1
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Parker KA, Beratan DN. Undulating Free Energy Landscapes Buffer Redox Chains from Environmental Fluctuations. J Phys Chem B 2024; 128:8933-8945. [PMID: 39244677 DOI: 10.1021/acs.jpcb.4c04637] [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: 09/10/2024]
Abstract
Roller-coaster or undulating free energy landscapes, with alternating high and low potential cofactors, occur frequently in biological redox chains. Yet, there is little understanding of the possible advantages created by these landscapes. We examined the tetraheme subunit associated with Blastochloris viridis reaction centers, comparing the dynamics of the native protein and of hypothetical (in silico) mutants. We computed the variation in the total number of electrons in wild type (WT) and mutant tetrahemes connected to an electron reservoir in the presence of a time-varying potential, as a model for a fluctuating redox environment. We found that roller-coaster free energy landscapes buffer the redox cofactor populations from these fluctuations. The WT roller-coaster landscape slows forward and backward electron transfer in the face of fluctuations, and may offer the advantage of sustaining the reduction of essential cofactors, such as the chlorophyll special pair in photosynthesis, even though an undulating landscape introduces thermodynamically uphill steps in multistep redox chains.
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Affiliation(s)
- Kelsey A Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
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2
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Hu P, Qian Y, Xu Y, Radian A, Yang Y, Gu JD. A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system. WATER RESEARCH X 2024; 24:100237. [PMID: 39155949 PMCID: PMC11327836 DOI: 10.1016/j.wroa.2024.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 08/20/2024]
Abstract
Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.
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Affiliation(s)
- Pengfei Hu
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Youfen Qian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Yanbin Xu
- School of Environmental Sciences and Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Adi Radian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong 510275, People’s Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
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3
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Giri NC, Mintmier B, Radhakrishnan M, Mielke JW, Wilcoxen J, Basu P. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions. J Biol Inorg Chem 2024; 29:395-405. [PMID: 38782786 DOI: 10.1007/s00775-024-02057-x] [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: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.
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Affiliation(s)
- Nitai C Giri
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Jonathan W Mielke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA.
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4
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Louie TS, Kumar A, Bini E, Häggblom MM. Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T. Lett Appl Microbiol 2024; 77:ovae038. [PMID: 38573838 DOI: 10.1093/lambio/ovae038] [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: 11/10/2023] [Revised: 02/12/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.
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Affiliation(s)
- Tiffany S Louie
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Anil Kumar
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences,, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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5
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Askari MJ, Kallick JD, McCrory CCL. Selective Reduction of Aqueous Nitrate to Ammonium with an Electropolymerized Chromium Molecular Catalyst. J Am Chem Soc 2024; 146:7439-7455. [PMID: 38465608 DOI: 10.1021/jacs.3c12783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nitrate (NO3-) is a common nitrogen-containing contaminant in agricultural, industrial, and low-level nuclear wastewater that causes significant environmental damage. In this work, we report a bioinspired Cr-based molecular catalyst incorporated into a redox polymer that selectively and efficiently reduces aqueous NO3- to ammonium (NH4+), a desirable value-added fertilizer component and industrial precursor, at rates of ∼0.36 mmol NH4+ mgcat-1 h-1 with >90% Faradaic efficiency for NH4+. The NO3- reduction reaction occurs through a cascade catalysis mechanism involving the stepwise reduction of NO3- to NH4+ via observed NO2- and NH2OH intermediates. To our knowledge, this is one of the first examples of a molecular catalyst, homogeneous or heterogenized, that is reported to reduce aqueous NO3- to NH4+ with rates and Faradaic efficiencies comparable to those of state-of-the-art solid-state electrocatalysts. This work highlights a promising and previously unexplored area of electrocatalyst research using polymer-catalyst composites containing complexes with oxophilic transition metal active sites for electrochemical nitrate remediation with nutrient recovery.
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Affiliation(s)
- Maiko J Askari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeremy D Kallick
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles C L McCrory
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Song WS, Kim JH, Namgung B, Cho HY, Shin H, Oh HB, Ha NC, Yoon SI. Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG. Int J Biol Macromol 2024; 262:129620. [PMID: 38262549 DOI: 10.1016/j.ijbiomac.2024.129620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
In bacteria, NarJ plays an essential role as a redox enzyme maturation protein in the assembly of the nitrate reductase NarGHI by interacting with the N-terminal signal peptide of NarG to facilitate cofactor incorporation into NarG. The purpose of our research was to elucidate the exact mechanism of NarG signal peptide recognition by NarJ. We determined the structures of NarJ alone and in complex with the signal peptide of NarG via X-ray crystallography and verified the NarJ-NarG interaction through mutational, binding, and molecular dynamics simulation studies. NarJ adopts a curved α-helix bundle structure with a U-shaped hydrophobic groove on its concave side. This groove accommodates the signal peptide of NarG via a dual binding mode in which the left and right parts of the NarJ groove each interact with two consecutive hydrophobic residues from the N- and C-terminal regions of the NarG signal peptide, respectively, through shape and chemical complementarity. This binding is accompanied by unwinding of the helical structure of the NarG signal peptide and by stabilization of the NarG-binding loop of NarJ. We conclude that NarJ recognizes the NarG signal peptide through a complementary hydrophobic interaction mechanism that mediates a structural rearrangement.
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Affiliation(s)
- Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jee-Hyeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Byeol Namgung
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hye Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyunwoo Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung-Il Yoon
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea; Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
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7
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Mollania H, Oloomi-Buygi M, Mollania N. Catalytic and anti-cancer properties of platinum, gold, silver, and bimetallic Au-Ag nanoparticles synthesized by Bacillus sp. bacteria. J Biotechnol 2024; 379:33-45. [PMID: 38049076 DOI: 10.1016/j.jbiotec.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/30/2023] [Indexed: 12/06/2023]
Abstract
Metallic nanoparticles play a significant role in the catalysis of chemical processes, besides, bimetallic nanoparticles with abundant active sites can reduce metallic nanoparticles toxicity in addition to increasing their catalytic performances. In this work, the platinum, gold, and silver nanoparticles are bio-synthesized using a native bacterium (GFCr-4). Also, the Au-Ag and Au@Ag bimetallic nanoparticles with alloy and core-shell structures, respectively, are biologically synthesized. To improve the synthesis, the effects of various factors like pH, temperature, electron donor, and ionic liquids were investigated. The as-synthesized nanoparticles were characterized with different techniques. The microscope images and dynamic light scattering (DLS) analysis confirm the uniform distribution of as-synthesized nanoparticles with average sizes of 25, 30, 47, 77, and 86 nm obtained for Ag, Au, Pt, Au-Ag alloy, and Au@Ag core-shell, respectively. The catalytic performances of as-synthesized nanoparticles were investigated. The Au-Ag alloy nanoparticles exhibit better catalytic performance than the as-synthesized metallic Au nanoparticles, according to the Gewald reaction. According to the photocatalytic study, the yield can be increased by up to 92% by using PtNPs in the presence of a green LED. Additionally, for the first time, PtNPs were utilized as an effective catalyst in a peroxyoxalate chemiluminescence (POCL) system in the presence of nuclear fast red (NFR) as a novel fluorophore. In addition, the results of the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay revealed that the synthesized eco-friendly nanoparticles have a low effect on the lethality of 3T3 normal cells whereas MCF-7 cancer cells were inhibited up to 77.3% after treatment by PtNPs nanoparticles.
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Affiliation(s)
- Hamid Mollania
- Ferdowsi University of Mashhad, Department of Electrical Engineering, Mashhad, Iran
| | - Majid Oloomi-Buygi
- Ferdowsi University of Mashhad, Department of Electrical Engineering, Mashhad, Iran.
| | - Nasrin Mollania
- Hakim Sabzevari University, Faculty of Basic Sciences, Department of Biology, Sabzevar, Iran.
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8
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Ouyang B, Wei D, Wu B, Yan L, Gang H, Cao Y, Chen P, Zhang T, Wang H. In the View of Electrons Transfer and Energy Conversion: The Antimicrobial Activity and Cytotoxicity of Metal-Based Nanomaterials and Their Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2303153. [PMID: 37721195 DOI: 10.1002/smll.202303153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/28/2023] [Indexed: 09/19/2023]
Abstract
The global pandemic and excessive use of antibiotics have raised concerns about environmental health, and efforts are being made to develop alternative bactericidal agents for disinfection. Metal-based nanomaterials and their derivatives have emerged as promising candidates for antibacterial agents due to their broad-spectrum antibacterial activity, environmental friendliness, and excellent biocompatibility. However, the reported antibacterial mechanisms of these materials are complex and lack a comprehensive understanding from a coherent perspective. To address this issue, a new perspective is proposed in this review to demonstrate the toxic mechanisms and antibacterial activities of metal-based nanomaterials in terms of energy conversion and electron transfer. First, the antimicrobial mechanisms of different metal-based nanomaterials are discussed, and advanced research progresses are summarized. Then, the biological intelligence applications of these materials, such as biomedical implants, stimuli-responsive electronic devices, and biological monitoring, are concluded based on trappable electrical signals from electron transfer. Finally, current improvement strategies, future challenges, and possible resolutions are outlined to provide new insights into understanding the antimicrobial behaviors of metal-based materials and offer valuable inspiration and instructional suggestions for building future intelligent environmental health.
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Affiliation(s)
- Baixue Ouyang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Dun Wei
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Bichao Wu
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Lvji Yan
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Haiying Gang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Yiyun Cao
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Peng Chen
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Tingzheng Zhang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
| | - Haiying Wang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, P. R. China
- School of Metallurgy and Environment and Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Central South, University, Changsha, 410083, China
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9
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Burgmayer SJN, Kirk ML. Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis. Molecules 2023; 28:7456. [PMID: 38005178 PMCID: PMC10673323 DOI: 10.3390/molecules28227456] [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: 10/03/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.
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Affiliation(s)
| | - Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM 87131, USA
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10
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Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
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Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
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11
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Burgmayer SJN. Making Moco: A Personal History. Molecules 2023; 28:7296. [PMID: 37959716 PMCID: PMC10649979 DOI: 10.3390/molecules28217296] [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: 09/06/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
This contribution describes the path of my nearly forty-year quest to understand the special ligand coordinated to molybdenum and tungsten ions in their respective enzymes. Through this quest, I aimed to discover why nature did not simply use a methyl group on the dithiolene that chelates Mo and W but instead chose a complicated pyranopterin. My journey sought answers through the synthesis of model Mo compounds that allowed systematic investigations of the interactions between molybdenum and pterin and molybdenum and pterin-dithiolene and revealed special features of the pyranopterin dithiolene chelate bound to molybdenum.
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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13
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Dupuy P, Gutierrez C, Neyrolles O. Modulation of bacterial membrane proteins activity by clustering into plasma membrane nanodomains. Mol Microbiol 2023; 120:502-507. [PMID: 37303242 DOI: 10.1111/mmi.15105] [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: 02/27/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Recent research has demonstrated specific protein clustering within membrane subdomains in bacteria, challenging the long-held belief that prokaryotes lack these subdomains. This mini review provides examples of bacterial membrane protein clustering, discussing the benefits of protein assembly in membranes and highlighting how clustering regulates protein activity.
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Affiliation(s)
- Pierre Dupuy
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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Wells M, Kim M, Akob DM, Basu P, Stolz JF. Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles. Microbiol Spectr 2023; 11:e0414522. [PMID: 36951557 PMCID: PMC10100899 DOI: 10.1128/spectrum.04145-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.
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Affiliation(s)
- Michael Wells
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Denise M. Akob
- United States Geological Survey, Geology, Energy, and Minerals Science Center, Reston, Virginia, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana, USA
| | - John F. Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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15
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Huang Y, Chen J, Jiang Q, Huang N, Ding X, Peng L, Deng X. The molybdate-binding protein ModA is required for Proteus mirabilis-induced UTI. Front Microbiol 2023; 14:1156273. [PMID: 37180242 PMCID: PMC10174112 DOI: 10.3389/fmicb.2023.1156273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 05/16/2023] Open
Abstract
Background Proteus mirabilis is one of the pathogens commonly causing urinary tract infections (UTIs). The molybdate-binding protein ModA encoded by modA binds molybdate with high affinity and transports it. Increasing evidence shows that ModA promotes the survival of bacteria in anaerobic environments and participates in bacterial virulence by obtaining molybdenum. However, the role of ModA in the pathogenesis of P. mirabilis remains unknown. Results In this study, a series of phenotypic assays and transcriptomic analyses were used to study the role of ModA in the UTIs induced by P. mirabilis. Our data showed that ModA absorbed molybdate with high affinity and incorporated it into molybdopterin, thus affecting the anaerobic growth of P. mirabilis. Loss of ModA enhanced bacterial swarming and swimming and up-regulated the expression of multiple genes in flagellar assembly pathway. The loss of ModA also resulted in decreased biofilm formation under anaerobic growth conditions. The modA mutant significantly inhibited bacterial adhesion and invasion to urinary tract epithelial cells and down-regulated the expression of multiple genes associated with pilus assembly. Those alterations were not due to anaerobic growth defects. In addition, the decreased bacteria in the bladder tissue, the weakened inflammatory damage, the low level of IL-6, and minor weight change was observed in the UTI mouse model infected with modA mutant. Conclusion Here, we reported that in P. mirabilis, ModA mediated the transport of molybdate, thereby affecting the activity of nitrate reductase and thus affecting the growth of bacteria under anaerobic conditions. Overall, this study clarified the indirect role of ModA in the anaerobic growth, motility, biofilm formation, and pathogenicity of P. mirabilis and its possible pathway, and emphasized the importance of the molybdate-binding protein ModA to P. mirabilis in mediating molybdate uptake, allowing the bacterium to adapt to complex environmental conditions and cause UTIs. Our results provided valuable information on the pathogenesis of ModA-induced P. mirabilis UTIs and may facilitate the development of new treatment strategies.
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Affiliation(s)
- Yi Huang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinbin Chen
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiao Jiang
- Guangdong 999 Brain Hospital, Guangzhou, Guangdong, China
| | - Nan Huang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Ding
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liang Peng
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- *Correspondence: Xiaoyan Deng, ; Liang Peng,
| | - Xiaoyan Deng
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, China
- *Correspondence: Xiaoyan Deng, ; Liang Peng,
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16
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Formate Dehydrogenase Mimics as Catalysts for Carbon Dioxide Reduction. Molecules 2022; 27:molecules27185989. [PMID: 36144724 PMCID: PMC9506188 DOI: 10.3390/molecules27185989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Formate dehydrogenases (FDH) reversibly catalyze the interconversion of CO2 to formate. They belong to the family of molybdenum and tungsten-dependent oxidoreductases. For several decades, scientists have been synthesizing structural and functional model complexes inspired by these enzymes. These studies not only allow for finding certain efficient catalysts but also in some cases to better understand the functioning of the enzymes. However, FDH models for catalytic CO2 reduction are less studied compared to the oxygen atom transfer (OAT) reaction. Herein, we present recent results of structural and functional models of FDH.
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Gates C, Varnum H, Getty C, Loui N, Chen J, Kirk ML, Yang J, Nieter Burgmayer SJ. Protonation and Non-Innocent Ligand Behavior in Pyranopterin Dithiolene Molybdenum Complexes. Inorg Chem 2022; 61:13728-13742. [PMID: 36000991 PMCID: PMC10544801 DOI: 10.1021/acs.inorgchem.2c01234] [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] [Indexed: 11/28/2022]
Abstract
The complex [TEA][Tp*MoIV(O)(S2BMOPP)] (1) [TEA = tetraethylammonium, Tp* = tris(3,5-dimethylpyrazolyl)hydroborate, and BMOPP = 6-(3-butynyl-2-methyl-2-ol)-2-pivaloyl pterin] is a structural analogue of the molybdenum cofactor common to all pyranopterin molybdenum enzymes because it possesses a pyranopterin-ene-1,2-dithiolate ligand (S2BMOPP) that exists primarily in the ring-closed pyrano structure as a resonance hybrid of ene-dithiolate and thione-thiolate forms. Compound 1, the protonated [Tp*MoIV(O)(S2BMOPP-H)] (1-H) and one-electron-oxidized [Tp*MoV(O)(S2BMOPP)] [1-Mo(5+)] species have been studied using a combination of electrochemistry, electronic absorption, and electron paramagnetic resonance (EPR) spectroscopy. Additional insight into the nature of these molecules has been derived from electronic structure computations. Differences in dithiolene C-S bond lengths correlate with relative contributions from both ene-dithiolate and thione-thiolate resonance structures. Upon protonation of 1 to form 1-H, large spectroscopic changes are observed with transitions assigned as Mo(xy) → pyranopterin metal-to-ligand charge transfer and dithiolene → pyranopterin intraligand charge transfer, respectively, and this underscores a dramatic change in electronic structure between 1 and 1-H. The changes in electronic structure that occur upon protonation of 1 are also reflected in a large >300 mV increase in the Mo(V/IV) redox potential for 1-H, resulting from the greater thione-thiolate resonance contribution and decreased charge donation that stabilize the Mo(IV) state in 1-H with respect to one-electron oxidation. EPR spin Hamiltonian parameters for one-electron-oxidized 1-Mo(5+) and uncyclized [Tp*MoV(O)(S2BDMPP)] [3-Mo(5+)] [BDMPP = 6-(3-butynyl-2,2-dimethyl)-2-pivaloyl pterin] are very similar to each other and to those of [Tp*MoVO(bdt)] (bdt = 1,2-ene-dithiolate). This indicates that the dithiolate form of the ligand dominates at the Mo(V) level, consistent with the demand for greater S → Mo charge donation and a corresponding increase in Mo-S covalency as the oxidation state of the metal is increased. Protonation of 1 represents a simple reaction that models how the transfer of a proton from neighboring acidic amino acid residues to the Mo cofactor at a nitrogen atom within the pyranopterin dithiolene (PDT) ligand in pyranopterin molybdenum enzymes can impact the electronic structure of the Mo-PDT unit. This work also illustrates how pyran ring-chain tautomerization drives changes in resonance contributions to the dithiolene chelate and may adjust the reduction potential of the Mo ion.
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Affiliation(s)
- Cassandra Gates
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Haley Varnum
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Catherine Getty
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Natalie Loui
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Ju Chen
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Martin L Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
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18
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Bian J, Liao Y, Liu R, An X, Hu C, Liu H, Qu J. Synergy of cyano groups and cobalt single atoms in graphitic carbon nitride for enhanced bio-denitrification. WATER RESEARCH 2022; 218:118465. [PMID: 35461103 DOI: 10.1016/j.watres.2022.118465] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Bio-denitrification plays a crucial role in the purification of nitrogen contaminated water, yet the low efficiency of the pure biological system often leads to the accumulation of harmful intermediates. Semi-biological catalysis provides an effective approach to improving the reaction efficiency through hybridizing artificial nanomaterials with natural organisms, yet the application of this strategy in bio-denitrification is limited. In this study, the effect of surface engineered carbon nitride on the denitrification capability of denitrifying bacteria was investigated. We found that cyano groups availed the biotic-abiotic interactions, while immobilized cobalt single atoms attenuated the local electrostatic repulsion. This synergistic effect endowed carbon nitride modified with cobalt atoms and cyano groups (Co/C3N4-C) with the unexpected acceleration of bio-denitrification reaction, without the accumulation of harmful intermediates. According to the metabolomics analysis, this improvement was attributed to the moderate metabolic adaptation caused by nanoelicitor, which induced dramatically boosted electron transfer and energy supply for extracellular polymeric substance (EPS) secretion. The elevation of intracellular iron level increased the activities of denitrification reductase, which was evidenced by metatranscriptomic analysis. Our results not only demonstrate the great potential of carbon nitride as an artificial elicitor for biological regulation, but also shed light on comprehending the complicated biotic-abiotic interactions for versatile application.
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Affiliation(s)
- Jiyong Bian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiaoqiang An
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Chengzhi Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Maunders EA, Ngu DHY, Ganio K, Hossain SI, Lim BYJ, Leeming MG, Luo Z, Tan A, Deplazes E, Kobe B, McDevitt CA. The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis. Front Microbiol 2022; 13:903146. [PMID: 35685933 PMCID: PMC9171197 DOI: 10.3389/fmicb.2022.903146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bryan Y. J. Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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20
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Modularity of membrane-bound charge-translocating protein complexes. Biochem Soc Trans 2021; 49:2669-2685. [PMID: 34854900 DOI: 10.1042/bst20210462] [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: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023]
Abstract
Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δμ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.
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21
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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22
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Khasimov MK, Petushkova EP, Khusnutdinova AN, Zorin NA, Batyrova KA, Yakunin AF, Tsygankov AA. The HydS C-terminal domain of the Thiocapsa bogorovii HydSL hydrogenase is involved in membrane anchoring and electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148492. [PMID: 34487705 DOI: 10.1016/j.bbabio.2021.148492] [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: 05/27/2021] [Revised: 07/18/2021] [Accepted: 08/28/2021] [Indexed: 10/20/2022]
Abstract
Thiocapsa bogorovii BBS (former name Thiocapsa roseopersicina) contains HydSL hydrogenase belonging to 1e subgroup of NiFe hydrogenases (isp-type). The operon of these hydrogenases contains gene for small subunit (hydS), gene for large subunit (hupL), and genes isp1 and isp2 between them. It is predicted that last two genes code electron transport careers for electron transfer from/to HydSL hydrogenase. However, the interaction between them is unclear. The aim of this study was to determine structural and functional role of T. bogorovii HydS C-terminal end. For this purpose, we modelled all subunits of the complex HydS-HydL-Isp1-Isp2. Hydrophobicity surface analysis of the Isp1 model revealed highly hydrophobic helices suggesting potential membrane localization, as well as the hydrophilic C-terminus, which is likely localized outside of membrane. Isp1 model was docked with models of full length and C-terminal truncated HydSL hydrogenases and results illustrate the possibility of HydSL membrane anchoring via transmembrane Isp1 with essential participation of C-terminal end of HydS in the interaction. C-terminal end of HydS subunit was deleted and our studies revealed that the truncated HydSL hydrogenase detached from cellular membranes in contrast to native hydrogenase. It is known that HydSL hydrogenase in T. bogorovii performs the reaction of elemental sulfur reduction (S0 + H2 = ≥H2S). Cells with truncated HydS produced much less H2S in the presence of H2 and S0. Thus, our data support the conclusion that C-terminal end of HydS subunit participates in interaction of HydSL hydrogenase with Isp1 protein for membrane anchoring and electron transfer.
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Affiliation(s)
- Makhmadyusuf K Khasimov
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia
| | - Ekaterina P Petushkova
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia
| | - Anna N Khusnutdinova
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia
| | - Nikolay A Zorin
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia
| | - Khorcheska A Batyrova
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Anatoly A Tsygankov
- Federal Research Center "Pushchino's center of Biological Research", Institute of Basic Biological Problems of Russian Academy of Sciences, Institutskaya st., 2, Pushchino, Moscow region 142290, Russia.
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Wang B, Zhai Y, Li S, Li C, Zhu Y, Xu M. Catalytic enhancement of hydrogenation reduction and oxygen transfer reaction for perchlorate removal: A review. CHEMOSPHERE 2021; 284:131315. [PMID: 34323780 DOI: 10.1016/j.chemosphere.2021.131315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/11/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Perchlorate is the main contaminant in surface water and groundwater, and it is of current urgency to remove due to its high water solubility, mobility, and endocrine-disrupting properties. The conversion of perchlorate into harmless chloride ions by using appropriate catalysts is the most promising and effective route to overcome its high activation energy and kinetic stability. Perchlorate is usually reduced in two ways: (1) indirect reduction via oxygen atom transfer (OAT) reaction or (2) hydrodeoxygenation through highly active reducing H atoms. This paper discusses the mechanisms underlying both the OAT reaction catalyzed by homogenous rhenium-oxo complexes or biological Mo-based enzymes and the heterogeneous hydrogenation for perchlorate reduction. Particular emphasis is placed on the factors affecting the catalytic process and the synergy between the (1) and (2) reactions. For completeness, the applicability of different electrolysis devices, electrodes, and bioreactors is also illustrated. Finally, this article gives prospects for the synthesis and application of catalysts in different pathways.
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Affiliation(s)
- Bei Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, China
| | - Yunbo Zhai
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, China.
| | - Shanhong Li
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, China
| | - Caiting Li
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, China
| | - Yun Zhu
- College of Electrical and Information Engineering, Hunan University, Changsha, 410082, China
| | - Min Xu
- Chinese Academy for Environmental Planning, Beijing, 100012, China.
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24
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Hagel C, Blaum B, Friedrich T, Heider J. Characterisation of the redox centers of ethylbenzene dehydrogenase. J Biol Inorg Chem 2021; 27:143-154. [PMID: 34843002 PMCID: PMC8840923 DOI: 10.1007/s00775-021-01917-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/29/2021] [Indexed: 01/18/2023]
Abstract
Ethylbenzene dehydrogenase (EbDH), the initial enzyme of anaerobic ethylbenzene degradation from the beta-proteobacterium Aromatoleum aromaticum, is a soluble periplasmic molybdenum enzyme consisting of three subunits. It contains a Mo-bis-molybdopterin guanine dinucleotide (Mo-bis-MGD) cofactor and an 4Fe-4S cluster (FS0) in the α-subunit, three 4Fe-4S clusters (FS1 to FS3) and a 3Fe-4S cluster (FS4) in the β-subunit and a heme b cofactor in the γ-subunit. Ethylbenzene is hydroxylated by a water molecule in an oxygen-independent manner at the Mo-bis-MGD cofactor, which is reduced from the MoVI to the MoIV state in two subsequent one-electron steps. The electrons are then transferred via the Fe-S clusters to the heme b cofactor. In this report, we determine the midpoint redox potentials of the Mo-bis-MGD cofactor and FS1-FS4 by EPR spectroscopy, and that of the heme b cofactor by electrochemically induced redox difference spectroscopy. We obtained relatively high values of > 250 mV both for the MoVI-MoV redox couple and the heme b cofactor, whereas FS2 is only reduced at a very low redox potential, causing magnetic coupling with the neighboring FS1 and FS3. We compare the results with the data on related enzymes and interpret their significance for the function of EbDH.
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Affiliation(s)
- Corina Hagel
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany
| | - Bärbel Blaum
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany.
| | - Johann Heider
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany.
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25
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Al-Attar S, Rendon J, Sidore M, Duneau JP, Seduk F, Biaso F, Grimaldi S, Guigliarelli B, Magalon A. Gating of Substrate Access and Long-Range Proton Transfer in Escherichia coli Nitrate Reductase A: The Essential Role of a Remote Glutamate Residue. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sinan Al-Attar
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Julia Rendon
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Marlon Sidore
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Jean-Pierre Duneau
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Farida Seduk
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Frédéric Biaso
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Stéphane Grimaldi
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Bruno Guigliarelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
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26
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The missing enzymatic link in syntrophic methane formation from fatty acids. Proc Natl Acad Sci U S A 2021; 118:2111682118. [PMID: 34583996 DOI: 10.1073/pnas.2111682118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 12/30/2022] Open
Abstract
The microbial production of methane from organic matter is an essential process in the global carbon cycle and an important source of renewable energy. It involves the syntrophic interaction between methanogenic archaea and bacteria that convert primary fermentation products such as fatty acids to the methanogenic substrates acetate, H2, CO2, or formate. While the concept of syntrophic methane formation was developed half a century ago, the highly endergonic reduction of CO2 to methane by electrons derived from β-oxidation of saturated fatty acids has remained hypothetical. Here, we studied a previously noncharacterized membrane-bound oxidoreductase (EMO) from Syntrophus aciditrophicus containing two heme b cofactors and 8-methylmenaquinone as key redox components of the redox loop-driven reduction of CO2 by acyl-coenzyme A (CoA). Using solubilized EMO and proteoliposomes, we reconstituted the entire electron transfer chain from acyl-CoA to CO2 and identified the transfer from a high- to a low-potential heme b with perfectly adjusted midpoint potentials as key steps in syntrophic fatty acid oxidation. The results close our gap of knowledge in the conversion of biomass into methane and identify EMOs as key players of β-oxidation in (methyl)menaquinone-containing organisms.
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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28
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Ren C, Yang P, Sun J, Bi EY, Gao J, Palmer J, Zhu M, Wu Y, Liu J. A Bioinspired Molybdenum Catalyst for Aqueous Perchlorate Reduction. J Am Chem Soc 2021; 143:7891-7896. [PMID: 34003633 DOI: 10.1021/jacs.1c00595] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Perchlorate (ClO4-) is a pervasive, harmful, and inert anion on both Earth and Mars. Current technologies for ClO4- reduction entail either harsh conditions or multicomponent enzymatic processes. Herein, we report a heterogeneous (L)Mo-Pd/C catalyst directly prepared from Na2MoO4, a bidentate nitrogen ligand (L), and Pd/C to reduce aqueous ClO4- into Cl- with 1 atm of H2 at room temperature. A suite of instrument characterizations and probing reactions suggest that the MoVI precursor and L at the optimal 1:1 ratio are transformed in situ into oligomeric MoIV active sites at the carbon-water interface. For each Mo site, the initial turnover frequency (TOF0) for oxygen atom transfer from ClOx- substrates reached 165 h-1. The turnover number (TON) reached 3840 after a single batch reduction of 100 mM ClO4-. This study provides a water-compatible, efficient, and robust catalyst to degrade and utilize ClO4- for water purification and space exploration.
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Affiliation(s)
- Changxu Ren
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Peng Yang
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Jiaonan Sun
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eric Y Bi
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States.,Martin Luther King High School, Riverside, California 92508, United States
| | - Jinyu Gao
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jacob Palmer
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Mengqiang Zhu
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Yiying Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jinyong Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
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29
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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30
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Ren C, Liu J. Bioinspired Catalytic Reduction of Aqueous Perchlorate by One Single-Metal Site with High Stability against Oxidative Deactivation. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05276] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Changxu Ren
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jinyong Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
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31
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He Y, Chen R, Qi Y, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. Int J Food Microbiol 2021; 348:109201. [PMID: 33930836 DOI: 10.1016/j.ijfoodmicro.2021.109201] [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: 12/26/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/21/2023]
Abstract
Salmonella enterica is frequently implicated in foodborne disease outbreaks associated with fresh-cut fruits. In the U.S., more than one third of fruit-related outbreaks have been linked to two S. enterica serotypes Newport and Typhimurium. Approximately 80% of fruit-related human salmonellosis cases were associated with tomatoes, cantaloupes and cucumbers. In this study, we investigated the population dynamics of S. Newport and S. Typhimurium on fresh-cut tomato, cantaloupe, cucumber and apple under short-term storage conditions. We further compared the transcriptomic profiles of a S. Newport strain on fresh-cut tomato and cantaloupe using high-throughput RNA-seq. We demonstrated that both S. enterica Newport and Typhimurium survived well on various fresh-cut fruit items under refrigeration storage conditions, independent of inoculation levels. However, S. enterica displayed variable survival behaviors on different types of fruits. For example, at 7 d storage, the population of S. enterica reduced less than 0.2 log (p > 0.05) on fresh-cut tomato and cantaloupe, in contrast to ~0.5 log (p < 0.05) on cucumber and apple. RNA-seq analysis suggested that S. enterica mediates its survival on fresh-cut fruits through differentially regulating genes involved in specific carbon utilization and metabolic pathways. Several known bacterial virulence factors (e.g., pag gene) were found to be differentially regulated on fresh-cut tomato and cantaloupe, suggesting a link between the events of food contamination and subsequent human infection. Findings from this study contribute to a better understanding of S. enterica survival mechanisms on fresh-cut produce.
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Affiliation(s)
- Yingshu He
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA; Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA.
| | - Ruixi Chen
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Yan Qi
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Joelle K Salazar
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Shimei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Mary Lou Tortorello
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Xiangyu Deng
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Wei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
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Aiding a Better Understanding of Molybdopterin: Syntheses, Structures, and pKa Value Determinations of Varied Pterin-Derived Organic Scaffolds Including Oxygen, Sulfur and Phosphorus Bearing Substituents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical SAM protein MoaA for the synthesis of active molybdoenzymes. J Bacteriol 2021; 203:e0008621. [PMID: 33782054 DOI: 10.1128/jb.00086-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them were characterized in detail in Escherichia coli, namely IscA, SufA and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli Our studies include the identification of the A-type carrier proteins ErpA and IscA involved in [4Fe-4S] cluster insertion into the S-adenosyl-methionine dependent radical SAM protein MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth of nitrate respiration, based on low gene expression levels.IMPORTANCEUnderstanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics and gene regulation. Still remaining critical gaps in our knowledge are how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SusA and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.
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Zuchan K, Baymann F, Baffert C, Brugna M, Nitschke W. The dyad of the Y-junction- and a flavin module unites diverse redox enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148401. [PMID: 33684340 DOI: 10.1016/j.bbabio.2021.148401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
The concomitant presence of two distinctive polypeptide modules, which we have chosen to denominate as the "Y-junction" and the "flavin" module, is observed in 3D structures of enzymes as functionally diverse as complex I, NAD(P)-dependent [NiFe]-hydrogenases and NAD(P)-dependent formate dehydrogenases. Amino acid sequence conservation furthermore suggests that both modules are also part of NAD(P)-dependent [FeFe]-hydrogenases for which no 3D structure model is available yet. The flavin module harbours the site of interaction with the substrate NAD(P) which exchanges two electrons with a strictly conserved flavin moiety. The Y-junction module typically contains four iron-sulphur centres arranged to form a Y-shaped electron transfer conduit and mediates electron transfer between the flavin module and the catalytic units of the respective enzymes. The Y-junction module represents an electron transfer hub with three potential electron entry/exit sites. The pattern of specific redox centres present both in the Y-junction and the flavin module is correlated to present knowledge of these enzymes' functional properties. We have searched publicly accessible genomes for gene clusters containing both the Y-junction and the flavin module to assemble a comprehensive picture of the diversity of enzymes harbouring this dyad of modules and to reconstruct their phylogenetic relationships. These analyses indicate the presence of the dyad already in the last universal common ancestor and the emergence of complex I's EFG-module out of a subgroup of NAD(P)- dependent formate dehydrogenases.
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Affiliation(s)
- Kilian Zuchan
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Frauke Baymann
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Myriam Brugna
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France.
| | - Wolfgang Nitschke
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
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Falke D, Fischer M, Ihling C, Hammerschmidt C, Sinz A, Sawers G. Co-purification of nitrate reductase 1 with components of the cytochrome bcc-aa 3 oxidase supercomplex from spores of Streptomyces coelicolor A3(2). FEBS Open Bio 2021; 11:652-669. [PMID: 33462996 PMCID: PMC7931247 DOI: 10.1002/2211-5463.13086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 11/30/2022] Open
Abstract
In order to reduce nitrate in vivo, the spore‐specific respiratory nitrate reductase, Nar1, of Streptomyces coelicolor relies on an active cytochrome bcc‐aa3 oxidase supercomplex (bcc‐aa3 supercomplex). This suggests that membrane‐associated Nar1, comprising NarG1, NarH1, and NarI1 subunits, might not act as a classical menaquinol oxidase but could either receive electrons from the bcc‐aa3 supercomplex, or require the supercomplex to stabilize the reductase in the membrane to allow it to function. To address the biochemical basis for this dependence on the bcc‐aa3 supercomplex, we purified two different Strep‐tagged variants of Nar1 and enriched the native enzyme complex from spore extracts using different chromatographic and electrophoretic procedures. Polypeptides associated with the isolated Nar1 complexes were identified using mass spectrometry and included components of the bcc‐aa3 supercomplex, along with an alternative, spore‐specific cytochrome b component, QcrB3. Surprisingly, we also co‐enriched the Nar3 enzyme with Nar1 from the wild‐type strain of S. coelicolor. Two differentially migrating active Nar1 complexes could be identified after clear native polyacrylamide gel electrophoresis; these had masses of approximately 450 and 250 kDa. The distribution of active Nar1 in these complexes was influenced by the presence of cytochrome bd oxidase and by QcrB3; the presence of the latter shifted Nar1 into the larger complex. Together, these data suggest that several respiratory complexes can associate in the spore membrane, including Nar1, Nar3, and the bcc‐aa3 supercomplex. Moreover, these findings provide initial support for the hypothesis that Nar1 and the bcc‐aa3 supercomplex physically associate.
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Affiliation(s)
- Dörte Falke
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Marco Fischer
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy, Charles Tanford Protein Center, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Claudia Hammerschmidt
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy, Charles Tanford Protein Center, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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36
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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Watanabe T, Shima S. MvhB-type Polyferredoxin as an Electron-transfer Chain in Putative Redox-enzyme Complexes. CHEM LETT 2021. [DOI: 10.1246/cl.200774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Hederstedt L. Molecular Biology of Bacillus subtilis Cytochromes anno 2020. BIOCHEMISTRY (MOSCOW) 2021; 86:8-21. [DOI: 10.1134/s0006297921010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Pamplona R, Jové M, Mota-Martorell N, Barja G. Is the NDUFV2 subunit of the hydrophilic complex I domain a key determinant of animal longevity? FEBS J 2021; 288:6652-6673. [PMID: 33455045 DOI: 10.1111/febs.15714] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022]
Abstract
Complex I, a component of the electron transport chain, plays a central functional role in cell bioenergetics and the biology of free radicals. The structural and functional N module of complex I is one of the main sites of the generation of free radicals. The NDUFV2 subunit/N1a cluster is a component of this module. Furthermore, the rate of free radical production is linked to animal longevity. In this review, we explore the hypothesis that NDUFV2 is the only conserved core subunit designed with a regulatory function to ensure correct electron transfer and free radical production, that low gene expression and protein abundance of the NDUFV2 subunit is an evolutionary adaptation needed to achieve a longevity phenotype, and that these features are determinants of the lower free radical generation at the mitochondrial level and a slower rate of aging of long-lived animals.
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Affiliation(s)
- Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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Pfendler S, Einhorn O, Alaoui-Sossé L, Bousta F, Alaoui-Sossé B, Aleya L. Factors inducing bryophyte growth on prehistoric pigments and effect of UV-C treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2987-2994. [PMID: 32901409 DOI: 10.1007/s11356-020-10681-8] [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: 03/23/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
In La Glacière cave (France), the touristic activity has been conducted to an environmental parameter change that has led to photosynthetic organism proliferation (microalgae, diatoms, cyanobacteria, bryophytes). The present study is focused on bryophyte development occurring in the show cave that was responsible of limestone biodeterioration. In order to understand the colonization process of limestone, we have maintained limestone blocks under optimal Lampenflora growth conditions. Moreover, some limestone blocks were painted with several pigments that were used in the prehistory (e.g., red ocher, bone char). Microorganisms and bryophyte growth were monitored during 1 year, and then, the block samples were treated using UV-C light (254 nm). Thus, obtained results were compared with in situ treatment in La Glacière cave. Results have showed dense bryophyte propagation on the several blocks. However, the growth rate was correlated with the chemical composition of the pigment. In fact, the presence of some chemical elements such as As, Cr, Ti, and Co contributed to reduce bryophyte growth. Finally, moss treatment using UV-C light has demonstrated high efficiency under in situ condition, while a fast recolonization has been observed for samples maintained in laboratory. This difference was explained by the high bryophyte density under laboratory conditions that make UV-C light penetration difficult.
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Affiliation(s)
- Stéphane Pfendler
- University of Lyon, UJM-Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023, Saint-Etienne, France.
| | - Olympe Einhorn
- Laboratoire Chrono-Environnement - UMR 6249, Université de Bourgogne Franche-Comté, 16, route de Gray, 25 000, Besançon, France
| | - Laurence Alaoui-Sossé
- Laboratoire Chrono-Environnement - UMR 6249, Université de Bourgogne Franche-Comté, 16, route de Gray, 25 000, Besançon, France
| | - Faisl Bousta
- Laboratoire de Recherche des Monuments Historiques, USR 3224, Champs-Sur-Marne, France
| | - Badr Alaoui-Sossé
- Laboratoire Chrono-Environnement - UMR 6249, Université de Bourgogne Franche-Comté, 16, route de Gray, 25 000, Besançon, France
| | - Lotfi Aleya
- Laboratoire Chrono-Environnement - UMR 6249, Université de Bourgogne Franche-Comté, 16, route de Gray, 25 000, Besançon, France
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Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol 2021; 6:1129-1139. [PMID: 34267357 PMCID: PMC8387239 DOI: 10.1038/s41564-021-00934-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023]
Abstract
Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein's electron transport chain, and elucidate the electron transfer pathways within the complex.
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Abstract
Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.
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Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution. Genes (Basel) 2020; 11:genes11111308. [PMID: 33158244 PMCID: PMC7694296 DOI: 10.3390/genes11111308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.
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Sulfite oxidation by the quinone-reducing molybdenum sulfite dehydrogenase SoeABC from the bacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148279. [DOI: 10.1016/j.bbabio.2020.148279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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47
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AbdelGawwad MR, Mahmutović E, Al Farraj DA, Elshikh MS. In silico prediction of silver nitrate nanoparticles and Nitrate Reductase A (NAR A) interaction in the treatment of infectious disease causing clinical strains of E. coli. J Infect Public Health 2020; 13:1580-1585. [PMID: 32855089 DOI: 10.1016/j.jiph.2020.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND The interaction of specially designed nanoparticles with proteins is the basis of formation of a nanoparticle-protein corona. Silver nanoparticles and molecules have been used in many fields due to their strong antimicrobial activity against pathogenic microorganisms such as bacteria, yeast and fungi. E. coli is a Gram-negative bacteria that has the genome completely sequenced and determined majority of its protein 3D structures. Nitrate Reductase A is a cellular protein often found in many bacteria that uses nitrate as an electron acceptor during anaerobic growth. The enzyme is composed of three different chains α, β and γ, all having properties of metal binding regions and domains. METHODS Bioinformatics tools were used to investigate the structure, domains, interactomes, and docking sites of E. coli Nitrate Reductase A in order to predict the possible site of interaction of silver nitrate AgNO3 with the protein. The 3D structure of the NAR A protein was predicted with the Phyre2 protein modeling software. The generated structures from Phyre2 were validated and evaluated by analysis of Ramachandran plots using RAMPAGE online software. To understand the evolutionary relationships between the subunits of Nitrate Reductase A, a phylogenetic tree was constructed using Phylogeny.fr. RESULTS All cysteine and histidine residues in amino acid sequences were identified; 3D structure of subunits predicted together with Ramachandran plots, and the electrostatic potential was computed using various bioinformatics tools. The reactive cationic property of silver ion leads to attachment to specific anionic regions and active sites of the three subunits causing in many prokaryotic cells deactivation of nitrate reductase. Obtained results showed the possible sites of attachment of silver ions and their reactivity with domains that have metal bonding properties. In silico analysis of silver nanoparticles and nitrate reductase is helpful to treat various infections diseases caused by E. coli.
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Affiliation(s)
- Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Ensar Mahmutović
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
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Yang J, Feng L, Pi S, Cui D, Ma F, Zhao HP, Li A. A critical review of aerobic denitrification: Insights into the intracellular electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139080. [PMID: 32417477 DOI: 10.1016/j.scitotenv.2020.139080] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/04/2020] [Accepted: 04/26/2020] [Indexed: 05/23/2023]
Abstract
Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.
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Affiliation(s)
- Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Di Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China; Engineering Research Center for Medicine, College of Pharmacy, Harbin University of Commerce, Harbin 150076, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
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1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148203. [PMID: 32305411 DOI: 10.1016/j.bbabio.2020.148203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 11/23/2022]
Abstract
The quinol oxidation site QD in E. coli respiratory nitrate reductase A (EcNarGHI) reacts with the three isoprenoid quinones naturally synthesized by the bacterium, i.e. ubiquinones (UQ), menaquinones (MK) and demethylmenaquinones (DMK). The binding mode of the demethylmenasemiquinone (DMSK) intermediate to the EcNarGHI QD quinol oxidation site is analyzed in detail using 1,2H hyperfine (hf) spectroscopy in combination with H2O/D2O exchange experiments and DFT modeling, and compared to the menasemiquinone one bound to the QD site (MSKD) previously studied by us. DMSKD and MSKD are shown to bind in a similar and strongly asymmetric manner through a short (~1.7 Å) H-bond. The origin of the specific hf pattern resolved on the DMSKD field-swept EPR spectrum is unambiguously ascribed to slightly inequivalent contributions from two β-methylene protons of the isoprenoid side chain. DFT calculations show that their large isotropic hf coupling constants (Aiso ~12 and 15 MHz) are consistent with both (i) a specific highly asymmetric binding mode of DMSKD and (ii) a near in-plane orientation of its isoprenyl chain at Cβ relative to the aromatic ring, which differs by ~90° to that predicted for free or NarGHI-bound MSK. Our results provide new insights into how the conformation and the redox properties of different natural quinones are selectively fine-tuned by the protein environment at a single Q site. Such a fine-tuning most likely contributes to render NarGHI as an efficient and flexible respiratory enzyme to be used upon rapid variations of the Q-pool content.
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Methane, arsenic, selenium and the origins of the DMSO reductase family. Sci Rep 2020; 10:10946. [PMID: 32616801 PMCID: PMC7331816 DOI: 10.1038/s41598-020-67892-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.
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