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Graça AP, Nikitushkin V, Ellerhorst M, Vilhena C, Klassert TE, Starick A, Siemers M, Al-Jammal WK, Vilotijevic I, Slevogt H, Papenfort K, Lackner G. MftG is crucial for ethanol metabolism of mycobacteria by linking mycofactocin oxidation to respiration. eLife 2025; 13:RP97559. [PMID: 39878311 PMCID: PMC11778925 DOI: 10.7554/elife.97559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2025] Open
Abstract
Mycofactocin is a redox cofactor essential for the alcohol metabolism of mycobacteria. While the biosynthesis of mycofactocin is well established, the gene mftG, which encodes an oxidoreductase of the glucose-methanol-choline superfamily, remained functionally uncharacterized. Here, we show that MftG enzymes are almost exclusively found in genomes containing mycofactocin biosynthetic genes and are present in 75% of organisms harboring these genes. Gene deletion experiments in Mycolicibacterium smegmatis demonstrated a growth defect of the ∆mftG mutant on ethanol as a carbon source, accompanied by an arrest of cell division reminiscent of mild starvation. Investigation of carbon and cofactor metabolism implied a defect in mycofactocin reoxidation. Cell-free enzyme assays and respirometry using isolated cell membranes indicated that MftG acts as a mycofactocin dehydrogenase shuttling electrons toward the respiratory chain. Transcriptomics studies also indicated remodeling of redox metabolism to compensate for a shortage of redox equivalents. In conclusion, this work closes an important knowledge gap concerning the mycofactocin system and adds a new pathway to the intricate web of redox reactions governing the metabolism of mycobacteria.
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Affiliation(s)
- Ana Patrícia Graça
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Junior Research Group Synthetic MicrobiologyJenaGermany
| | - Vadim Nikitushkin
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Junior Research Group Synthetic MicrobiologyJenaGermany
- University of Bayreuth, Chair of Biochemistry of MicroorganismsKulmbachGermany
| | - Mark Ellerhorst
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Junior Research Group Synthetic MicrobiologyJenaGermany
- University of Bayreuth, Chair of Biochemistry of MicroorganismsKulmbachGermany
| | - Cláudia Vilhena
- Leibniz Institute for Natural Product Research and Infection Biology– Hans Knöll Institute, Department of Infection BiologyJenaGermany
| | - Tilman E Klassert
- Respiratory Infection Dynamics, Helmholtz Centre for Infection Research - HZI BraunschweigBraunschweigGermany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATHHannoverGermany
| | - Andreas Starick
- Friedrich Schiller University Jena, Institute of MicrobiologyJenaGermany
- Microverse Cluster, Friedrich Schiller University JenaJenaGermany
| | - Malte Siemers
- Friedrich Schiller University Jena, Institute of MicrobiologyJenaGermany
- Microverse Cluster, Friedrich Schiller University JenaJenaGermany
| | - Walid K Al-Jammal
- Friedrich Schiller University Jena, Institute of Organic Chemistry and Macromolecular ChemistryJenaGermany
| | - Ivan Vilotijevic
- Friedrich Schiller University Jena, Institute of Organic Chemistry and Macromolecular ChemistryJenaGermany
| | - Hortense Slevogt
- Respiratory Infection Dynamics, Helmholtz Centre for Infection Research - HZI BraunschweigBraunschweigGermany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATHHannoverGermany
| | - Kai Papenfort
- Friedrich Schiller University Jena, Institute of MicrobiologyJenaGermany
- Microverse Cluster, Friedrich Schiller University JenaJenaGermany
| | - Gerald Lackner
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Junior Research Group Synthetic MicrobiologyJenaGermany
- University of Bayreuth, Chair of Biochemistry of MicroorganismsKulmbachGermany
- Microverse Cluster, Friedrich Schiller University JenaJenaGermany
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Zampieri G, Santinello D, Palù M, Orellana E, Costantini P, Favaro L, Campanaro S, Treu L. Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota. THE ISME JOURNAL 2025; 19:wraf017. [PMID: 39893570 PMCID: PMC11844248 DOI: 10.1093/ismejo/wraf017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/27/2024] [Accepted: 01/29/2025] [Indexed: 02/04/2025]
Abstract
Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by Sphaerobacter thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.
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Affiliation(s)
- Guido Zampieri
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Davide Santinello
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Matteo Palù
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Esteban Orellana
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Paola Costantini
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Lorenzo Favaro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, Viale dell'Università 16, Legnaro, 35020, Italy
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35131, Italy
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Lettau E, Lorent C, Appel J, Boehm M, Cordero PRF, Lauterbach L. Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2025; 1866:149508. [PMID: 39245309 DOI: 10.1016/j.bbabio.2024.149508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
The NAD+-reducing soluble [NiFe] hydrogenase (SH) is the key enzyme for production and consumption of molecular hydrogen (H2) in Synechocystis sp. PCC6803. In this study, we focused on the reductase module of the SynSH and investigated the structural and functional aspects of its subunits, particularly the so far elusive role of HoxE. We demonstrated the importance of HoxE for enzyme functionality, suggesting a regulatory role in maintaining enzyme activity and electron supply. Spectroscopic analysis confirmed that HoxE and HoxF each contain one [2Fe2S] cluster with an almost identical electronic structure. Structure predictions, alongside experimental evidence for ferredoxin interactions, revealed a remarkable similarity between SynSH and bifurcating hydrogenases, suggesting a related functional mechanism. Our study unveiled the subunit arrangement and cofactor composition essential for biological electron transfer. These findings enhance our understanding of NAD+-reducing [NiFe] hydrogenases in terms of their physiological function and structural requirements for biotechnologically relevant modifications.
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Affiliation(s)
- Elisabeth Lettau
- RWTH Aachen University, iAMB - Institute of Applied Microbiology, Worringerweg 1, 52074 Aachen, Germany; Technische Universität Berlin, Institute of Chemistry, Straße des 14. Juni 135, 10623 Berlin, Germany.
| | - Christian Lorent
- Technische Universität Berlin, Institute of Chemistry, Straße des 14. Juni 135, 10623 Berlin, Germany
| | - Jens Appel
- Universität Kassel, Molecular Plant Biology, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Marko Boehm
- Universität Kassel, Molecular Plant Biology, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Paul R F Cordero
- RWTH Aachen University, iAMB - Institute of Applied Microbiology, Worringerweg 1, 52074 Aachen, Germany
| | - Lars Lauterbach
- RWTH Aachen University, iAMB - Institute of Applied Microbiology, Worringerweg 1, 52074 Aachen, Germany.
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Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [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: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
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Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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Marbehan X, Roger M, Fournier F, Infossi P, Guedon E, Delecourt L, Lebrun R, Giudici-Orticoni MT, Delaunay S. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2024; 15:1336360. [PMID: 38463485 PMCID: PMC10920352 DOI: 10.3389/fmicb.2024.1336360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions. Methods To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). Results The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. Discussion In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
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Affiliation(s)
| | - Magali Roger
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Pascale Infossi
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Louis Delecourt
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
- LISM-UMR 7255, Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Aix-Marseille Université, CNRS, Marseille, France
| | - Régine Lebrun
- IMM-FR3479, Marseille Protéomique, Aix-Marseille Université, CNRS, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
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