1
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Kang W. Structural Insights and Mechanistic Understanding of Iron-Molybdenum Cofactor Biosynthesis by NifB in Nitrogenase Assembly Process. Mol Cells 2023; 46:736-742. [PMID: 38052488 PMCID: PMC10701300 DOI: 10.14348/molcells.2023.0140] [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: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 12/07/2023] Open
Abstract
NifB, a radical S-adenosylmethionine (SAM) enzyme, is pivotal in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), commonly referred to as the M-cluster. This cofactor, located within the active site of nitrogenase, is essential for the conversion of dinitrogen (N2) to NH3. Recognized as the most intricate metallocluster in nature, FeMo-co biosynthesis involves multiple proteins and a sequence of steps. Of particular significance, NifB directs the fusion of two [Fe4S4] clusters to assemble the 8Fe core, while also incorporating an interstitial carbide. Although NifB has been extensively studied, its molecular mechanisms remain elusive. In this review, we explore recent structural analyses of NifB and provide a comprehensive overview of the established catalytic mechanisms. We propose prospective directions for future research, emphasizing the relevance to biochemistry, agriculture, and environmental science. The goal of this review is to lay a solid foundation for future endeavors aimed at elucidating the atomic details of FeMo-co biosynthesis.
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Affiliation(s)
- Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
- Department of Green Chemistry and Materials Engineering, Soongsil University, Seoul 06978, Korea
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2
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Quechol R, Solomon JB, Liu YA, Lee CC, Jasniewski AJ, Górecki K, Oyala P, Hedman B, Hodgson KO, Ribbe MW, Hu Y. Heterologous synthesis of the complex homometallic cores of nitrogenase P- and M-clusters in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2314788120. [PMID: 37871225 PMCID: PMC10622910 DOI: 10.1073/pnas.2314788120] [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: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Nitrogenase is an active target of heterologous expression because of its importance for areas related to agronomy, energy, and environment. One major hurdle for expressing an active Mo-nitrogenase in Escherichia coli is to generate the complex metalloclusters (P- and M-clusters) within this enzyme, which involves some highly unique bioinorganic chemistry/metalloenzyme biochemistry that is not generally dealt with in the heterologous expression of proteins via synthetic biology; in particular, the heterologous synthesis of the homometallic P-cluster ([Fe8S7]) and M-cluster core (or L-cluster; [Fe8S9C]) on their respective protein scaffolds, which represents two crucial checkpoints along the biosynthetic pathway of a complete nitrogenase, has yet to be demonstrated by biochemical and spectroscopic analyses of purified metalloproteins. Here, we report the heterologous formation of a P-cluster-containing NifDK protein upon coexpression of Azotobacter vinelandii nifD, nifK, nifH, nifM, and nifZ genes, and that of an L-cluster-containing NifB protein upon coexpression of Methanosarcina acetivorans nifB, nifS, and nifU genes alongside the A. vinelandii fdxN gene, in E. coli. Our metal content, activity, EPR, and XAS/EXAFS data provide conclusive evidence for the successful synthesis of P- and L-clusters in a nondiazotrophic host, thereby highlighting the effectiveness of our metallocentric, divide-and-conquer approach that individually tackles the key events of nitrogenase biosynthesis prior to piecing them together into a complete pathway for the heterologous expression of nitrogenase. As such, this work paves the way for the transgenic expression of an active nitrogenase while providing an effective tool for further tackling the biosynthetic mechanism of this important metalloenzyme.
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Affiliation(s)
- Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Andrew J. Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Paul Oyala
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
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3
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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4
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Scott AG, Agapie T. Synthesis of a Fe 3-Carbyne Motif by Oxidation of an Alkyl Ligated Iron-Sulfur (WFe 3S 3) Cluster. J Am Chem Soc 2023; 145:2-6. [PMID: 36537723 PMCID: PMC10575540 DOI: 10.1021/jacs.2c04826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The presence of a carbide ligand in the active site of nitrogenases remains an unusual example of organometallic chemistry employed by a protein. Carbide incorporation into the MFe7S9C cluster involves complex biosynthesis, but analogous synthetic methodologies are limited. Herein, we present a new synthetic strategy for incorporating carbon based bridging ligands into iron-sulfur clusters. Starting from a halide precursor, a WFe3S3 cluster displaying three terminal alkyl ligands and an open Fe3 face was prepared. Oxidation results in loss of alkane and formation of a μ3-carbyne. Characterization of these clusters and mechanistic studies are presented.
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Affiliation(s)
- Anna G Scott
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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5
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Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio 2022; 13:e0244322. [PMID: 36409126 PMCID: PMC9765008 DOI: 10.1128/mbio.02443-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N2 and CO2 into NH3 and CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2 fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.
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6
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Nguyen TQ, Nicolet Y. Structure and Catalytic Mechanism of Radical SAM Methylases. Life (Basel) 2022; 12:1732. [PMID: 36362886 PMCID: PMC9692996 DOI: 10.3390/life12111732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/14/2023] Open
Abstract
Methyl transfer is essential in myriad biological pathways found across all domains of life. Unlike conventional methyltransferases that catalyze this reaction through nucleophilic substitution, many members of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily use radical-based chemistry to methylate unreactive carbon centers. These radical SAM methylases reductively cleave SAM to generate a highly reactive 5'-deoxyadenosyl radical, which initiates a broad range of transformations. Recently, crystal structures of several radical SAM methylases have been determined, shedding light on the unprecedented catalytic mechanisms used by these enzymes to overcome the substantial activation energy barrier of weakly nucleophilic substrates. Here, we review some of the discoveries on this topic over the last decade, focusing on enzymes for which three-dimensional structures are available to identify the key players in the mechanisms, highlighting the dual function of SAM as a methyl donor and a 5'-deoxyadenosyl radical or deprotonating base source. We also describe the role of the protein matrix in orchestrating the reaction through different strategies to catalyze such challenging methylations.
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Affiliation(s)
| | - Yvain Nicolet
- Metalloproteins Unit, Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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7
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Zhang Q, Liu H, Shui X, Li Y, Zhang Z. Research progress of additives in photobiological hydrogen production system to enhance biohydrogen. BIORESOURCE TECHNOLOGY 2022; 362:127787. [PMID: 35985465 DOI: 10.1016/j.biortech.2022.127787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Photosynthetic biohydrogen has the advantages of extensive raw materials, clean and renewable, etc. But, its low substrate utilization rate limit its commercial application. It is reported that the use of additives in the process of biohydrogen by photofermentation is beneficial to increase biohydrogen. However, in practical application, the mechanism of additives in hydrogen production is not understood. This paper, the promotion effect of some additives on biohydrogen by photofermentation was reviewed. Whatever, the existing problems and development trends of various additives are also discussed. It is necessary to select appropriate additives according to the hydrogen-producing characteristics. The use of composite additives may further enhance biohydrogen, but the specific situation needs further exploration. The research results of this paper can help readers to further understand the role of additives in the crouse of photofermentative biohydrogen, provide reference for the research of photofermentative biohydrogen.
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Affiliation(s)
- Quanguo Zhang
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy (MOA of China), Henan Agricultural University, Zhengzhou 450002, China; Institute of Agricultural Engineering, Huanghe S & T University, Zhengzhou 450006, China.
| | - Hong Liu
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy (MOA of China), Henan Agricultural University, Zhengzhou 450002, China; Institute of Agricultural Engineering, Huanghe S & T University, Zhengzhou 450006, China
| | - Xuenan Shui
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy (MOA of China), Henan Agricultural University, Zhengzhou 450002, China
| | - Yameng Li
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy (MOA of China), Henan Agricultural University, Zhengzhou 450002, China
| | - Zhiping Zhang
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy (MOA of China), Henan Agricultural University, Zhengzhou 450002, China
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8
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He W, Burén S, Baysal C, Jiang X, Capell T, Christou P, Rubio LM. Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis. ACS Synth Biol 2022; 11:3028-3036. [PMID: 35998307 PMCID: PMC9486962 DOI: 10.1021/acssynbio.2c00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The engineering of nitrogen fixation in plants requires assembly of an active prokaryotic nitrogenase complex, which is yet to be achieved. Nitrogenase biogenesis relies on NifB, which catalyzes the formation of the [8Fe-9S-C] metal cluster NifB-co. This is the first committed step in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found at the nitrogenase active site. The production of NifB in plants is challenging because this protein is often insoluble in eukaryotic cells, and its [Fe-S] clusters are extremely unstable and sensitive to O2. As a first step to address this challenge, we generated transgenic rice plants expressing NifB from the Archaea Methanocaldococcus infernus and Methanothermobacter thermautotrophicus. The recombinant proteins were targeted to the mitochondria to limit exposure to O2 and to have access to essential [4Fe-4S] clusters required for NifB-co biosynthesis. M. infernus and M. thermautotrophicus NifB accumulated as soluble proteins in planta, and the purified proteins were functional in the in vitro FeMo-co synthesis assay. We thus report NifB protein expression and purification from an engineered staple crop, representing a first step in the biosynthesis of a functional NifDK complex, as required for independent biological nitrogen fixation in cereals.
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Affiliation(s)
- Wenshu He
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Stefan Burén
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Can Baysal
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Xi Jiang
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Teresa Capell
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Paul Christou
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain,ICREA,
Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain,
| | - Luis M. Rubio
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain,
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9
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Jeyachandran VR, Boal AK. Structural insights into auxiliary cofactor usage by radical S-adenosylmethionine enzymes. Curr Opin Chem Biol 2022; 68:102153. [PMID: 35512465 DOI: 10.1016/j.cbpa.2022.102153] [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: 12/31/2021] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/03/2022]
Abstract
Radical S-adenosylmethionine (SAM) enzymes use a common catalytic core for diverse transformations. While all radical SAM enzymes bind a Fe4S4 cluster via a characteristic tri-cysteine motif, many bind additional metal cofactors. Recently reported structures of radical SAM enzymes that use methylcobalamin or additional iron-sulfur clusters as cosubstrates show that these auxiliary units are anchored by N- and C-terminal domains that vary significantly in size and topology. Despite this architectural diversity, all use a common surface for auxiliary cofactor docking. In the sulfur insertion and metallocofactor assembly systems evaluated here, interaction with iron-sulfur cluster assembly proteins or downstream scaffold proteins is an important component of catalysis. Structures of these complexes represent important new frontiers in structural analysis of radical SAM enzymes.
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Affiliation(s)
- Vivian Robert Jeyachandran
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA; Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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10
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Liu YA, Quechol R, Solomon JB, Lee CC, Ribbe MW, Hu Y, Hedman B, Hodgson KO. Radical SAM-dependent formation of a nitrogenase cofactor core on NifB. J Inorg Biochem 2022; 233:111837. [PMID: 35550498 PMCID: PMC9526504 DOI: 10.1016/j.jinorgbio.2022.111837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022]
Abstract
Nitrogenase is a versatile metalloenzyme that reduces N2, CO and CO2 at its cofactor site. Designated the M-cluster, this complex cofactor has a composition of [(R-homocitrate)MoFe7S9C], and it is assembled through the generation of a unique [Fe8S9C] core prior to the insertion of Mo and homocitrate. NifB is a radical S-adenosyl-L-methionine (SAM) enzyme that is essential for nitrogenase cofactor assembly. This review focuses on the recent work that sheds light on the role of NifB in the formation of the [Fe8S9C] core of the nitrogenase cofactor, highlighting the structure, function and mechanism of this unique radical SAM methyltransferase.
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Affiliation(s)
- Yiling A Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Joseph B Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America; Department of Chemistry, University of California, Irvine, CA 92697-2025, United States of America
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America; Department of Chemistry, University of California, Irvine, CA 92697-2025, United States of America.
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America.
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States of America.
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States of America; Department of Chemistry, Stanford University, Stanford, CA 94305, United States of America.
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11
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Lénon M, Arias-Cartín R, Barras F. The Fe-S proteome of Escherichia coli: prediction, function and fate. Metallomics 2022; 14:6555457. [PMID: 35349713 DOI: 10.1093/mtomcs/mfac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic ubiquitous and ancient cofactors. Fe-S bound proteins contribute to most cellular processes, including DNA replication and integrity, genetic expression and regulation, metabolism, biosynthesis and most bioenergetics systems. Also, Fe-S proteins hold a great biotechnological potential in metabolite and chemical production, including antibiotics. From classic biophysics and spectroscopy methodologies to recent development in bioinformatics, including structural modeling and chemoproteomics, our capacity to predict and identify Fe-S proteins has spectacularly increased over the recent years. Here, these developments are presented and collectively used to update the composition of Escherichia coli Fe-S proteome, for which we predict 181 occurrences, i.e. 40 more candidates than in our last catalog (Py and Barras, 2010), and equivalent to 4% of its total proteome. Besides, Fe-S clusters can be targeted by redox active compounds or reactive oxygen and nitrosative species, and even be destabilized by contaminant metals. Accordingly, we discuss how cells handle damaged Fe-S proteins, i.e. degradation, recycling or repair.
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Affiliation(s)
- Marine Lénon
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
| | - Rodrigo Arias-Cartín
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
| | - Frédéric Barras
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, F-75015 Paris, France
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12
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Nicolet Y, Cherrier MV, Amara P. Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View. ACS BIO & MED CHEM AU 2022; 2:36-52. [PMID: 37102176 PMCID: PMC10114646 DOI: 10.1021/acsbiomedchemau.1c00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
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Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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13
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Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Van Stappen C, Jiménez-Vicente E, Pérez-González A, Yang ZY, Seefeldt LC, DeBeer S, Dean DR, Decamps L. A Conformational Role for NifW in the Maturation of Molybdenum Nitrogenase P-cluster. Chem Sci 2022; 13:3489-3500. [PMID: 35432878 PMCID: PMC8943848 DOI: 10.1039/d1sc06418e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Reduction of dinitrogen by molybdenum nitrogenase relies on complex metalloclusters: the [8Fe:7S] P-cluster and the [7Fe:9S:Mo:C:homocitrate] FeMo-cofactor. Although both clusters bear topological similarities and require the reductive fusion of [4Fe:4S] sub-clusters to achieve their respective assemblies, P-clusters are assembled directly on the NifD2K2 polypeptide prior to the insertion of FeMo-co, which is fully assembled separately from NifD2K2. P-cluster maturation involves the iron protein NifH2 as well as several accessory proteins, whose role has not been elucidated. In the present work, two NifD2K2 species bearing immature P-clusters were isolated from an Azotobacter vinelandii strain in which the genes encoding NifH and the accessory protein NifZ were deleted, and characterized by X-ray absorption spectroscopy and EPR. These analyses showed that both NifD2K2 complexes harbor clusters that are electronically and structurally similar, with each NifDK unit containing two [4Fe:4S]2+/+ clusters. Binding of the accessory protein NifW parallels a decrease in the distance between these clusters, as well as a subtle change in their coordination. These results support a conformational role for NifW in P-cluster biosynthesis, bringing the two [4Fe:4S] precursors closer prior to their fusion, which may be crucial in challenging cellular contexts. Upon binding of NifW, a subtle conformation change occurs in NifD2K2, decreasing the distance between the two [4Fe:4S] clusters precursors of the P-cluster in nitrogenase.![]()
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Emilio Jiménez-Vicente
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg VA 24061 USA
| | - Ana Pérez-González
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg VA 24061 USA
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Dennis R Dean
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg VA 24061 USA
| | - Laure Decamps
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
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