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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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Yang J, Gao M, Wang J, He C, Wang X, Liu L. Structural basis of copper binding by a dimeric periplasmic protein forming a six-helical bundle. J Inorg Biochem 2022; 229:111728. [DOI: 10.1016/j.jinorgbio.2022.111728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
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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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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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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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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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Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ. Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR. Inorg Chem 2017; 56:6459-6476. [PMID: 28517938 DOI: 10.1021/acs.inorgchem.7b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli RcnR (resistance to cobalt and nickel regulator, EcRcnR) is a metal-responsive repressor of the genes encoding the Ni(II) and Co(II) exporter proteins RcnAB by binding to PRcnAB. The DNA binding affinity is weakened when the cognate ions Ni(II) and Co(II) bind to EcRcnR in a six-coordinate site that features a (N/O)5S ligand donor-atom set in distinct sites: while both metal ions are bound by the N terminus, Cys35, and His64, Co(II) is additionally bound by His3. On the other hand, the noncognate Zn(II) and Cu(I) ions feature a lower coordination number, have a solvent-accessible binding site, and coordinate protein ligands that do not include the N-terminal amine. A molecular model of apo-EcRcnR suggested potential roles for Glu34 and Glu63 in binding Ni(II) and Co(II) to EcRcnR. The roles of Glu34 and Glu63 in metal binding, metal selectivity, and function were therefore investigated using a structure/function approach. X-ray absorption spectroscopy was used to assess the structural changes in the Ni(II), Co(II), and Zn(II) binding sites of Glu → Ala and Glu → Cys variants at both positions. The effect of these structural alterations on the regulation of PrcnA by EcRcnR in response to metal binding was explored using LacZ reporter assays. These combined studies indicate that while Glu63 is a ligand for both metal ions, Glu34 is a ligand for Co(II) but possibly not for Ni(II). The Glu34 variants affect the structure of the cognate metal sites, but they have no effect on the transcriptional response. In contrast, the Glu63 variants affect both the structure and transcriptional response, although they do not completely abolish the function of EcRcnR. The structure of the Zn(II) site is not significantly perturbed by any of the glutamic acid variations. The spectroscopic and functional data obtained on the mutants were used to calculate models of the metal-site structures of EcRcnR bound to Ni(II), Co(II), and Zn(II). The results are interpreted in terms of a switch mechanism, in which a subset of the metal-binding ligands is responsible for the allosteric response required for DNA release.
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Affiliation(s)
- Carolyn E Carr
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University , Durham DH1 3LE, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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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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