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Galea D, Herzberg M, Nies DH. The metal-binding GTPases CobW2 and CobW3 are at the crossroads of zinc and cobalt homeostasis in Cupriavidus metallidurans. J Bacteriol 2024; 206:e0022624. [PMID: 39041725 PMCID: PMC11340326 DOI: 10.1128/jb.00226-24] [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: 05/31/2024] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
The metal-resistant beta-proteobacterium Cupriavidus metallidurans is also able to survive conditions of metal starvation. We show that zinc-starved cells can substitute some of the required zinc with cobalt but not with nickel ions. The zinc importer ZupT was necessary for this process but was not essential for either zinc or cobalt import. The cellular cobalt content was also influenced by the two COG0523-family proteins, CobW2 and CobW3. Pulse-chase experiments with radioactive and isotope-enriched zinc demonstrated that both proteins interacted with ZupT to control the cellular flow-equilibrium of zinc, a central process of zinc homeostasis. Moreover, an antagonistic interplay of CobW2 and CobW3 in the presence of added cobalt caused a growth defect in mutant cells devoid of the cobalt efflux system DmeF. Full cobalt resistance also required a synergistic interaction of ZupT and DmeF. Thus, the two transporters along with CobW2 and CobW3 interact to control cobalt homeostasis in a process that depends on zinc availability. Because ZupT, CobW2, and CobW3 also direct zinc homeostasis, this process links the control of cobalt and zinc homeostasis, which subsequently protects C. metallidurans against cadmium stress and general metal starvation.IMPORTANCEIn bacterial cells, zinc ions need to be allocated to zinc-dependent proteins without disturbance of this process by other transition metal cations. Under zinc-starvation conditions, C. metallidurans floods the cell with cobalt ions, which protect the cell against cadmium toxicity, help withstand metal starvation, and provide cobalt to metal-promiscuous paralogs of essential zinc-dependent proteins. The number of cobalt ions needs to be carefully controlled to avoid a toxic cobalt overload. This is accomplished by an interplay of the zinc importer ZupT with the COG0523-family proteins, CobW3, and CobW2. At high external cobalt concentrations, this trio of proteins additionally interacts with the cobalt efflux system, DmeF, so that these four proteins form an inextricable link between zinc and cobalt homeostasis.
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Affiliation(s)
- Diana Galea
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Department of Environmental Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Dietrich H. Nies
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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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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Cupriavidus sp. strain Ni-2 resistant to high concentration of nickel and its genes responsible for the tolerance by genome comparison. Arch Microbiol 2019; 201:1323-1331. [DOI: 10.1007/s00203-019-01700-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
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5
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Characterization of phthalate reductase from Ralstonia eutropha CH34 and in silico study of phthalate dioxygenase and phthalate reductase interaction. J Mol Graph Model 2019; 90:161-170. [DOI: 10.1016/j.jmgm.2019.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
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6
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Moraleda-Muñoz A, Marcos-Torres FJ, Pérez J, Muñoz-Dorado J. Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors. Mol Microbiol 2019; 112:385-398. [PMID: 31187912 PMCID: PMC6851896 DOI: 10.1111/mmi.14328] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
In order to survive, bacteria must adapt to multiple fluctuations in their environment, including coping with changes in metal concentrations. Many metals are essential for viability, since they act as cofactors of indispensable enzymes. But on the other hand, they are potentially toxic because they generate reactive oxygen species or displace other metals from proteins, turning them inactive. This dual effect of metals forces cells to maintain homeostasis using a variety of systems to import and export them. These systems are usually inducible, and their expression is regulated by metal sensors and signal‐transduction mechanisms, one of which is mediated by extracytoplasmic function (ECF) sigma factors. In this review, we have focused on the metal‐responsive ECF sigma factors, several of which are activated by iron depletion (FecI, FpvI and PvdS), while others are activated by excess of metals such as nickel and cobalt (CnrH), copper (CarQ and CorE) or cadmium and zinc (CorE2). We focus particularly on their physiological roles, mechanisms of action and signal transduction pathways.
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Affiliation(s)
- Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
| | - Francisco Javier Marcos-Torres
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, Granada, E-18071, Spain
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7
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Nshogozabahizi J, Aubrey K, Ross J, Thakor N. Applications and limitations of regulatory
RNA
elements in synthetic biology and biotechnology. J Appl Microbiol 2019; 127:968-984. [DOI: 10.1111/jam.14270] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/09/2019] [Accepted: 03/21/2019] [Indexed: 12/13/2022]
Affiliation(s)
- J.C. Nshogozabahizi
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - K.L. Aubrey
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - J.A. Ross
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
| | - N. Thakor
- Department of Chemistry and Biochemistry Alberta RNA Research and Training Institute (ARRTI) University of Lethbridge Lethbridge AB Canada
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8
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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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9
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Millacura FA, Janssen PJ, Monsieurs P, Janssen A, Provoost A, Van Houdt R, Rojas LA. Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance. Genes (Basel) 2018; 9:E551. [PMID: 30428624 PMCID: PMC6266692 DOI: 10.3390/genes9110551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 12/04/2022] Open
Abstract
For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.
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Affiliation(s)
- Felipe A Millacura
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK.
| | - Paul J Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Pieter Monsieurs
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Provoost
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Rob Van Houdt
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Luis A Rojas
- Chemistry Department, Faculty of Sciences, Universidad Católica del Norte, UCN, Antofagasta 1240000, Chile.
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Van Houdt R, Provoost A, Van Assche A, Leys N, Lievens B, Mijnendonckx K, Monsieurs P. Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. Genes (Basel) 2018; 9:genes9100507. [PMID: 30340417 PMCID: PMC6210171 DOI: 10.3390/genes9100507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022] Open
Abstract
Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Kristel Mijnendonckx
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
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Asaf S, Khan AL, Khan MA, Al-Harrasi A, Lee IJ. Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth. 3 Biotech 2018; 8:389. [PMID: 30175026 PMCID: PMC6111035 DOI: 10.1007/s13205-018-1403-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022] Open
Abstract
Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
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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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13
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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Vandecraen J, Monsieurs P, Mergeay M, Leys N, Aertsen A, Van Houdt R. Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans. Front Microbiol 2016; 7:359. [PMID: 27047473 PMCID: PMC4803752 DOI: 10.3389/fmicb.2016.00359] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on medium supplemented with a toxic zinc concentration, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive. Interestingly, deletion of cnrH, and consequently the CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.
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Affiliation(s)
- Joachim Vandecraen
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN)Mol, Belgium; Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Max Mergeay
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven Leuven, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
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Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants. Appl Microbiol Biotechnol 2016; 100:2967-84. [PMID: 26860944 DOI: 10.1007/s00253-016-7364-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
Abstract
Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.
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16
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Maillard AP, Künnemann S, Große C, Volbeda A, Schleuder G, Petit-Härtlein I, de Rosny E, Nies DH, Covès J. Response of CnrX from Cupriavidus metallidurans CH34 to nickel binding. Metallomics 2016; 7:622-31. [PMID: 25628016 DOI: 10.1039/c4mt00293h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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.
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Affiliation(s)
- Antoine P Maillard
- Institut de Biologie Structurale, UMR 5075 CNRS-CEA-Université Grenoble-Alpes, 71, Avenue des Martyrs, 38044 Grenoble Cedex 9, France
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Durand MJ, Hua A, Jouanneau S, Cregut M, Thouand G. Detection of Metal and Organometallic Compounds with Bioluminescent Bacterial Bioassays. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015:77-99. [PMID: 26475470 DOI: 10.1007/10_2015_332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Chemical detection of metal and organometallic compounds is very specific and sensitive, but these techniques are time consuming and expensive. Although these techniques provide information about the concentrations of compounds, they fail to inform us about the toxicity of a sample. Because the toxic effects of metals and organometallic compounds are influenced by a multitude of environmental factors, such as pH, the presence of chelating agents, speciation, and organic matter, bioassays have been developed for ecotoxicological studies. Among these bioassays, recombinant luminescent bacteria have been developed over the past 20 years, and many of them are specific for the detection of metals and metalloids. These bioassays are simple to use, are inexpensive, and provide information on the bioavailable fraction of metals and organometals. Thus, they are an essential complementary tool for providing information beyond chemical analysis. In this chapter, we propose to investigate the detection of metals and organometallic compounds with bioluminescent bacterial bioassays and the applications of these bioassays to environmental samples. Graphical Abstract.
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Affiliation(s)
- M J Durand
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France.
| | - A Hua
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
| | - S Jouanneau
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
| | - M Cregut
- Capacités SAS, 26 Bd Vincent Gâche, 44200, Nantes, France
| | - G Thouand
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
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Monsieurs P, Hobman J, Vandenbussche G, Mergeay M, Van Houdt R. Response of Cupriavidus metallidurans CH34 to Metals. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20594-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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19
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Herzberg M, Schüttau M, Reimers M, Große C, Hans-Günther-Schlegel HGS, Nies DH. Synthesis of nickel–iron hydrogenase in Cupriavidus metallidurans is controlled by metal-dependent silencing and un-silencing of genomic islands. Metallomics 2015; 7:632-49. [DOI: 10.1039/c4mt00297k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Trepreau J, Grosse C, Mouesca JM, Sarret G, Girard E, Petit-Haertlein I, Kuennemann S, Desbourdes C, de Rosny E, Maillard AP, Nies DH, Covès J. Metal sensing and signal transduction by CnrX from Cupriavidus metallidurans CH34: role of the only methionine assessed by a functional, spectroscopic, and theoretical study. Metallomics 2014; 6:263-73. [PMID: 24154823 DOI: 10.1039/c3mt00248a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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.
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Affiliation(s)
- Juliette Trepreau
- Institut de Biologie Structurale, UMR 5075 CNRS-CEA-UJF-Grenoble-1, 6 Rue Jules Horowitz, 38042 Grenoble, France.
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21
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Ziani W, Maillard AP, Petit-Härtlein I, Garnier N, Crouzy S, Girard E, Covès J. The X-ray structure of NccX from Cupriavidus metallidurans 31A illustrates potential dangers of detergent solubilization when generating and interpreting crystal structures of membrane proteins. J Biol Chem 2014; 289:31160-72. [PMID: 25258316 DOI: 10.1074/jbc.m114.586537] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The x-ray structure of NccX, a type II transmembrane metal sensor, from Cupriavidus metallidurans 31A has been determined at a resolution of 3.12 Å. This was achieved after solubilization by dodecylphosphocholine and purification in the presence of the detergent. NccX crystal structure did not match the model based on the extensively characterized periplasmic domain of its closest homologue CnrX. Instead, the periplasmic domains of NccX appeared collapsed against the hydrophobic transmembrane segments, leading to an aberrant topology incompatible with membrane insertion. This was explained by a detergent-induced redistribution of the hydrophobic interactions among the transmembrane helices and a pair of hydrophobic patches keeping the periplasmic domains together in the native dimer. Molecular dynamics simulations performed with the full-length protein or with the transmembrane segments were used along with in vivo homodimerization assays (TOXCAT) to evaluate the determinants of the interactions between NccX protomers. Taken as a whole, computational and experimental results are in agreement with the structural model of CnrX where a cradle-shaped periplasmic metal sensor domain is anchored into the inner membrane by two N-terminal helices. In addition, they show that the main determinant of NccX dimerization is the periplasmic soluble domain and that the interaction between transmembrane segments is highly dynamic. The present work introduces a new crystal structure for a transmembrane protein and, in line with previous studies, substantiates the use of complementary theoretical and in vivo investigations to rationalize a three-dimensional structure obtained in non-native conditions.
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Affiliation(s)
- Widade Ziani
- From the Institut de Biologie Structurale, UMR 5075 CNRS-Commissariat à l'Energie Atomique (CEA)-Université Grenoble-Alpes, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Antoine P Maillard
- From the Institut de Biologie Structurale, UMR 5075 CNRS-Commissariat à l'Energie Atomique (CEA)-Université Grenoble-Alpes, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Isabelle Petit-Härtlein
- From the Institut de Biologie Structurale, UMR 5075 CNRS-Commissariat à l'Energie Atomique (CEA)-Université Grenoble-Alpes, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire, CNRS UPR4301 affiliated to the University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France, and
| | - Serge Crouzy
- Laboratoire de Chimie et Biologie des Métaux, UMR 5249, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Eric Girard
- From the Institut de Biologie Structurale, UMR 5075 CNRS-Commissariat à l'Energie Atomique (CEA)-Université Grenoble-Alpes, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France
| | - Jacques Covès
- From the Institut de Biologie Structurale, UMR 5075 CNRS-Commissariat à l'Energie Atomique (CEA)-Université Grenoble-Alpes, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France,
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22
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Chivers PT. Cobalt and Nickel. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cobalt and nickel play key roles in biological systems as cofactors in a small number of important enzymes. The majority of these are found in microbes. Evidence for direct roles for Ni(II) and Co(II) enzymes in higher organisms is limited, with the exception of the well-known requirement for the cobalt-containing vitamin B12 cofactor and the Ni-dependent urease in plants. Nonetheless, nickel in particular plays a key role in human health because of its essential role in microbes that inhabit various growth niches within the body. These roles can be beneficial, as can be seen with the anaerobic production and consumption of H2 in the digestive tract by bacteria and archaea that results in increased yields of short-chain fatty acids. In other cases, nickel has an established role in the establishment of pathogenic infection (Helicobacter pylori urease and colonization of the stomach). The synthesis of Co- and Ni-containing enzymes requires metal import from the extracellular milieu followed by the targeting of these metals to the appropriate protein and enzymes involved in metallocluster or cofactor biosynthesis. These metals are toxic in excess so their levels must be regulated carefully. This complex pathway of metalloenzyme synthesis and intracellular homeostasis requires proteins that can specifically recognize these metals in a hierarchical manner. This chapter focuses on quantitative and structural details of the cobalt and nickel binding sites in transport, trafficking and regulatory proteins involved in cobalt and nickel metabolism in microbes.
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Affiliation(s)
- Peter T. Chivers
- Department of Chemistry, School of Biological and Biomedical Sciences, and Biophysical Sciences Institute, Durham University Durham UK
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23
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Hynninen A, Virta M. Whole-cell bioreporters for the detection of bioavailable metals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 118:31-63. [PMID: 19543702 DOI: 10.1007/10_2009_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Whole-cell bioreporters are living microorganisms that produce a specific, quantifiable output in response to target chemicals. Typically, whole-cell bioreporters combine a sensor element for the substance of interest and a reporter element coding for an easily detectable protein. The sensor element is responsible for recognizing the presence of an analyte. In the case of metal bioreporters, the sensor element consists of a DNA promoter region for a metal-binding transcription factor fused to a promoterless reporter gene that encodes a signal-producing protein. In this review, we provide an overview of specific whole-cell bioreporters for heavy metals. Because the sensing of metals by bioreporter microorganisms is usually based on heavy metal resistance/homeostasis mechanisms, the basis of these mechanisms will also be discussed. The goal here is not to present a comprehensive summary of individual metal-specific bioreporters that have been constructed, but rather to express views on the theory and applications of metal-specific bioreporters and identify some directions for future research and development.
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Affiliation(s)
- Anu Hynninen
- Department of Applied Chemistry and Microbiology, University of Helsinki, 56, 00014, Helsinki, Finland
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24
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San Martin-Uriz P, Mirete S, Alcolea PJ, Gomez MJ, Amils R, Gonzalez-Pastor JE. Nickel-resistance determinants in Acidiphilium sp. PM identified by genome-wide functional screening. PLoS One 2014; 9:e95041. [PMID: 24740277 PMCID: PMC3989265 DOI: 10.1371/journal.pone.0095041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/23/2014] [Indexed: 11/18/2022] Open
Abstract
Acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. Indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. Acidiphilium sp. PM is an environmental isolate from Rio Tinto, an acidic, metal-laden river located in southwestern Spain. The characterization of its metal resistance revealed a remarkable ability to tolerate high Ni concentrations. Here we report the screening of a genomic library of Acidiphilium sp. PM to identify genes involved in Ni resistance. This approach revealed seven different genes conferring Ni resistance to E. coli, two of which form an operon encoding the ATP-dependent protease HslVU (ClpQY). This protease was found to enhance resistance to both Ni and Co in E. coli, a function not previously reported. Other Ni-resistance determinants include genes involved in lipopolysaccharide biosynthesis and the synthesis of branched amino acids. The diversity of molecular functions of the genes recovered in the screening suggests that Ni resistance in Acidiphilium sp. PM probably relies on different molecular mechanisms.
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Affiliation(s)
- Patxi San Martin-Uriz
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Salvador Mirete
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Pedro J. Alcolea
- Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel J. Gomez
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose E. Gonzalez-Pastor
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
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25
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Maillard AP, Girard E, Ziani W, Petit-Härtlein I, Kahn R, Covès J. The crystal structure of the anti-σ factor CnrY in complex with the σ factor CnrH shows a new structural class of anti-σ factors targeting extracytoplasmic function σ factors. J Mol Biol 2014; 426:2313-27. [PMID: 24727125 DOI: 10.1016/j.jmb.2014.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/19/2014] [Accepted: 04/03/2014] [Indexed: 11/25/2022]
Abstract
Gene expression in bacteria is regulated at the level of transcription initiation, a process driven by σ factors. The regulation of σ factor activity proceeds from the regulation of their cytoplasmic availability, which relies on specific inhibitory proteins called anti-σ factors. With anti-σ factors regulating their availability according to diverse cues, extracytoplasmic function σ factors (σ(ECF)) form a major signal transduction system in bacteria. Here, structure:function relationships have been characterized in an emerging class of minimal-size transmembrane anti-σ factors, using CnrY from Cupriavidus metallidurans CH34 as a model. This study reports the 1.75-Å-resolution structure of CnrY cytosolic domain in complex with CnrH, its cognate σ(ECF), and identifies a small hydrophobic knob in CnrY as the major determinant of this interaction in vivo. Unsuspected structural similarity with the molecular switch regulating the general stress response in α-proteobacteria unravels a new class of anti-σ factors targeting σ(ECF). Members of this class carry out their function via a 30-residue stretch that displays helical propensity but no canonical structure on its own.
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Affiliation(s)
- Antoine P Maillard
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France.
| | - Eric Girard
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Widade Ziani
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Isabelle Petit-Härtlein
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Richard Kahn
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Jacques Covès
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, and Institut de Biologie Structurale, F-38000 Grenoble, France
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Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter. Proc Natl Acad Sci U S A 2013; 110:18484-9. [PMID: 24173033 DOI: 10.1073/pnas.1318705110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Efflux pumps belonging to the ubiquitous resistance-nodulation-cell division (RND) superfamily transport substrates out of cells by coupling proton conduction across the membrane to a conformationally driven pumping cycle. The heavy metal-resistant bacteria Cupriavidus metallidurans CH34 relies notably on as many as 12 heavy metal efflux pumps of the RND superfamily. Here we show that C. metallidurans CH34 ZneA is a proton driven efflux pump specific for Zn(II), and that transport of substrates through the transmembrane domain may be electrogenic. We report two X-ray crystal structures of ZneA in intermediate transport conformations, at 3.0 and 3.7 Å resolution. The trimeric ZneA structures capture protomer conformations that differ in the spatial arrangement and Zn(II) occupancies at a proximal and a distal substrate binding site. Structural comparison shows that transport of substrates through a tunnel that links the two binding sites, toward an exit portal, is mediated by the conformation of a short 14-aa loop. Taken together, the ZneA structures presented here provide mechanistic insights into the conformational changes required for substrate efflux by RND superfamily transporters.
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27
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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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The evolution of the bacterial luciferase gene cassette (lux) as a real-time bioreporter. SENSORS 2012; 12:732-52. [PMID: 22368493 PMCID: PMC3279237 DOI: 10.3390/s120100732] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 12/30/2011] [Accepted: 01/09/2012] [Indexed: 01/23/2023]
Abstract
The bacterial luciferase gene cassette (lux) is unique among bioluminescent bioreporter systems due to its ability to synthesize and/or scavenge all of the substrate compounds required for its production of light. As a result, the lux system has the unique ability to autonomously produce a luminescent signal, either continuously or in response to the presence of a specific trigger, across a wide array of organismal hosts. While originally employed extensively as a bacterial bioreporter system for the detection of specific chemical signals in environmental samples, the use of lux as a bioreporter technology has continuously expanded over the last 30 years to include expression in eukaryotic cells such as Saccharomyces cerevisiae and even human cell lines as well. Under these conditions, the lux system has been developed for use as a biomedical detection tool for toxicity screening and visualization of tumors in small animal models. As the technologies for lux signal detection continue to improve, it is poised to become one of the first fully implantable detection systems for intra-organismal optical detection through direct marriage to an implantable photon-detecting digital chip. This review presents the basic biochemical background that allows the lux system to continuously autobioluminesce and highlights the important milestones in the use of lux-based bioreporters as they have evolved from chemical detection platforms in prokaryotic bacteria to rodent-based tumorigenesis study targets. In addition, the future of lux imaging using integrated circuit microluminometry to image directly within a living host in real-time will be introduced and its role in the development of dose/response therapeutic systems will be highlighted.
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Trepreau J, de Rosny E, Duboc C, Sarret G, Petit-Hartlein I, Maillard AP, Imberty A, Proux O, Covès J. Spectroscopic characterization of the metal-binding sites in the periplasmic metal-sensor domain of CnrX from Cupriavidus metallidurans CH34. Biochemistry 2011; 50:9036-45. [PMID: 21942751 DOI: 10.1021/bi201031q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CnrX, the dimeric metal sensor of the three-protein transmembrane signal transduction complex CnrYXH of Cupriavidus metallidurans CH34, contains one metal-binding site per monomer. Both Ni and Co elicit a biological response and bind the protein in a 3N2O1S coordination sphere with a nearly identical octahedral geometry as shown by the X-ray structure of CnrXs, the soluble domain of CnrX. However, in solution CnrXs is titrated by 4 Co-equiv and exhibits an unexpected intense band at 384 nm that was detected neither by single-crystal spectroscopy nor under anaerobiosis. The data from a combination of spectroscopic techniques (spectrophotometry, electron paramagnetic resonance, X-ray absorption spectroscopy) showed that two sites correspond to those identified by crystallography. The two extra binding sites accommodate Co(II) in an octahedral geometry in the absence of oxygen and are occupied in air by a mixture of low-spin Co(II) as well as EPR-silent Co(III). These extra sites, located at the N-terminus of the protein, are believed to participate to the formation of peroxo-bridged dimers. Accordingly, we hypothesize that the intense band at 384 nm relies on the formation of a binuclear μ-peroxo Co(III) complex. These metal binding sites are not physiologically relevant since they are not detected in full-length NccX, the closest homologue of CnrX. X-ray absorption spectroscopy demonstrates that NccX stabilizes Co(II) in two-binding sites similar to those characterized by crystallography in its soluble counterpart. Nevertheless, the original spectroscopic properties of the extra Co-binding sites are of interest because they are susceptible to be detected in other Co-bound proteins.
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Affiliation(s)
- Juliette Trepreau
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075, CNRS-CEA-UJF-Grenoble-1, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
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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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Thede GL, Arthur DC, Edwards RA, Buelow DR, Wong JL, Raivio TL, Glover JNM. Structure of the periplasmic stress response protein CpxP. J Bacteriol 2011; 193:2149-57. [PMID: 21317318 PMCID: PMC3133086 DOI: 10.1128/jb.01296-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 02/03/2011] [Indexed: 01/10/2023] Open
Abstract
CpxP is a novel bacterial periplasmic protein with no homologues of known function. In gram-negative enteric bacteria, CpxP is thought to interact with the two-component sensor kinase, CpxA, to inhibit induction of the Cpx envelope stress response in the absence of protein misfolding. CpxP has also been shown to facilitate DegP-mediated proteolysis of misfolded proteins. Six mutations that negate the ability of CpxP to function as a signaling protein are localized in or near two conserved LTXXQ motifs that define a class of proteins with similarity to CpxP, Pfam PF07813. To gain insight into how these mutations might affect CpxP signaling and/or proteolytic adaptor functions, the crystal structure of CpxP from Escherichia coli was determined to 2.85-Å resolution. The structure revealed an antiparallel dimer of intertwined α-helices with a highly basic concave surface. Each protomer consists of a long, hooked and bent hairpin fold, with the conserved LTXXQ motifs forming two diverging turns at one end. Biochemical studies demonstrated that CpxP maintains a dimeric state but may undergo a slight structural adjustment in response to the inducing cue, alkaline pH. Three of the six previously characterized cpxP loss-of-function mutations, M59T, Q55P, and Q128H, likely result from a destabilization of the protein fold, whereas the R60Q, D61E, and D61V mutations may alter intermolecular interactions.
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Affiliation(s)
- Gina L. Thede
- Department of Biochemistry, School of Molecular and Systems Medicine
| | - David C. Arthur
- Department of Biochemistry, School of Molecular and Systems Medicine
| | - Ross A. Edwards
- Department of Biochemistry, School of Molecular and Systems Medicine
| | - Daelynn R. Buelow
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Julia L. Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tracy L. Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - J. N. Mark Glover
- Department of Biochemistry, School of Molecular and Systems Medicine
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Insertion sequence elements in Cupriavidus metallidurans CH34: Distribution and role in adaptation. Plasmid 2011; 65:193-203. [DOI: 10.1016/j.plasmid.2010.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/20/2010] [Indexed: 11/20/2022]
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34
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Trepreau J, Girard E, Maillard AP, de Rosny E, Petit-Haertlein I, Kahn R, Covès J. Structural basis for metal sensing by CnrX. J Mol Biol 2011; 408:766-79. [PMID: 21414325 DOI: 10.1016/j.jmb.2011.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/03/2011] [Accepted: 03/07/2011] [Indexed: 11/19/2022]
Abstract
CnrX is the metal sensor and signal modulator of the three-protein transmembrane signal transduction complex CnrYXH of Cupriavidus metallidurans CH34 that is involved in the setup of cobalt and nickel resistance. We have determined the atomic structure of the soluble domain of CnrX in its Ni-bound, Co-bound, or Zn-bound form. Ni and Co ions elicit a biological response, while the Zn-bound form is inactive. The structures presented here reveal the topology of intraprotomer and interprotomer interactions and the ability of metal-binding sites to fine-tune the packing of CnrX dimer as a function of the bound metal. These data suggest an allosteric mechanism to explain how the complex is switched on and how the signal is modulated by Ni or Co binding. These results provide clues to propose a model for signal propagation through the membrane in the complex.
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Affiliation(s)
- Juliette Trepreau
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CNRS-CEA-UJF Grenoble 1, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
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35
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He Z, Van Nostrand JD, Deng Y, Zhou J. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11783-011-0301-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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36
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Olsson-Francis K, VAN Houdt R, Mergeay M, Leys N, Cockell CS. Microarray analysis of a microbe-mineral interaction. GEOBIOLOGY 2010; 8:446-456. [PMID: 20718869 DOI: 10.1111/j.1472-4669.2010.00253.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and long-term climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Micro-organisms are known to play a role in rock weathering yet the genomics and genetics of biological rock weathering are unknown. We apply DNA microarray technology to determine putative genes involved in weathering using the heavy metal-resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium does not depend on siderophores. Instead, the up-regulation of porins and transporters which are employed concomitantly with genes associated with biofilm formation suggests that novel passive and active iron uptake systems are involved. We hypothesize that these mechanisms induce rock weathering by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal-resistant genes. Some of the earliest environments on the Earth were volcanic. Therefore, these results not only elucidate the mechanisms by which micro-organisms might have sequestered nutrients on the early Earth but also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.
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38
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Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes. Proc Natl Acad Sci U S A 2010; 107:13461-6. [PMID: 20628010 DOI: 10.1073/pnas.1008285107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lantibiotics are ribosomally synthesized, posttranslationally modified peptide antibiotics. The biosynthetic gene cluster for microbisporicin, a potent lantibiotic produced by the actinomycete Microbispora corallina containing chlorinated tryptophan and dihydroxyproline residues, was identified by genome scanning and isolated from an M. corallina cosmid library. Heterologous expression in Nonomuraea sp. ATCC 39727 confirmed that all of the genes required for microbisporicin biosynthesis were present in the cluster. Deletion, in M. corallina, of the gene (mibA) predicted to encode the prepropeptide abolished microbisporicin production. Further deletion analysis revealed insights into the biosynthesis of this unusual and potentially clinically useful lantibiotic, shedding light on mechanisms of regulation and self-resistance. In particular, we report an example of the involvement of a tryptophan halogenase in the modification of a ribosomally synthesized peptide and the pathway-specific regulation of an antibiotic biosynthetic gene cluster by an extracytoplasmic function sigma factor-anti-sigma factor complex.
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Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 2010; 5:e10433. [PMID: 20463976 PMCID: PMC2864759 DOI: 10.1371/journal.pone.0010433] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 03/29/2010] [Indexed: 11/21/2022] Open
Abstract
Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.
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Affiliation(s)
- Paul J Janssen
- Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium.
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Thakur KG, Praveena T, Gopal B. Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA. J Mol Biol 2010; 397:1199-208. [PMID: 20184899 PMCID: PMC2877774 DOI: 10.1016/j.jmb.2010.02.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 02/12/2010] [Accepted: 02/16/2010] [Indexed: 12/03/2022]
Abstract
An effective transcriptional response to redox stimuli is of particular importance for Mycobacterium tuberculosis, as it adapts to the environment of host alveoli and macrophages. The M. tuberculosis sigma factor sigma(L) regulates the expression of genes involved in cell-wall and polyketide syntheses. sigma(L) interacts with the cytosolic anti-sigma domain of a membrane-associated protein, RslA. Here we demonstrate that RslA binds Zn(2+) and can sequester sigma(L) in a reducing environment. In response to an oxidative stimulus, proximal cysteines in the CXXC motif of RslA form a disulfide bond, releasing bound Zn(2+). This results in a substantial rearrangement of the sigma(L)/RslA complex, leading to an 8-fold decrease in the affinity of RslA for sigma(L). The crystal structure of the -35-element recognition domain of sigma(L), sigma(4)(L), bound to RslA reveals that RslA inactivates sigma(L) by sterically occluding promoter DNA and RNA polymerase binding sites. The crystal structure further reveals that the cysteine residues that coordinate Zn(2+) in RslA are solvent exposed in the complex, thus providing a structural basis for the redox sensitivity of RslA. The biophysical parameters of sigma(L)/RslA interactions provide a template for understanding how variations in the rate of Zn(2+) release and associated conformational changes could regulate the activity of a Zn(2+)-associated anti-sigma factor.
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Key Words
- rnap, rna polymerase
- asd, anti-σ domain
- ecf, extracytoplasmic function
- mtb, mycobacterium tuberculosis
- ec, escherichia coli
- sco, streptomyces coelicolor
- zas, zinc-associated anti-σ
- rsp, rhodobacter sphaeroides
- pdb, protein data bank
- par, 4-(2-pyridylazo)-resorcinol
- spr, surface plasmon resonance
- lc-esi-ms, liquid chromatography–electrospray ionization–mass spectrometry
- maldi-tof, matrix-assisted laser desorption/ionization time-of-flight
- wt, wild type
- dls, dynamic light scattering
- tpen, n,n,n′,n′-tetrakis(2-pyridylmethyl) ethylenediamine
- extracytoplasmic function σ factor
- zinc binding
- redox sensitivity
- anti-σ factor
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Affiliation(s)
| | | | - B. Gopal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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41
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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42
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The response of Cupriavidus metallidurans CH34 to spaceflight in the international space station. Antonie van Leeuwenhoek 2009; 96:227-45. [DOI: 10.1007/s10482-009-9360-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 06/17/2009] [Indexed: 01/30/2023]
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43
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Van Houdt R, Monchy S, Leys N, Mergeay M. New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria. Antonie van Leeuwenhoek 2009; 96:205-26. [DOI: 10.1007/s10482-009-9345-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 03/18/2009] [Indexed: 10/20/2022]
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44
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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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45
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Pompidor G, Maillard AP, Girard E, Gambarelli S, Kahn R, Covès J. X-ray structure of the metal-sensor CnrX in both the apo- and copper-bound forms. FEBS Lett 2008; 582:3954-8. [PMID: 18992246 DOI: 10.1016/j.febslet.2008.10.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 10/17/2008] [Accepted: 10/24/2008] [Indexed: 10/21/2022]
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46
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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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47
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Biostructural analysis of the metal-sensor domain of CnrX from Cupriavidus metallidurans CH34. Antonie van Leeuwenhoek 2008; 96:141-8. [PMID: 18825506 DOI: 10.1007/s10482-008-9283-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 10/21/2022]
Abstract
In Cupriavidus metallidurans CH34, the proteins CnrX, CnrY, and CnrH regulate the expression of the cnrCBA operon that codes for a cation-efflux pump involved in cobalt and nickel resistance. The periplasmic part of CnrX can be defined as the metal sensor in the signal transduction complex composed of the membrane-bound anti-sigma factor CnrY and the extra-cytoplasmic function sigma factor CnrH. A soluble form of CnrX was overproduced and purified. This protein behaves as a dimer in solution as judged from gel filtration, sedimentation velocity experiments, and NMR. Native crystals diffracting to 2.3 A using synchrotron radiation were obtained using the hanging-drop vapor-diffusion method. They belong to the primitive monoclinic space group P2(1), with unit cell parameters a = 31.87, b = 74.80, c = 93.67 A, beta = 90.107 degrees. NMR data and secondary structure prediction suggest that this protein is essentially formed by helices.
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48
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Grosse C, Friedrich S, Nies DH. Contribution of extracytoplasmic function sigma factors to transition metal homeostasis in Cupriavidus metallidurans strain CH34. J Mol Microbiol Biotechnol 2007; 12:227-40. [PMID: 17587871 DOI: 10.1159/000099644] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Cornelia Grosse
- Institut für Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Deutschland
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49
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Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, Mergeay M. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 2007; 189:7417-25. [PMID: 17675385 PMCID: PMC2168447 DOI: 10.1128/jb.00375-07] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We fully annotated two large plasmids, pMOL28 (164 open reading frames [ORFs]; 171,459 bp) and pMOL30 (247 ORFs; 233,720 bp), in the genome of Cupriavidus metallidurans CH34. pMOL28 contains a backbone of maintenance and transfer genes resembling those found in plasmid pSym of C. taiwanensis and plasmid pHG1 of C. eutrophus, suggesting that they belong to a new class of plasmids. Genes involved in resistance to the heavy metals Co(II), Cr(VI), Hg(II), and Ni(II) are concentrated in a 34-kb region on pMOL28, and genes involved in resistance to Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Pb(II), and Zn(II) occur in a 132-kb region on pMOL30. We identified three putative genomic islands containing metal resistance operons flanked by mobile genetic elements, one on pMOL28 and two on pMOL30. Transcriptomic analysis using quantitative PCR and microarrays revealed metal-mediated up-regulation of 83 genes on pMOL28 and 143 genes on pMOL30 that coded for all known heavy metal resistance proteins, some new heavy metal resistance proteins (czcJ, mmrQ, and pbrU), membrane proteins, truncated transposases, conjugative transfer proteins, and many unknown proteins. Five genes on each plasmid were down-regulated; for one of them, chrI localized on pMOL28, the down-regulation occurred in the presence of five cations. We observed multiple cross-responses (induction of specific metal resistance by other metals), suggesting that the cellular defense of C. metallidurans against heavy metal stress involves various regulons and probably has multiple stages, including a more general response and a more metal-specific response.
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Affiliation(s)
- Sébastien Monchy
- Molecular & Cellular Biology, Institute for Health, Environment & Safety, Center of Studies for Nuclear Energy, SCK CEN, B-2400, Mol, Belgium
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50
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Bhadra B, Nanda AK, Chakraborty R. Fluctuation in recoverable nickel and zinc resistant copiotrophic bacteria explained by the varying zinc ion content of Torsa River in different months. Arch Microbiol 2007; 188:215-24. [PMID: 17464499 DOI: 10.1007/s00203-007-0236-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2006] [Revised: 02/28/2007] [Accepted: 03/19/2007] [Indexed: 10/23/2022]
Abstract
Heavy metal content analysis of River Torsa in India did not indicate any alarming level of toxicity for human consumption but revealed variation at the ppb level in different months. The variation in recoverable nickel and zinc resistant copiotrophic (or eutrophic) bacterial counts was explained by the variation of the zinc content (34.0-691.3 ppb) of the river water in different sampling months. Growth studies conducted with some purified nickel and/or zinc resistant strains revealed that pre-exposure of the cells to ppb levels of Zn(2+), comparable to the indigenous zinc ion concentration of the river, could induce the nickel or zinc resistance. A minimum concentration of 5-10 microM Zn(2+ )(325-650 ppb) was found effective in inducing the Nickel resistance of the isolates. Zinc resistance of the isolates was tested by pre-exposing the cells to 4 microM Zn(2+ )(260 ppb). The lag phase was reduced by 6-8 h in all the cases. Biochemical characteristics and phylogenetic analysis based on 16S rDNA sequence indicated that some of the Torsa River isolates, having inducible nickel and zinc resistance, are members of the genus Pseudomonas, Acinetobacter, Bacillus, Enterobacter, Serratia and Moraxella.
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Affiliation(s)
- Bhaskar Bhadra
- Department of Biotechnology, North Bengal University, Siliguri 734430, West Bengal, India
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