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Liu D, Bandyopadhyay A, Liberton M, Pakrasi HB, Bhattacharyya-Pakrasi M. Investigation of the Cyanothece nitrogenase cluster in Synechocystis: a blueprint for engineering nitrogen-fixing photoautotrophs. mBio 2025:e0405224. [PMID: 39998212 DOI: 10.1128/mbio.04052-24] [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: 01/14/2025] [Accepted: 02/04/2025] [Indexed: 02/26/2025] Open
Abstract
The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria, such as Cyanothece, is frequently selected by nature for nitrogen-fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain underexplored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of a Synechocystis 6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, the nif genes from Cyanothece 51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genes nifHDK, nifBSUENPVZTXW, as well as hesAB, are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar-powered conversion of atmospheric nitrogen into nitrogen-rich compounds, a stride toward a greener world.IMPORTANCEIntegrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen-rich products in a green and energy-efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen-fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen-fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen-fixing ability.
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Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Michelle Liberton
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri, USA
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2
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Wen ZP, Sha C, Nawab S, Lu ZJ, Yong YC. One-step transformation of CO 2 to methane by Escherichia coli with a synthetic biomethanation module. Biochem Biophys Res Commun 2025; 746:151284. [PMID: 39761619 DOI: 10.1016/j.bbrc.2024.151284] [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: 12/18/2024] [Accepted: 12/31/2024] [Indexed: 01/15/2025]
Abstract
The biomethanation process is widely recognized as a significant approach to mitigating carbon dioxide emissions while simultaneously generating methane. However, only a few microorganisms that required intricate culturing conditions were identified for biomethanation. Here, Escherichia coli that featured easy cultivation and versatile chassis was genetically modified for biomethanation for the first time. The nif-related gene cluster with methanogenic capability from Rhodopseudomonas palustris was systematically analyzed, cloned, and integrated into a synthetic biomethanation module. As a result, E. coli BL21 (DE3) and Rosetta (DE3) carrying this synthetic biomethanation module exhibited significant methane production activity, with methane yields reaching 50 nmol/mL and 159 nmol/mL, respectively. This finding provided a simple route to construct synthetic strain for biomethanation, which would advance the fundamental research and be beneficial to further harness the power of biomethanation for practical application.
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Affiliation(s)
- Ze-Peng Wen
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Chong Sha
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Said Nawab
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Zi-Jie Lu
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China; School of Emergency Management, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, 215009, China.
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3
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Ito Y, Yoshidome D, Hidaka M, Araki Y, Ito K, Kosono S, Nishiyama M. Improvement of the nitrogenase activity in Escherichia coli that expresses the nitrogen fixation-related genes from Azotobacter vinelandii. Biochem Biophys Res Commun 2024; 728:150345. [PMID: 38971001 DOI: 10.1016/j.bbrc.2024.150345] [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: 04/09/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The transfer of nitrogen fixation (nif) genes from diazotrophs to non-diazotrophic hosts is of increasing interest for engineering biological nitrogen fixation. A recombinant Escherichia coli strain expressing Azotobacter vinelandii 18 nif genes (nifHDKBUSVQENXYWZMF, nifiscA, and nafU) were previously constructed and showed nitrogenase activity. In the present study, we constructed several E. coli strain derivatives in which all or some of the 18 nif genes were additionally integrated into the fliK locus of the chromosome in various combinations. E. coli derivatives with the chromosomal integration of nifiscA, nifU, and nifS, which are involved in the biosynthesis of the [4Fe-4S] cluster of dinitrogenase reductase, exhibited enhanced nitrogenase activity. We also revealed that overexpression of E. coli fldA and ydbK, which encode flavodoxin and flavodoxin-reducing enzyme, respectively, enhanced nitrogenase activity, likely by facilitating electron transfer to dinitrogenase reductase. The additional expression of nifM, putatively involved in maturation of dinitrogenase reductase, further enhanced nitrogenase activity and the amount of soluble NifH. By combining these factors, we successfully improved nitrogenase activity 10-fold.
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Affiliation(s)
- Yusuke Ito
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Daisuke Yoshidome
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Makoto Hidaka
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yasuko Araki
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Saori Kosono
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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4
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Solomon JB, Lee CC, Liu YA, Duffin C, Ribbe MW, Hu Y. Ammonia synthesis via an engineered nitrogenase assembly pathway in Escherichia coli. Nat Catal 2024; 7:1130-1141. [PMID: 39713742 PMCID: PMC11661828 DOI: 10.1038/s41929-024-01229-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/19/2024] [Indexed: 12/24/2024]
Abstract
Heterologous expression of nitrogenase has been actively pursued because of the far-reaching impact of this enzyme on agriculture, energy and environment. Yet, isolation of an active two-component, metallocentre-containing nitrogenase from a non-diazotrophic host has yet to be accomplished. Here, we report the heterologous synthesis of an active Mo-nitrogenase by combining genes from Azotobacter vinelandii and Methanosarcina acetivorans in Escherichia coli. Metal, activity and EPR analyses demonstrate the integrity of the metallocentres in the purified nitrogenase enzyme; whereas growth, nanoSIMS and NMR experiments illustrate diazotrophic growth and 15N enrichment by the E. coli expression strain, as well as accumulation of extracellular ammonia upon deletion of the ammonia transporter that permits incorporation of thus-generated N into the cellular mass of a non-diazotrophic E. coli strain. As such, this study provides a crucial prototype system that could be optimized/modified to enable future transgenic expression and biotechnological adaptations of nitrogenase.
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Affiliation(s)
- Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
| | - Calder Duffin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
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5
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Lewis NM, Kisgeropoulos EC, Lubner CE, Fixen KR. Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity. J Inorg Biochem 2024; 254:112521. [PMID: 38471286 DOI: 10.1016/j.jinorgbio.2024.112521] [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: 10/11/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1T11I). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1T11I. Electrochemical characterization revealed both Fer1 and Fer1T11I have similar redox transitions (-480 mV and - 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron‑sulfur (FeS) cluster of Fer1. Additionally, disruption of hydrogen bonding around an FeS cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1T11I. Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1T11I, which indicate changes to the high spin states and/or spin-spin coupling between the FeS clusters of Fer1. Our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.
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Affiliation(s)
- Nathan M Lewis
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO, United States of America.
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America.
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6
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Venkataraman M, Yñigez-Gutierrez A, Infante V, MacIntyre A, Fernandes-Júnior PI, Ané JM, Pfleger B. Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes. ACS Synth Biol 2023; 12:3623-3634. [PMID: 37988619 PMCID: PMC10754042 DOI: 10.1021/acssynbio.3c00414] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. This work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.
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Affiliation(s)
- Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Audrey Yñigez-Gutierrez
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - April MacIntyre
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Valent BioSciences, Libertyville, Illinois 60048, United States
| | - Paulo Ivan Fernandes-Júnior
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Brazilian Agricultural Research Corporation (Embrapa), Tropical Semi-Arid Research Center (Embrapa Semiárido), Petrolina, Pernambuco 56302-970, Brazil
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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7
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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8
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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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9
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Johnston E, Okada S, Gregg CM, Warden AC, Rolland V, Gillespie V, Byrne K, Colgrave ML, Eamens AL, Allen RS, Wood CC. The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01363-3. [PMID: 37326800 DOI: 10.1007/s11103-023-01363-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
A long-held goal of synthetic biology has been the transfer of a bacterial nitrogen-fixation pathway into plants to reduce the use of chemical fertiliser on crops such as rice, wheat and maize. There are three classes of bacterial nitrogenase, named after their metal requirements, containing either a MoFe-, VFe- or FeFe-cofactor, that converts N2 gas to ammonia. Relative to the Mo-nitrogenase the Fe-nitrogenase is not as efficient for catalysis but has less complex genetic and metallocluster requirements, features that may be preferable for engineering into crops. Here we report the successful targeting of bacterial Fe-nitrogenase proteins, AnfD, AnfK, AnfG and AnfH, to plant mitochondria. When expressed as a single protein AnfD was mostly insoluble in plant mitochondria, but coexpression of AnfD with AnfK improved its solubility. Using affinity-based purification of mitochondrially expressed AnfK or AnfG we were able to demonstrate a strong interaction of AnfD with AnfK and a weaker interaction of AnfG with AnfDK. This work establishes that the structural components of the Fe-nitrogenase can be engineered into plant mitochondria and form a complex, which will be a requirement for function. This report outlines the first use of Fe-nitrogenase proteins within a plant as a preliminary step towards engineering an alternative nitrogenase into crops.
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Affiliation(s)
- E Johnston
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
- School of Environmental and Life Sciences, University of Newcastle, University Dr, Callaghan NSW 2308, Callaghan, Australia
| | - S Okada
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
| | - C M Gregg
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - A C Warden
- CSIRO Environment, GPO Box 1700, Acton, ACT, 2601, Australia
| | - V Rolland
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - V Gillespie
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
| | - K Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - M L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - A L Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - R S Allen
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia.
| | - C C Wood
- CSIRO Agriculture and Food, GPO Box 1700, Acton, ACT, 2601, Australia
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10
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Yu G, Li X, Duan Q, Fu J, Zhang Y, Wang H, Luan J. Systematic identification of endogenous strong constitutive promoters from the diazotrophic rhizosphere bacterium Pseudomonas stutzeri DSM4166 to improve its nitrogenase activity. Microb Cell Fact 2023; 22:91. [PMID: 37138314 PMCID: PMC10155442 DOI: 10.1186/s12934-023-02085-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Biological nitrogen fixation converting atmospheric dinitrogen to ammonia is an important way to provide nitrogen for plants. Pseudomonas stutzeri DSM4166 is a diazotrophic Gram-negative bacterium isolated from the rhizosphere of cereal Sorghum nutans. Endogenous constitutive promoters are important for engineering of the nitrogen fixation pathway, however, they have not been systematically characterized in DSM4166. RESULTS Twenty-six candidate promoters were identified from DSM4166 by RNA-seq analysis. These 26 promoters were cloned and characterized using the firefly luciferase gene. The strengths of nineteen promoters varied from 100 to 959% of the strength of the gentamicin resistance gene promoter. The strongest P12445 promoter was used to overexpress the biological nitrogen fixation pathway-specific positive regulator gene nifA. The transcription level of nitrogen fixation genes in DSM4166 were significantly increased and the nitrogenase activity was enhanced by 4.1 folds determined by the acetylene reduction method. The nifA overexpressed strain produced 359.1 µM of extracellular ammonium which was 25.6 times higher than that produced by the wild-type strain. CONCLUSIONS The endogenous strong constitutive promoters identified in this study will facilitate development of DSM4166 as a microbial cell factory for nitrogen fixation and production of other useful compounds.
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Affiliation(s)
- Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Qiuyue Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China.
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11
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Guo K, Yang J, Yu N, Luo L, Wang E. Biological nitrogen fixation in cereal crops: Progress, strategies, and perspectives. PLANT COMMUNICATIONS 2023; 4:100499. [PMID: 36447432 PMCID: PMC10030364 DOI: 10.1016/j.xplc.2022.100499] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 05/04/2023]
Abstract
Nitrogen is abundant in the atmosphere but is generally the most limiting nutrient for plants. The inability of many crop plants, such as cereals, to directly utilize freely available atmospheric nitrogen gas means that their growth and production often rely heavily on the application of chemical fertilizers, which leads to greenhouse gas emissions and the eutrophication of water. By contrast, legumes gain access to nitrogen through symbiotic association with rhizobia. These bacteria convert nitrogen gas into biologically available ammonia in nodules through a process termed symbiotic biological nitrogen fixation, which plays a decisive role in ecosystem functioning. Engineering cereal crops that can fix nitrogen like legumes or associate with nitrogen-fixing microbiomes could help to avoid the problems caused by the overuse of synthetic nitrogen fertilizer. With the development of synthetic biology, various efforts have been undertaken with the aim of creating so-called "N-self-fertilizing" crops capable of performing autonomous nitrogen fixation to avoid the need for chemical fertilizers. In this review, we briefly summarize the history and current status of engineering N-self-fertilizing crops. We also propose several potential biotechnological approaches for incorporating biological nitrogen fixation capacity into non-legume plants.
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Affiliation(s)
- Kaiyan Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Li Luo
- School of Life Sciences, Shanghai Key Laboratory of Bioenergy Crops, Shanghai University, Shanghai 200444, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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12
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Bennett EM, Murray JW, Isalan M. Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution. BIODESIGN RESEARCH 2023; 5:0005. [PMID: 37849466 PMCID: PMC10521693 DOI: 10.34133/bdr.0005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/24/2022] [Indexed: 10/19/2023] Open
Abstract
Globally, agriculture depends on industrial nitrogen fertilizer to improve crop growth. Fertilizer production consumes fossil fuels and contributes to environmental nitrogen pollution. A potential solution would be to harness nitrogenases-enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions. It is therefore a major goal of synthetic biology to engineer functional nitrogenases into crop plants, or bacteria that form symbiotic relationships with crops, to support growth and reduce dependence on industrially produced fertilizer. This review paper highlights recent work toward understanding the functional requirements for nitrogenase expression and manipulating nitrogenase gene expression in heterologous hosts to improve activity and oxygen tolerance and potentially to engineer synthetic symbiotic relationships with plants.
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Affiliation(s)
- Emily M. Bennett
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - James W. Murray
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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13
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Watanabe Y, Aoki W, Ueda M. Ammonia Production Using Bacteria and Yeast toward a Sustainable Society. Bioengineering (Basel) 2023; 10:82. [PMID: 36671654 PMCID: PMC9854848 DOI: 10.3390/bioengineering10010082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/29/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.
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Affiliation(s)
- Yukio Watanabe
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Wataru Aoki
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8501, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8501, Japan
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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: 0.3] [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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Decamps L, Rice DB, DeBeer S. An Fe 6 C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022; 61:e202209190. [PMID: 35975943 PMCID: PMC9826452 DOI: 10.1002/anie.202209190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Indexed: 01/11/2023]
Abstract
The biological process of dinitrogen reduction to ammonium occurs at the cofactors of nitrogenases, the only enzymes that catalyze this challenging chemical reaction. Three types of nitrogenases have been described, named according to the heterometal in their cofactor: molybdenum, vanadium or iron nitrogenases. Spectroscopic and structural characterization allowed the unambiguous identification of the cofactors of molybdenum and vanadium nitrogenases and revealed a central μ6 -carbide in both of them. Although genetic studies suggested that the cofactor of the iron nitrogenase contains a similar Fe6 C core, this has not been experimentally demonstrated. Here we report Valence-to-Core X-ray Emission Spectroscopy providing experimental evidence that this cofactor contains a carbide, thereby making the Fe6 C core a feature of all nitrogenase cofactors.
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Affiliation(s)
- Laure Decamps
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Derek B. Rice
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
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16
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Decamps L, Rice D, DeBeer S. An Fe6C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laure Decamps
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Derek Rice
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Serena DeBeer
- MPI CEC Molecular Theory and Spectroscopy Stidtstr. 34-36 45470 Muelheim an der Ruhr GERMANY
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17
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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18
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Payá-Tormo L, Coroian D, Martín-Muñoz S, Badalyan A, Green RT, Veldhuizen M, Jiang X, López-Torrejón G, Balk J, Seefeldt LC, Burén S, Rubio LM. A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation. Sci Rep 2022; 12:10367. [PMID: 35725884 PMCID: PMC9209457 DOI: 10.1038/s41598-022-14453-x] [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] [Received: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
Biological nitrogen fixation (BNF) is the reduction of N2 into NH3 in a group of prokaryotes by an extremely O2-sensitive protein complex called nitrogenase. Transfer of the BNF pathway directly into plants, rather than by association with microorganisms, could generate crops that are less dependent on synthetic nitrogen fertilizers and increase agricultural productivity and sustainability. In the laboratory, nitrogenase activity is commonly determined by measuring ethylene produced from the nitrogenase-dependent reduction of acetylene (ARA) using a gas chromatograph. The ARA is not well suited for analysis of large sample sets nor easily adapted to automated robotic determination of nitrogenase activities. Here, we show that a reduced sulfonated viologen derivative (S2Vred) assay can replace the ARA for simultaneous analysis of isolated nitrogenase proteins using a microplate reader. We used the S2Vred to screen a library of NifH nitrogenase components targeted to mitochondria in yeast. Two NifH proteins presented properties of great interest for engineering of nitrogen fixation in plants, namely NifM independency, to reduce the number of genes to be transferred to the eukaryotic host; and O2 resistance, to expand the half-life of NifH iron-sulfur cluster in a eukaryotic cell. This study established that NifH from Dehalococcoides ethenogenes did not require NifM for solubility, [Fe-S] cluster occupancy or functionality, and that NifH from Geobacter sulfurreducens was more resistant to O2 exposure than the other NifH proteins tested. It demonstrates that nitrogenase components with specific biochemical properties such as a wider range of O2 tolerance exist in Nature, and that their identification should be an area of focus for the engineering of nitrogen-fixing crops.
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Affiliation(s)
- Lucía Payá-Tormo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Silvia Martín-Muñoz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 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
| | - Artavazd Badalyan
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Robert T Green
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 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
| | - Gema López-Torrejón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 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
| | - Janneke Balk
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 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.
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Crta M-40 km 38 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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19
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A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants. Nat Commun 2022; 13:3361. [PMID: 35688828 PMCID: PMC9187771 DOI: 10.1038/s41467-022-31113-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/06/2022] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are important for crop performance. However, a deeper knowledge of crop-associated microbial communities is needed to harness beneficial host-microbe interactions. Here, by assessing the assembly and functions of maize microbiomes across soil types, climate zones, and genotypes, we found that the stem xylem selectively recruits highly conserved microbes dominated by Gammaproteobacteria. We showed that the proportion of bacterial taxa carrying the nitrogenase gene (nifH) was larger in stem xylem than in other organs such as root and leaf endosphere. Of the 25 core bacterial taxa identified in xylem sap, several isolated strains were confirmed to be active nitrogen-fixers or to assist with biological nitrogen fixation. On this basis, we established synthetic communities (SynComs) consisting of two core diazotrophs and two helpers. GFP-tagged strains and 15N isotopic dilution method demonstrated that these SynComs do thrive and contribute, through biological nitrogen fixation, 11.8% of the total N accumulated in maize stems. These core taxa in xylem sap represent an untapped resource that can be exploited to increase crop productivity. The plant xylem microbiota remains understudied. Here, the authors characterise the xylem microbiota in maize plants finding that some bacteria carried N fixing genes. By using synthetic communities the authors confirm that xylem inhabiting and N fixing bacteria provide the host plant with N.
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20
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Takimoto R, Tatemichi Y, Aoki W, Kosaka Y, Minakuchi H, Ueda M, Kuroda K. A critical role of an oxygen-responsive gene for aerobic nitrogenase activity in Azotobacter vinelandii and its application to Escherichia coli. Sci Rep 2022; 12:4182. [PMID: 35264690 PMCID: PMC8907163 DOI: 10.1038/s41598-022-08007-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Since nitrogenase is irreversibly inactivated within a few minutes after exposure to oxygen, current studies on the heterologous expression of nitrogenase are limited to anaerobic conditions. This study comprehensively identified genes showing oxygen-concentration-dependent expression only under nitrogen-fixing conditions in Azotobacter vinelandii, an aerobic diazotroph. Among the identified genes, nafU, with an unknown function, was greatly upregulated under aerobic nitrogen-fixing conditions. Through replacement and overexpressing experiments, we suggested that nafU is involved in the maintenance of nitrogenase activity under aerobic nitrogenase activity. Furthermore, heterologous expression of nafU in nitrogenase-producing Escherichia coli increased nitrogenase activity under aerobic conditions by 9.7 times. Further analysis of NafU protein strongly suggested its localization in the inner membrane and raised the possibility that this protein may lower the oxygen concentration inside the cells. These findings provide new insights into the mechanisms for maintaining stable nitrogenase activity under aerobic conditions in A. vinelandii and provide a platform to advance the use of nitrogenase under aerobic conditions.
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Affiliation(s)
- Ren Takimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuki Tatemichi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuishin Kosaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | | | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
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21
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Pérez‐González A, Jimenez‐Vicente E, Salinero‐Lanzarote A, Harris DF, Seefeldt LC, Dean DR. AnfO
controls fidelity of nitrogenase
FeFe
protein maturation by preventing misincorporation of
FeV
‐cofactor. Mol Microbiol 2022; 117:1080-1088. [PMID: 35220629 PMCID: PMC9310841 DOI: 10.1111/mmi.14890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/26/2022]
Abstract
Azotobacter vinelandii produces three genetically distinct, but structurally and mechanistically similar nitrogenase isozymes designated as Mo‐dependent, V‐dependent, or Fe‐only based on the heterometal contained within their associated active site cofactors. These catalytic cofactors, which provide the site for N2 binding and reduction, are, respectively, designated as FeMo‐cofactor, FeV‐cofactor, and FeFe‐cofactor. Fe‐only nitrogenase is a poor catalyst for N2 fixation, when compared to the Mo‐dependent and V‐dependent nitrogenases and is only produced when neither Mo nor V is available. Under conditions favoring the production of Fe‐only nitrogenase a gene product designated AnfO preserves the fidelity of Fe‐only nitrogenase by preventing the misincorporation of FeV‐cofactor, which results in the accumulation of a hybrid enzyme that cannot reduce N2. These results are interpreted to indicate that AnfO controls the fidelity of Fe‐only nitrogenase maturation during the physiological transition from conditions that favor V‐dependent nitrogenase utilization to Fe‐only nitrogenase utilization to support diazotrophic growth.
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Affiliation(s)
| | | | - Alvaro Salinero‐Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223 Madrid Spain
| | - Derek F. Harris
- Department of Chemistry and Biochemistry Utah State University Logan UT USA
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry Utah State University Logan UT USA
| | - Dennis R. Dean
- Department of Biochemistry, Virginia Tech, Blacksburg Virginia USA
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22
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A Red Fluorescent Protein Reporter System Developed for Measuring Gene Expression in Photosynthetic Bacteria under Anaerobic Conditions. Microorganisms 2022; 10:microorganisms10020201. [PMID: 35208656 PMCID: PMC8880563 DOI: 10.3390/microorganisms10020201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
The photosynthetic bacterium Rhodopseudomonas palustris converts nitrogen gas (N2) to fertilizer ammonia (NH3) and also produces clean energy hydrogen gas (H2) from protons (H+) when it is grown anaerobically in nitrogen fixing medium with illumination, a condition that promotes the expression of active nitrogenase. Compared with quantitative real-time PCR (qRT-PCR) and the lacZ reporter system, two methods commonly used for in vivo study of nitrogenase regulation in photosynthetic bacteria, the fluorescent protein reporter system has advantages in terms of its simplicity and sensitivity. However, little is known concerning if the fluorescent protein reporter system can be used in bacterial cells that need to grow anaerobically. Here, we developed an RFP-based method to measure the nitrogenase gene expression in photosynthetic bacteria grown anaerobically. This method was able to determine the levels of both the genome-based and the plasmid-based nitrogenase expression under anaerobic conditions, providing a better method for in vivo study of gene expression affected by oxygen. The RFP reporter system developed here will promote a better understanding of the molecular mechanism of nitrogenase regulation and will be used on other genes of interest in a wider range of anaerobic bacteria.
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23
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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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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: 0.8] [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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Priyadarshini P, Choudhury S, Tilgam J, Bharati A, Sreeshma N. Nitrogen fixing cereal: A rising hero towards meeting food security. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:912-920. [PMID: 34547550 DOI: 10.1016/j.plaphy.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen serves as one of the primary components of major biomolecules and thus extends a significant contribution to crop growth and yield. But the inability of plants to utilize freely available atmospheric N2 makes the whole agricultural system dependent on chemical fertilizers, which incur significant input cost to supplement required quantities of nitrogen to crops. Only bacteria and archaea have been gifted with the power of drawing free N2 from air to convert them into NH3, which is one of the two utilizable forms of nitrogen taken up by plants. Legumes, the only family of crops, can engage themselves in symbiotic nitrogen fixation where they establish a mutualistic relationship with nitrogen-fixing bacteria and in turn, can waive off the necessity of adding nitrogen fertilizers. Sincere effort, therefore, has been undertaken to incorporate this capability of nitrogen-fixation into non-legume crops, especially cereals which make up a vital portion in the food basket. Biotechnological interventions have also played important role in providing nitrogen fixing trait to non-legumes. This review takes up an effort to look into and accumulate all the important updates to date regarding nitrogen-fixing non-legumes with a special focus on cereals, which is one of the most important future goals in the field of science in the present era.
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Affiliation(s)
- Parichita Priyadarshini
- ICAR-Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, U.P., 284003, India
| | - Sharani Choudhury
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotsana Tilgam
- ICAR- National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, U.P., 274103, India.
| | - Alka Bharati
- ICAR-Central Agroforestry Research Institute, Jhansi, U.P., 284003, India
| | - N Sreeshma
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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Tatemichi Y, Nakahara T, Ueda M, Kuroda K. Construction of recombinant Escherichia coli producing nitrogenase-related proteins from Azotobacter vinelandii. Biosci Biotechnol Biochem 2021; 85:2209-2216. [PMID: 34387317 DOI: 10.1093/bbb/zbab144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/05/2021] [Indexed: 11/12/2022]
Abstract
Biological nitrogen fixation by nitrogenase has attracted attention as an alternative method to chemical nitrogen fixation, which requires large amounts of fossil fuels. Azotobacter vinelandii, which produces an oxygen-sensitive nitrogenase, can fix nitrogen even under aerobic conditions; therefore, the heterologous expression of nif-related genes from A. vinelandii is a promising strategy for developing a biological nitrogen fixation method. We assembled 17 nif-related genes, which are scattered throughout the genome of A. vinelandii, into synthetic gene clusters by overlap-extension-PCR and seamless cloning and expressed them in Escherichia coli. The transcription and translation of the 17 nif-related genes were evaluated by RT-qPCR and LC-MS/MS, respectively. The constructed E. coli showed nitrogenase activity under anaerobic and microaerobic conditions. This strain would be a useful model for examining the effect of other genes from A. vinelandii on nitrogen fixation by expressing them in addition to the minimal set of nif-related genes.
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Affiliation(s)
- Yuki Tatemichi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
- Research and Development Division, Kikkoman Corporation, Noda-City, Chiba, Japan
| | - Takeharu Nakahara
- Research and Development Division, Kikkoman Corporation, Noda-City, Chiba, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, Japan
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Sustainable Biological Ammonia Production towards a Carbon-Free Society. SUSTAINABILITY 2021. [DOI: 10.3390/su13179496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A sustainable society was proposed more than 50 years ago. However, it is yet to be realised. For example, the production of ammonia, an important chemical widely used in the agriculture, steel, chemical, textile, and pharmaceutical industries, still depends on fossil fuels. Recently, biological approaches to achieve sustainable ammonia production have been gaining attention. Moreover, unlike chemical methods, biological approaches have a lesser environmental impact because ammonia can be produced under mild conditions of normal temperature and pressure. Therefore, in previous studies, nitrogen fixation by nitrogenase, including enzymatic ammonia production using food waste, has been attempted. Additionally, the production of crops using nitrogen-fixing bacteria has been implemented in the industry as one of the most promising approaches to achieving a sustainable ammonia economy. Thus, in this review, we described previous studies on biological ammonia production and showed the prospects for realising a sustainable society.
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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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Specificity of NifEN and VnfEN for the Assembly of Nitrogenase Active Site Cofactors in Azotobacter vinelandii. mBio 2021; 12:e0156821. [PMID: 34281397 PMCID: PMC8406325 DOI: 10.1128/mbio.01568-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nitrogen-fixing microbe Azotobacter vinelandii has the ability to produce three genetically distinct, but mechanistically similar, components that catalyze nitrogen fixation. For two of these components, the Mo-dependent and V-dependent components, their corresponding metal-containing active site cofactors, designated FeMo-cofactor and FeV-cofactor, respectively, are preformed on separate molecular scaffolds designated NifEN and VnfEN, respectively. From prior studies, and the present work, it is now established that neither of these scaffolds can replace the other with respect to their in vivo cofactor assembly functions. Namely, a strain inactivated for NifEN cannot produce active Mo-dependent nitrogenase nor can a strain inactivated for VnfEN produce an active V-dependent nitrogenase. It is therefore proposed that metal specificities for FeMo-cofactor and FeV-cofactor formation are supplied by their respective assembly scaffolds. In the case of the third, Fe-only component, its associated active site cofactor, designated FeFe-cofactor, requires neither the NifEN nor VnfEN assembly scaffold for its formation. Furthermore, there are no other genes present in A. vinelandii that encode proteins having primary structure similarity to either NifEN or VnfEN. It is therefore concluded that FeFe-cofactor assembly is completed within its cognate catalytic protein partner without the aid of an intermediate assembly site. IMPORTANCE Biological nitrogen fixation is a complex process involving the nitrogenases. The biosynthesis of an active nitrogenase involves a large number of genes and the coordinated function of their products. Understanding the details of the assembly and activation of the different nitrogen fixation components, in particular the simplest one known so far, the Fe-only nitrogenase, would contribute to the goal of transferring the necessary genetic elements of bacterial nitrogen fixation to cereal crops to endow them with the capacity for self-fertilization. In this work, we show that there is no need for a scaffold complex for the assembly of the FeFe-cofactor, which provides the active site for Fe-only nitrogenase. These results are in agreement with previously reported genetic reconstruction experiments using a non-nitrogen-fixing microbe. In aggregate, these findings provide a high degree of confidence that the Fe-only system represents the simplest and, therefore, most attractive target for mobilizing nitrogen fixation into plants.
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Li Q, Zhang H, Zhang L, Chen S. Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases. Microb Cell Fact 2021; 20:139. [PMID: 34281551 PMCID: PMC8287671 DOI: 10.1186/s12934-021-01629-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/10/2021] [Indexed: 12/16/2022] Open
Abstract
Background Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known. Results A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results. Conclusions The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01629-9.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.,Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Liqun Zhang
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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Vladimirova AA, Gumenko RS, Akimova ES, Baymiev AK, Baymiev AK. Functional Specificity of the nifA Gene Product within the Group of Root Nodule Bacteria. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Jung D, Park S, Ruffini J, Dussault F, Dufour S, Ronholm J. Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. Microb Genom 2021; 7:000597. [PMID: 34227932 PMCID: PMC8477405 DOI: 10.1099/mgen.0.000597] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/29/2021] [Indexed: 01/03/2023] Open
Abstract
Escherichia coli is a major causative agent of environmental bovine mastitis and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic E. coli (MPEC) is indeed a unique E. coli pathotype, or whether this infection is merely an opportunistic infection caused by any E. coli isolate being displaced from the bovine gastrointestinal tract to the environment and, then, into the udder. In this study, we conducted a thorough genomic analysis of 113 novel MPEC isolates from clinical mastitis cases and 100 bovine commensal E. coli isolates. A phylogenomic analysis indicated that MPEC and commensal E. coli isolates formed clades based on common sequence types and O antigens, but did not cluster based on mammary pathogenicity. A comparative genomic analysis of MPEC and commensal isolates led to the identification of nine genes that were part of either the core or the soft-core MPEC genome, but were not found in any bovine commensal isolates. These apparent MPEC marker genes were genes involved with nutrient intake and metabolism [adeQ, adenine permease; nifJ, pyruvate-flavodoxin oxidoreductase; and yhjX, putative major facilitator superfamily (MFS)-type transporter], included fitness and virulence factors commonly seen in uropathogenic E. coli (pqqL, zinc metallopeptidase, and fdeC, intimin-like adhesin, respectively), and putative proteins [yfiE, uncharacterized helix-turn-helix-type transcriptional activator; ygjI, putative inner membrane transporter; and ygjJ, putative periplasmic protein]. Further characterization of these highly conserved MPEC genes may be critical to understanding the pathobiology of MPEC.
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Affiliation(s)
- Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Sainte Anne de Bellevue, Quebec, Canada
- Mastitis Network, Saint-Hyacinthe, Quebec J2S 2M2, Canada
| | - Soyoun Park
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Sainte Anne de Bellevue, Quebec, Canada
- Mastitis Network, Saint-Hyacinthe, Quebec J2S 2M2, Canada
| | - Janina Ruffini
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | | | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Quebec J2S 2M2, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec J2S 2M2, Canada
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Sainte Anne de Bellevue, Quebec, Canada
- Mastitis Network, Saint-Hyacinthe, Quebec J2S 2M2, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec J2S 2M2, Canada
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López‐Torrejón G, Burén S, Veldhuizen M, Rubio LM. Biosynthesis of cofactor-activatable iron-only nitrogenase in Saccharomyces cerevisiae. Microb Biotechnol 2021; 14:1073-1083. [PMID: 33507628 PMCID: PMC8085987 DOI: 10.1111/1751-7915.13758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/02/2022] Open
Abstract
Engineering nitrogenase in eukaryotes is hampered by its genetic complexity and by the oxygen sensitivity of its protein components. Of the three types of nitrogenases, the Fe-only nitrogenase is considered the simplest one because its function depends on fewer gene products than the homologous and more complex Mo and V nitrogenases. Here, we show the expression of stable Fe-only nitrogenase component proteins in the low-oxygen mitochondria matrix of S. cerevisiae. As-isolated Fe protein (AnfH) was active in electron donation to NifDK to reduce acetylene into ethylene. Ancillary proteins NifU, NifS and NifM were not required for Fe protein function. The FeFe protein existed as apo-AnfDK complex with the AnfG subunit either loosely bound or completely unable to interact with it. Apo-AnfDK could be activated for acetylene reduction by the simple addition of FeMo-co in vitro, indicating preexistence of the P-clusters even in the absence of coexpressed NifU and NifS. This work reinforces the use of Fe-only nitrogenase as simple model to engineer nitrogen fixation in yeast and plant mitochondria.
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Affiliation(s)
- Gema López‐Torrejón
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Pozuelo de Alarcón, Madrid28223Spain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaría y de BiosistemasUPMMadridSpain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Pozuelo de Alarcón, Madrid28223Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Pozuelo de Alarcón, Madrid28223Spain
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Pozuelo de Alarcón, Madrid28223Spain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaría y de BiosistemasUPMMadridSpain
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Sheoran S, Kumar S, Kumar P, Meena RS, Rakshit S. Nitrogen fixation in maize: breeding opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1263-1280. [PMID: 33677701 DOI: 10.1007/s00122-021-03791-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH4+). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Sandeep Kumar
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462 030, India
| | - Pradeep Kumar
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India
| | - Ram Swaroop Meena
- Department of Agronomy, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 1410 04, India.
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Watanabe Y, Aoki W, Ueda M. Improved ammonia production from soybean residues by cell surface-displayed l-amino acid oxidase on yeast. Biosci Biotechnol Biochem 2021; 85:972-980. [PMID: 33580695 DOI: 10.1093/bbb/zbaa112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022]
Abstract
Ammonia is critical for agricultural and chemical industries. The extracellular production of ammonia by yeast (Saccharomyces cerevisiae) using cell surface engineering can be efficient approach because yeast can avoid growth deficiencies caused by knockout of genes for ammonia assimilation. In this study, we produced ammonia outside the yeast cells by displaying an l-amino acid oxidase with a wide substrate specificity derived from Hebeloma cylindrosporum (HcLAAO) on yeast cell surfaces. The HcLAAO-displaying yeast successfully produced 12.6 m m ammonia from a mixture of 20 proteinogenic amino acids (the theoretical conversion efficiency was 63%). We also succeeded in producing ammonia from a food processing waste, soybean residues (okara) derived from tofu production. The conversion efficiency was 88.1%, a higher yield than reported in previous studies. Our study demonstrates that ammonia production outside of yeast cells is a promising strategy to utilize food processing wastes.
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Affiliation(s)
- Yukio Watanabe
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), Tokyo, Japan
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Soumare A, Diedhiou AG, Thuita M, Hafidi M, Ouhdouch Y, Gopalakrishnan S, Kouisni L. Exploiting Biological Nitrogen Fixation: A Route Towards a Sustainable Agriculture. PLANTS 2020; 9:plants9081011. [PMID: 32796519 PMCID: PMC7464700 DOI: 10.3390/plants9081011] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022]
Abstract
For all living organisms, nitrogen is an essential element, while being the most limiting in ecosystems and for crop production. Despite the significant contribution of synthetic fertilizers, nitrogen requirements for food production increase from year to year, while the overuse of agrochemicals compromise soil health and agricultural sustainability. One alternative to overcome this problem is biological nitrogen fixation (BNF). Indeed, more than 60% of the fixed N on Earth results from BNF. Therefore, optimizing BNF in agriculture is more and more urgent to help meet the demand of the food production needs for the growing world population. This optimization will require a good knowledge of the diversity of nitrogen-fixing microorganisms, the mechanisms of fixation, and the selection and formulation of efficient N-fixing microorganisms as biofertilizers. Good understanding of BNF process may allow the transfer of this ability to other non-fixing microorganisms or to non-leguminous plants with high added value. This minireview covers a brief history on BNF, cycle and mechanisms of nitrogen fixation, biofertilizers market value, and use of biofertilizers in agriculture. The minireview focuses particularly on some of the most effective microbial products marketed to date, their efficiency, and success-limiting in agriculture. It also highlights opportunities and difficulties of transferring nitrogen fixation capacity in cereals.
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Affiliation(s)
- Abdoulaye Soumare
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir 43150, Morocco; (M.H.); (Y.O.); (L.K.)
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar 1386, Senegal
- Correspondence: (A.S.); (A.G.D.)
| | - Abdala G. Diedhiou
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar 1386, Senegal
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD) de Dakar, Dakar 1386, Senegal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar 18524, Senegal
- Correspondence: (A.S.); (A.G.D.)
| | - Moses Thuita
- International Institute of Tropical Agriculture, Nairobi PO BOX 30772-00100, Kenya;
| | - Mohamed Hafidi
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir 43150, Morocco; (M.H.); (Y.O.); (L.K.)
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Yedir Ouhdouch
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir 43150, Morocco; (M.H.); (Y.O.); (L.K.)
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | | | - Lamfeddal Kouisni
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir 43150, Morocco; (M.H.); (Y.O.); (L.K.)
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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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Burén S, Jiménez-Vicente E, Echavarri-Erasun C, Rubio LM. Biosynthesis of Nitrogenase Cofactors. Chem Rev 2020; 120:4921-4968. [PMID: 31975585 PMCID: PMC7318056 DOI: 10.1021/acs.chemrev.9b00489] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/30/2022]
Abstract
Nitrogenase harbors three distinct metal prosthetic groups that are required for its activity. The simplest one is a [4Fe-4S] cluster located at the Fe protein nitrogenase component. The MoFe protein component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase metalloclusters requires the participation of the structural nitrogenase components and many accessory proteins, and occurs both in situ, for the P-cluster, and in external assembly sites for FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves molecular scaffolds, metallochaperones, radical chemistry, and novel and unique biosynthetic intermediates. This review provides a critical overview of discoveries on nitrogenase cofactor structure, function, and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria
y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department
of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria
y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, 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), Pozuelo de Alarcón, 28223 Madrid, Spain
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Li Q, Chen S. Transfer of Nitrogen Fixation (nif) Genes to Non-diazotrophic Hosts. Chembiochem 2020; 21:1717-1722. [PMID: 32009294 DOI: 10.1002/cbic.201900784] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Indexed: 12/20/2022]
Abstract
Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture. Biological nitrogen fixation, the conversion of atmospheric N2 to NH3 , is an important source of nitrogen input in agriculture and represents a promising substitute for chemical nitrogen fertilizers. However, nitrogen fixation is only sporadically distributed within bacteria and archaea (diazotrophs). Thus, many biologists hope to reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host, with the final aim of developing N2 -fixing cereal crops. With the advent of synthetic biology and a deep understanding of the fundamental genetic determinants necessary to sustain nitrogen fixation in bacteria, much progress has been made toward this goal. Transfer of native and refactored nif (nitrogen fixation) genes to non-diazotrophs has been attempted in model bacteria, yeast, and plants. Specifically, nif genes from Klebsiella oxytoca, Azotobacter vinelandii, and Paenibacillus polymyxa have been successfully transferred and expressed in Escherichia coli, Saccharomyces cerevisiae, and even in the tobacco plant. These advances have laid the groundwork to enable cereal crops to "fix" nitrogen themselves to sustain their growth and yield.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
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40
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Abstract
As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce N2, nitrogenase must also hydrolyze at least 16 equivalents of adenosine triphosphate (MgATP), representing the consumption of a significant quantity of energy available to biological systems. Here, we review natural and engineered electron transfer pathways to nitrogenase, including strategies to redirect or redistribute electron flow in vivo towards NH3 production. Further, we also review strategies to artificially reduce nitrogenase in vitro, where MgATP hydrolysis is necessary for turnover, in addition to strategies that are capable of bypassing the requirement of MgATP hydrolysis to achieve MgATP-independent N2 reduction.
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Addo MA, Dos Santos PC. Distribution of Nitrogen‐Fixation Genes in Prokaryotes Containing Alternative Nitrogenases. Chembiochem 2020; 21:1749-1759. [DOI: 10.1002/cbic.202000022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/04/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Maame A. Addo
- Department of Chemistry Wake Forest University Winston-Salem NC 27106 USA
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Bloch SE, Ryu MH, Ozaydin B, Broglie R. Harnessing atmospheric nitrogen for cereal crop production. Curr Opin Biotechnol 2020; 62:181-188. [DOI: 10.1016/j.copbio.2019.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
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Demtröder L, Pfänder Y, Masepohl B. Rhodobacter capsulatus AnfA is essential for production of Fe-nitrogenase proteins but dispensable for cofactor biosynthesis and electron supply. Microbiologyopen 2020; 9:1234-1246. [PMID: 32207246 PMCID: PMC7294313 DOI: 10.1002/mbo3.1033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/07/2023] Open
Abstract
The photosynthetic α‐proteobacterium Rhodobacter capsulatus reduces and thereby fixes atmospheric dinitrogen (N2) by a molybdenum (Mo)‐nitrogenase and an iron‐only (Fe)‐nitrogenase. Differential expression of the structural genes of Mo‐nitrogenase (nifHDK) and Fe‐nitrogenase (anfHDGK) is strictly controlled and activated by NifA and AnfA, respectively. In contrast to NifA‐binding sites, AnfA‐binding sites are poorly defined. Here, we identified two highly similar AnfA‐binding sites in the R. capsulatus anfH promoter by studying the effects of promoter mutations on in vivo anfH expression and in vitro promoter binding by AnfA. Comparison of the experimentally determined R. capsulatus AnfA‐binding sites and presumed AnfA‐binding sites from other α‐proteobacteria revealed a consensus sequence of dyad symmetry, TAC–N6–GTA, suggesting that AnfA proteins bind their target promoters as dimers. Chromosomal replacement of the anfH promoter by the nifH promoter restored anfHDGK expression and Fe‐nitrogenase activity in an R. capsulatus strain lacking AnfA suggesting that AnfA is required for AnfHDGK production, but dispensable for biosynthesis of the iron‐only cofactor and electron delivery to Fe‐nitrogenase, pathways activated by NifA. These observations strengthen our model, in which the Fe‐nitrogenase system in R. capsulatus is largely integrated into the Mo‐nitrogenase system.
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Affiliation(s)
- Lisa Demtröder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yvonne Pfänder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bernd Masepohl
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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44
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Okada S, Gregg CM, Allen RS, Menon A, Hussain D, Gillespie V, Johnston E, Byrne K, Colgrave ML, Wood CC. A Synthetic Biology Workflow Reveals Variation in Processing and Solubility of Nitrogenase Proteins Targeted to Plant Mitochondria, and Differing Tolerance of Targeting Sequences in a Bacterial Nitrogenase Assay. FRONTIERS IN PLANT SCIENCE 2020; 11:552160. [PMID: 33013970 PMCID: PMC7511584 DOI: 10.3389/fpls.2020.552160] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/21/2020] [Indexed: 05/13/2023]
Abstract
While industrial nitrogen fertilizer is intrinsic to modern agriculture, it is expensive and environmentally harmful. One approach to reduce fertilizer usage is to engineer the bacterial nitrogenase enzyme complex within plant mitochondria, a location that may support enzyme function. Our current strategy involves fusing a mitochondrial targeting peptide (MTP) to nitrogenase (Nif) proteins, enabling their import to the mitochondrial matrix. However, the process of import modifies the N-terminus of each Nif protein and may impact nitrogenase assembly and function. Here we present our workflow assessing the mitochondrial processing, solubility and relative abundance of 16 Klebsiella oxytoca Nif proteins targeted to the mitochondrial matrix in Nicotiana benthamiana leaf. We found that processing and abundance of MTP::Nif proteins varied considerably, despite using the same constitutive promoter and MTP across all Nif proteins tested. Assessment of the solubility for all MTP::Nif proteins when targeted to plant mitochondria found NifF, M, N, S, U, W, X, Y, and Z were soluble, while NifB, E, H, J, K, Q, and V were mostly insoluble. The functional consequence of the N-terminal modifications required for mitochondrial targeting of Nif proteins was tested using a bacterial nitrogenase assay. With the exception of NifM, the Nif proteins generally tolerated the N-terminal extension. Proteomic analysis of Nif proteins expressed in bacteria found that the relative abundance of NifM with an N-terminal extension was increased ~50-fold, while that of the other Nif proteins was not influenced by the N-terminal extension. Based on the solubility, processing and functional assessments, our workflow identified that K. oxytoca NifF, N, S, U, W, Y, and Z successfully met these criteria. For the remaining Nif proteins, their limitations will need to be addressed before proceeding towards assembly of a complete set of plant-ready Nif proteins for reconstituting nitrogenase in plant mitochondria.
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Affiliation(s)
- Shoko Okada
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Christina M. Gregg
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Robert Silas Allen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Amratha Menon
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Dawar Hussain
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Vanessa Gillespie
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ema Johnston
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Keren Byrne
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
| | - Michelle Lisa Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Queensland Biosciences Precinct, St. Lucia, QLD, Australia
| | - Craig C. Wood
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
- *Correspondence: Craig C. Wood,
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Nag P, Shriti S, Das S. Microbiological strategies for enhancing biological nitrogen fixation in nonlegumes. J Appl Microbiol 2020; 129:186-198. [PMID: 31858682 DOI: 10.1111/jam.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 01/17/2023]
Abstract
In an agro-ecosystem, industrially produced nitrogenous fertilizers are the principal sources of nitrogen for plant growth; unfortunately these also serve as the leading sources of pollution. Hence, it becomes imperative to find pollution-free methods of providing nitrogen to crop plants. A diverse group of free-living, plant associative and symbiotic prokaryotes are able to perform biological nitrogen fixation (BNF). BNF is a two component process involving the nitrogen fixing diazotrophs and the host plant. Symbiotic nitrogen fixation is most efficient as it can fix nitrogen inside the nodule formed on the roots of the plant; delivering nitrogen directly to the host. However, most of the important crop plants are nonleguminous and are unable to form symbiotic associations. In this context, the plant associative and endophytic diazotrophs assume importance. BNF in nonlegumes can be encouraged either through the transfer of BNF traits from legumes or by elevating the nitrogen fixing capacity of the associative and endophytic diazotrophs. In this review we discuss mainly the microbiological strategies which may be used in nonleguminous crops for enhancement of BNF.
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Affiliation(s)
- P Nag
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Shriti
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
| | - S Das
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
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Van Langenhove L, Depaepe T, Vicca S, van den Berge J, Stahl C, Courtois E, Weedon J, Urbina I, Grau O, Asensio D, Peñuelas J, Boeckx P, Richter A, Van Der Straeten D, Janssens IA. Regulation of nitrogen fixation from free-living organisms in soil and leaf litter of two tropical forests of the Guiana shield. PLANT AND SOIL 2020; 450:93-110. [PMID: 32624623 PMCID: PMC7319290 DOI: 10.1007/s11104-019-04012-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/25/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Biological fixation of atmospheric nitrogen (N2) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana. METHODS We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates. RESULTS Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites. CONCLUSIONS Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.
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Affiliation(s)
- Leandro Van Langenhove
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Thomas Depaepe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, KL Belgium
| | - Sara Vicca
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Joke van den Berge
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Clement Stahl
- INRA, UMR Ecology of Guiana Forests (Ecofog), AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, 97387 Kourou, French Guiana
| | - Elodie Courtois
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
- Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, French Guiana, 97300 Cayenne, France
| | - James Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ifigenia Urbina
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Oriol Grau
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Dolores Asensio
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Pascal Boeckx
- Department of Applied Analytical and Physical Chemistry, Faculty of Bioscience Engineering, Isotope Bioscience Laboratory – ISOFYS, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, KL Belgium
| | - Ivan A. Janssens
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
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Pankievicz VCS, Irving TB, Maia LGS, Ané JM. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol 2019; 17:99. [PMID: 31796086 PMCID: PMC6889567 DOI: 10.1186/s12915-019-0710-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
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Affiliation(s)
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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48
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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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49
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Abinandan S, Subashchandrabose SR, Venkateswarlu K, Megharaj M. Soil microalgae and cyanobacteria: the biotechnological potential in the maintenance of soil fertility and health. Crit Rev Biotechnol 2019; 39:981-998. [PMID: 31455102 DOI: 10.1080/07388551.2019.1654972] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The soil microbiota plays a major role in maintaining the nutrient balance, carbon sink, and soil health. Numerous studies reported on the function of microbiota such as plant growth-promoting bacteria and fungi in soil. Although microalgae and cyanobacteria are ubiquitous in soil, very less attention has been paid on the potential of these microorganisms. The indiscriminate use of various chemicals to enhance agricultural productivity led to serious consequences like structure instability, accumulation of toxic contaminants, etc., leading to an ecological imbalance between soil, plant, and microbiota. However, the significant role of microalgae and cyanobacteria in crop productivity and other potential options has been so far undermined. The intent of the present critical review is to highlight the significance of this unique group of microorganisms in terms of maintaining soil fertility and soil health. Beneficial soil ecological applications of these two groups in enhancing plant growth, establishing interrelationships among other microbes, and detoxifying chemical agents such as insecticides, herbicides, etc. through mutualistic cooperation by synthesizing enzymes and phytohormones are presented. Since recombinant technology involving genomic integration favors the development of useful traits in microalgae and cyanobacteria for their potential application in improvement of soil fertility and health, the merits and demerits of various such advanced methodologies associated in harnessing the biotechnological potential of these photosynthetic microorganisms for sustainable agriculture were also discussed.
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Affiliation(s)
- Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle , Callaghan , Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle , Callaghan , Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle , Callaghan , Australia
| | | | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle , Callaghan , Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle , Callaghan , Australia
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Demtröder L, Pfänder Y, Schäkermann S, Bandow JE, Masepohl B. NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus. Microbiologyopen 2019; 8:e921. [PMID: 31441241 PMCID: PMC6925177 DOI: 10.1002/mbo3.921] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/09/2023] Open
Abstract
Rhodobacter capsulatus fixes atmospheric nitrogen (N2) by a molybdenum (Mo)‐nitrogenase and a Mo‐free iron (Fe)‐nitrogenase, whose production is induced or repressed by Mo, respectively. At low nanomolar Mo concentrations, both isoenzymes are synthesized and contribute to nitrogen fixation. Here we examined the regulatory interplay of the central transcriptional activators NifA and AnfA by proteome profiling. As expected from earlier studies, synthesis of the structural proteins of Mo‐nitrogenase (NifHDK) and Fe‐nitrogenase (AnfHDGK) required NifA and AnfA, respectively, both of which depend on the alternative sigma factor RpoN to activate expression of their target genes. Unexpectedly, NifA was found to be essential for the synthesis of Fe‐nitrogenase, electron supply to both nitrogenases, biosynthesis of their cofactors, and production of RpoN. Apparently, RpoN is the only NifA‐dependent factor required for target gene activation by AnfA, since plasmid‐borne rpoN restored anfH transcription in a NifA‐deficient strain. However, plasmid‐borne rpoN did not restore Fe‐nitrogenase activity in this strain. Taken together, NifA requirement for synthesis and activity of both nitrogenases suggests that Fe‐nitrogenase functions as a complementary nitrogenase rather than an alternative isoenzyme in R. capsulatus.
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Affiliation(s)
- Lisa Demtröder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yvonne Pfänder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bernd Masepohl
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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