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Hossain S, Morey JR, Neville SL, Ganio K, Radin JN, Norambuena J, Boyd JM, McDevitt CA, Kehl-Fie TE. Host subversion of bacterial metallophore usage drives copper intoxication. mBio 2023; 14:e0135023. [PMID: 37737591 PMCID: PMC10653882 DOI: 10.1128/mbio.01350-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE During infection, bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes S. aureus to copper intoxication. In response to zinc starvation, S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.
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Affiliation(s)
- Saika Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jacqueline R. Morey
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jana N. Radin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Jeff M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas E. Kehl-Fie
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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2
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Bonhomme L, Dubard L, Riha M, Rodrigues A, Aussel L. [Metallophores: The metal rush]. Med Sci (Paris) 2023; 39:676-680. [PMID: 37695159 DOI: 10.1051/medsci/2023104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Affiliation(s)
- Laura Bonhomme
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Ludovic Dubard
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Melvin Riha
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Anthony Rodrigues
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
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3
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Seregin IV, Kozhevnikova AD. Nicotianamine: A Key Player in Metal Homeostasis and Hyperaccumulation in Plants. Int J Mol Sci 2023; 24:10822. [PMID: 37446000 DOI: 10.3390/ijms241310822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Nicotianamine (NA) is a low-molecular-weight N-containing metal-binding ligand, whose accumulation in plant organs changes under metal deficiency or excess. Although NA biosynthesis can be induced in vivo by various metals, this non-proteinogenic amino acid is mainly involved in the detoxification and transport of iron, zinc, nickel, copper and manganese. This review summarizes the current knowledge on NA biosynthesis and its regulation, considers the mechanisms of NA secretion by plant roots, as well as the mechanisms of intracellular transport of NA and its complexes with metals, and its role in radial and long-distance metal transport. Its role in metal tolerance is also discussed. The NA contents in excluders, storing metals primarily in roots, and in hyperaccumulators, accumulating metals mainly in shoots, are compared. The available data suggest that NA plays an important role in maintaining metal homeostasis and hyperaccumulation mechanisms. The study of metal-binding compounds is of interdisciplinary significance, not only regarding their effects on metal toxicity in plants, but also in connection with the development of biofortification approaches to increase the metal contents, primarily of iron and zinc, in agricultural plants, since the deficiency of these elements in food crops seriously affects human health.
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Affiliation(s)
- Ilya V Seregin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St., 35, 127276 Moscow, Russia
| | - Anna D Kozhevnikova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St., 35, 127276 Moscow, Russia
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4
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Hossain S, Morey JR, Neville SL, Ganio K, Radin JN, Norambuena J, Boyd JM, McDevitt CA, Kehl-Fie TE. Host subversion of bacterial metallophore usage drives copper intoxication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542972. [PMID: 37398167 PMCID: PMC10312489 DOI: 10.1101/2023.05.30.542972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microorganisms can acquire metal ions in metal-limited environments using small molecules called metallophores. While metals and their importers are essential, metals can also be toxic, and metallophores have limited ability to discriminate metals. The impact of the metallophore-mediated non-cognate metal uptake on bacterial metal homeostasis and pathogenesis remains to be defined. The globally significant pathogen Staphylococcus aureus uses the Cnt system to secrete the metallophore staphylopine in zinc-limited host niches. Here, we show that staphylopine and the Cnt system facilitate bacterial copper uptake, potentiating the need for copper detoxification. During in vivo infection, staphylopine usage increased S. aureus susceptibility to host-mediated copper stress, indicating that the innate immune response can harness the antimicrobial potential of altered elemental abundances in host niches. Collectively, these observations show that while the broad-spectrum metal-chelating properties of metallophores can be advantageous, the host can exploit these properties to drive metal intoxication and mediate antibacterial control. IMPORTANCE During infection bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes Staphylococcus aureus to copper intoxication. In response to zinc starvation S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.
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Affiliation(s)
- Saika Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jacqueline R Morey
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Jana N Radin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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5
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Seebach H, Radow G, Brunek M, Schulz F, Piotrowski M, Krämer U. Arabidopsis Nicotianamine Synthases (NAS) comprise a common core-NAS domain fused to a variable auto-inhibitory C-terminus. J Biol Chem 2023:104732. [PMID: 37086785 DOI: 10.1016/j.jbc.2023.104732] [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: 10/14/2022] [Revised: 03/07/2023] [Accepted: 04/12/2023] [Indexed: 04/24/2023] Open
Abstract
Nicotianamine Synthase (NAS) catalyzes the biosynthesis of the low-molecular-mass metal chelator nicotianamine (NA) from the 2-aminobutyrate moieties of three S-adenosylmethionine molecules. NA has central roles in metal nutrition and metal homeostasis of flowering plants. The enzymatic function of NAS remains poorly understood. Crystal structures are available of archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyl transferase reactions. Here we report amino acids essential for the activity of AtNAS1 based on structural modeling and site-directed mutagenesis. Using a newly developed enzyme-coupled continuous activity assay, we compare differing NAS proteins identified through multiple sequence alignments and phylogenetic analyses. In most NAS of dicotyledonous and monocotyledonous plants (class Ia and Ib), the core-NAS domain is fused to a variable C-terminal domain. Compared to fungal and moss NAS that comprise merely a core-NAS domain (class III), NA biosynthetic activities of the four paralogous Arabidopsis thaliana NAS proteins were far lower. C-terminally trimmed core-AtNAS variants exhibited strongly elevated activities. Of 320 amino acids of AtNAS1, twelve, 287-TRGCMFMPCNCS-298, accounted for the auto-inhibitory effect of the C-terminus, of which approximately one-third was attributed to N296 within a CNCS motif that is fully conserved in Arabidopsis. No detectable NA biosynthesis was mediated by two representative plant NAS proteins that naturally lack the C-terminal domain, class Ia Arabidopsis halleri NAS5, and Medicago truncatula NAS2 of class II which is found in dicots and diverged early during the evolution of flowering plants. Next we will address a possible post-translational release of auto-inhibition in class I NAS proteins.
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Affiliation(s)
- Hiroyuki Seebach
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Radow
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Brunek
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Frank Schulz
- Chemistry and Biochemistry of Natural Products, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Markus Piotrowski
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
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6
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Tian L, Wang L, Zhang X, Huang X, Wang F, Zhu S, Li X, Guan Y. Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:24284-24298. [PMID: 36334202 DOI: 10.1007/s11356-022-23539-y] [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: 01/11/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.
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Affiliation(s)
- Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Lin Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Xiaofeng Zhang
- Qingdao Water Development Service Center, Qingdao, 266071, China
| | - Xuda Huang
- Qingdao Water Development Service Center, Qingdao, 266071, China
| | - Fuhao Wang
- Qingdao Water Affairs Group, Environmental Energy Co., Ltd, Qingdao, 266075, China
| | - Sifu Zhu
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
| | - Xueqiang Li
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
| | - Ying Guan
- Qingdao Haibo River Water Operation Co., Ltd, Qingdao, 266021, China
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7
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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8
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Secli V, Di Biagio C, Martini A, Michetti E, Pacello F, Ammendola S, Battistoni A. Localized Infections with P. aeruginosa Strains Defective in Zinc Uptake Reveal That Zebrafish Embryos Recapitulate Nutritional Immunity Responses of Higher Eukaryotes. Int J Mol Sci 2023; 24:ijms24020944. [PMID: 36674459 PMCID: PMC9862628 DOI: 10.3390/ijms24020944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
The innate immune responses of mammals to microbial infections include strategies based on manipulating the local concentration of metals such as iron (Fe) and zinc (Zn), commonly described as nutritional immunity. To evaluate whether these strategies are also present in zebrafish embryos, we have conducted a series of heart cavity-localized infection experiments with Pseudomonas aeruginosa strains characterized by a different ability to acquire Zn. We have found that, 48 h after infection, the bacterial strains lacking critical components of the Zn importers ZnuABC and ZrmABCD have a reduced colonization capacity compared to the wild-type strain. This observation, together with the finding of a high level of expression of Zur-regulated genes, suggests the existence of antimicrobial mechanisms based on Zn sequestration. However, we have observed that strains lacking such Zn importers have a selective advantage over the wild-type strain in the early stages of infection. Analysis of the expression of the gene that encodes for a Zn efflux pump has revealed that at short times after infection, P. aeruginosa is exposed to high concentrations of Zn. At the same time, zebrafish respond to the infection by activating the expression of the Zn transporters Slc30a1 and Slc30a4, whose mammalian homologs mediate a redistribution of Zn in phagocytes aimed at intoxicating bacteria with a metal excess. These observations indicate that teleosts share similar nutritional immunity mechanisms with higher vertebrates, and confirm the usefulness of the zebrafish model for studying host-pathogen interactions.
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Affiliation(s)
- Valerio Secli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Claudia Di Biagio
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Arianna Martini
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Council for Agricultural Research and Economics, Research, Centre for Animal Production and Aquaculture, Via Salaria 31, 00015 Monterotondo, Italy
| | - Emma Michetti
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Serena Ammendola
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
- Correspondence:
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9
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Harrington SA, Connorton JM, Nyangoma NIM, McNelly R, Morgan YML, Aslam MF, Sharp PA, Johnson AAT, Uauy C, Balk J. A two-gene strategy increases iron and zinc concentrations in wheat flour, improving mineral bioaccessibility. PLANT PHYSIOLOGY 2023; 191:528-541. [PMID: 36308454 PMCID: PMC9806615 DOI: 10.1093/plphys/kiac499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/13/2022] [Indexed: 05/09/2023]
Abstract
Dietary deficiencies of iron and zinc cause human malnutrition that can be mitigated by biofortified staple crops. Conventional breeding approaches to increase grain mineral concentrations in wheat (Triticum aestivum L.) have had only limited success, and our understanding of the genetic and physiological barriers to altering this trait is incomplete. Here we demonstrate that a transgenic approach combining endosperm-specific expression of the wheat VACUOLAR IRON TRANSPORTER gene TaVIT2-D with constitutive expression of the rice (Oryza sativa) NICOTIANAMINE SYNTHASE gene OsNAS2 significantly increases the total concentration of zinc and relocates iron to white-flour fractions. In two distinct bread wheat cultivars, we show that the so called VIT-NAS construct led to a two-fold increase in zinc in wholemeal flour, to ∼50 µg g-1. Total iron was not significantly increased, but redistribution within the grain resulted in a three-fold increase in iron in highly pure, roller-milled white flour, to ∼25 µg g-1. Interestingly, expression of OsNAS2 partially restored iron translocation to the aleurone, which is iron depleted in grain overexpressing TaVIT2 alone. A greater than three-fold increase in the level of the natural plant metal chelator nicotianamine in the grain of VIT-NAS lines corresponded with improved iron and zinc bioaccessibility in white flour. The growth of VIT-NAS plants in the greenhouse was indistinguishable from untransformed controls. Our results provide insights into mineral translocation and distribution in wheat grain and demonstrate that the individual and combined effects of the two transgenes can enhance the nutritional quality of wheat beyond what is possible by conventional breeding.
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Affiliation(s)
| | - James M Connorton
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Rose McNelly
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Yvie M L Morgan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Mohamad F Aslam
- Department of Nutritional Sciences, King’s College London, London SE1 9NH, UK
| | - Paul A Sharp
- Department of Nutritional Sciences, King’s College London, London SE1 9NH, UK
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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10
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Ducret V, Gonzalez D, Perron K. Zinc homeostasis in Pseudomonas. Biometals 2022:10.1007/s10534-022-00475-5. [PMID: 36472780 PMCID: PMC10393844 DOI: 10.1007/s10534-022-00475-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
AbstractIn the genus Pseudomonas, zinc homeostasis is mediated by a complete set of import and export systems, whose expression is precisely controlled by three transcriptional regulators: Zur, CzcR and CadR. In this review, we describe in detail our current knowledge of these systems, their regulation, and the biological significance of zinc homeostasis, taking Pseudomonas aeruginosa as our paradigm. Moreover, significant parts of this overview are dedicated to highlight interactions and cross-regulations between zinc and copper import/export systems, and to shed light, through a review of the literature and comparative genomics, on differences in gene complement and function across the whole Pseudomonas genus. The impact and importance of zinc homeostasis in Pseudomonas and beyond will be discussed throughout this review.
Graphical abstract
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11
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Reitz ZL, Medema MH. Genome mining strategies for metallophore discovery. Curr Opin Biotechnol 2022; 77:102757. [PMID: 35914390 DOI: 10.1016/j.copbio.2022.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Many bacteria use small-molecule chelators called metallophores to acquire trace metals from their environment. These molecules play a central role in interactions between bacteria, plants, and animals. Hence, knowing their full diversity is key to combatting infectious diseases as well as harnessing beneficial microbial communities. Metallophore discovery has been streamlined by advances in genome mining, where genomes are scanned for genes involved in metallophore biosynthesis. This review highlights recent trends and advances in predicting the presence and structure of metallophores based solely on genomic information. Recent work suggests new families of metallophores remain hidden from current homology-based approaches. Their discovery will require new genome mining approaches that move beyond biosynthesis to consider metallophore transporters, regulation, and evolution.
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Affiliation(s)
- Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
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12
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Chorianopoulou SN, Bouranis DL. The Role of Sulfur in Agronomic Biofortification with Essential Micronutrients. PLANTS 2022; 11:plants11151979. [PMID: 35956455 PMCID: PMC9370111 DOI: 10.3390/plants11151979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Sulfur (S) is an essential macronutrient for plants, being necessary for their growth and metabolism and exhibiting diverse roles throughout their life cycles. Inside the plant body, S is present either in one of its inorganic forms or incorporated in an organic compound. Moreover, organic S compounds may contain S in its reduced or oxidized form. Among others, S plays roles in maintaining the homeostasis of essential micronutrients, e.g., iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn). One of the most well-known connections is homeostasis between S and Fe, mainly in terms of the role of S in uptake, transportation, and distribution of Fe, as well as the functional interactions of S with Fe in the Fe-S clusters. This review reports the available information describing the connections between the homeostasis of S and Fe, Cu, Zn, and Mn in plants. The roles of S- or sulfur-derived organic ligands in metal uptake and translocation within the plant are highlighted. Moreover, the roles of these micronutrients in S homeostasis are also discussed.
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13
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Kumar S, Vinella D, De Reuse H. Nickel, an essential virulence determinant of Helicobacter pylori: Transport and trafficking pathways and their targeting by bismuth. Adv Microb Physiol 2022; 80:1-33. [PMID: 35489790 DOI: 10.1016/bs.ampbs.2022.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Nickel is required for the pathogenicity of H. pylori. This bacterial pathogen colonizes the stomach of about half of the human population worldwide and is associated with gastric cancer that is responsible for 800,000 deaths per year. H. pylori possesses two nickel-enzymes that are essential for in vivo colonization, a [NiFe] hydrogenase and an abundant urease responsible for resistance to gastric acidity. Because of these two enzymes, survival of H. pylori relies on an important supply of nickel, implying tight control strategies to avoid its toxic accumulation or deprivation. H. pylori possesses original mechanisms for nickel uptake, distribution, storage and trafficking that will be discussed in this review. During evolution, acquisition of nickel transporters and specific nickel-binding proteins has been a decisive event to allow Helicobacter species to become able to colonize the stomach. Accordingly, many of the factors involved in these mechanisms are required for mouse colonization by H. pylori. These mechanisms are controlled at different levels including protein interaction networks, transcriptional, post-transcriptional and post-translational regulation. Bismuth is another metal used in combination with antibiotics to efficiently treat H. pylori infections. Although the precise mode of action of bismuth is unknown, many targets have been identified in H. pylori and there is growing evidence that bismuth interferes with the essential nickel pathways. Understanding the metal pathways will help improve treatments against H. pylori and other pathogens.
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Affiliation(s)
- Sumith Kumar
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Daniel Vinella
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France.
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. MICROBIOME 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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Luo Z, Luo S, Ju Y, Ding P, Xu J, Gu Q, Zhou H. Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis. FASEB J 2021; 35:e21575. [PMID: 33826776 DOI: 10.1096/fj.202002287rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 11/11/2022]
Abstract
Staphylopine (StP) and other nicotianamine-like metallophores are crucial for many pathogens to acquire the transition metals from hosts during invasion. CntL from Staphylococcus aureus (SaCntL) catalyzes the condensation of the 2-aminobutyrate (Ab) moiety of S-adenosylmethionine (SAM) with D-histidine in the biosynthesis of StP. Here, we report the crystal structures of SaCntL in complex with either SAM or two products. The structure of SaCntL consists of an N-terminal four-helix bundle (holding catalytic residue E84) and a C-terminal Rossmann fold (binding the substrates). The sequence connecting the N- and C-terminal domains (N-C linker) in SaCntL was found to undergo conformational alternation between open and closed states. Our structural and biochemical analyses suggested that this intrinsically dynamic interdomain linker forms an additional structural module that plays essential roles in ligand diffusion, recognition, and catalysis. We confirmed that SaCntL stereoselectively carries out the catalysis of D-His but not its enantiomer, L-His, and we found that the N-C linker and active site of SaCntL could accommodate both enantiomers. SaCntL is likely able to bind L-His without catalysis, and as a result, L-His could show inhibitory effects toward SaCntL. These findings provide critical structural and mechanistic insights into CntL, which facilitates a better understanding of the biosynthesis of nicotianamine-like metallophores and the discovery of inhibitors of this process.
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Affiliation(s)
- Zhiteng Luo
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Siting Luo
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingchen Ju
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Ding
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Xu
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiong Gu
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huihao Zhou
- Research Center for Drug Discovery and Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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Abstract
Drug-resistant infections pose a significant risk to global health as pathogenic bacteria become increasingly difficult to treat. The rapid selection of resistant strains through poor antibiotic stewardship has reduced the number of viable treatments and increased morbidity of infections, especially among the immunocompromised. To circumvent such challenges, new strategies are required to stay ahead of emerging resistance trends, yet research and funding for antibiotic development lags other classes of therapeutics. Though the use of metals in therapeutics has been around for centuries, recent strategies have devoted a great deal of effort into the pathways through which bacteria acquire and utilize iron, which is critical for the establishment of infection. To target iron uptake systems, siderophore-drug conjugates have been developed that hijack siderophore-based iron uptake for delivery of antibiotics. While this strategy has produced several potential leads, the use of siderophores in infection is diminished over time when bacteria adapt to utilize heme as an iron source, leading to a need for the development of porphyrin mimetics as therapeutics. The use of such strategies as well as the inclusion of gallium, a redox-inert iron mimic, are herein reviewed.
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Affiliation(s)
- Garrick Centola
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA.
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