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Prakasha G, Revanasiddappa H, Jayalakshmi B, Borappa S, Siddaiah K, Shivamallu C, Shati AA, Alfaifi MY, Elbehairi SEI, Singh P, Setty PBS, Kollur SP. Co(III), Ni(II), Pd(II) and Pt(II) complexes derived from new benzimidazole-based imine ligands: Preparation, structure, antibacterial, HSA binding and DNA interaction studies. Inorganica Chim Acta 2024; 565:121981. [DOI: 10.1016/j.ica.2024.121981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
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2
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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024. [PMID: 38555564 DOI: 10.1111/febs.17125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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3
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Basak P, Cabelli DE, Chivers PT, Farquhar ER, Maroney MJ. In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation. Metallomics 2023; 15:mfad054. [PMID: 37723610 PMCID: PMC10628968 DOI: 10.1093/mtomcs/mfad054] [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: 06/13/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
The importance of cellular low molecular weight ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of nickel-dependent superoxide dismutase (NiSOD) from Streptomyces coelicolor. In vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.
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Affiliation(s)
- Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Diane E Cabelli
- Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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4
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Aptekmann AA, Buongiorno J, Giovannelli D, Glamoclija M, Ferreiro DU, Bromberg Y. mebipred: identifying metal binding potential in protein sequence. Bioinformatics 2022; 38:3532-3540. [PMID: 35639953 PMCID: PMC9272798 DOI: 10.1093/bioinformatics/btac358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/27/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Motivation metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Results we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred’s utility in analyzing microbiome metal requirements. Availability and implementation mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA.,Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | | | - D Giovannelli
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,Department of Biology, University of Naples Federico II, Naples, Italy.,Institute for Marine Biological Resources and Biotechnology-IRBIM, National Research Council of Italy, CNR, Ancona, Italy
| | - M Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, New Brunswick, NJ, 07102, USA
| | - D U Ferreiro
- Protein Physiology Lab, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, 1428, Argentina
| | - Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA
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5
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Kelley BR, Lu J, Haley KP, Gaddy JA, Johnson JG. Metal homeostasis in pathogenic Epsilonproteobacteria: mechanisms of acquisition, efflux, and regulation. Metallomics 2021; 13:mfaa002. [PMID: 33570133 PMCID: PMC8043183 DOI: 10.1093/mtomcs/mfaa002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
Epsilonproteobacteria are a diverse class of eubacteria within the Proteobacteria phylum that includes environmental sulfur-reducing bacteria and the human pathogens, Campylobacter jejuni and Helicobacter pylori. These pathogens infect and proliferate within the gastrointestinal tracts of multiple animal hosts, including humans, and cause a variety of disease outcomes. While infection of these hosts provides nutrients for the pathogenic Epsilonproteobacteria, many hosts have evolved a variety of strategies to either sequester metals from the invading pathogen or exploit the toxicity of metals and drive their accumulation as an antimicrobial strategy. As a result, C. jejuni and H. pylori have developed mechanisms to sense changes in metal availability and regulate their physiology in order to respond to either metal limitation or accumulation. In this review, we will discuss the challenges of metal availability at the host-pathogen interface during infection with C. jejuni and H. pylori and describe what is currently known about how these organisms alter their gene expression and/or deploy bacterial virulence factors in response to these environments.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Jacky Lu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
| | - Kathryn P Haley
- Department of Biology, Grand Valley State University, Grand Rapids, MI, USA
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Liu Y, Serrano A, Wyman V, Marcellin E, Southam G, Vaughan J, Villa-Gomez D. Nickel complexation as an innovative approach for nickel-cobalt selective recovery using sulfate-reducing bacteria. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123506. [PMID: 32712361 DOI: 10.1016/j.jhazmat.2020.123506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
This study evaluated the differences in nickel (Ni) and cobalt (Co) solubility in the presence of sulfate reducing bacteria (SRB) to evaluate the feasibility of selective recovery of both metals from mine-impacted waters. A series of sulfate reducing activity tests with Ni, Co and both metals showed that up to 99 % Ni remained soluble despite the availability of sulfide for precipitation, while Co sulfide precipitation always occurred (over 84.5 %). The characterization of proteins in the liquid phase of the experiments revealed that some proteins were only produced in the experiments where Ni displayed higher solubility, suggesting their involvement in metal complexation. Some functions of these proteins included maintaining Ni homeostasis, acting as metalloenzymes and containing Ni-binding ligands. Desulfomicrobium baculatum, Stenotrophomonas maltophilia, and Desulfovibrio magneticus, were the main responsible species producing these proteins.
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Affiliation(s)
- Yun Liu
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia.
| | - Antonio Serrano
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
| | - Valentina Wyman
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 QLD, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, 4072 QLD, Australia
| | - James Vaughan
- School of Chemical Engineering, The University of Queensland, 4072 QLD, Australia
| | - Denys Villa-Gomez
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
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Kambunga SN, Candeias C, Hasheela I, Mouri H. Review of the nature of some geophagic materials and their potential health effects on pregnant women: some examples from Africa. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:2949-2975. [PMID: 30977022 DOI: 10.1007/s10653-019-00288-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The voluntary human consumption of soil known as geophagy is a global practice and deep-rooted in many African cultures. The nature of geophagic material varies widely from the types to the composition. Generally, clay and termite mound soils are the main materials consumed by geophagists. Several studies revealed that gestating women across the world consume more soil than other groups for numerous motives. These motivations are related to medicinal, cultural and nutrients supplementation. Although geophagy in pregnancy (GiP) is a universal dynamic habit, the highest prevalence has been reported in African countries such as Kenya, Ghana, Rwanda, Nigeria, Tanzania, and South Africa. Geophagy can be both beneficial and detrimental. Its health effects depend on the amount and composition of the ingested soils, which is subjective to the geology and soil formation processes. In most cases, the negative health effects concomitant with the practice of geophagy eclipse the positive effects. Therefore, knowledge about the nature of geophagic material and the health effects that might arise from their consumption is important.
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Affiliation(s)
- Selma N Kambunga
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - Carla Candeias
- GeoBioTec, Geosciences Department, University of Aveiro, Aveiro, Portugal
- EpiUnit, Public Health Institute, University of Porto, Porto, Portugal
| | - Israel Hasheela
- Environmental and Engineering Geology Division, Geological Survey of Namibia, Windhoek, Namibia
| | - Hassina Mouri
- Department of Geology, University of Johannesburg, Johannesburg, South Africa.
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8
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Knuutinen J, Bomberg M, Kemell M, Lusa M. Ni(II) Interactions in Boreal Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. Strains Isolated From an Acidic, Ombrotrophic Bog. Front Microbiol 2019; 10:2677. [PMID: 31849859 PMCID: PMC6901981 DOI: 10.3389/fmicb.2019.02677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/04/2019] [Indexed: 12/04/2022] Open
Abstract
The uptake of nickel [Ni(II)] by Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. strains isolated from a boreal bog was studied using batch experiments. All strains removed Ni(II) from the solution and the uptake efficiency was affected by the nutrient source, incubation temperature, time, and pH. As highest Ni uptake (with a maximum Kd of 1890 L/kg DW) was recorded for the Pseudomonas sp. strains, these bacteria were used in the following protein expression (SDS-PAGE and MALDI-TOFF), transmission electron microscopy (TEM) and EDS experiments. In addition, Freundlich and Langmuir sorption isotherms were determined. In the Ni(II) treated cells, dense crystalline intra-cellular accumulations were observed in TEM examinations, which were identified as Ni accumulations using EDS. SDS-PAGE and MALDI-TOFF spectra of Ni(II) treated cells showed several changes in the protein profiles, which can indicate active accumulation of Ni in these bacteria. Concurrently, we observed Ni(II) uptake to follow Freundlich and Langmuir isotherms, suggesting straight cellular biosorption in addition to the intra-cellular accumulation. The role of cellular (cell membrane and cell wall) functional groups involved in Ni(II) binding were therefore studied using Fourier transformation infrared spectroscopy. These analyses supported the potential role of the alcoholic hydroxyl, carboxyl and amine groups in Ni(II) binding in these bacteria, therefore suggesting two different Ni(II) uptake mechanisms; (i) intra-cellular accumulation [possibly connected to detoxification of Ni(II)], and (ii) straight biosorption on cell membrane/wall functional groups.
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Affiliation(s)
- Jenna Knuutinen
- Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Marianna Kemell
- Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Merja Lusa
- Department of Chemistry, University of Helsinki, Helsinki, Finland
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9
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Abstract
Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.
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10
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Gomathi V, Selvameena R. Spectroscopic investigation, fluorescence quenching, in vitro antibacterial and cytotoxicity assay of Co(II) and Ni(II) complexes containing 4-((3-ethoxy-2-hydroxy benzylidene)amino)-N-(pyridin-2-yl)benzenesulfonamide. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Grim KP, San Francisco B, Radin JN, Brazel EB, Kelliher JL, Párraga Solórzano PK, Kim PC, McDevitt CA, Kehl-Fie TE. The Metallophore Staphylopine Enables Staphylococcus aureus To Compete with the Host for Zinc and Overcome Nutritional Immunity. mBio 2017; 8:e01281-17. [PMID: 29089427 PMCID: PMC5666155 DOI: 10.1128/mbio.01281-17] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/27/2017] [Indexed: 12/18/2022] Open
Abstract
During infection, the host sequesters essential nutrients, such as zinc, to combat invading microbes. Despite the ability of the immune effector protein calprotectin to bind zinc with subpicomolar affinity, Staphylococcus aureus is able to successfully compete with the host for zinc. However, the zinc importers expressed by S. aureus remain unknown. Our investigations have revealed that S. aureus possesses two importers, AdcABC and CntABCDF, which are induced in response to zinc limitation. While AdcABC is similar to known zinc importers in other bacteria, CntABCDF has not previously been associated with zinc acquisition. Concurrent loss of the two systems severely impairs the ability of S. aureus to obtain zinc and grow in zinc-limited environments. Further investigations revealed that the Cnt system is responsible for the ability of S. aureus to compete with calprotectin for zinc in culture and contributes to acquisition of zinc during infection. The cnt locus also enables S. aureus to produce the broad-spectrum metallophore staphylopine. Similarly to the Cnt transporter, loss of staphylopine severely impairs the ability of S. aureus to resist host-imposed zinc starvation, both in culture and during infection. Further investigations revealed that together staphylopine and the Cnt importer function analogously to siderophore-based iron acquisition systems in order to facilitate zinc acquisition by S. aureus Analogous systems are found in a broad range of Gram-positive and Gram-negative bacterial pathogens, suggesting that this new type of zinc importer broadly contributes to the ability of bacteria to cause infection.IMPORTANCE A critical host defense against infection is the restriction of zinc availability. Despite the subpicomolar affinity of the immune effector calprotectin for zinc, Staphylococcus aureus can successfully compete for this essential metal. Here, we describe two zinc importers, AdcABC and CntABCDF, possessed by S. aureus, the latter of which has not previously been associated with zinc acquisition. The ability of S. aureus to compete with the host for zinc is dependent on CntABCDF and the metallophore staphylopine, both in culture and during infection. These results expand the mechanisms utilized by bacteria to obtain zinc, beyond Adc-like systems, and demonstrate that pathogens utilize strategies similar to siderophore-based iron acquisition to obtain other essential metals during infection. The staphylopine synthesis machinery is present in a diverse collection of bacteria, suggesting that this new family of zinc importers broadly contributes to the ability of numerous pathogens to cause infection.
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Affiliation(s)
- Kyle P Grim
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Brian San Francisco
- Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jana N Radin
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Erin B Brazel
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jessica L Kelliher
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Paola K Párraga Solórzano
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Philip C Kim
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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12
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Elucidation of the biosynthesis of the methane catalyst coenzyme F 430. Nature 2017; 543:78-82. [PMID: 28225763 PMCID: PMC5337119 DOI: 10.1038/nature21427] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Methane biogenesis in methanogens is mediated by methyl-coenzyme M reductase, an enzyme that is also responsible for the utilisation of methane through anaerobic methane oxidation. The enzyme employs an ancillary factor called coenzyme F430, a nickel-containing modified tetrapyrrole that promotes catalysis through a novel methyl radical/Ni(II)-thiolate intermediate. However, the biosynthesis of coenzyme F430 from the common primogenitor uroporphyrinoge III, incorporating 11 steric centres into the macrocycle, has remained poorly understood although the pathway must involve chelation, amidation, macrocyclic ring reduction, lactamisation and carbocyclic ring formation. We have now identified the proteins that catalyse coenzyme F430 biosynthesis from sirohydrochlorin, termed CfbA-E, and shown their activity. The research completes our understanding of how nature is able to construct its repertoire of tetrapyrrole-based life pigments, permitting the development of recombinant systems to utilise these metalloprosthetic groups more widely.
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13
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Zeer-Wanklyn CJ, Zamble DB. Microbial nickel: cellular uptake and delivery to enzyme centers. Curr Opin Chem Biol 2017; 37:80-88. [PMID: 28213182 DOI: 10.1016/j.cbpa.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 01/29/2023]
Abstract
Nickel enzymes allow microorganisms to access chemistry that can be vital for survival and virulence. In this review we highlight recent work on several systems that import nickel ions and deliver them to the active sites of these enzymes. Small molecules, in particular l-His and derivatives, may chelate nickel ions before import at TonB-dependent outer-membrane and ABC-type inner-membrane transporters. Inside the cell, nickel ions are used by maturation factors required to produce nickel enzymes such as [NiFe]-hydrogenase, urease and lactate racemase. These accessory proteins often exhibit metal selectivity and frequently include an NTP-hydrolyzing metallochaperone protein. The research described provides a deeper understanding of the processes that allow microorganisms to access nickel ions from the environment and incorporate them into nickel proteins.
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Affiliation(s)
- Conor J Zeer-Wanklyn
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
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14
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Fischer F, Robbe-Saule M, Turlin E, Mancuso F, Michel V, Richaud P, Veyrier FJ, De Reuse H, Vinella D. Characterization in Helicobacter pylori of a Nickel Transporter Essential for Colonization That Was Acquired during Evolution by Gastric Helicobacter Species. PLoS Pathog 2016; 12:e1006018. [PMID: 27923069 PMCID: PMC5140060 DOI: 10.1371/journal.ppat.1006018] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/21/2016] [Indexed: 12/23/2022] Open
Abstract
Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease. Using a genetic screen, we identified an ABC transporter, that we designated NiuBDE, as a novel H. pylori nickel transport system. Unmarked mutants carrying deletions of nixA, niuD and/or niuB, were constructed and used to measure (i) tolerance to toxic nickel exposure, (ii) intracellular nickel content by ICP-OES, (iii) transport of radioactive nickel and (iv) expression of a reporter gene controlled by nickel concentration. We demonstrated that NiuBDE and NixA function separately and are the sole nickel transporters in H. pylori. NiuBDE, but not NixA, also transports cobalt and bismuth, a metal currently used in H. pylori eradication therapy. Both NiuBDE and NixA participate in nickel-dependent urease activation at pH 5 and survival under acidic conditions mimicking those encountered in the stomach. However, only NiuBDE is able to carry out this activity at neutral pH and is essential for colonization of the mouse stomach. Phylogenomic analyses indicated that both nixA and niuBDE genes have been acquired via horizontal gene transfer by the last common ancestor of the gastric Helicobacter species. Our work highlights the importance of this evolutionary event for the emergence of Helicobacter gastric species that are adapted to the hostile environment of the stomach where the capacity of Helicobacter to import nickel and thereby activate urease needs to be optimized.
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Affiliation(s)
- Frédéric Fischer
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
| | - Marie Robbe-Saule
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
| | - Evelyne Turlin
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
| | - Francesco Mancuso
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
| | - Valérie Michel
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
| | - Pierre Richaud
- CEA, DRF, BIAM SBVME and CNRS, UMR 7265, Saint-Paul-lez-Durance, Aix Marseille Université, Marseille, FRANCE
| | - Frédéric J. Veyrier
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, Laval, Quebec, CANADA
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
- * E-mail:
| | - Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, FRANCE
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