can attack and destroy iron-sulfur clusters thereby releasing iron which can in turn cause oxidative stress. Therefore, copper homeostasis has to be highly balanced to ensure proper cellular function while avoiding cell damage.Throughout evolution bacteria and archaea have developed a highly regulated balance in copper metabolism. While for many prokaryotes copper uptake seems to be unspecific, others have developed highly sophisticated uptake mechanisms to ensure the availability of sufficient amounts of copper. Within the cytoplasm copper is sequestered by various proteins and molecules, including specific copper chaperones, to prevent cellular damage. Copper-containing proteins are usually located in the cytoplasmic membrane with the catalytic domain facing the periplasm, in the periplasm of Gram-negative bacteria, or they are secreted, limiting the necessity of copper to accumulate in the cytoplasm. To prevent cellular damage due to excess copper, bacteria and archaea have developed various copper detoxification strategies. In this chapter we attempt to give an overview of the mechanisms employed by bacteria and archaea to handle copper and the importance of the metal for cellular function as well as in the global nutrient cycle.
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Affiliation(s)
- Christopher Rensing
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1870, Frederiksberg C, Denmark
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Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 2011; 24:1133-51. [DOI: 10.1007/s10534-011-9473-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
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Ribeiro-dos-Santos G, Biondo R, Quadros ODF, Vicente EJ, Schenberg ACG. A metal-repressed promoter from gram-positive Bacillus subtilis is highly active and metal-induced in gram-negative Cupriavidus metallidurans. Biotechnol Bioeng 2010; 107:469-77. [DOI: 10.1002/bit.22820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Petit-Haertlein I, Girard E, Sarret G, Hazemann JL, Gourhant P, Kahn R, Covès J. Evidence for conformational changes upon copper binding to Cupriavidus metallidurans CzcE. Biochemistry 2010; 49:1913-22. [PMID: 20112954 DOI: 10.1021/bi100001z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CzcE is a periplasmic protein from Cupriavidus metallidurans CH34 that can bind four copper atoms per dimer. We have crystallized the apo form of the protein and determined its structure at 1.85 A resolution. Three Cu atoms were localized by soaking apo-CzcE crystals into a CuCl(2) solution. We identified His24 as a Cu(II) ligand in each protomer and Asp100 as a key residue for Cu binding at the interface of the dimer. The role of these amino acids was confirmed by site-directed mutagenesis and UV-visible spectroscopy. The fourth Cu atom was not located. The oxidized form of CzcE contains four Cu(II) atoms, while the reduced form contains four Cu(I) atoms. Average coordination spheres of four N or O atoms for Cu(II) and of one N or O atom and two S atoms for Cu(I) were determined by X-ray absorption spectroscopy. As there is no evidence for preformed metal-binding sites in apo-CzcE, we suggest that different conformational changes occurred upon Cu(II) or Cu(I) binding. These changes were further demonstrated by digestion experiments that gave different proteolysis patterns depending not only on the presence of the metal but also on its speciation. The ability of CzcE to bind copper and to adapt its conformation to different copper oxidation states could be related to a role in copper sensing for this protein.
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Affiliation(s)
- Isabelle Petit-Haertlein
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
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Molina-Henares AJ, Godoy P, Duque E, Ramos JL. A general profile for the MerR family of transcriptional regulators constructed using the semi-automated Provalidator tool. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:518-523. [PMID: 23765930 DOI: 10.1111/j.1758-2229.2009.00067.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Provalidator is a web-based tool that facilitates the design and validation of generalized profiles of protein families in prokaryotes. This tool combines the nearly full automation of profile building with a search for family members in all available databases. The tool is useful for assigning a given protein to a specific family, and is also useful for genome mining in annotated prokaryotic genomes. The tool is freely available at http://www.bactregulators.org. As proof of concept we constructed a profile that best defines the MerR family of transcriptional regulators. The profile created includes functional residues that are part of the helix-turn-helix DNA binding domain and accessory elements defined as wings 1 and 2, suggesting that members of the MerR family of regulators may exhibit conserved 3D structure in the region that defines the family profile. The profile defined for MerR was used to search for members of this family in the Swiss-Prot and TrEMBL databases, and also to identify members of the family in the genome of Pseudomonas putida. One of these identified regulators was found to be involved in zinc tolerance, showing the usefulness of identifying family members and assigning phenotypes.
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Affiliation(s)
- Antonio J Molina-Henares
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, E-18008 Granada, Spain
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Scherer J, Nies DH. CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34. Mol Microbiol 2009; 73:601-21. [PMID: 19602147 DOI: 10.1111/j.1365-2958.2009.06792.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cupriavidus metallidurans CH34 possesses a multitude of metal efflux systems. Here, the function of the novel P(IB4)-type ATPase CzcP is characterized, which belongs to the plasmid pMOL30-mediated cobalt-zinc-cadmium (Czc) resistance system. Contribution of CzcP to transition metal resistance in C. metallidurans was compared with that of three P(IB2)-type ATPases (CadA, ZntA, PrbA) and to other efflux proteins by construction and characterization of multiple deletion mutants. These data also yielded additional evidence for an export of metal cations from the periplasm to the outside of the cell rather than from the cytoplasm to the outside. Moreover, metal-sensitive Escherichia coli strains were functionally substituted in trans with CzcP and the three P(IB2)-type ATPases. Metal transport kinetics performed with inside-out vesicles identified the main substrates for these four exporters, the K(m) values and apparent turn-over numbers. In combination with the mutant data, transport kinetics indicated that CzcP functions as 'resistance enhancer': this P(IB4)-type ATPase exports transition metals Zn(2+), Cd(2+) and Co(2+) much more rapidly than the three P(IB2)-type proteins. However, a basic resistance level has to be provided by the P(IB2)-type efflux pumps because CzcP may not be able to reach all different speciations of these metals in the cytoplasm.
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Affiliation(s)
- Judith Scherer
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University, Halle-Wittenberg, Germany
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32
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Mergeay M, Monchy S, Janssen P, Houdt RV, Leys N. Megaplasmids in Cupriavidus Genus and Metal Resistance. MICROBIAL MEGAPLASMIDS 2009. [DOI: 10.1007/978-3-540-85467-8_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Cupriavidus metallidurans: evolution of a metal-resistant bacterium. Antonie van Leeuwenhoek 2008; 96:115-39. [DOI: 10.1007/s10482-008-9284-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 09/17/2008] [Indexed: 10/21/2022]
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Abstract
Porphyromonas gingivalis is a Gram-negative oral anaerobe associated with chronic adult periodontitis. Its ecological niche is the gingival crevice, where the organism adapts to the challenges of the infectious process such as host defence and bacterial products. Bacterial responses to environmental changes are partly regulated by two-component signal transduction systems. Several intact systems were annotated in the genome of P. gingivalis, as well as an orphan regulator encoding a homologue of RprY, a response regulator from Bacteroides fragilis. With the goal of defining the environmental cues that activate RprY in P. gingivalis, we used several strategies to identify its regulon. Results from gene expression and DNA-protein binding assays identified target genes that were either involved in transport functions or associated with oxidative stress, and indicated that RprY can act as an activator and a repressor. RprY positively activated the primary sodium pump, NADH : ubiquinone oxidoreductase (NQR), and RprY protein also interacted with the promoter regions of nqrA genes from B. fragilis and Vibrio cholerae. Given that gingival bleeding and infiltration of host defence cells are symptoms of periodontal infection, iron products released from blood and reactive oxygen species from polymorphonuclear leucocytes may be potential inducers of the RprY regulon.
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Affiliation(s)
- Ana E Duran-Pinedo
- Department of Molecular Genetics, Forsyth Institute, Boston, MA 02115, USA
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35
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Zoropogui A, Gambarelli S, Covès J. CzcE from Cupriavidus metallidurans CH34 is a copper-binding protein. Biochem Biophys Res Commun 2007; 365:735-9. [PMID: 18029263 DOI: 10.1016/j.bbrc.2007.11.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 11/08/2007] [Indexed: 11/18/2022]
Abstract
CzcE is encoded by the most distal gene of the czc determinant that allows Cupriavidus metallidurans CH34 to modulate its internal concentrations of cobalt, zinc and cadmium by regulation of the expression of the efflux pump CzcCBA. We have overproduced and purified CzcE. CzcE is a periplasm-located dimeric protein able to bind specifically 4 Cu-equivalent per dimer. Spectrophotometry and EPR are indicative of type II copper with typical d-d transitions. Re-oxidation of fully reduced CzcE led to the formation of an air stable semi-reduced form binding both 2 Cu(I) and 2 Cu(II) ions. The spectroscopic characteristics of the semi-reduced form are different of those of the oxidized one, suggesting a change in the environment of Cu(II).
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Affiliation(s)
- Anthony Zoropogui
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
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36
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Pompidor G, Zoropogui A, Kahn R, Covès J. Overproduction, purification and preliminary X-ray diffraction analysis of CzcE from Cupriavidus metallidurans CH34. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:884-6. [PMID: 17909296 PMCID: PMC2339729 DOI: 10.1107/s1744309107043709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 09/06/2007] [Indexed: 11/10/2022]
Abstract
CzcE is encoded by the czc determinant that allows Cupriavidus metallidurans CH34 to modulate its internal concentrations of cobalt, zinc and cadmium. This periplasmic protein was overproduced in its mature form in Escherichia coli and purified in two steps. After preliminary screening of crystallization conditions using a robot, well diffracting crystals were obtained using the hanging-drop vapour-diffusion method. Crystals diffracted to 1.96 A using synchrotron radiation. They belonged to the monoclinic space group C2, with unit-cell parameters a = 105.54, b = 29.68, c = 71.10 A. The asymmetric unit is expected to contain a dimer, in agreement with the quaternary structure deduced from gel-filtration experiments.
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Affiliation(s)
- Guillaume Pompidor
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS–CEA–UJF, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX, France
| | - Anthony Zoropogui
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS–CEA–UJF, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX, France
| | - Richard Kahn
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS–CEA–UJF, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX, France
| | - Jacques Covès
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS–CEA–UJF, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX, France
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Reith F, Lengke MF, Falconer D, Craw D, Southam G. The geomicrobiology of gold. ISME JOURNAL 2007; 1:567-84. [DOI: 10.1038/ismej.2007.75] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kloosterman TG, van der Kooi-Pol MM, Bijlsma JJE, Kuipers OP. The novel transcriptional regulator SczA mediates protection against Zn2+ stress by activation of the Zn2+-resistance gene czcD in Streptococcus pneumoniae. Mol Microbiol 2007; 65:1049-63. [PMID: 17640279 DOI: 10.1111/j.1365-2958.2007.05849.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Maintenance of the intracellular homeostasis of metal ions is important for the virulence of many bacterial pathogens. Here, we demonstrate that the czcD gene of the human pathogen Streptococcus pneumoniae is involved in resistance against Zn2+, and that its transcription is induced by the transition-metal ions Zn2+, Co2+ and Ni2+. Upstream of czcD a gene was identified, encoding a novel TetR family regulator, SczA, that is responsible for the metal ion-dependent activation of czcD expression. Transcriptome analyses revealed that in a sczA mutant expression of czcD, a gene encoding a MerR-family transcriptional regulator and a gene encoding a zinc-containing alcohol dehydrogenase (adhB) were downregulated. Activation of the czcD promoter by SczA is shown to proceed by Zn2+-dependent binding of SczA to a conserved DNA motif. In the absence of Zn2+, SczA binds to a second site in the czcD promoter, thereby fully blocking czcD expression. This is the first example of a metalloregulatory protein belonging to the TetR family that has been described. The presence in S. pneumoniae of the Zn2+-resistance system characterized in this study might reflect the need for adjustment to a fluctuating Zn2+ pool encountered by this pathogen during infection of the human body.
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Affiliation(s)
- Tomas G Kloosterman
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands
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Schmidt A, Schmidt A, Haferburg G, Kothe E. Superoxide dismutases of heavy metal resistant streptomycetes. J Basic Microbiol 2007; 47:56-62. [PMID: 17304620 DOI: 10.1002/jobm.200610213] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Heavy metal tolerant and resistant strains of streptomycetes isolated from a former uranium mining site were screened for their superoxide dismutase expression. From the strains tolerating high concentrations of different heavy metals, one was selected for its tolerance of concentrations of heavy metals (Ni, Cu, Cd, Cr, Mn, Zn, Fe). This strain, Streptomyces acidiscabies E13, was chosen for the purpose of superoxide dismutase analysis. Gel electrophoresis and activity staining revealed only one each of a nickel (NiSOD) and an iron (FeZnSOD) containing superoxide dismutase as shown by differential enzymatic repression studies. The gene for nickel containing superoxide dismutase, sodN, was cloned and sequenced from this strain. The genomic sequence shows 92.7% nucleotide identity and 96.1% amino acid identity to sodN of S. coelicolor. Expression can be activated by nickel as well as other heavy metals and active enzyme is produced in media lacking nickel but containing copper, iron or zinc. Thus, the selected strain is well suited for further characterization of the enzyme encoded by sodN.
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Affiliation(s)
- Astrid Schmidt
- Microbial Phytopathology, Institute of Microbiology, Friedrich-Schiller-University, Jena, Germany
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Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T. Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. MICROBIOLOGY-SGM 2006; 152:1765-1776. [PMID: 16735739 DOI: 10.1099/mic.0.28593-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The four replicons of Cupriavidus metallidurans CH34 (the genome sequence was provided by the US Department of Energy-University of California Joint Genome Institute) contain two gene clusters putatively encoding periplasmic resistance to copper, with an arrangement of genes resembling that of the copSRABCD locus on the 2.1 Mb megaplasmid (MPL) of Ralstonia solanacearum, a closely related plant pathogen. One of the copSRABCD clusters was located on the 2.6 Mb MPL, while the second was found on the pMOL30 (234 kb) plasmid as part of a larger group of genes involved in copper resistance, spanning 17 857 bp in total. In this region, 19 ORFs (copVTMKNSRABCDIJGFLQHE) were identified based on the sequencing of a fragment cloned in an IncW vector, on the preliminary annotation by the Joint Genome Institute, and by using transcriptomic and proteomic data. When introduced into plasmid-cured derivatives of C. metallidurans CH34, the cop locus was able to restore the wild-type MIC, albeit with a biphasic survival curve, with respect to applied Cu(II) concentration. Quantitative-PCR data showed that the 19 ORFs were induced from 2- to 1159-fold when cells were challenged with elevated Cu(II) concentrations. Microarray data showed that the genes that were most induced after a Cu(II) challenge of 0.1 mM belonged to the pMOL30 cop cluster. Megaplasmidic cop genes were also induced, but at a much lower level, with the exception of the highly expressed MPL copD. Proteomic data allowed direct observation on two-dimensional gel electrophoresis, and via mass spectrometry, of pMOL30 CopK, CopR, CopS, CopA, CopB and CopC proteins. Individual cop gene expression depended on both the Cu(II) concentration and the exposure time, suggesting a sequential scheme in the resistance process, involving genes such as copK and copT in an initial phase, while other genes, such as copH, seem to be involved in a late response phase. A concentration of 0.4 mM Cu(II) was the highest to induce maximal expression of most cop genes.
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Affiliation(s)
- Sébastien Monchy
- Service de Confirmation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, Belgium
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Mohammed A Benotmane
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Ruddy Wattiez
- Département de Protéomique et de Biochimie des Protéines, University of Mons-Hainaut, B-7000 Mons, Belgium
| | - Sébastien van Aelst
- Laboratoire de Microbiologie de l'Université Libre de Bruxelles, campus CERIA, 1 av. E. Gryzon, 1070 Brussels, Belgium
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Vanessa Auquier
- Centre de Biologie Structurale et de Bioinformatique: Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Belgium
| | | | - Max Mergeay
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Safiyh Taghavi
- Brookhaven National Laboratory, Biology Department, Upton, NY 11973-5000, USA
- Environmental Technology, Vito, B-2400 Mol, Belgium
| | | | - Tatiana Vallaeys
- INRA, Département de Microbiologie, F-78850 Thiverval Grignon, France
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
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Nies DH, Rehbein G, Hoffmann T, Baumann C, Grosse C. Paralogs of Genes Encoding Metal Resistance Proteins in Cupriavidus metallidurans Strain CH34. J Mol Microbiol Biotechnol 2006; 11:82-93. [PMID: 16825791 DOI: 10.1159/000092820] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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.
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