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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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2
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Garcia PS, Gribaldo S, Barras F. When iron and sulfur met on an anoxic planet and eventually made clusters essential for life. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119730. [PMID: 38631441 DOI: 10.1016/j.bbamcr.2024.119730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
[FeS] clusters are co-factors that are essential for life and are synthesized by dedicated multiprotein cellular machineries. In this review, we present the current scenario for the emergence and the diversification of the [FeS] cluster biosynthesis machineries. In addition to well-known NIF, ISC and SUF machineries, two alternative minimal systems, SMS, and MIS, were recently identified. Taxonomic distribution and phylogeny analyses indicate that SMS and MIS were present in the Last Universal Common Ancestor (LUCA), well before the increase of oxygen on Earth. ISC, SUF and NIF systems emerged later in the history of life. The possible reasons for the emergence and diversification of these machineries are discussed.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Paris, France; Institut Pasteur, Université Paris Cité, Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Frédéric Barras
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Paris, France.
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3
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Sourice M, Oriol C, Aubert C, Mandin P, Py B. Genetic dissection of the bacterial Fe-S protein biogenesis machineries. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119746. [PMID: 38719030 DOI: 10.1016/j.bbamcr.2024.119746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
Iron‑sulfur (Fe-S) clusters are one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters are essential cofactors for the activity of a large variety of metalloproteins that play crucial physiological roles. Fe-S protein biogenesis is a complex process that starts with the acquisition of the elements (iron and sulfur atoms) and their assembly into an Fe-S cluster that is subsequently inserted into the target proteins. The Fe-S protein biogenesis is ensured by multiproteic systems conserved across all domains of life. Here, we provide an overview on how bacterial genetics approaches have permitted to reveal and dissect the Fe-S protein biogenesis process in vivo.
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Affiliation(s)
- Mathieu Sourice
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Charlotte Oriol
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - BĂ©atrice Py
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.
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4
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Saini J, Deere TM, Lessner DJ. The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans. Sci Rep 2023; 13:15120. [PMID: 37704679 PMCID: PMC10500019 DOI: 10.1038/s41598-023-42400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.
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Affiliation(s)
- Jasleen Saini
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA.
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5
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Garcia PS, D'Angelo F, Ollagnier de Choudens S, Dussouchaud M, Bouveret E, Gribaldo S, Barras F. An early origin of iron-sulfur cluster biosynthesis machineries before Earth oxygenation. Nat Ecol Evol 2022; 6:1564-1572. [PMID: 36109654 DOI: 10.1038/s41559-022-01857-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors essential for life. It is largely thought that the emergence of oxygenic photosynthesis and progressive oxygenation of the atmosphere led to the origin of multiprotein machineries (ISC, NIF and SUF) assisting Fe-S cluster synthesis in the presence of oxidative stress and shortage of bioavailable iron. However, previous analyses have left unclear the origin and evolution of these systems. Here, we combine exhaustive homology searches with genomic context analysis and phylogeny to precisely identify Fe-S cluster biogenesis systems in over 10,000 archaeal and bacterial genomes. We highlight the existence of two additional and clearly distinct 'minimal' Fe-S cluster assembly machineries, MIS (minimal iron-sulfur) and SMS (SUF-like minimal system), which we infer in the last universal common ancestor (LUCA) and we experimentally validate SMS as a bona fide Fe-S cluster biogenesis system. These ancestral systems were kept in archaea whereas they went through stepwise complexification in bacteria to incorporate additional functions for higher Fe-S cluster synthesis efficiency leading to SUF, ISC and NIF. Horizontal gene transfers and losses then shaped the current distribution of these systems, driving ecological adaptations such as the emergence of aerobic lifestyles in archaea. Our results show that dedicated machineries were in place early in evolution to assist Fe-S cluster biogenesis and that their origin is not directly linked to Earth oxygenation.
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Affiliation(s)
- Pierre Simon Garcia
- Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | - Francesca D'Angelo
- Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | | | - Macha Dussouchaud
- Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | - Emmanuelle Bouveret
- Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France.
| | - Frédéric Barras
- Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France.
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6
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Li J, Ran X, Zhou M, Wang K, Wang H, Wang Y. Oxidative stress and antioxidant mechanisms of obligate anaerobes involved in biological waste treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156454. [PMID: 35667421 DOI: 10.1016/j.scitotenv.2022.156454] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
In-depth understanding of the molecular mechanisms and physiological consequences of oxidative stress is still limited for anaerobes. Anaerobic biotechnology has become widely accepted by the wastewater/sludge industry as a better alternative to more conventional but costly aerobic processes. However, the functional anaerobic microorganisms used in anaerobic biotechnology are frequently hampered by reactive oxygen/nitrogen species (ROS/RNS)-mediated oxidative stress caused by exposure to stressful factors (e.g., oxygen and heavy metals), which negatively impact treatment performance. Thus, identifying stressful factors and understanding antioxidative defense mechanisms of functional obligate anaerobes are crucial for the optimization of anaerobic bioprocesses. Herein, we present a comprehensive overview of oxidative stress and antioxidant mechanisms of obligate anaerobes involved in anaerobic bioprocesses; as examples, we focus on anaerobic ammonium oxidation bacteria and methanogenic archaea. We summarize the primary stress factors in anaerobic bioprocesses and the cellular antioxidant defense systems of functional anaerobes, a consortia of enzymatic and nonenzymatic mechanisms. The dual role of ROS/RNS in cellular processes is elaborated; at low concentrations, they have vital cell signaling functions, but at high concentrations, they cause oxidative damage. Finally, we highlight gaps in knowledge and future work to uncover antioxidant and damage repair mechanisms in obligate anaerobes. This review provides in-depth insights and guidance for future research on oxidative stress of obligate anaerobes to boost the accurate regulation of anaerobic bioprocesses in challenging and changing operating conditions.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Mingda Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
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7
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Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
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8
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Oral Iron Supplementation—Gastrointestinal Side Effects and the Impact on the Gut Microbiota. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Iron deficiency anaemia (IDA) is a worldwide healthcare problem affecting approximately 25% of the global population. The most common IDA treatment is oral iron supplementation, which has been associated with gastrointestinal (GI) side effects such as constipation and bloating. These can result in treatment non-adherence and the persistence of IDA. Intravenous iron does not cause GI side effects, which may be due to the lack of exposure to the intestinal lumen. Luminal iron can cause changes to the gut microbiota, aiding the promotion of pathogenic species and decreasing beneficial protective species. Iron is vital for methanogenic archaea, which rely on iron for growth and metabolism. Increased intestinal methane has been associated with slowing of intestinal transit, constipation, and bloating. Here we explore the literature to understand a potential link between iron and methanogenesis as a novel way to understand the mechanism of oral iron supplementation induced GI side effects.
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