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Obayori OS, Salam LB, Ashade AO, Oseni TD, Kalu MD, Mustapha FM. An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria. World J Microbiol Biotechnol 2024; 40:327. [PMID: 39299940 DOI: 10.1007/s11274-024-04136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.
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Affiliation(s)
| | - Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Ondo State, Nigeria
| | - Ahmeed Olalekan Ashade
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | | | - Mandy Divine Kalu
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
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Xu J, Ma S, Huang Y, Zhang Q, Huang L, Xu H, Suleiman IM, Li P, Wang Z, Xie J. Mycobacterium marinum MMAR_0267-regulated copper utilization facilitates bacterial escape from phagolysosome. Commun Biol 2024; 7:1180. [PMID: 39300168 DOI: 10.1038/s42003-024-06860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024] Open
Abstract
The host limits Mycobacterium tuberculosis (Mtb) by enriching copper in high concentrations. This research investigates how Mtb escapes copper stress. The membrane protein encoded by Mtb Rv0102, when its homolog in M. smegmatis (MSMEG_4702) was knocked out, resulted in a fourfold decrease in intracellular copper levels and enhanced tolerance to elevated extracellular copper concentrations. Similarly, knockout mutants of its homolog in M. marinum (MMAR_0267) showed increased virulence in zebrafish and higher bacterial load within macrophages. In THP-1 cells infected with MMAR_0267 deletion mutants, the intracellular survival of these mutants increased, along with reduced THP-1 cell apoptosis. Deficiency in copper down-regulated the transcriptional level of the virulence factor CFP-10 in M. marinum, suppressed cytosolic signaling via the macrophage STING pathway, leading to decreased production of IFN-β and reduced cell apoptosis. In conclusion, these findings highlight the significant impact of copper on the survival and reproduction of mycobacteria, underscoring the importance of studying mycobacterial adaptation mechanisms in copper-rich environments.
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Affiliation(s)
- Junqi Xu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shaying Ma
- Chongqing Public Health Medical Center, Chongqing, China
| | - Yu Huang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Qiao Zhang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Lingxi Huang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Hongxiang Xu
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Ismail Mohamed Suleiman
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Peibo Li
- Chongqing Public Health Medical Center, Chongqing, China.
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Public Health Medical Center, Chongqing, China.
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Cuaxinque-Flores G, Talavera-Mendoza O, Aguirre-Noyola JL, Hernández-Flores G, Martínez-Miranda V, Rosas-Guerrero V, Martínez-Romero E. Molecular and geochemical basis of microbially induced carbonate precipitation for treating acid mine drainage: The case of a novel Sporosarcina genomospecies from mine tailings. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135005. [PMID: 38996684 DOI: 10.1016/j.jhazmat.2024.135005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/12/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Microbially induced carbonate precipitation (MICP) immobilizes toxic metals and reduces their bioavailability in aqueous systems. However, its application in the treatment of acid mine drainage (AMD) is poorly understood. In this study, the genomes of Sporosarcina sp. UB5 and UB10 were sequenced. Urease, carbonic anhydrases, and metal resistance genes were identified and enzymatic assays were performed for their validation. The geochemical mechanism of precipitation in AMD was elucidated through geo-mineralogical analysis. Sporosarcina sp. UB5 was shown to be a new genomospecies, with an average nucleotide identity < 95 % (ANI) and DNA-DNA hybridization < 70 % (DDH) whereas UB10 is close to S. pasteurii. UB5 contained two urease operons, whereas only one was identified in UB10. The ureolytic activities of UB5 and UB10 were 122.67 ± 15.74 and 131.70 ± 14.35 mM NH4+ min-1, respectively. Both strains feature several carbonic anhydrases of the α, β, or γ families, which catalyzed the precipitation of CaCO3. Only Sporosarcina sp. UB5 was able to immobilize metals and neutralize AMD. Geo-mineralogical analyses revealed that UB5 directly immobilized Fe (1-23 %), Mn (0.65-1.33 %) and Zn (0.8-3 %) in AMD via MICP and indirectly through adsorption to calcite and binding to bacterial cell walls. The MICP-treated AMD exhibited high removal rates (>67 %) for Ag, Al, As, Ca, Cd, Co, Cu, Fe, Mn, Pb, and Zn, and a removal rate of 15 % for Mg. This study provides new insights into the MICP process and its applications to AMD treatment using autochthonous strains.
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Affiliation(s)
- Gustavo Cuaxinque-Flores
- Doctorado en Recursos Naturales y Ecologia, Facultad de Ecología Marina, Universidad Autónoma de Guerrero, Gran vía tropical 20, Fraccionamiento Las playas, Acapulco de Juárez, Guerrero, Mexico
| | - Oscar Talavera-Mendoza
- Doctorado en Recursos Naturales y Ecologia, Facultad de Ecología Marina, Universidad Autónoma de Guerrero, Gran vía tropical 20, Fraccionamiento Las playas, Acapulco de Juárez, Guerrero, Mexico; Escuela Superior de Ciencias de la Tierra, Universidad Autónoma de Guerrero, Ex-hacienda, San Juan Bautista s/n, CP 40323 Taxco el Viejo, Guerrero, Mexico.
| | - José Luis Aguirre-Noyola
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 47600, Jalisco, Mexico
| | - Giovanni Hernández-Flores
- CONAHCyT-Escuela Superior de Ciencias de la Tierra, Universidad Autónoma de Guerrero, Ex Hacienda San Juan Bautista s/n, Taxco de Alarcón 40323, Mexico
| | - Verónica Martínez-Miranda
- Instituto Interamericano de Tecnología y Ciencias del Agua (IITCA), Universidad Autónoma del Estado de México, Unidad San Cayetano, Km. 14.5, Carretera, Toluca-Atlacomulco, C.P. 50200 Toluca, Estado de México, Mexico
| | - Víctor Rosas-Guerrero
- Escuela Superior en Desarrollo Sustentable, Universidad Autónoma de Guerrero, Tecpan de Galeana 40900, Mexico
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, UNAM, Av. Universidad s/n, Chamilpa, 62210 Cuernavaca, Morelos, Mexico.
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Munzone A, Pujol M, Tamhankar A, Joseph C, Mazurenko I, Réglier M, Jannuzzi SAV, Royant A, Sicoli G, DeBeer S, Orio M, Simaan AJ, Decroos C. Integrated Experimental and Theoretical Investigation of Copper Active Site Properties of a Lytic Polysaccharide Monooxygenase from Serratia marcescens. Inorg Chem 2024; 63:11063-11078. [PMID: 38814816 DOI: 10.1021/acs.inorgchem.4c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens (SmAA10). The structure of the holo-enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca. 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of SmAA10 but also establishes a robust framework for future studies of similar enzymatic systems.
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Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Manon Pujol
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Ashish Tamhankar
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Chris Joseph
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Sergio A V Jannuzzi
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
- European Synchrotron Radiation Facility, Grenoble 38043, France
| | - Giuseppe Sicoli
- LASIRE UMR CNRS 8516, Université de Lille, Villeneuve-d'Arcy 59655, France
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Christophe Decroos
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
- Department of Integrative Structural Biology, Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch 67400, France
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5
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Hirth N, Wiesemann N, Krüger S, Gerlach MS, Preußner K, Galea D, Herzberg M, Große C, Nies DH. A gold speciation that adds a second layer to synergistic gold-copper toxicity in Cupriavidus metallidurans. Appl Environ Microbiol 2024; 90:e0014624. [PMID: 38557120 PMCID: PMC11022561 DOI: 10.1128/aem.00146-24] [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: 01/25/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024] Open
Abstract
The metal-resistant bacterium Cupriavidus metallidurans occurs in metal-rich environments. In auriferous soils, the bacterium is challenged by a mixture of copper ions and gold complexes, which exert synergistic toxicity. The previously used, self-made Au(III) solution caused a synergistic toxicity of copper and gold that was based on the inhibition of the CupA-mediated efflux of cytoplasmic Cu(I) by Au(I) in this cellular compartment. In this publication, the response of the bacterium to gold and copper was investigated by using a commercially available Au(III) solution instead of the self-made solution. The new solution was five times more toxic than the previously used one. Increased toxicity was accompanied by greater accumulation of gold atoms by the cells. The contribution of copper resistance determinants to the commercially available Au(III) solution and synergistic gold-copper toxicity was studied using single- and multiple-deletion mutants. The commercially available Au(III) solution inhibited periplasmic Cu(I) homeostasis, which is required for the allocation of copper ions to copper-dependent proteins in this compartment. The presence of the gene for the periplasmic Cu(I) and Au(I) oxidase, CopA, decreased the cellular copper and gold content. Transcriptional reporter gene fusions showed that up-regulation of gig, encoding a minor contributor to copper resistance, was strictly glutathione dependent. Glutathione was also required to resist synergistic gold-copper toxicity. The new data indicated a second layer of synergistic copper-gold toxicity caused by the commercial Au(III) solution, inhibition of the periplasmic copper homeostasis in addition to the cytoplasmic one.IMPORTANCEWhen living in auriferous soils, Cupriavidus metallidurans is not only confronted with synergistic toxicity of copper ions and gold complexes but also by different gold species. A previously used gold solution made by using aqua regia resulted in the formation of periplasmic gold nanoparticles, and the cells were protected against gold toxicity by the periplasmic Cu(I) and Au(I) oxidase CopA. To understand the role of different gold species in the environment, another Au(III) solution was commercially acquired. This compound was more toxic due to a higher accumulation of gold atoms by the cells and inhibition of periplasmic Cu(I) homeostasis. Thus, the geo-biochemical conditions might influence Au(III) speciation. The resulting Au(III) species may subsequently interact in different ways with C. metallidurans and its copper homeostasis system in the cytoplasm and periplasm. This study reveals that the geochemical conditions may decide whether bacteria are able to form gold nanoparticles or not.
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Affiliation(s)
- Niklas Hirth
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Nicole Wiesemann
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Stephanie Krüger
- Microscopy Unit, Biocenter, Martin Luther University Halle Wittenberg, Wittenberg, Germany
| | - Michelle-Sophie Gerlach
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kilian Preußner
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - 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 Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Cornelia Große
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Dietrich H Nies
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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de Oliveira Silva YR, Zheng D, Peters SC, Fisher OS. Stabilization of a Cu-binding site by a highly conserved tryptophan residue. J Inorg Biochem 2024; 253:112501. [PMID: 38342077 DOI: 10.1016/j.jinorgbio.2024.112501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Copper serves as an essential cofactor for nearly all living organisms. There are still many gaps remaining in our knowledge of how Gram-positive bacteria import copper and maintain homeostasis. To obtain a better understanding of how these processes work, here we focus on the ycnKJI operon responsible for regulating copper levels in the Gram-positive bacterium Bacillus subtilis. This operon encodes three Cu-related proteins: a copper-dependent transcriptional repressor (YcnK), a putative copper importer (YcnJ), and a copper-binding protein of unknown function (YcnI). We previously found that YcnI's extracellular Domain of Unknown Function 1775 (DUF1775) houses a monohistidine brace motif that coordinates a single Cu(II) ion. The Cu(II) binding site includes a highly conserved tryptophan residue. Here, we investigate the role of that tryptophan and the ability of the protein to interact with other oxidation states of Cu. We find that YcnI exhibits strong preference for binding Cu in the oxidized Cu(II) state, and that the conserved tryptophan residue is not essential for the interaction. We determine the structure of a tryptophan variant to 1.95 Å resolution that indicates that the tryptophan is needed to stabilize the metal binding interaction, and find that this variant has weaker affinity for Cu(II) than the wild-type protein. Together, these data provide further insights into the DUF1775 domain family and reveal the role of the conserved tryptophan residue.
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Affiliation(s)
| | - Dia Zheng
- Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA 18015, USA
| | - Stephen C Peters
- Department of Earth and Environmental Sciences, Lehigh University, 1 W Packer Ave, Bethlehem, PA 18015, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA 18015, USA.
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7
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Morobane DM, Tshishonga K, Serepa-Dlamini MH. Draft Genome Sequence of Pantoea sp. Strain MHSD4, a Bacterial Endophyte With Bioremediation Potential. Evol Bioinform Online 2024; 20:11769343231217908. [PMID: 38487815 PMCID: PMC10938601 DOI: 10.1177/11769343231217908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/14/2023] [Indexed: 03/17/2024] Open
Abstract
Pantoea sp. strain MHSD4 is a bacterial endophyte isolated from the leaves of the medicinal plant Pellaea calomelanos. Here, we report on strain MHSD4 draft whole genome sequence and annotation. The draft genome size of Pantoea sp. strain MHSD4 is 4 647 677 bp with a G+C content of 54.2% and 41 contigs. The National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline tool predicted a total of 4395 genes inclusive of 4235 protein-coding genes, 87 total RNA genes, 14 non-coding (nc) RNAs and 70 tRNAs, and 73 pseudogenes. Biosynthesis pathways for naphthalene and anthracene degradation were identified. Putative genes involved in bioremediation such as copA, copD, cueO, cueR, glnGm, and trxC were identified. Putative genes involved in copper homeostasis and tolerance were identified which may suggest that Pantoea sp. strain MHSD4 has biotechnological potential for bioremediation of heavy metals.
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Affiliation(s)
- Dimpho Michelle Morobane
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Doornfontein, Johannesburg, South Africa
| | - Khuthadzo Tshishonga
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Doornfontein, Johannesburg, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Doornfontein, Johannesburg, South Africa
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Ramdass AC, Rampersad SN. Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains. DNA Res 2023; 30:dsad025. [PMID: 37952165 PMCID: PMC10710014 DOI: 10.1093/dnares/dsad025] [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: 07/20/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.
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Affiliation(s)
- Amanda Christine Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
| | - Sephra Nalini Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
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10
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Liu Y, Harnden KA, Van Stappen C, Dikanov SA, Lu Y. A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase. Proc Natl Acad Sci U S A 2023; 120:e2308286120. [PMID: 37844252 PMCID: PMC10614608 DOI: 10.1073/pnas.2308286120] [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: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 10/18/2023] Open
Abstract
The "Histidine-brace" (His-brace) copper-binding site, composed of Cu(His)2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.
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Affiliation(s)
- Yiwei Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Kevin A. Harnden
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
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11
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Ma L, Zhou Y, Wang A, Li Q. A potential heavy metals detoxification system in composting: Biotic and abiotic synergy mediated by shell powder. BIORESOURCE TECHNOLOGY 2023; 386:129576. [PMID: 37506928 DOI: 10.1016/j.biortech.2023.129576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Regulating heavy metal resistance genes (HMRGs) was an effective method for heavy metal resistant bacteria (HMRB) to cope with heavy metal stress during dairy manure composting. This research aimed to investigate heavy metal detoxification mediated by shell powder (SP) in composting and the response of HMRB and HMRGs to changes in heavy metal bioavailability during composting. Research showed that SP additive reduced the bioavailability of Zu, Cu, and Mn by 10.64%, 13.90% and 14.14%, respectively. SP increased the composition percentage of humic acid (HA) in humus (HS) by 8%. SP enhanced the resistance of Actinobacteria to heavy metals and improved the regulation of HMRGs. Correlation analysis demonstrated that the bioavailability of heavy metals was positively correlated with most HMRGs. HA was significantly negatively correlated with the bioavailability of Zn, Cu and Mn. Therefore, SP additive could be a novel strategy for heavy metals detoxification during composting.
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Affiliation(s)
- Liangcai Ma
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yucheng Zhou
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ao Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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12
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Hirth N, Gerlach MS, Wiesemann N, Herzberg M, Große C, Nies DH. Full Copper Resistance in Cupriavidus metallidurans Requires the Interplay of Many Resistance Systems. Appl Environ Microbiol 2023:e0056723. [PMID: 37191542 DOI: 10.1128/aem.00567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
The metal-resistant bacterium Cupriavidus metallidurans uses its copper resistance components to survive the synergistic toxicity of copper ions and gold complexes in auriferous soils. The cup, cop, cus, and gig determinants encode as central component the Cu(I)-exporting PIB1-type ATPase CupA, the periplasmic Cu(I)-oxidase CopA, the transenvelope efflux system CusCBA, and the Gig system with unknown function, respectively. The interplay of these systems with each other and with glutathione (GSH) was analyzed. Copper resistance in single and multiple mutants up to the quintuple mutant was characterized in dose-response curves, Live/Dead-staining, and atomic copper and glutathione content of the cells. The regulation of the cus and gig determinants was studied using reporter gene fusions and in case of gig also RT-PCR studies, which verified the operon structure of gigPABT. All five systems contributed to copper resistance in the order of importance: Cup, Cop, Cus, GSH, and Gig. Only Cup was able to increase copper resistance of the Δcop Δcup Δcus Δgig ΔgshA quintuple mutant but the other systems were required to increase copper resistance of the Δcop Δcus Δgig ΔgshA quadruple mutant to the parent level. Removal of the Cop system resulted in a clear decrease of copper resistance in most strain backgrounds. Cus cooperated with and partially substituted Cop. Gig and GSH cooperated with Cop, Cus, and Cup. Copper resistance is thus the result of an interplay of many systems. IMPORTANCE The ability of bacteria to maintain homeostasis of the essential-but-toxic "Janus"-faced element copper is important for their survival in many natural environments but also in case of pathogenic bacteria in their respective host. The most important contributors to copper homeostasis have been identified in the last decades and comprise PIB1-type ATPases, periplasmic copper- and oxygen-dependent copper oxidases, transenvelope efflux systems, and glutathione; however, it is not known how all these players interact. This publication investigates this interplay and describes copper homeostasis as a trait emerging from a network of interacting resistance systems.
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Affiliation(s)
- Niklas Hirth
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | | | - Nicole Wiesemann
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Martin Herzberg
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Cornelia Große
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Dietrich H Nies
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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13
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The Extracellular Electron Transport Pathway Reduces Copper for Sensing by the CopRS Two-Component System under Anaerobic Conditions in Listeria monocytogenes. J Bacteriol 2023; 205:e0039122. [PMID: 36622231 PMCID: PMC9879103 DOI: 10.1128/jb.00391-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The renowned antimicrobial activity of copper stems in part from its ability to undergo redox cycling between Cu1+/2+ oxidation states. Bacteria counter copper toxicity with a network of sensors that often include two-component signaling systems to direct transcriptional responses. As in typical two-component systems, ligand binding by the extracellular domain of the membrane bound copper sensor component leads to phosphorylation and activation of the cognate response regulator transcription factor. In Listeria monocytogenes, the plasmid-borne CopRS two-component system upregulates both copper resistance and lipoprotein remodeling genes upon copper challenge, but the oxidation state of copper bound by CopS is unknown. Herein, we show CopS utilizes a triad of key residues (His-His-Phe) that are predicted to be at the dimerization interface and that are analogous with the Escherichia coli CusS copper sensor to specifically bind Cu1+/Ag1+ and activate CopR transcription. We demonstrate Cu2+ only induces CopRS if first reduced by electron transport systems, as strains lacking menaquinone carriers were unable to respond to Cu2+. The flavin-dependent extracellular electron transport system (EET) was the main mechanism for metal reduction, capable of either generating inducing ligand (Cu2+ to Cu1+) or removing it by precipitation (Ag1+ to Ag0). We show that EET flux is directly proportional to the rate of Cu2+ reduction and that since EET activity is low under oxygenated conditions when a competing respiratory chain is operating, CopRS signaling in turn is activated only under anaerobic conditions. EET metal reduction thus sensitizes cells to copper while providing resistance to silver under anaerobic growth. IMPORTANCE Two-component extracellular copper sensing from the periplasm of Gram-negative bacteria has been well studied, but copper detection at the cell surface of the Gram-positive L. monocytogenes is less understood. Collectively, our results show that EET is most active under anaerobic conditions and reduces Cu2+ and Ag1+ to, respectively, generate or remove the monovalent ligands that directly bind to CopS and lead to the induction of lipoprotein remodeling genes. This reducing activity regulates CopRS signaling and links the upregulation of copper resistance genes with increasing EET flux. Our studies provide insight into how a two-component copper sensing system is integrated into a model monoderm Firmicute to take cues from the electron transport chain activity.
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14
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Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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15
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Ares Á, Sakai S, Sasaki T, Shimamura S, Mitarai S, Nunoura T. Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Environ Microbiol 2022; 24:6144-6163. [PMID: 36284406 PMCID: PMC10092412 DOI: 10.1111/1462-2920.16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Sanae Sakai
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Toshio Sasaki
- Imaging section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Shigeru Shimamura
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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16
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Siles JA, Hendrickson AJ, Terry N. Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116132. [PMID: 36067666 DOI: 10.1016/j.jenvman.2022.116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.
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Affiliation(s)
- José A Siles
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
| | - Andrew J Hendrickson
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Norman Terry
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
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17
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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18
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Abstract
Copper is essential to most living beings but also highly toxic and as such is an important player at the host-pathogen interface. Bacteria have thus developed homeostatic mechanisms to tightly control its intracellular concentration. Known Cu export and import systems are under transcriptional control, whereas posttranscriptional regulatory mechanisms are yet to be characterized. We identified a three-gene operon, bp2923-bfrG-bp2921, downregulated by copper and notably encoding a TonB-dependent transporter in Bordetella pertussis. We show here that the protein encoded by the first gene, which is a member of the DUF2946 protein family, represents a new type of upstream Open Reading Frame (uORF) involved in posttranscriptional regulation of the downstream genes. In the absence of copper, the entire operon is transcribed and translated. Perception of copper by the nascent bp2923-coded protein via its conserved CXXC motif triggers Rho-dependent transcription termination between the first and second genes by relieving translation arrest on a conserved C-terminal RAPP motif. Homologs of bp2923 are widespread in bacterial genomes, where they head operons predicted to participate in copper homeostasis. This work has thus unveiled a new mode of genetic regulation by a transition metal and identified a regulatory function for a member of an uncharacterized family of bacterial proteins that we have named CruR, for copper-responsive upstream regulator.
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19
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Novoa-Aponte L, Argüello JM. Unique underlying principles shaping copper homeostasis networks. J Biol Inorg Chem 2022; 27:509-528. [PMID: 35802193 PMCID: PMC9470648 DOI: 10.1007/s00775-022-01947-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 12/27/2022]
Abstract
Abstract Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria. Graphical Abstract ![]()
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Affiliation(s)
- Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.,Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.
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20
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Kekez I, Faletar M, Kekez M, Cendron L, Wright M, Zanotti G, Matković-Čalogović D. Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori. Molecules 2022; 27:molecules27113387. [PMID: 35684325 PMCID: PMC9182242 DOI: 10.3390/molecules27113387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.
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Affiliation(s)
- Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
- Correspondence: (I.K.); (D.M.-Č.); Tel.: +385-14-606-345 (D.M.-Č.)
| | - Mihovil Faletar
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
| | - Mario Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
| | - Laura Cendron
- Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Maya Wright
- Fluidic Analytics Ltd., Unit A Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK;
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Dubravka Matković-Čalogović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (M.F.); (M.K.)
- Correspondence: (I.K.); (D.M.-Č.); Tel.: +385-14-606-345 (D.M.-Č.)
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21
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Gómez-Piñeiro R, Drosou M, Bertaina S, Decroos C, Simaan AJ, Pantazis DA, Orio M. Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens. Inorg Chem 2022; 61:8022-8035. [PMID: 35549254 PMCID: PMC9131454 DOI: 10.1021/acs.inorgchem.2c00766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 11/29/2022]
Abstract
Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.
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Affiliation(s)
| | - Maria Drosou
- Inorganic
Chemistry Laboratory, National and Kapodistrian
University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Sylvain Bertaina
- Aix-Marseille
Université, CNRS, IM2NP UMR 7334, Marseille 13397, France
| | - Christophe Decroos
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | - A. Jalila Simaan
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an
der Ruhr 45470, Germany
| | - Maylis Orio
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
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22
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Guo HN, Liu HT, Wu S. Immobilization pathways of heavy metals in composting: Interactions of microbial community and functional gene under varying C/N ratios and bulking agents. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128103. [PMID: 34952492 DOI: 10.1016/j.jhazmat.2021.128103] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Excessive heavy metals (HMs) in livestock manure due to additives over-use limits its recycling through composting. However, few studies have investigated the interactive influence of microbial communities, functional genes, and environmental factors in HM immobilization during composting. Therefore, treatments with different C/N ratios (15:1, 20:1, 25:1) and bulking agents (maize straw, green waste, vinasse) were conducted to explore the HMs immobilization pathways using structural equation model (SEM). Results confirmed the promoting effect of C/N ratio of 20:1 and vinasse on microbial diversity, thus leading to greater HMs immobilization rate. Meanwhile, the dominant microbial phyla of Cu/Zn, Cd, As, and Cr were identified as Proteobacteria, Firmicutes, Chytridiomycota, and Bacteroidota, respectively. Moreover, the significant correlation between functional genes (copC, mt, cbh1, aoxB, yieF) and HMs illustrated potential immobilization effects of metal-binding proteins on Cu and Zn, humus complexation on Zn, and oxidase/reductase on As/Cr. Finally, SEM indicated that the redistribution of Cu, Zn, As, and Cr fractions was interactively influenced by environmental factors (organic matter, pH, electrical conductivity, and total phosphorus), microbial communities, and functional genes, while Cd was directly regulated by organic matter and total phosphorus. These results may provide a deeper understanding of HM immobilization pathways during swine manure composting.
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Affiliation(s)
- Hao-Nan Guo
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Tao Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Engineering Laboratory for Yellow River Delta Modern Agriculture, Chinese Academy of Sciences, Beijing 100101, China.
| | - Shubiao Wu
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
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23
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Complete Genome Sequence of Micrococcus luteus Strain CW.Ay, Isolated from Indoor Air in a Hong Kong School. Microbiol Resour Announc 2022; 11:e0119421. [PMID: 35175116 PMCID: PMC8852316 DOI: 10.1128/mra.01194-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Micrococcus luteus strain CW.Ay was isolated from indoor air in Hong Kong. The complete genome (2,543,764 bp; GC content, 72.93%) was established by hybrid assembly and comprised a linear plasmid and a single chromosome featuring many genes to account for its broad distribution in very diverse habitats.
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Plasmids Bring Additional Capabilities to Caulobacter Isolates. Curr Microbiol 2022; 79:45. [PMID: 34982248 PMCID: PMC8812328 DOI: 10.1007/s00284-021-02742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Caulobacter is a well-studied bacterial genus, but little is known about the plasmids that are found in some wild Caulobacter isolates. We used bioinformatic approaches to identify nine plasmids from seven different Caulobacter strains and grouped them based on their size and the similarity of their repABC, parAB, and mobAB genes. Protein pathway analysis of the genes on the K31p1 and K31p2 plasmids showed many metabolic pathways that would enhance the metabolic versatility of the host strain. In contrast, the CB4 plasmid contained 21 heavy metal resistance genes with the majority coding for proteins that enhance copper resistance. Growth assays of C. henricii CB4 demonstrated increased copper resistance and quantitative PCR showed an increase in the expression of eight heavy metal genes when induced with copper.
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Hadley RC, Zhitnitsky D, Livnat-Levanon N, Masrati G, Vigonsky E, Rose J, Ben-Tal N, Rosenzweig AC, Lewinson O. The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery. J Biol Chem 2022; 298:101445. [PMID: 34822841 PMCID: PMC8689200 DOI: 10.1016/j.jbc.2021.101445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
The Escherichia coli yobA-yebZ-yebY (AZY) operon encodes the proteins YobA, YebZ, and YebY. YobA and YebZ are homologs of the CopC periplasmic copper-binding protein and the CopD putative copper importer, respectively, whereas YebY belongs to the uncharacterized Domain of Unknown Function 2511 family. Despite numerous studies of E. coli copper homeostasis and the existence of the AZY operon in a range of bacteria, the operon's proteins and their functional roles have not been explored. In this study, we present the first biochemical and functional studies of the AZY proteins. Biochemical characterization and structural modeling indicate that YobA binds a single Cu2+ ion with high affinity. Bioinformatics analysis shows that YebY is widespread and encoded either in AZY operons or in other genetic contexts unrelated to copper homeostasis. We also determined the 1.8 Å resolution crystal structure of E. coli YebY, which closely resembles that of the lantibiotic self-resistance protein MlbQ. Two strictly conserved cysteine residues form a disulfide bond, consistent with the observed periplasmic localization of YebY. Upon treatment with reductants, YebY binds Cu+ and Cu2+ with low affinity, as demonstrated by metal-binding analysis and tryptophan fluorescence. Finally, genetic manipulations show that the AZY operon is not involved in copper tolerance or antioxidant defense. Instead, YebY and YobA are required for the activity of the copper-related NADH dehydrogenase II. These results are consistent with a potential role of the AZY operon in copper delivery to membrane proteins.
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Affiliation(s)
- Rose C Hadley
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Daniel Zhitnitsky
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Nurit Livnat-Levanon
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elena Vigonsky
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Jessica Rose
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois, USA.
| | - Oded Lewinson
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel.
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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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Prospects for the creation of antimicrobial preparations based on copper and copper oxides nanoparticles. ACTA BIOMEDICA SCIENTIFICA 2021. [DOI: 10.29413/abs.2021-6.6-2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The spread of strains of microorganisms that are multidrug resistant to modern antimicrobial drugs is still an urgent problem in the treatment and prevention of infectious diseases and public health in general.Currently, the possibility of using metal nanopreparations in various fields of medicine is being actively studied. Nanoparticles of metals and metal oxides are promising antimicrobial agents and are attracting growing interest due to their effectiveness. Nanoscale copper metal particles have shown high antimicrobial activity againstvarious types of gram-positive and gram-negative bacteria, as well as fungi. Taking into account the potential of copper nanoparticles in antimicrobial therapy, we present an overview of the current state of research related to their antimicrobial properties, consideration of the mechanisms of action, key factors affecting antimicrobial activity, including the polymer matrix. The issues of toxicity and resistance to copper are considered. The advantage of copper nanoparticles over other metal nanoparticles is shown.The studies summarized in this review have shown the promise of copper nanoparticles in the creation of new antimicrobial drugs that can be used in the future to control, prevent, and treat various diseases.
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Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings. PLoS One 2021; 16:e0257800. [PMID: 34582496 PMCID: PMC8478169 DOI: 10.1371/journal.pone.0257800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/12/2021] [Indexed: 11/19/2022] Open
Abstract
Copper is prevalent in coastal ecosystems due to its use as an algaecide and as an anti-fouling agent on ship hulls. Alteromonas spp. have previously been shown to be some of the early colonizers of copper-based anti-fouling paint but little is known about the mechanisms they use to overcome this initial copper challenge. The main models of copper resistance include the Escherichia coli chromosome-based Cue and Cus systems; the plasmid-based E. coli Pco system; and the plasmid-based Pseudomonas syringae Cop system. These were all elucidated from strains isolated from copper-rich environments of agricultural and/or enteric origin. In this work, copper resistance assays demonstrated the ability of Alteromonas macleodii strains CUKW and KCC02 to grow at levels lethal to other marine bacterial species. A custom database of Hidden Markov Models was designed based on proteins from the Cue, Cus, and Cop/Pco systems and used to identify potential copper resistance genes in CUKW and KCC02. Comparative genomic analyses with marine bacterial species and bacterial species isolated from copper-rich environments demonstrated that CUKW and KCC02 possess genetic elements of all systems, oftentimes with multiple copies, distributed throughout the chromosome and mega-plasmids. In particular, two copies of copA (the key player in cytoplasmic detoxification), each with its own apparent MerR-like transcriptional regulator, occur on a mega-plasmid, along with multiple copies of Pco homologs. Genes from both systems were induced upon exposure to elevated copper levels (100 μM- 3 mM). Genomic analysis identified one of the merR-copA clusters occurs on a genomic island (GI) within the plasmid, and comparative genomic analysis found that either of the merR-copA clusters, which also includes genes coding for a cupredoxin domain-containing protein and an isoprenylcysteine methyltransferase, occurs on a GI across diverse bacterial species. These genomic findings combined with the ability of CUKW and KCC02 to grow in copper-challenged conditions are couched within the context of the genome flexibility of the Alteromonas genus.
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Damle MS, Singh AN, Peters SC, Szalai VA, Fisher OS. The YcnI protein from Bacillus subtilis contains a copper-binding domain. J Biol Chem 2021; 297:101078. [PMID: 34400169 PMCID: PMC8424229 DOI: 10.1016/j.jbc.2021.101078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Abstract
Bacteria require a precise balance of copper ions to ensure that essential cuproproteins are fully metalated while also avoiding copper-induced toxicity. The Gram-positive bacterium Bacillus subtilis maintains appropriate copper homeostasis in part through the ycn operon. The ycn operon comprises genes encoding three proteins: the putative copper importer YcnJ, the copper-dependent transcriptional repressor YcnK, and the uncharacterized Domain of Unknown Function 1775 (DUF1775) containing YcnI. DUF1775 domains are found across bacterial phylogeny, and bioinformatics analyses indicate that they frequently neighbor domains implicated in copper homeostasis and transport. Here, we investigated whether YcnI can interact with copper and, using electron paramagnetic resonance and inductively coupled plasma-MS, found that this protein can bind a single Cu(II) ion. We determine the structure of both the apo and copper-bound forms of the protein by X-ray crystallography, uncovering a copper-binding site featuring a unique monohistidine brace ligand set that is highly conserved among DUF1775 domains. These data suggest a possible role for YcnI as a copper chaperone and that DUF1775 domains in other bacterial species may also function in copper homeostasis.
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Affiliation(s)
- Madhura S Damle
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Aarshi N Singh
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Stephen C Peters
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Veronika A Szalai
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA.
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Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Copper binding by a unique family of metalloproteins is dependent on kynurenine formation. Proc Natl Acad Sci U S A 2021; 118:2100680118. [PMID: 34074779 DOI: 10.1073/pnas.2100680118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Some methane-oxidizing bacteria use the ribosomally synthesized, posttranslationally modified natural product methanobactin (Mbn) to acquire copper for their primary metabolic enzyme, particulate methane monooxygenase. The operons encoding the machinery to biosynthesize and transport Mbns typically include genes for two proteins, MbnH and MbnP, which are also found as a pair in other genomic contexts related to copper homeostasis. While the MbnH protein, a member of the bacterial diheme cytochrome c peroxidase (bCcP)/MauG superfamily, has been characterized, the structure and function of MbnP, the relationship between the two proteins, and their role in copper homeostasis remain unclear. Biochemical characterization of MbnP from the methanotroph Methylosinus trichosporium OB3b now reveals that MbnP binds a single copper ion, present in the +1 oxidation state, with high affinity. Copper binding to MbnP in vivo is dependent on oxidation of the first tryptophan in a conserved WxW motif to a kynurenine, a transformation that occurs through an interaction of MbnH with MbnP. The 2.04-Å-resolution crystal structure of MbnP reveals a unique fold and an unusual copper-binding site involving a histidine, a methionine, a solvent ligand, and the kynurenine. Although the kynurenine residue may not serve as a CuI primary-sphere ligand, being positioned ∼2.9 Å away from the CuI ion, its presence is required for copper binding. Genomic neighborhood analysis indicates that MbnP proteins, and by extension kynurenine-containing copper sites, are widespread and may play diverse roles in microbial copper homeostasis.
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Ipsen JØ, Hernández-Rollán C, Muderspach SJ, Brander S, Bertelsen AB, Jensen PE, Nørholm MHH, Lo Leggio L, Johansen KS. Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC. FEBS Lett 2021; 595:1708-1720. [PMID: 33896006 DOI: 10.1002/1873-3468.14092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/11/2022]
Abstract
The histidine brace (His-brace) is a copper-binding motif that is associated with both oxidative enzymes and proteinaceous copper chaperones. Here, we used biochemical and structural methods to characterize mutants of a His-brace-containing copper chaperone from Pseudomonas fluorescens (PfCopC). A total of 15 amino acid variants in primary and second-sphere residues were produced and characterized in terms of their copper binding and redox properties. PfCopC has a very high affinity for Cu(II) and also binds Cu(I). A high reorganization barrier likely prevents redox cycling and, thus, catalysis. In contrast, mutations in the conserved second-sphere Glu27 enable slow oxidation of ascorbate. The crystal structure of the variant E27A confirmed copper binding at the His-brace. Unexpectedly, Asp83 at the equatorial position was shown to be indispensable for Cu(II) binding in the His-brace of PfCopC. A PfCopC mutant that was designed to mimic the His-brace from lytic polysaccharide monooxygenase-like family X325 did not bind Cu(II), but was still able to bind Cu(I). These results highlight the importance of the proteinaceous environment around the copper His-brace for reactivity and, thus, the difference between enzyme and chaperone.
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Affiliation(s)
- Johan Ø Ipsen
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Søren Brander
- Department of Geosciences and Natural Resource Management, Copenhagen University, Frederiksberg, Denmark
| | - Andreas B Bertelsen
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, Copenhagen University, Frederiksberg, Denmark
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Giachino A, Focarelli F, Marles-Wright J, Waldron KJ. Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling. FEMS Microbiol Ecol 2021; 97:6021318. [PMID: 33501489 DOI: 10.1093/femsec/fiaa249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022] Open
Abstract
One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.
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Affiliation(s)
- Andrea Giachino
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Francesca Focarelli
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Kevin J Waldron
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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Shafiee RT, Diver PJ, Snow JT, Zhang Q, Rickaby REM. Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches. ISME COMMUNICATIONS 2021; 1:1. [PMID: 37938628 PMCID: PMC9723733 DOI: 10.1038/s43705-021-00001-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK.
| | - Poppy J Diver
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Joseph T Snow
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
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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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Reyes C, Hodgskiss LH, Kerou M, Pribasnig T, Abby SS, Bayer B, Kraemer SM, Schleper C. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. THE ISME JOURNAL 2020; 14:2659-2674. [PMID: 32665710 PMCID: PMC7785015 DOI: 10.1038/s41396-020-0715-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/09/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
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Affiliation(s)
- Carolina Reyes
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Sophie S Abby
- University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Barbara Bayer
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Department of Limnology and Oceanography, Division of Bio-oceanography, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106-9620, USA
| | - Stephan M Kraemer
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. mBio 2020; 11:mBio.02371-20. [PMID: 33051370 PMCID: PMC7554672 DOI: 10.1128/mbio.02371-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
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Brander S, Horvath I, Ipsen JØ, Peciulyte A, Olsson L, Hernández-Rollán C, Nørholm MHH, Mossin S, Leggio LL, Probst C, Thiele DJ, Johansen KS. Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace. Sci Rep 2020; 10:16369. [PMID: 33004835 PMCID: PMC7529816 DOI: 10.1038/s41598-020-73266-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
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Affiliation(s)
- Søren Brander
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Istvan Horvath
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Johan Ø Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Ausra Peciulyte
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Susanne Mossin
- Centre for Catalysis and Sustainable Chemistry, Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Corinna Probst
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dennis J Thiele
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Katja S Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
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Hamdy AA, Esawy MA, Elattal NA, Amin MA, Ali AE, Awad GEA, Connerton I, Mansour NM. Complete genome sequence and comparative analysis of two potential probiotics Bacillus subtilis isolated from honey and honeybee microbiomes. J Genet Eng Biotechnol 2020; 18:34. [PMID: 32700263 PMCID: PMC7376800 DOI: 10.1186/s43141-020-00050-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND We have previously isolated Bacillus subtilis HMNig-2 and MENO2 strains, from honey and the honeybee gut microbiome respectively, and demonstrated these strains to produce levansucrase with potential probiotics characteristics. Here we report their complete genome sequence and comparative analysis with other and other B. subtilis strains. RESULTS The complete genome sequences of Bacillus subtilis HMNig-2 and MENO2 were de novo assembled from MiSeq paired-end sequence reads and annotated using the RAST tool. Whole-genome alignments were performed to identify functional differences associated with their potential use as probiotics. CONCLUSIONS The comparative analysis and the availability of the genome sequence of these two strains will provide comprehensive analysis about the diversity of these valuable Bacillus strains and the possible impact of the environment on bacterial evolution. SIGNIFICANCE AND IMPACT OF STUDY We introduce complete genome sequence of two new B. subtilis strains HMNig-2 and MENO2 with probiotic potential and as cell factories for the production of levan and other valuable components for pharmaceutical and industrial applications.
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Affiliation(s)
- Abdelhamid A. Hamdy
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Div., National Research Centre, 33 El Bohouth St., Dokki, P.O. Box: 12622, Cairo, Egypt
| | - Mona A. Esawy
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Div., National Research Centre, 33 El Bohouth St., Dokki, P.O. Box: 12622, Cairo, Egypt
| | - Nouran A. Elattal
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Div., National Research Centre, 33 El Bohouth St., Dokki, P.O. Box: 12622, Cairo, Egypt
| | - Magdy A. Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Amal E. Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ghada E. A. Awad
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Div., National Research Centre, 33 El Bohouth St., Dokki, P.O. Box: 12622, Cairo, Egypt
| | - Ian Connerton
- Division of Food Sciences, School of Biosciences, University of Nottingham Loughborough, Sutton Bonington Campus, Leicestershire, LE12 5RD UK
| | - Nahla M. Mansour
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Div., National Research Centre, 33 El Bohouth St., Dokki, P.O. Box: 12622, Cairo, Egypt
- Gut Microbiology & Immunology Group, Chemistry of Natural & Microbial Products Department, Pharmaceutical Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, 12622, Cairo, Egypt
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Mahamoud Ahmed A, Tardy V, Bonnineau C, Billard P, Pesce S, Lyautey E. Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122197. [PMID: 32058227 DOI: 10.1016/j.jhazmat.2020.122197] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
Sediment microbial communities were exposed for 21 days to an environmental concentration of copper to assess Cu-induced composition changes and resulting effects on microbial sensitivity to acute Cu and As toxicity. Chronic Cu exposure reduced the diversity of the bacterial and archaeal communities from Day 0 to Day 21. The pollution-induced community tolerance concept (PICT) predicts that loss of the most sensitive taxa and gain of more tolerant ones should increase the capacity of Cu-exposed communities to tolerate acute Cu toxicity. Although diversity loss and functional costs of adaptation could have increased their sensitivity to subsequent toxic stress, no increased sensitivity to As was observed. PICT responses varied according to heterotrophic activity, selected as the functional endpoint for toxicity testing, with different results for Cu and As. This suggests that induced tolerance to Cu and As was supported by different species with different metabolic capacities. Ecological risk assessment of contaminants would gain accuracy from further research on the relative contribution of tolerance acquisition and co-tolerance processes on the functional response of microbial communities.
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Affiliation(s)
- Ayanleh Mahamoud Ahmed
- INRAE, UR RiverLy, 69625 Villeurbanne, France; Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France; Centre de Recherche, Université de Djibouti, BP 1904 Djibouti Ville, Djibouti
| | - Vincent Tardy
- INRAE, UR RiverLy, 69625 Villeurbanne, France; Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | | | - Patrick Billard
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, 54501, France
| | | | - Emilie Lyautey
- INRAE, UR RiverLy, 69625 Villeurbanne, France; Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France.
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42
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Selamoglu N, Önder Ö, Öztürk Y, Khalfaoui-Hassani B, Blaby-Haas CE, Garcia BA, Koch HG, Daldal F. Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins. Metallomics 2020; 12:572-591. [PMID: 32149296 PMCID: PMC7192791 DOI: 10.1039/c9mt00314b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/28/2020] [Indexed: 12/20/2022]
Abstract
Copper (Cu) is an essential, but toxic, micronutrient for living organisms and cells have developed sophisticated response mechanisms towards both the lack and the excess of Cu in their environments. In this study, we achieved a global view of Cu-responsive changes in the prokaryotic model organism Rhodobacter capsulatus using label-free quantitative differential proteomics. Semi-aerobically grown cells under heterotrophic conditions in minimal medium (∼0.3 μM Cu) were compared with cells supplemented with either 5 μM Cu or with 5 mM of the Cu-chelator bathocuproine sulfonate. Mass spectrometry based bottom-up proteomics of unfractionated cell lysates identified 2430 of the 3632 putative proteins encoded by the genome, producing a robust proteome dataset for R. capsulatus. Use of biological and technical replicates for each growth condition yielded high reproducibility and reliable quantification for 1926 of the identified proteins. Comparison of cells grown under Cu-excess or Cu-depleted conditions to those grown under minimal Cu-sufficient conditions revealed that 75 proteins exhibited statistically significant (p < 0.05) abundance changes, ranging from 2- to 300-fold. A subset of the highly Cu-responsive proteins was orthogonally probed using molecular genetics, validating that several of them were indeed involved in cellular Cu homeostasis.
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Affiliation(s)
- Nur Selamoglu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Garcia-Santamarina S, Probst C, Festa RA, Ding C, Smith AD, Conklin SE, Brander S, Kinch LN, Grishin NV, Franz KJ, Riggs-Gelasco P, Lo Leggio L, Johansen KS, Thiele DJ. A lytic polysaccharide monooxygenase-like protein functions in fungal copper import and meningitis. Nat Chem Biol 2020; 16:337-344. [PMID: 31932719 PMCID: PMC7036007 DOI: 10.1038/s41589-019-0437-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
Infection by the fungal pathogen Cryptococcus neoformans causes lethal meningitis, primarily in immune-compromised individuals. Colonization of the brain by C. neoformans is dependent on copper (Cu) acquisition from the host, which drives critical virulence mechanisms. While C. neoformans Cu+ import and virulence are dependent on the Ctr1 and Ctr4 proteins, little is known concerning extracellular Cu ligands that participate in this process. We identified a C. neoformans gene, BIM1, that is strongly induced during Cu limitation and which encodes a protein related to lytic polysaccharide monooxygenases (LPMOs). Surprisingly, bim1 mutants are Cu deficient, and Bim1 function in Cu accumulation depends on Cu2+ coordination and cell-surface association via a glycophosphatidyl inositol anchor. Bim1 participates in Cu uptake in concert with Ctr1 and expression of this pathway drives brain colonization in mouse infection models. These studies demonstrate a role for LPMO-like proteins as a critical factor for Cu acquisition in fungal meningitis.
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Affiliation(s)
- Sarela Garcia-Santamarina
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Genome Biology Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Corinna Probst
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Richard A Festa
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Irvine Scientific, Santa Ana, CA, USA
| | - Chen Ding
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Aaron D Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Steven E Conklin
- Department of Chemistry, Duke University, Durham, NC, USA
- Division of Clinical Chemistry, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Søren Brander
- Department of Geoscience and Natural Resource, University of Copenhagen, Copenhagen, Denmark
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource, University of Copenhagen, Copenhagen, Denmark
| | - Dennis J Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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Munzone A, El Kerdi B, Fanuel M, Rogniaux H, Ropartz D, Réglier M, Royant A, Simaan AJ, Decroos C. Characterization of a bacterial copper‐dependent lytic polysaccharide monooxygenase with an unusual second coordination sphere. FEBS J 2020; 287:3298-3314. [DOI: 10.1111/febs.15203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/05/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Bilal El Kerdi
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Mathieu Fanuel
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - Hélène Rogniaux
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - David Ropartz
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - Marius Réglier
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Antoine Royant
- Univ. Grenoble Alpes CNRS CEA Institut de Biologie Structurale (IBS) Grenoble France
- European Synchrotron Radiation Facility Grenoble France
| | - A. Jalila Simaan
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
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Multiple Megaplasmids Confer Extremely High Levels of Metal Tolerance in Alteromonas Strains. Appl Environ Microbiol 2020; 86:AEM.01831-19. [PMID: 31757820 DOI: 10.1128/aem.01831-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/25/2019] [Indexed: 02/08/2023] Open
Abstract
Alteromonas is a widely distributed genus of marine Gammaproteobacteria, with representatives shown to be key players in diverse processes, including biogeochemical cycling and biofouling of marine substrata. While Alteromonas spp. are early colonizers of copper-based antifouling paints on marine vessels, their mechanism of tolerance is poorly understood. PacBio whole-genome sequencing of Alteromonas macleodii strains CUKW and KCC02, isolated from Cu/Ni alloy test coupons submerged in oligotrophic coastal waters, indicated the presence of multiple megaplasmids (ca. 200 kb) in both. A pulsed-field gel electrophoresis method was developed and used to confirm the presence of multiple megaplasmids in these two strains; it was then used to screen additional Alteromonas strains for which little to no sequencing data exist. Plasmids were not detected in any of the other strains. Bioinformatic analysis of the CUKW and KCC02 plasmids identified numerous genes associated with metal resistance. Copper resistance orthologs from both the Escherichia coli Cue and Cus and Pseudomonas syringae Cop systems were present, at times as multiple copies. Metal growth assays in the presence of copper, cobalt, manganese, and zinc performed with 10 Alteromonas strains demonstrated the ability of CUKW and KCC02 to grow at metal concentrations inhibitory to all the other strains tested. This study reports multiple megaplasmids in Alteromonas strains. Bioinformatic analysis of the CUKW and KCC02 plasmids indicate that they harbor elements of the Tra system conjugation apparatus, although their type of mobility remains to be experimentally verified.IMPORTANCE Copper is commonly used as an antifouling agent on ship hulls. Alteromonas spp. are early colonizers of copper-based antifouling paint, but their mechanism of tolerance is poorly understood. Sequencing of A. macleodii strains isolated from copper test materials for marine ships indicated the presence of multiple megaplasmids. Plasmids serve as key vectors in horizontal gene transfer and confer traits such as metal resistance, detoxification, ecological interaction, and antibiotic resistance. Bioinformatic analysis identified many metal resistance genes and genes associated with mobility. Understanding the molecular mechanisms and capacity for gene transfer within marine biofilms provides a platform for the development of novel antifouling solutions targeting genes involved in copper tolerance and biofilm formation.
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47
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A fungal family of lytic polysaccharide monooxygenase-like copper proteins. Nat Chem Biol 2020; 16:345-350. [DOI: 10.1038/s41589-019-0438-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/22/2019] [Indexed: 11/08/2022]
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Kenney GE, Dassama LMK, Manesis AC, Ross MO, Chen S, Hoffman BM, Rosenzweig AC. MbnH is a diheme MauG-like protein associated with microbial copper homeostasis. J Biol Chem 2019; 294:16141-16151. [PMID: 31511324 PMCID: PMC6827288 DOI: 10.1074/jbc.ra119.010202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/06/2019] [Indexed: 01/09/2023] Open
Abstract
Methanobactins (Mbns) are ribosomally-produced, post-translationally modified peptidic copper-binding natural products produced under conditions of copper limitation. Genes encoding Mbn biosynthetic and transport proteins have been identified in a wide variety of bacteria, indicating a broader role for Mbns in bacterial metal homeostasis. Many of the genes in the Mbn operons have been assigned functions, but two genes usually present, mbnP and mbnH, encode uncharacterized proteins predicted to reside in the periplasm. MbnH belongs to the bacterial diheme cytochrome c peroxidase (bCcP)/MauG protein family, and MbnP contains no domains of known function. Here, we performed a detailed bioinformatic analysis of both proteins and have biochemically characterized MbnH from Methylosinus (Ms.) trichosporium OB3b. We note that the mbnH and mbnP genes typically co-occur and are located proximal to genes associated with microbial copper homeostasis. Our bioinformatics analysis also revealed that the bCcP/MauG family is significantly more diverse than originally appreciated, and that MbnH is most closely related to the MauG subfamily. A 2.6 Å resolution structure of Ms. trichosporium OB3b MbnH combined with spectroscopic data and peroxidase activity assays provided evidence that MbnH indeed more closely resembles MauG than bCcPs, although its redox properties are significantly different from those of MauG. The overall similarity of MbnH to MauG suggests that MbnH could post-translationally modify a macromolecule, such as internalized CuMbn or its uncharacterized partner protein, MbnP. Our results indicate that MbnH is a MauG-like diheme protein that is likely involved in microbial copper homeostasis and represents a new family within the bCcP/MauG superfamily.
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Affiliation(s)
- Grace E. Kenney
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Laura M. K. Dassama
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Anastasia C. Manesis
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Matthew O. Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Siyu Chen
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208, To whom correspondence should be addressed. Tel.:
847-467-5301; Fax:
847-467-6489; E-mail:
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Fisher OS, Sendzik MR, Ross MO, Lawton TJ, Hoffman BM, Rosenzweig AC. PCu AC domains from methane-oxidizing bacteria use a histidine brace to bind copper. J Biol Chem 2019; 294:16351-16363. [PMID: 31527086 PMCID: PMC6827282 DOI: 10.1074/jbc.ra119.010093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
Copper is critically important for methanotrophic bacteria because their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is copper-dependent. In addition to pMMO, many other copper proteins are encoded in the genomes of methanotrophs, including proteins that contain periplasmic copper-Achaperone (PCuAC) domains. Using bioinformatics analyses, we identified three distinct classes of PCuAC domain-containing proteins in methanotrophs, termed PmoF1, PmoF2, and PmoF3. PCuAC domains from other types of bacteria bind a single Cu(I) ion via an HXnMX21/22HXM motif, which is also present in PmoF3, but PmoF1 and PmoF2 lack this motif entirely. Instead, the PCuAC domains of PmoF1 and PmoF2 bind only Cu(II), and PmoF1 binds additional Cu(II) ions in a His-rich extension to its PCuAC domain. Crystal structures of the PmoF1 and PmoF2 PCuAC domains reveal that Cu(II) is coordinated by an N-terminal histidine brace HX10H motif. This binding site is distinct from those of previously characterized PCuAC domains but resembles copper centers in CopC proteins and lytic polysaccharide monooxygenase (LPMO) enzymes. Bioinformatics analysis of the entire PCuAC family reveals previously unappreciated diversity, including sequences that contain both the HXnMX21/22HXM and HX10H motifs, and sequences that lack either set of copper-binding ligands. These findings provide the first characterization of an additional class of copper proteins from methanotrophs, further expand the PCuAC family, and afford new insight into the biological significance of histidine brace-mediated copper coordination.
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Affiliation(s)
- Oriana S. Fisher
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Madison R. Sendzik
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Matthew O. Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Thomas J. Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, To whom correspondence should be addressed:
Depts. of Molecular Biosciences and Chemistry, Northwestern University, Evanston, IL 60208. Tel.:
847-467-5301; Fax:
847-467-6489; E-mail:
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Kruse T, Ratnadevi CM, Erikstad HA, Birkeland NK. Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives. BMC Genomics 2019; 20:642. [PMID: 31399023 PMCID: PMC6688271 DOI: 10.1186/s12864-019-5995-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The candidate genus "Methylacidiphilum" comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizers. The genes pmoCAB, encoding the particulate methane monooxygenase do not originate from horizontal gene transfer from proteobacteria. Instead, the "Ca. Methylacidiphilum" and the sister genus "Ca. Methylacidimicrobium" represent a novel and hitherto understudied evolutionary lineage of aerobic methane oxidizers. Obtaining and comparing the full genome sequences is an important step towards understanding the evolution and physiology of this novel group of organisms. RESULTS Here we present the closed genome of "Ca. Methylacidiphilum kamchatkense" strain Kam1 and a comparison with the genomes of its two closest relatives "Ca. Methylacidiphilum fumariolicum" strain SolV and "Ca. Methylacidiphilum infernorum" strain V4. The genome consists of a single 2,2 Mbp chromosome with 2119 predicted protein coding sequences. Genome analysis showed that the majority of the genes connected with metabolic traits described for one member of "Ca. Methylacidiphilum" is conserved between all three genomes. All three strains encode class I CRISPR-cas systems. The average nucleotide identity between "Ca. M. kamchatkense" strain Kam1 and strains SolV and V4 is ≤95% showing that they should be regarded as separate species. Whole genome comparison revealed a high degree of synteny between the genomes of strains Kam1 and SolV. In contrast, comparison of the genomes of strains Kam1 and V4 revealed a number of rearrangements. There are large differences in the numbers of transposable elements found in the genomes of the three strains with 12, 37 and 80 transposable elements in the genomes of strains Kam1, V4 and SolV respectively. Genomic rearrangements and the activity of transposable elements explain much of the genomic differences between strains. For example, a type 1h uptake hydrogenase is conserved between strains Kam1 and SolV but seems to have been lost from strain V4 due to genomic rearrangements. CONCLUSIONS Comparing three closed genomes of "Ca. Methylacidiphilum" spp. has given new insights into the evolution of these organisms and revealed large differences in numbers of transposable elements between strains, the activity of these explains much of the genomic differences between strains.
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Affiliation(s)
- Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
| | | | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
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