1
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Deng Y, Wang JX, Ghosh B, Lu Y. Enzymatic CO 2 reduction catalyzed by natural and artificial Metalloenzymes. J Inorg Biochem 2024; 259:112669. [PMID: 39059175 DOI: 10.1016/j.jinorgbio.2024.112669] [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: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Barshali Ghosh
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America.
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2
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Mrnjavac N, Degli Esposti M, Mizrahi I, Martin WF, Allen JF. Three enzymes governed the rise of O 2 on Earth. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149495. [PMID: 39004113 DOI: 10.1016/j.bbabio.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK.
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3
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Fritz G, Kroneck PMH, Steuber J. The power supply for biological nitrogen fixation. Nat Chem Biol 2024:10.1038/s41589-024-01663-9. [PMID: 38987384 DOI: 10.1038/s41589-024-01663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Affiliation(s)
- Günter Fritz
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Peter M H Kroneck
- Department of Biology, Faculty of Sciences, University of Konstanz, Konstanz, Germany
| | - Julia Steuber
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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4
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [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: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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5
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Vazquez Ramos J, Kulka-Peschke CJ, Bechtel DF, Zebger I, Pierik AJ, Layer G. Characterization of the iron-sulfur clusters in the nitrogenase-like reductase CfbC/D required for coenzyme F 430 biosynthesis. FEBS J 2024; 291:3233-3248. [PMID: 38588274 DOI: 10.1111/febs.17134] [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: 11/17/2023] [Revised: 02/14/2024] [Accepted: 03/28/2024] [Indexed: 04/10/2024]
Abstract
Coenzyme F430 is a nickel-containing tetrapyrrole, serving as the prosthetic group of methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. During coenzyme F430 biosynthesis, the tetrapyrrole macrocycle is reduced by the nitrogenase-like CfbC/D system consisting of the reductase component CfbC and the catalytic component CfbD. Both components are homodimeric proteins, each carrying a [4Fe-4S] cluster. Here, the ligands of the [4Fe-4S] clusters of CfbC2 and CfbD2 were identified revealing an all cysteine ligation of both clusters. Moreover, the midpoint potentials of the [4Fe-4S] clusters were determined to be -256 mV for CfbC2 and -407 mV for CfbD2. These midpoint potentials indicate that the consecutive thermodynamically unfavorable 6 individual "up-hill" electron transfers to the organic moiety of the Ni2+-sirohydrochlorin a,c-diamide substrate require an intricate interplay of ATP-binding, hydrolysis, protein complex formation and release to drive product formation, which is a common theme in nitrogenase-like systems.
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Affiliation(s)
- José Vazquez Ramos
- Pharmazeutische Biologie, Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Germany
| | | | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Germany
| | | | - Gunhild Layer
- Pharmazeutische Biologie, Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Germany
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6
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Lee M, Magante K, Gómez-Garzón C, Payne SM, Smith AT. Structural Determinants of Vibrio cholerae FeoB Nucleotide Promiscuity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595361. [PMID: 38826458 PMCID: PMC11142208 DOI: 10.1101/2024.05.22.595361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Ferrous iron (Fe2+) is required for the growth and virulence of many pathogenic bacteria, including Vibrio cholerae (Vc), the causative agent of the disease cholera. For this bacterium, Feo is the primary system that transports Fe2+ into the cytosol. FeoB, the main component of this system, is regulated by a soluble cytosolic domain termed NFeoB. Recent reanalysis has shown that NFeoBs can be classified as either GTP-specific or NTP-promiscuous, but the structural and mechanistic bases for these differences were not known. To explore this intriguing property of FeoB, we solved the X-ray crystal structures of VcNFeoB in both the apo and GDP-bound forms. Surprisingly, this promiscuous NTPase displayed a canonical NFeoB G-protein fold like GTP-specific NFeoBs. Using structural bioinformatics, we hypothesized that residues surrounding the nucleobase could be important for both nucleotide affinity and specificity. We then solved the X-ray crystal structures of N150T VcNFeoB in the apo and GDP-bound forms to reveal H-bonding differences surround the guanine nucleobase. Interestingly, isothermal titration calorimetry revealed similar binding thermodynamics of the WT and N150T proteins to guanine nucleotides, while the behavior in the presence of adenine nucleotides was dramatically different. AlphaFold models of VcNFeoB in the presence of ADP and ATP showed important conformational changes that contribute to nucleotide specificity among FeoBs. Combined, these results provide a structural framework for understanding FeoB nucleotide promiscuity, which could be an adaptive measure utilized by pathogens to ensure adequate levels of intracellular iron across multiple metabolic landscapes.
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Affiliation(s)
- Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Kate Magante
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Camilo Gómez-Garzón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712 USA
| | - Shelley M. Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712 USA
- John Ring LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, Texas, 78712 USA
| | - Aaron T. Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
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7
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Maslać N, Cadoux C, Bolte P, Murken F, Gu W, Milton RD, Wagner T. Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. FEBS J 2024. [PMID: 38696373 DOI: 10.1111/febs.17148] [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: 08/16/2023] [Revised: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N2) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP·AlF 4 - $$ {\mathrm{AlF}}_4^{-} $$ is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N2-machinery from these ancient archaea.
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Affiliation(s)
- Nevena Maslać
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Pauline Bolte
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Fenja Murken
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wenyu Gu
- Laboratory of Microbial Physiology and Resource Biorecovery, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédéral de Lausanne, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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8
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Ribeiro IDA, Paes JA, Wendisch VF, Ferreira HB, Passaglia LMP. Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5 T under conventional and alternative nitrogen fixation. J Proteomics 2024; 294:105061. [PMID: 38154550 DOI: 10.1016/j.jprot.2023.105061] [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: 08/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil
| | - Jéssica Andrade Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Volker F Wendisch
- Institute for Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil.
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9
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Wendisch VF, Brito LF, Passaglia LM. Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T. Genet Mol Biol 2024; 46:e20230115. [PMID: 38224489 PMCID: PMC10789242 DOI: 10.1590/1678-4685-gmb-2023-0115] [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: 04/21/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024] Open
Abstract
Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.
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Affiliation(s)
- Volker F. Wendisch
- Bielefeld University, Faculty of Biology, Genetics of Prokaryotes, Bielefeld, Germany
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Luciana F. Brito
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Luciane M.P. Passaglia
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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10
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Barchenko M, Malcomson T, de Visser SP, O’Malley PJ. Computational Study on the Influence of Mo/V Centers on the Electronic Structure and Hydrazine Reduction Capability of [MFe 3S 4] 3+/2+ Complexes. Inorg Chem 2023; 62:16401-16411. [PMID: 37756478 PMCID: PMC10565805 DOI: 10.1021/acs.inorgchem.3c02072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 09/29/2023]
Abstract
[MFe3S4] cubanes have for some time been of interest for their ability to mimic the electronic and geometric structure of the active site of nitrogenase, the enzyme responsible for fixing N2 to NH3. Nitrogenase naturally occurs in three forms, with the major difference being that the metal ion present in the cofactor active site is either molybdenum (FeMoco), vanadium (FeVco), or iron. The molybdenum and vanadium versions of these cofactors are more closely studied, owing to their larger abundance and rate of catalysis. In this study, we compare free energy profiles and electronic properties of the Mo/V cubanes at various stages during the reduction of N2H4 to NH3. Our findings highlight the differences in how the complexes facilitate the reaction, in particular, vanadium's comparatively weaker ability to interact with the Fe/S network and stabilize reducing electrons prior to N-N bond cleavage, which may have implications when considering the lower efficiency of the vanadium-dependent nitrogenase.
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Affiliation(s)
- Maxim Barchenko
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
| | - Thomas Malcomson
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Patrick J. O’Malley
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
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11
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Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
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Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
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12
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Tzaguy A, Masip-Sánchez A, Avram L, Solé-Daura A, López X, Poblet JM, Neumann R. Electrocatalytic Reduction of Dinitrogen to Ammonia with Water as Proton and Electron Donor Catalyzed by a Combination of a Tri-ironoxotungstate and an Alkali Metal Cation. J Am Chem Soc 2023; 145:19912-19924. [PMID: 37642197 PMCID: PMC10510311 DOI: 10.1021/jacs.3c06167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 08/31/2023]
Abstract
The electrification of ammonia synthesis is a key target for its decentralization and lowering impact on atmospheric CO2 concentrations. The lithium metal electrochemical reduction of nitrogen to ammonia using alcohols as proton/electron donors is an important advance, but requires rather negative potentials, and anhydrous conditions. Organometallic electrocatalysts using redox mediators have also been reported. Water as a proton and electron donor has not been demonstrated in these reactions. Here a N2 to NH3 electrocatalytic reduction using an inorganic molecular catalyst, a tri-iron substituted polyoxotungstate, {SiFe3W9}, is presented. The catalyst requires the presence of Li+ or Na+ cations as promoters through their binding to {SiFe3W9}. Experimental NMR, CV and UV-vis measurements, and MD simulations and DFT calculations show that the alkali metal cation enables the decrease of the redox potential of {SiFe3W9} allowing the activation of N2. Controlled potential electrolysis with highly purified 14N2 and 15N2 ruled out formation of NH3 from contaminants. Importantly, using Na+ cations and polyethylene glycol as solvent, the anodic oxidation of water can be used as a proton and electron donor for the formation of NH3. In an undivided cell electrolyzer under 1 bar N2, rates of NH3 formation of 1.15 nmol sec-1 cm-2, faradaic efficiencies of ∼25%, 5.1 equiv of NH3 per equivalent of {SiFe3W9} in 10 h, and a TOF of 64 s-1 were obtained. The future development of suitable high surface area cathodes and well solubilized N2 and the use of H2O as the reducing agent are important keys to the future deployment of an electrocatalytic ammonia synthesis.
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Affiliation(s)
- Avra Tzaguy
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Albert Masip-Sánchez
- Department
de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Liat Avram
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot, Israel 76100
| | - Albert Solé-Daura
- Department
de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Xavier López
- Department
de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Josep M. Poblet
- Department
de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Ronny Neumann
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel 76100
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13
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Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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14
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Ribeiro IDA, Bach E, Passaglia LMP. Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family. Mol Phylogenet Evol 2022; 177:107624. [PMID: 36084857 DOI: 10.1016/j.ympev.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
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15
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Ribbe MW, Górecki K, Grosch M, Solomon JB, Quechol R, Liu YA, Lee CC, Hu Y. Nitrogenase Fe Protein: A Multi-Tasking Player in Substrate Reduction and Metallocluster Assembly. Molecules 2022; 27:molecules27196743. [PMID: 36235278 PMCID: PMC9571451 DOI: 10.3390/molecules27196743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
The Fe protein of nitrogenase plays multiple roles in substrate reduction and metallocluster assembly. Best known for its function to transfer electrons to its catalytic partner during nitrogenase catalysis, the Fe protein is also a key player in the biosynthesis of the complex metalloclusters of nitrogenase. In addition, it can function as a reductase on its own and affect the ambient reduction of CO2 or CO to hydrocarbons. This review will provide an overview of the properties and functions of the Fe protein, highlighting the relevance of this unique FeS enzyme to areas related to the catalysis, biosynthesis, and applications of the fascinating nitrogenase system.
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Affiliation(s)
- Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Correspondence: (M.W.R.); (Y.H.)
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Correspondence: (M.W.R.); (Y.H.)
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16
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Sestok AE, O'Sullivan SM, Smith AT. A general protocol for the expression and purification of the intact transmembrane transporter FeoB. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183973. [PMID: 35636558 PMCID: PMC9203943 DOI: 10.1016/j.bbamem.2022.183973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 04/27/2023]
Abstract
Ferrous iron (Fe2+) transport is an essential process that supports the growth, intracellular survival, and virulence of several drug-resistant pathogens, and the ferrous iron transport (Feo) system is the most important and widespread protein complex that mediates Fe2+ transport in these organisms. The Feo system canonically comprises three proteins (FeoA/B/C). FeoA and FeoC are both small, accessory proteins localized to the cytoplasm, and their roles in the Fe2+ transport process have been of great debate. FeoB is the only wholly-conserved component of the Feo system and serves as the inner membrane-embedded Fe2+ transporter with a soluble G-protein-like N-terminal domain. In vivo studies have underscored the importance of Feo during infection, emphasizing the need to better understand Feo-mediated Fe2+ uptake, although a paucity of research exists on intact FeoB. To surmount this problem, we designed an overproduction and purification system that can be applied generally to a suite of intact FeoBs from several organisms. Importantly, we noted that FeoB is extremely sensitive to excess salt while in the membrane of a recombinant host, and we designed a workflow to circumvent this issue. We also demonstrated effective protein extraction from the lipid bilayer through small-scale solubilization studies. We then applied this approach to the large-scale purifications of Escherichia coli and Pseudomonas aeruginosa FeoBs to high purity and homogeneity. Lastly, we show that our protocol can be generally applied to various FeoB proteins. Thus, this workflow allows for isolation of suitable quantities of FeoB for future biochemical and biophysical characterization.
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Affiliation(s)
- Alex E Sestok
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Sean M O'Sullivan
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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17
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Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
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Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
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18
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Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein. Proc Natl Acad Sci U S A 2022; 119:e2203576119. [PMID: 35905315 PMCID: PMC9351452 DOI: 10.1073/pnas.2203576119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Electron transfers coupled to the hydrolysis of ATP allow various metalloenzymes to catalyze reductions at very negative reduction potentials. The double-cubane cluster protein (DCCP) catalyzes the reduction of small molecules, such as acetylene and hydrazine, with electrons provided by its cognate ATP-hydrolyzing reductase (DCCP-R). How ATP-driven electron transfer occurs is not known. To resolve the structural basis for ATP-driven electron transfer, we solved the structures of the DCCP:DCCP-R complex in three different states. The structures show that the DCCP-R homodimer is covalently bridged by a [4Fe4S] cluster that is aligned with the twofold axis of the DCCP homodimer, positioning the [4Fe4S] cluster to enable electron transfer to both double-cubane clusters in the DCCP dimer. DCCP and DCCP-R form stable complexes independent of oxidation state or nucleotides present, and electron transfer requires the hydrolysis of ATP. Electron transfer appears to be additionally driven by modulating the angle between the helices binding the [4Fe4S] cluster. We observed hydrogen bond networks running from the ATP binding site via the [4Fe4S] cluster in DCCP-R to the double-cubane cluster in DCCP, allowing the propagation of conformational changes. Remarkable similarities between the DCCP:DCCP-R complex and the nonhomologous nitrogenases suggest a convergent evolution of catalytic strategies to achieve ATP-driven electron transfers between iron-sulfur clusters.
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19
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Garibello CF, Simonov AN, Eldridge DS, Mahlerbe F, Hocking RK. Redox properties of iron sulfides: direct versus catalytic reduction and implications for catalyst design. ChemCatChem 2022. [DOI: 10.1002/cctc.202200270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- C. Felipe Garibello
- Swinburne University of Technology - Hawthorn Campus: Swinburne University of Technology Chemistry and Biotechnology AUSTRALIA
| | | | - Daniel S. Eldridge
- Swinburne University of Technology - Hawthorn Campus: Swinburne University of Technology Chemistry and Biotechnology AUSTRALIA
| | - Francois Mahlerbe
- Swinburne University of Technology - Hawthorn Campus: Swinburne University of Technology Chemistry and Biotechnology AUSTRALIA
| | - Rosalie Katherine Hocking
- Swinburne University of Technology Chemistry and Biotechnology John Street Hawthorn 3128 Melbourne AUSTRALIA
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20
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Sestok AE, Brown JB, Obi JO, O'Sullivan SM, Garcin ED, Deredge DJ, Smith AT. A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB. J Biol Chem 2022; 298:101808. [PMID: 35271852 PMCID: PMC8980893 DOI: 10.1016/j.jbc.2022.101808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022] Open
Abstract
Iron is an essential element for nearly all organisms, and under anoxic and/or reducing conditions, Fe2+ is the dominant form of iron available to bacteria. The ferrous iron transport (Feo) system is the primary prokaryotic Fe2+ import machinery, and two constituent proteins (FeoA and FeoB) are conserved across most bacterial species. However, how FeoA and FeoB function relative to one another remains enigmatic. In this work, we explored the distribution of feoAB operons encoding a fusion of FeoA tethered to the N-terminal, G-protein domain of FeoB via a connecting linker region. We hypothesized that this fusion poises FeoA to interact with FeoB to affect function. To test this hypothesis, we characterized the soluble NFeoAB fusion protein from Bacteroides fragilis, a commensal organism implicated in drug-resistant infections. Using X-ray crystallography, we determined the 1.50-Å resolution structure of BfFeoA, which adopts an SH3-like fold implicated in protein–protein interactions. Using a combination of structural modeling, small-angle X-ray scattering, and hydrogen–deuterium exchange mass spectrometry, we show that FeoA and NFeoB interact in a nucleotide-dependent manner, and we mapped the protein–protein interaction interface. Finally, using guanosine triphosphate (GTP) hydrolysis assays, we demonstrate that BfNFeoAB exhibits one of the slowest known rates of Feo-mediated GTP hydrolysis that is not potassium-stimulated. Importantly, truncation of FeoA from this fusion demonstrates that FeoA–NFeoB interactions function to stabilize the GTP-bound form of FeoB. Taken together, our work reveals a role for FeoA function in the fused FeoAB system and suggests a function for FeoA among prokaryotes.
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Affiliation(s)
- Alex E Sestok
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Juliet O Obi
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, 21201 USA
| | - Sean M O'Sullivan
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA; Laboratoire d'Information Génomique et Structurale, UMR7256, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, 21201 USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA.
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21
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Gee LB, Scott AD, Dapper CH, Newton WE, Cramer SP. Carbon monoxide binding to α-R277H Mo-nitrogenase – Evidence for multiple pH-dependent species from IR-monitored photolysis. J Inorg Biochem 2022; 232:111806. [DOI: 10.1016/j.jinorgbio.2022.111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
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22
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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González-Cabaleiro R, Thompson JA, Vilà-Nadal L. Looking for Options to Sustainably Fixate Nitrogen. Are Molecular Metal Oxides Catalysts a Viable Avenue? Front Chem 2021; 9:742565. [PMID: 34595154 PMCID: PMC8476845 DOI: 10.3389/fchem.2021.742565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Fast and reliable industrial production of ammonia (NH3) is fundamentally sustaining modern society. Since the early 20th Century, NH3 has been synthesized via the Haber-Bosch process, running at conditions of around 350-500°C and 100-200 times atmospheric pressure (15-20 MPa). Industrial ammonia production is currently the most energy-demanding chemical process worldwide and contributes up to 3% to the global carbon dioxide emissions. Therefore, the development of more energy-efficient pathways for ammonia production is an attractive proposition. Over the past 20 years, scientists have imagined the possibility of developing a milder synthesis of ammonia by mimicking the nitrogenase enzyme, which fixes nitrogen from the air at ambient temperatures and pressures to feed leguminous plants. To do this, we propose the use of highly reconfigurable molecular metal oxides or polyoxometalates (POMs). Our proposal is an informed design of the polyoxometalate after exploring the catabolic pathways that cyanobacteria use to fix N2 in nature, which are a different route than the one followed by the Haber-Bosch process. Meanwhile, the industrial process is a "brute force" system towards breaking the triple bond N-N, needing high pressure and high temperature to increase the rate of reaction, nature first links the protons to the N2 to later easier breaking of the triple bond at environmental temperature and pressure. Computational chemistry data on the stability of different polyoxometalates will guide us to decide the best design for a catalyst. Testing different functionalized molecular metal oxides as ammonia catalysts laboratory conditions will allow for a sustainable reactor design of small-scale production.
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Affiliation(s)
| | - Jake A Thompson
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Laia Vilà-Nadal
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
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24
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Larrea-Álvarez M, Purton S. The Chloroplast of Chlamydomonas reinhardtii as a Testbed for Engineering Nitrogen Fixation into Plants. Int J Mol Sci 2021; 22:8806. [PMID: 34445505 PMCID: PMC8395883 DOI: 10.3390/ijms22168806] [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: 06/19/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic organisms such as plants are unable to utilise nitrogen gas (N2) directly as a source of this essential element and are dependent either on its biological conversion to ammonium by diazotrophic prokaryotes, or its supply as chemically synthesised nitrate fertiliser. The idea of genetically engineering crops with the capacity to fix N2 by introduction of the bacterial nitrogenase enzyme has long been discussed. However, the expression of an active nitrogenase must overcome several major challenges: the coordinated expression of multiple genes to assemble an enzyme complex containing several different metal cluster co-factors; the supply of sufficient ATP and reductant to the enzyme; the enzyme's sensitivity to oxygen; and the intracellular accumulation of ammonium. The chloroplast of plant cells represents an attractive location for nitrogenase expression, but engineering the organelle's genome is not yet feasible in most crop species. However, the unicellular green alga Chlamydomonas reinhardtii represents a simple model for photosynthetic eukaryotes with a genetically tractable chloroplast. In this review, we discuss the main advantages, and limitations, of this microalga as a testbed for producing such a complex multi-subunit enzyme. Furthermore, we suggest that a minimal set of six transgenes are necessary for chloroplast-localised synthesis of an 'Fe-only' nitrogenase, and from this set we demonstrate the stable expression and accumulation of the homocitrate synthase, NifV, under aerobic conditions. Arguably, further studies in C. reinhardtii aimed at testing expression and function of the full gene set would provide the groundwork for a concerted future effort to create nitrogen-fixing crops.
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Affiliation(s)
- Marco Larrea-Álvarez
- School of Biological Sciences and Engineering, Yachay-Tech University Hacienda San José, Urcuquí-Imbabura 100650, Ecuador;
- Algal Research Group, Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Saul Purton
- Algal Research Group, Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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25
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Koirala A, Brözel VS. Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea. Microorganisms 2021; 9:microorganisms9081662. [PMID: 34442741 PMCID: PMC8399215 DOI: 10.3390/microorganisms9081662] [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: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.
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Affiliation(s)
- Amrit Koirala
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA;
| | - Volker S. Brözel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA;
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
- Correspondence: ; Tel.: +1-605-688-6144
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Chernomor O, Peters L, Schneidewind J, Loeschcke A, Knieps-Grünhagen E, Schmitz F, von Lieres E, Kutta RJ, Svensson V, Jaeger KE, Drepper T, von Haeseler A, Krauss U. Complex Evolution of Light-Dependent Protochlorophyllide Oxidoreductases in Aerobic Anoxygenic Phototrophs: Origin, Phylogeny, and Function. Mol Biol Evol 2021; 38:819-837. [PMID: 32931580 PMCID: PMC7947762 DOI: 10.1093/molbev/msaa234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlorophyllide oxidoreductase are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in oxygenic phototrophs, we recently identified a functional LPOR in the aerobic anoxygenic phototrophic bacterium (AAPB) Dinoroseobacter shibae and attributed its presence to a single horizontal gene transfer event from cyanobacteria. Here, we provide evidence for the more widespread presence of genuine LPOR enzymes in AAPBs. An exhaustive bioinformatics search identified 36 putative LPORs outside of oxygenic phototrophic bacteria (cyanobacteria) with the majority being AAPBs. Using in vitro and in vivo assays, we show that the large majority of the tested AAPB enzymes are genuine LPORs. Solution structural analyses, performed for two of the AAPB LPORs, revealed a globally conserved structure when compared with a well-characterized cyanobacterial LPOR. Phylogenetic analyses suggest that LPORs were transferred not only from cyanobacteria but also subsequently between proteobacteria and from proteobacteria to Gemmatimonadetes. Our study thus provides another interesting example for the complex evolutionary processes that govern the evolution of bacteria, involving multiple horizontal gene transfer events that likely occurred at different time points and involved different donors.
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Affiliation(s)
- Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Lena Peters
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Judith Schneidewind
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Esther Knieps-Grünhagen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Fabian Schmitz
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg, Germany
| | - Vera Svensson
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Drepper
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
- Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans. Appl Environ Microbiol 2020; 86:AEM.01402-20. [PMID: 32826220 DOI: 10.1128/aem.01402-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/15/2020] [Indexed: 12/22/2022] Open
Abstract
CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI 1 I 2 DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N2 was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N2 Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N2 but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivorans IMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.
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Pence N, Lewis N, Alleman AB, Seefeldt LC, Peters JW. Revealing a role for the G subunit in mediating interactions between the nitrogenase component proteins. J Inorg Biochem 2020; 214:111273. [PMID: 33086169 DOI: 10.1016/j.jinorgbio.2020.111273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/16/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Azotobacter vinelandii contains three forms of nitrogenase known as the Mo-, V-, and Fe-nitrogenases. They are all two-component enzyme systems, where the catalytic component, referred to as NifDK, VnfDGK, and AnfDGK, associates with the reductase component, the Fe protein or NifH, VnfH, and AnfH respectively. AnfDGK and VnfDGK have an additional subunit compared to NifDK, termed gamma or AnfG and VnfG, whose role is unknown. The expression of each nitrogenase is tightly regulated by metal availability, however it is known that there is crosstalk between the Mo- and V‑nitrogenases but the Fe‑nitrogenase components cannot support substrate reduction with its Mo‑nitrogenase counterparts. Here, docking models for the nitrogenase complexes were generated in ClusPro 2.0 based on the crystal structure of the Mo‑nitrogenase and refined using the HADDOCK 2.2 refinement interface to identify structural determinants that enable crosstalk between the Mo- and V‑nitrogenase but not the Fe‑nitrogenase. Differing salt bridge interactions were identified at the binding interface of each complex. Specifically, positively charged residues of VnfG enable complementary interactions with NifH and VnfH but not AnfH. Similarly, negatively charged residues of AnfG enable interactions with AnfH but not NifH or VnfH. A role for the G subunit is revealed where VnfG could be mediating crosstalk between the Mo- and V‑nitrogenases while the AnfG subunit on AnfDGK makes interactions with NifH and VnfH unfavorable, reducing competition with NifDK and funneling electrons to the most efficient nitrogenase.
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Affiliation(s)
- Natasha Pence
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States of America
| | - Nathan Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America
| | - Alexander B Alleman
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States of America
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America.
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29
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Artificial, Photoinduced Activation of Nitrogenase Using Directed and Mediated Electron Transfer Processes. Catalysts 2020. [DOI: 10.3390/catal10090979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nitrogenase, a bacteria-based enzyme, is the sole enzyme that is able to generate ammonia by atmospheric nitrogen fixation. Thus, improved understanding of its utilization and developing methods to artificially activate it may contribute to basic research, as well as to the design of future artificial systems. Here, we present methods to artificially activate nitrogenase using photoinduced reactions. Two nitrogenase variants originating from Azotobacter vinelandii were examined using photoactivated CdS nanoparticles (NPs) capped with thioglycolic acid (TGA) or 2-mercaptoethanol (ME) ligands. The effect of methyl viologen (MV) as a redox mediator of hydrogen and ammonia generation was tested and analyzed. We further determined the NPs conductive band edges and their effect on the nitrogenase photoactivation. The nano-biohybrid systems comprising CdS NPs and nitrogenase were further imaged by transmission electron microscopy, visualizing their formation for the first time. Our results show that the ME-capped CdS NPs–nitrogenase enzyme biohybrid system with added MV as a redox mediator leads to a five-fold increase in the production of ammonia compared with the non-mediated biohybrid system; nevertheless, it stills lag behind the natural process rate. On the contrary, a maximal hydrogen generation amount was achieved by the αL158C MoFe-P and the ME-capped CdS NPs.
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30
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Méheust R, Castelle CJ, Matheus Carnevali PB, Farag IF, He C, Chen LX, Amano Y, Hug LA, Banfield JF. Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. ISME JOURNAL 2020; 14:2907-2922. [PMID: 32681159 DOI: 10.1038/s41396-020-0716-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/15/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
Abstract
Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Paula B Matheus Carnevali
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Lewes, DE, 19968, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Ibaraki, Japan
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Innovative Genomics Institute, Berkeley, CA, 94720, USA.
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31
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Abstract
The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are less efficient. The presumption has been that alternative nitrogenases are fail-safe enzymes that are used in situations where molybdenum is limiting. Recent work indicates that vanadium nitrogenase may play a role in the global biological nitrogen cycle and iron-only nitrogenase may contribute products that shape microbial community interactions in nature.
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Affiliation(s)
- Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
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32
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Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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33
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Garcia AK, McShea H, Kolaczkowski B, Kaçar B. Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization. GEOBIOLOGY 2020; 18:394-411. [PMID: 32065506 PMCID: PMC7216921 DOI: 10.1111/gbi.12381] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/23/2019] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon.
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Affiliation(s)
- Amanda K. Garcia
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonArizona
| | - Hanon McShea
- Department of Earth System ScienceStanford UniversityStanfordCalifornia
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell ScienceUniversity of FloridaGainesvilleFlorida
| | - Betül Kaçar
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonArizona
- Steward Observatory and the Lunar and Planetary LaboratoryUniversity of ArizonaTucsonArizona
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34
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Synthesis, spectral and structural characterization of vanadium lactate, malate and citrate with large counter cation. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Tsukada S, Abe T, Abe N, Nakashima S, Yamamoto K, Gunji T. Benzenedithiolate-bridged MoFe complexes: structures, oxidation states, and reactivities. Dalton Trans 2020; 49:9048-9056. [DOI: 10.1039/d0dt01428a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The benzenedithiolate-bridged MoFe complexes were synthesized and the oxidation states of the metal centers elucidated.
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Affiliation(s)
- Satoru Tsukada
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Takayuki Abe
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Naoya Abe
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Satoru Nakashima
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
- Natural Science Centre for Basic Research and Development
| | - Kazuki Yamamoto
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Takahiro Gunji
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
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36
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Newcomb MP, Lee CC, Tanifuji K, Jasniewski AJ, Liedtke J, Ribbe MW, Hu Y. A V‐Nitrogenase Variant Containing a Citrate‐Substituted Cofactor. Chembiochem 2019; 21:1742-1748. [DOI: 10.1002/cbic.201900654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Megan P. Newcomb
- Department of Chemistry University of California, Irvine Natural Sciences II Irvine CA 92697-2025 USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
| | - Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
| | - Andrew J. Jasniewski
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
| | - Jasper Liedtke
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
| | - Markus W. Ribbe
- Department of Chemistry University of California, Irvine Natural Sciences II Irvine CA 92697-2025 USA
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry University of California, Irvine 3205 McGaugh Hall Irvine CA 92697-3900 USA
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37
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Hickey DP, Cai R, Yang ZY, Grunau K, Einsle O, Seefeldt LC, Minteer SD. Establishing a Thermodynamic Landscape for the Active Site of Mo-Dependent Nitrogenase. J Am Chem Soc 2019; 141:17150-17157. [DOI: 10.1021/jacs.9b06546] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- David P. Hickey
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Rong Cai
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Katharina Grunau
- Institut für Biochemie and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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40
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X-ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin-Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019; 58:9373-9377. [PMID: 31119827 PMCID: PMC6772009 DOI: 10.1002/anie.201901899] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/17/2019] [Indexed: 11/23/2022]
Abstract
Nitrogenase enzymes catalyze the reduction of atmospheric dinitrogen to ammonia utilizing a Mo‐7Fe‐9S‐C active site, the so‐called FeMoco cluster. FeMoco and an analogous small‐molecule (Et4N)[(Tp)MoFe3S4Cl3] cubane have both been proposed to contain unusual spin‐coupled MoIII sites with an S(Mo)=1/2 non‐Hund configuration at the Mo atom. Herein, we present Fe and Mo L3‐edge X‐ray magnetic circular dichroism (XMCD) spectroscopy of the (Et4N)[(Tp)MoFe3S4Cl3] cubane and Fe L2,3‐edge XMCD spectroscopy of the MoFe protein (containing both FeMoco and the 8Fe‐7S P‐cluster active sites). As the P‐clusters of MoFe protein have an S=0 total spin, these are effectively XMCD‐silent at low temperature and high magnetic field, allowing for FeMoco to be selectively probed by Fe L2,3‐edge XMCD within the intact MoFe protein. Further, Mo L3‐edge XMCD spectroscopy of the cubane model has provided experimental support for a local S(Mo)=1/2 configuration, demonstrating the power and selectivity of XMCD.
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Affiliation(s)
- Joanna K Kowalska
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Justin T Henthorn
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - David Keavney
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Serena DeBeer
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X‐ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin‐Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joanna K. Kowalska
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Justin T. Henthorn
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - David Keavney
- Argonne National Laboratory 9700 S. Cass Ave Argonne IL 60439 USA
| | - Serena DeBeer
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
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Rutledge HL, Rittle J, Williamson LM, Xu WA, Gagnon DM, Tezcan FA. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J Am Chem Soc 2019; 141:10091-10098. [PMID: 31146522 DOI: 10.1021/jacs.9b04555] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molybdenum nitrogenase catalyzes the reduction of dinitrogen into ammonia, which requires the coordinated transfer of eight electrons to the active site cofactor (FeMoco) through the intermediacy of an [8Fe-7S] cluster (P-cluster), both housed in the molybdenum-iron protein (MoFeP). Previous studies on MoFeP from two different organisms, Azotobacter vinelandii ( Av) and Gluconacetobacter diazotrophicus ( Gd), have established that the P-cluster is conformationally flexible and can undergo substantial structural changes upon two-electron oxidation to the POX state, whereby a backbone amidate and an oxygenic residue (Ser or Tyr) ligate to two of the cluster's Fe centers. This redox-dependent change in coordination has been implicated in the conformationally gated electron transfer in nitrogenase. Here, we have investigated the role of the oxygenic ligand in Av MoFeP, which natively contains a Ser ligand (βSer188) to the P-cluster. Three variants were generated in which (1) the oxygenic ligand was eliminated (βSer188Ala), (2) the P-cluster environment was converted to the one in Gd MoFeP (βPhe99Tyr/βSer188Ala), and (3) two oxygenic ligands were simultaneously included (βPhe99Tyr). Our studies have revealed that the P-cluster can become compositionally labile upon oxidation and reversibly lose one or two Fe centers in the absence of the oxygenic ligand, while still retaining wild-type-like dinitrogen reduction activity. Our findings also suggest that Av and Gd MoFePs evolved with specific preferences for Ser and Tyr ligands, respectively, and that the structural control of these ligands must extend beyond the primary and secondary coordination spheres of the P-cluster. The P-cluster adds to the increasing number of examples of inherently labile Fe-S clusters whose compositional instability may be an obligatory feature to enable redox-linked conformational changes to facilitate multielectron redox reactions.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Jonathan Rittle
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Laura M Williamson
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Wanqing A Xu
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Derek M Gagnon
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
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Enzymatic Systems with Homology to Nitrogenase: Biosynthesis of Bacteriochlorophyll and Coenzyme F 430. Methods Mol Biol 2019; 1876:25-35. [PMID: 30317472 DOI: 10.1007/978-1-4939-8864-8_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Enzymes with homology to nitrogenase are essential for the reduction of chemically stable double bonds within the biosynthetic pathways of bacteriochlorophyll and coenzyme F430. These tetrapyrrole-based compounds are crucial for bacterial photosynthesis and the biogenesis of methane in methanogenic archaea. Formation of bacteriochlorophyll requires the unique ATP-dependent enzyme chlorophyllide oxidoreductase (COR) for the two-electron reduction of chlorophyllide to bacteriochlorophyllide. COR catalysis is based on the homodimeric protein subunit BchX2, which facilitates the transfer of electrons to the corresponding heterotetrameric catalytic subunit (BchY/BchZ)2. By analogy to the nitrogenase system, the dynamic switch protein BchX2 contains a [4Fe-4S] cluster that triggers the ATP-driven transfer of electrons onto a second [4Fe-4S] cluster located in (BchY/BchZ)2. The subsequent substrate reduction and protonation is unrelated to nitrogenase catalysis, with no further involvement of a molybdenum-containing cofactor. The biosynthesis of the nickel-containing coenzyme F430 includes the six-electron reduction of the tetrapyrrole macrocycle of Ni2+-sirohydrochlorin a,c-diamide to Ni2+-hexahydrosirohydrochlorin a,c-diamide catalyzed by CfbC/D. The homodimeric CfbC2 subunit carrying a [4Fe-4S] cluster shows close homology to BchX2. Accordingly, parallelism for the initial ATP-driven electron transfer steps of CfbC/D was proposed. Electrons are received by the dimeric catalytic subunit CfbD2, which contains a second [4Fe-4S] cluster and carries out the saturation of an overall of three double bonds in a highly orchestrated spatial and regioselective process. Following a short introduction to nitrogenase catalysis, this chapter will focus on the recent progress toward the understanding of the nitrogenase-like enzymes COR and CfbC/D, with special emphasis on the underlying enzymatic mechanism(s).
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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Denekamp IM, Veenstra FL, Jungbacker P, Rothenberg G. A simple synthesis of symmetric phthalocyanines and their respective perfluoro and transition‐metal complexes. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ilse M. Denekamp
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 Amsterdam 1098 XH The Netherlands
| | - Florentine L.P. Veenstra
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 Amsterdam 1098 XH The Netherlands
| | - Peter Jungbacker
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 Amsterdam 1098 XH The Netherlands
| | - Gadi Rothenberg
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 Amsterdam 1098 XH The Netherlands
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Bouchard S, Bruschi M, De Gioia L, Le Roy C, Pétillon FY, Schollhammer P, Talarmin J. FeMo Heterobimetallic Dithiolate Complexes: Investigation of Their Electron Transfer Chemistry and Reactivity toward Acids, a Density Functional Theory Rationalization. Inorg Chem 2019; 58:679-694. [PMID: 30561200 DOI: 10.1021/acs.inorgchem.8b02861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The electrochemical behavior of complexes [FeMo(CO)5(κ2-dppe)(μ-pdt)] (1) and [FeMo(CO)4(MeCN)(κ2-dppe)(μ-pdt)] (2), in the absence and in the presence of acid, has been investigated. The reduction of 1 follows at slow scan rates, in CH2Cl2-[NBu4][PF6] and acid-free media, an ECrevE mechanism that is supported by cyclic voltammetry (CV) experiments and digital CV simulations. In MeCN-[NBu4][PF6], the electrochemical reduction of 1 is the same as in dichloromethane and follows an ECE mechanism at slow scan rates, but with a positive shift of the redox potentials. In contrast, the oxidation of 1 is strongly solvent-dependent. In dichloromethane, the oxidation of 1 is reversible and involves a single electron, while in acetonitrile, it is irreversible at moderate and slow scan rates ( v ≤ ca. 1 V s-1), and some chemical reversibility is apparent at higher scan rates ( v = 10 V s-1). Density functional theory calculations revealed that the chemical step in the ECrevE mechanism corresponds to the dissociation of one PPh2 end of the diphosphine ligand and the transfer of the semibridging CO to the Fe atom, similarly to the mechanism observed in the FeFe analogue complex. However, in the case of 1, the subsequent coordination of the phosphine ligand to the other metal is an unfavorable process.
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Affiliation(s)
- Solène Bouchard
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Maurizio Bruschi
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , Piazza della Scienza 1 , 20126 Milan , Italy
| | - Luca De Gioia
- Department of Biotechnology and Bioscience , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Christine Le Roy
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - François Y Pétillon
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Philippe Schollhammer
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Jean Talarmin
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
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Gu NX, Ung G, Peters JC. Catalytic hydrazine disproportionation mediated by a thiolate-bridged VFe complex. Chem Commun (Camb) 2019; 55:5363-5366. [DOI: 10.1039/c9cc00345b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A heterobimetallic VFe complex is demonstrated to catalyse hydrazine disproportionation with yields of up to 1073 equivalents of NH3 per catalyst, comparable to the highest turnover known for any molecular catalyst.
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Affiliation(s)
- Nina X. Gu
- Division of Chemistry and Chemical Engineering
- California Institute of Technology
- Pasadena
- USA
| | - Gaël Ung
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - Jonas C. Peters
- Division of Chemistry and Chemical Engineering
- California Institute of Technology
- Pasadena
- USA
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48
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Abstract
Diphosphorous (P2) side-on coordinated to a dicobalt (Co–Co) moiety was described 45 years ago. This discovery had several links to actual problems of homogeneous molecular catalysis. The new type of organometallic complexes induced several ingenious new ramifications in main-group/transition metal cluster chemistry in the last decades. The present review traces the main lines of these research results and their contacts to actual problems of industrial catalysis.
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Demtröder L, Narberhaus F, Masepohl B. Coordinated regulation of nitrogen fixation and molybdate transport by molybdenum. Mol Microbiol 2018; 111:17-30. [PMID: 30325563 DOI: 10.1111/mmi.14152] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2018] [Indexed: 12/01/2022]
Abstract
Biological nitrogen fixation, the reduction of chemically inert dinitrogen to bioavailable ammonia, is a central process in the global nitrogen cycle highly relevant for life on earth. N2 reduction to NH3 is catalyzed by nitrogenases exclusively synthesized by diazotrophic prokaryotes. All diazotrophs have a molybdenum nitrogenase containing the unique iron-molybdenum cofactor FeMoco. In addition, some diazotrophs encode one or two alternative Mo-free nitrogenases that are less efficient at reducing N2 than Mo-nitrogenase. To permit biogenesis of Mo-nitrogenase and other molybdoenzymes when Mo is scarce, bacteria synthesize the high-affinity molybdate transporter ModABC. Generally, Mo supports expression of Mo-nitrogenase genes, while it represses production of Mo-free nitrogenases and ModABC. Since all three nitrogenases and ModABC can reach very high levels at suitable Mo concentrations, tight Mo-mediated control saves considerable resources and energy. This review outlines the similarities and differences in Mo-responsive regulation of nitrogen fixation and molybdate transport in diverse diazotrophs.
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Affiliation(s)
- Lisa Demtröder
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | - Bernd Masepohl
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S. Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs. Microbes Environ 2018; 33:357-365. [PMID: 30404970 PMCID: PMC6307998 DOI: 10.1264/jsme2.me18030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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