1
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Li Q, Shi M, Liao Q, Li K, Huang X, Sun Z, Yang W, Si M, Yang Z. Molecular response to the influences of Cu(II) and Fe(III) on forming biogenic manganese oxides by Pseudomonas putida MnB1. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135298. [PMID: 39053055 DOI: 10.1016/j.jhazmat.2024.135298] [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: 03/31/2024] [Revised: 06/29/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The biogeochemical cycle of biogenic manganese oxides (BioMnOx) is closely associated with the environmental behavior and fate of various pollutants. It is significantly interfered by many metals, such as Cu and Fe. However, the bacterial molecular responses are not clear. Here, the effects of Cu(II) and Fe(III) on oxidation of manganese by Pseudomonas putida MnB1 and the bacterial molecular response mechanisms have been studied. The bacterial oxidation of manganese were promoted by both Fe(III) and Cu(II) and the final manganese oxidation rate of the Cu(II) group exceeded 16 % that of the Fe(III) group. The results of transcriptome indicated that Cu(II) promoted manganese oxidation by up-regulating the expression levels of multicopper oxidase (MCO) and peroxidase(POD), and by stimulating electron transfer, while Fe(III) promoted this process by accelerating the electron transfer and nitrogen cycling, and activating POD. The protein-protein interaction (PPI) network indicated that the MCO genes (mnxG and mcoA) were directly linked to the copper homeostasis proteins (cusA, cusB, czcC and cusF). Cytochrome c was closely related to the genes related to nitrogen cycling (glnA, glnL, and putA) and electrons transfer (cycO, cycD, nuoA, nuoK, and nuoL), which also promoted manganese oxidation. This study provides a molecular level insight into the oxidation of Mn(II) by Pseudomonas putida MnB1 with Cu(II) and/or Fe(III) ions.
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Affiliation(s)
- Qingzhu Li
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; State Key Laboratory of Advanced Metallurgy for Non-ferrous Metals, Changsha 410083, China; National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha 410083, China; Water Pollution Control Technology Key Lab of Hunan Province, Changsha 410083, China
| | - Miao Shi
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Qi Liao
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; State Key Laboratory of Advanced Metallurgy for Non-ferrous Metals, Changsha 410083, China; National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha 410083, China; Water Pollution Control Technology Key Lab of Hunan Province, Changsha 410083, China.
| | - Kaizhong Li
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Xiaofeng Huang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Zhumei Sun
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; School of Environmental and Safety Engineering, North University of China, Taiyuan 030051, China
| | - Weichun Yang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; State Key Laboratory of Advanced Metallurgy for Non-ferrous Metals, Changsha 410083, China; National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha 410083, China; Water Pollution Control Technology Key Lab of Hunan Province, Changsha 410083, China
| | - Mengying Si
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; State Key Laboratory of Advanced Metallurgy for Non-ferrous Metals, Changsha 410083, China; National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha 410083, China; Water Pollution Control Technology Key Lab of Hunan Province, Changsha 410083, China
| | - Zhihui Yang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; State Key Laboratory of Advanced Metallurgy for Non-ferrous Metals, Changsha 410083, China; National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Central South University, Changsha 410083, China; Water Pollution Control Technology Key Lab of Hunan Province, Changsha 410083, China
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2
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Novikova IV, Soldatova AV, Moser TH, Thibert SM, Romano CA, Zhou M, Tebo BM, Evans JE, Spiro TG. Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization. J Am Chem Soc 2024; 146:22950-22958. [PMID: 39056168 DOI: 10.1021/jacs.3c06537] [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: 07/28/2024]
Abstract
The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The β-sheet-rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE3F3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.
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Affiliation(s)
- Irina V Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Trevor H Moser
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Stephanie M Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Bradley M Tebo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - James E Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
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3
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Gu T, Tong Z, Zhang X, Wang Z, Zhang Z, Hwang TS, Li L. Carbon Metabolism of a Soilborne Mn(II)-Oxidizing Escherichia coli Isolate Implicated as a Pronounced Modulator of Bacterial Mn Oxidation. Int J Mol Sci 2022; 23:ijms23115951. [PMID: 35682628 PMCID: PMC9180420 DOI: 10.3390/ijms23115951] [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: 03/22/2022] [Revised: 04/18/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Mn(II)-oxidizing microorganisms are generally considered the primary driving forces in the biological formation of Mn oxides. However, the mechanistic elucidation of the actuation and regulation of Mn oxidation in soilborne bacteria remains elusive. Here, we performed joint multiple gene-knockout analyses and comparative morphological and physiological determinations to characterize the influence of carbon metabolism on the Mn oxide deposit amount (MnODA) and the Mn oxide formation of a soilborne bacterium, Escherichia coli MB266. Different carbon source substances exhibited significantly varied effects on the MnODA of MB266. A total of 16 carbon metabolism-related genes with significant variant expression levels under Mn supplementation conditions were knocked out in the MB266 genome accordingly, but only little effect on the MnODA of each mutant strain was accounted for. However, a simultaneous four-gene-knockout mutant (namely, MB801) showed an overall remarkable MnODA reduction and an initially delayed Mn oxide formation compared with the wild-type MB266. The assays using scanning/transmission electron microscopy verified that MB801 exhibited not only a delayed Mn-oxide aggregate processing, but also relatively smaller microspherical agglomerations, and presented flocculent deposit Mn oxides compared with normal fibrous and crystalline Mn oxides formed by MB266. Moreover, the Mn oxide aggregate formation was highly related to the intracellular ROS level. Thus, this study demonstrates that carbon metabolism acts as a pronounced modulator of MnODA in MB266, which will provide new insights into the occurrence of Mn oxidation and Mn oxide formation by soilborne bacteria in habitats where Mn(II) naturally occurs.
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Affiliation(s)
- Tong Gu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
| | - Zhenghu Tong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
| | - Xue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
| | - Zhiyong Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei Minzu University, Enshi 445000, China
| | - Zhen Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
- College of Food and Bioengineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Tzann-Shun Hwang
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei 11114, Taiwan
- Correspondence: (T.-S.H.); (L.L.)
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (T.G.); (Z.T.); (X.Z.); (Z.W.); (Z.Z.)
- Correspondence: (T.-S.H.); (L.L.)
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4
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Soldatova AV, Fu W, Romano CA, Tao L, Casey WH, Britt RD, Tebo BM, Spiro TG. Metallo-inhibition of Mnx, a bacterial manganese multicopper oxidase complex. J Inorg Biochem 2021; 224:111547. [PMID: 34403930 DOI: 10.1016/j.jinorgbio.2021.111547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 11/29/2022]
Abstract
The manganese oxidase complex, Mnx, from Bacillus sp. PL-12 contains a multicopper oxidase (MCO) and oxidizes dissolved Mn(II) to form insoluble manganese oxide (MnO2) mineral. Previous kinetic and spectroscopic analyses have shown that the enzyme's mechanism proceeds through an activation step that facilitates formation of a series of binuclear Mn complexes in the oxidation states II, III, and IV on the path to MnO2 formation. We now demonstrate that the enzyme is inhibited by first-row transition metals in the order of the Irving-Williams series. Zn(II) strongly (Ki ~ 1.5 μM) inhibits both activation and turnover steps, as well as the rate of Mn(II) binding. The combined Zn(II) and Mn(II) concentration dependence establishes that the inhibition is non-competitive. This result is supported by electron paramagnetic resonance (EPR) spectroscopy, which reveals unaltered Mnx-bound Mn(II) EPR signals, both mono- and binuclear, in the presence of Zn(II). We infer that inhibitory metals bind at a site separate from the substrate sites and block the conformation change required to activate the enzyme, a case of allosteric inhibition. The likely biological role of this inhibitory site is discussed in the context of Bacillus spore physiology. While Cu(II) inhibits Mnx strongly, in accord with the Irving-Williams series, it increases Mnx activation at low concentrations, suggesting that weakly bound Cu, in addition to the four canonical MCO-Cu, may support enzyme activity, perhaps as an electron transfer agent.
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Wen Fu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - William H Casey
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States; Earth and Planetary Sciences Department, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States.
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5
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Kim J, Park S, Go YK, Jin K, Kim Y, Nam KT, Kim SH. Probing the Structure and Binding Mode of EDTA on the Surface of Mn 3O 4 Nanoparticles for Water Oxidation by Advanced Electron Paramagnetic Resonance Spectroscopy. Inorg Chem 2020; 59:8846-8854. [PMID: 32501692 DOI: 10.1021/acs.inorgchem.0c00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of the surface structure of nanoparticles is important for understanding the catalytic mechanism and improving the properties of the particles. Here, we provide a detailed description of the coordination modes of ethylenediaminetetraacetate (EDTA) on Mn3O4 nanoparticles at the atomic level, as obtained by advanced electron paramagnetic resonance (EPR) spectroscopy. Binding of EDTA to Mn3O4 leads to dramatic changes in the EPR spectrum, with a 5-fold increase in the axial zero-field splitting parameter of Mn(II). This indicates significant changes in the coordination environment of the Mn(II) site; hence, the binding of EDTA causes a profound change in the electronic structure of the manganese site. Furthermore, the electron spin echo envelope modulation results reveal that two 14N atoms of EDTA are directly coordinated to the Mn site and a water molecule is coordinated to the surface of the nanoparticles. An Fourier transform infrared spectroscopy study shows that the Ca(II) ion is coordinated to the carboxylic ligands via the pseudobridging mode. The EPR spectroscopic results provide an atomic picture of surface-modified Mn3O4 nanoparticles for the first time. These results can enhance our understanding of the rational design of catalysts, for example, for the water oxidation reaction.
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Affiliation(s)
- Jin Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Sunghak Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoo Kyung Go
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Kyoungsuk Jin
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yujeong Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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6
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Lingappa UF, Monteverde DR, Magyar JS, Valentine JS, Fischer WW. How manganese empowered life with dioxygen (and vice versa). Free Radic Biol Med 2019; 140:113-125. [PMID: 30738765 DOI: 10.1016/j.freeradbiomed.2019.01.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/25/2019] [Indexed: 01/02/2023]
Abstract
Throughout the history of life on Earth, abiotic components of the environment have shaped the evolution of life, and in turn life has shaped the environment. The element manganese embodies a special aspect of this collaboration; its history is closely entwined with those of photosynthesis and O2-two reigning features that characterize the biosphere today. Manganese chemistry was central to the environmental context and evolutionary innovations that enabled the origin of oxygenic photosynthesis and the ensuing rise of O2. It was also manganese chemistry that provided an early, fortuitous antioxidant system that was instrumental in how life came to cope with oxidative stress and ultimately thrive in an aerobic world. Subsequently, the presence of O2 transformed the biogeochemical dynamics of the manganese cycle, enabling a rich suite of environmental and biological processes involving high-valent manganese and manganese redox cycling. Here, we describe insights from chemistry, biology, and geology, to examine manganese dynamics in the environment, and its unique role in the history of life.
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Affiliation(s)
- Usha F Lingappa
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Danielle R Monteverde
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - John S Magyar
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Joan Selverstone Valentine
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA; Dept. of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Woodward W Fischer
- Div. of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
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7
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Fortman B, Takahashi S. Understanding the Linewidth of the ESR Spectrum Detected by a Single NV Center in Diamond. J Phys Chem A 2019; 123:6350-6355. [PMID: 31294988 DOI: 10.1021/acs.jpca.9b02445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectral analysis of electron spin resonance (ESR) is a powerful technique for various investigations including characterization of spin systems, measurements of spin concentration, and probing spin dynamics. The nitrogen-vacancy (NV) center in diamond is a promising magnetic sensor enabling improvement of ESR sensitivity to the level of a single spin. Therefore, understanding the nature of the NV-detected ESR (NV-ESR) spectrum is critical for applications to nanoscale ESR. Within this work, we investigate the linewidth of NV-ESR from single substitutional nitrogen centers (called P1 centers). NV-ESR is detected by a double electron-electron resonance (DEER) technique. By studying the dependence of the DEER excitation bandwidth on the NV-ESR linewidth, we find that the spectral resolution is improved significantly and eventually limited by inhomogeneous broadening of the detected P1 ESR. Moreover, we show that the NV-ESR linewidth can be as narrow as 0.3 MHz.
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Affiliation(s)
- Benjamin Fortman
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Susumu Takahashi
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States.,Department of Physics & Astronomy , University of Southern California , Los Angeles , California 90089 , United States
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8
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Gagnon DM, Hadley RC, Ozarowski A, Nolan EM, Britt RD. High-Field EPR Spectroscopic Characterization of Mn(II) Bound to the Bacterial Solute-Binding Proteins MntC and PsaA. J Phys Chem B 2019; 123:4929-4934. [PMID: 31117618 DOI: 10.1021/acs.jpcb.9b03633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During infection, the bacterial pathogens Staphylococcus aureus and Streptococcus pneumoniae employ ATP-binding cassette (ABC) transporters to acquire Mn(II), an essential nutrient, from the host environment. Staphylococcal MntABC and streptococcal PsaABC attract the attention of the biophysical and bacterial pathogenesis communities because of their established importance during infection. Previous biophysical examination of Mn(II)-MntC and Mn(II)-PsaA using continuous-wave (≈9 GHz) electron paramagnetic resonance (EPR) spectroscopy revealed broad, difficult-to-interpret spectra (Hadley et al. J. Am. Chem. Soc. 2018, 140, 110-113). Herein, we employ high-frequency (>90 GHz), high-field (>3 T) EPR spectroscopy to investigate the Mn(II)-binding sites of these proteins and determine the spin Hamiltonian parameters. Our analyses demonstrate that the zero-field splitting (ZFS) is large for Mn(II)-MntC and Mn(II)-PsaA at +2.72 and +2.87 GHz, respectively. The measured 55Mn hyperfine coupling values for Mn(II)-MntC and Mn(II)-PsaA of 241 and 236 MHz, respectively, demonstrate a more covalent interaction between Mn(II) and the protein compared to Mn(II) in aqueous solution (≈265 MHz). These studies indicate that MntC and PsaA bind Mn(II) in a similar coordination geometry. Comparison of the ZFS values determined herein with those ascertained for other Mn(II) proteins suggests that the Mn(II)-MntC and Mn(II)-PsaA coordination spheres are not five-coordinate in solution.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry , University of California Davis , Davis , California 95616 , United States
| | - Rose C Hadley
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Elizabeth M Nolan
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - R David Britt
- Department of Chemistry , University of California Davis , Davis , California 95616 , United States
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9
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Medina M, Rizo A, Dinh D, Chau B, Omidvar M, Juarez A, Ngo J, Johnson HA. MopA, the Mn Oxidizing Protein From Erythrobacter sp. SD-21, Requires Heme and NAD + for Mn(II) Oxidation. Front Microbiol 2018; 9:2671. [PMID: 30487779 PMCID: PMC6247904 DOI: 10.3389/fmicb.2018.02671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/19/2018] [Indexed: 11/15/2022] Open
Abstract
Bacterial manganese (Mn) oxidation is catalyzed by a diverse group of microbes and can affect the fate of other elements in the environment. Yet, we understand little about the enzymes that catalyze this reaction. The Mn oxidizing protein MopA, from Erythrobacter sp. strain SD-21, is a heme peroxidase capable of Mn(II) oxidation. Unlike Mn oxidizing multicopper oxidase enzymes, an understanding of MopA is very limited. Sequence analysis indicates that MopA contains an N-terminal heme peroxidase domain and a C-terminal calcium binding domain. Heterologous expression and nickel affinity chromatography purification of the N-terminal peroxidase domain (MopA-hp) from Erythrobacter sp. strain SD-21 led to partial purification. MopA-hp is a heme binding protein that requires heme, NAD+, and calcium (Ca2+) for activity. Mn oxidation is also stimulated by the presence of pyrroloquinoline quinone. MopA-hp has a KM for Mn(II) of 154 ± 46 μM and kcat = 1.6 min−1. Although oxygen requiring MopA-hp is homologous to peroxidases based on sequence, addition of hydrogen peroxide and hydrogen peroxide scavengers had little effect on Mn oxidation, suggesting this is not the oxidizing agent. These studies provide insight into the mechanism by which MopA oxidizes Mn.
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Affiliation(s)
- Michael Medina
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Antonia Rizo
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - David Dinh
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Briana Chau
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Moussa Omidvar
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Andrew Juarez
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Julia Ngo
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
| | - Hope A Johnson
- Department of Biological Science, Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, CA, United States
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10
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Tao L, Stich TA, Soldatova AV, Tebo BM, Spiro TG, Casey WH, Britt RD. Mn(III) species formed by the multi-copper oxidase MnxG investigated by electron paramagnetic resonance spectroscopy. J Biol Inorg Chem 2018; 23:1093-1104. [PMID: 29968177 DOI: 10.1007/s00775-018-1587-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023]
Abstract
The multi-copper oxidase (MCO) MnxG from marine Bacillus bacteria plays an essential role in geochemical cycling of manganese by oxidizing Mn2+(aq) to form manganese oxide minerals at rates that are three to five orders of magnitude faster than abiotic rates. The MCO MnxG protein is isolated as part of a multi-protein complex, denoted as Mnx, which includes one MnxG unit and a hexamer of MnxE3F3 subunit. During the oxidation of Mn2+(aq) catalyzed by the Mnx protein complex, an enzyme-bound Mn(III) species was trapped recently in the presence of pyrophosphate (PP) and analyzed using parallel-mode electron paramagnetic resonance (EPR) spectroscopy. Herein, we provide a full analysis of this enzyme-bound Mn(III) intermediate via temperature dependence studies and spectral simulations. This Mnx-bound Mn(III) species is characterized by a hyperfine-coupling value of A(55Mn) = 4.2 mT (corresponding to 120 MHz) and a negative zero-field splitting (ZFS) value of D = - 2.0 cm-1. These magnetic properties suggest that the Mnx-bound Mn(III) species could be either six-coordinate with a 5B1g ground state or square-pyramidal five-coordinate with a 5B1 ground state. In addition, as a control, Mn(III)PP is also analyzed by parallel-mode EPR spectroscopy. It exhibits distinctly different magnetic properties with a hyperfine-coupling value of A(55Mn) = 4.8 mT (corresponding to 140 MHz) and a negative ZFS value of D = - 2.5 cm-1. The different ZFS values suggest differences in ligand environment of Mnx-bound Mn(III) and aqueous Mn(III)PP species. These studies provide further insights into the mechanism of biological Mn2+(aq) oxidation.
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Affiliation(s)
- Lizhi Tao
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Troy A Stich
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - William H Casey
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Department of Geology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - R David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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11
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Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx. Nat Commun 2017; 8:746. [PMID: 28963463 PMCID: PMC5622069 DOI: 10.1038/s41467-017-00896-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 08/02/2017] [Indexed: 12/28/2022] Open
Abstract
Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes. Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products
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Soldatova AV, Romano CA, Tao L, Stich TA, Casey WH, Britt RD, Tebo BM, Spiro TG. Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Coordinated Two-Stage Mn(II)/(III) and Mn(III)/(IV) Mechanism. J Am Chem Soc 2017; 139:11381-11391. [PMID: 28712303 DOI: 10.1021/jacs.7b02772] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The bacterial manganese oxidase MnxG of the Mnx protein complex is unique among multicopper oxidases (MCOs) in carrying out a two-electron metal oxidation, converting Mn(II) to MnO2 nanoparticles. The reaction occurs in two stages: Mn(II) → Mn(III) and Mn(III) → MnO2. In a companion study , we show that the electron transfer from Mn(II) to the low-potential type 1 Cu of MnxG requires an activation step, likely forming a hydroxide bridge at a dinuclear Mn(II) site. Here we study the second oxidation step, using pyrophosphate (PP) as a Mn(III) trap. PP chelates Mn(III) produced by the enzyme and subsequently allows it to become a substrate for the second stage of the reaction. EPR spectroscopy confirms the presence of Mn(III) bound to the enzyme. The Mn(III) oxidation step does not involve direct electron transfer to the enzyme from Mn(III), which is shown by kinetic measurements to be excluded from the Mn(II) binding site. Instead, Mn(III) is proposed to disproportionate at an adjacent polynuclear site, thereby allowing indirect oxidation to Mn(IV) and recycling of Mn(II). PP plays a multifaceted role, slowing the reaction by complexing both Mn(II) and Mn(III) in solution, and also inhibiting catalysis, likely through binding at or near the active site. An overall mechanism for Mnx-catalyzed MnO2 production from Mn(II) is presented.
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | | | | | | | | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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13
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Soldatova AV, Tao L, Romano CA, Stich TA, Casey WH, Britt RD, Tebo BM, Spiro TG. Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism. J Am Chem Soc 2017; 139:11369-11380. [PMID: 28712284 DOI: 10.1021/jacs.7b02771] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO2 biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu2+, the electron acceptor. Indeed the type 1 Cu2+ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO2 formation from MnO2 nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pKa > 8.6 deprotonation, which is assigned to Mn(II)-bound H2O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pKa 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH)2Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O)2Mn(IV) or an oligomer, which subsequently nucleates MnO2 nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | | | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | | | | | | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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14
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Tao L, Simonov AN, Romano CA, Butterfield CN, Tebo BM, Bond AM, Spiccia L, Martin LL, Casey WH. Probing Electron Transfer in the Manganese‐Oxide‐Forming MnxEFG Protein Complex using Fourier Transformed AC Voltammetry: Understanding the Oxidative Priming Effect. ChemElectroChem 2017. [DOI: 10.1002/celc.201700563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lizhi Tao
- Department of Chemistry University of California One Shields Avenue Davis California 95616 United States
| | - Alexandr N. Simonov
- A School of Chemistry Monash University Victoria 3800 Australia
- ARC Centre of Excellence for Electromaterials Science Monash University Victoria 3800 Australia
| | - Christine A. Romano
- Division of Environmental and Biomolecular Systems Institute of Environmental Health Oregon Health & Science University Portland Oregon 97239 United States
| | - Cristina N. Butterfield
- Division of Environmental and Biomolecular Systems Institute of Environmental Health Oregon Health & Science University Portland Oregon 97239 United States
| | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems Institute of Environmental Health Oregon Health & Science University Portland Oregon 97239 United States
| | - Alan M. Bond
- A School of Chemistry Monash University Victoria 3800 Australia
- ARC Centre of Excellence for Electromaterials Science Monash University Victoria 3800 Australia
| | - Leone Spiccia
- A School of Chemistry Monash University Victoria 3800 Australia
- ARC Centre of Excellence for Electromaterials Science Monash University Victoria 3800 Australia
| | | | - William H. Casey
- Department of Chemistry University of California One Shields Avenue Davis California 95616 United States
- Department of Earth and Planetary Sciences University of California One Shields Avenue Davis California 95616 United States
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Tao L, Stich TA, Liou SH, Soldatova AV, Delgadillo DA, Romano CA, Spiro TG, Goodin DB, Tebo BM, Casey WH, Britt RD. Copper Binding Sites in the Manganese-Oxidizing Mnx Protein Complex Investigated by Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc 2017; 139:8868-8877. [DOI: 10.1021/jacs.7b02277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Alexandra V. Soldatova
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - David A. Delgadillo
- Department of Chemistry & Chemical Biology, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Christine A. Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | | | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
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Manes TA, Rose MJ. Mono- and Dinuclear Manganese Carbonyls Supported by 1,8-Disubstituted (L = Py, SMe, SH) Anthracene Ligand Scaffolds. Inorg Chem 2016; 55:5127-38. [PMID: 27195661 DOI: 10.1021/acs.inorgchem.5b02737] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Presented herein is a synthetic scheme to generate symmetric and asymmetric ligands based on a 1,8-disubstituted anthracene scaffold. The metal-binding scaffolds were prepared by aryl chloride activation of 1,8-dichloroanthracene using Suzuki-type couplings facilitated by [Pd(dba)2] as a Pd source; the choice of cocatalyst (XPhos or SPhos) yielded symmetrically or asymmetrically substituted scaffolds (respectively): namely, Anth-SMe2 (3), Anth-N2 (4), and Anth-NSMe (6). The ligands exhibit a nonplanar geometry in the solid state (X-ray), owing to steric hindrance between the anthracene scaffold and the coupled aryl units. To determine the flexibility and binding characteristics of the anthracene-based ligands, the symmetric scaffolds were complexed with [Mn(CO)5Br] to afford the mononuclear species [(Anth-SMe2)Mn(CO)3Br] (8) and [(Anth-N2)Mn(CO)3Br] (9), in which the donor moieties chelate the Mn center in a cis fashion. The asymmetric ligand Anth-NSMe (6) binds preferentially through the py moieties, affording the bis-ligated complex [(Anth-NSMe)2Mn(CO)3Br] (10), wherein the thioether-S donors remain unbound. Alternatively, deprotection of the thioether in 6 affords the free thiol ligand Anth-NSH (7), which more readily binds the Mn center. Complexation of 7 ultimately affords the mixed-valence Mn(I)/Mn(II) dimer of formula [(Anth-NS)3Mn2(CO)3] (11), which exhibits a fac-{Mn(CO)3} unit supported by a triad of bridging thiolates, which are in turn ligated to a supporting Mn(II) center (EPR: |D| = 0.053 cm(-1), E/|D| = 0.3, Aiso = -150 MHz). All of the metal complexes have been characterized by single-crystal X-ray diffraction, IR spectroscopy and NMR/EPR measurements-all of which demonstrate that the meta-linked, anthracene-based ligand scaffold is a viable approach for the coordination of metal carbonyls.
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Affiliation(s)
- Taylor A Manes
- Department of Chemistry, The University of Texas at Austin , 1 University Station, A5300, Austin, Texas 78712, United States
| | - Michael J Rose
- Department of Chemistry, The University of Texas at Austin , 1 University Station, A5300, Austin, Texas 78712, United States
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The Role of Bacterial Spores in Metal Cycling and Their Potential Application in Metal Contaminant Bioremediation. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.tbs-0018-2013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
Bacteria are one of the premier biological forces that, in combination with chemical and physical forces, drive metal availability in the environment. Bacterial spores, when found in the environment, are often considered to be dormant and metabolically inactive, in a resting state waiting for favorable conditions for them to germinate. However, this is a highly oversimplified view of spores in the environment. The surface of bacterial spores represents a potential site for chemical reactions to occur. Additionally, proteins in the outer layers (spore coats or exosporium) may also have more specific catalytic activity. As a consequence, bacterial spores can play a role in geochemical processes and may indeed find uses in various biotechnological applications. The aim of this review is to introduce the role of bacteria and bacterial spores in biogeochemical cycles and their potential use as toxic metal bioremediation agents.
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