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Nomura S, Paczia N, Kahnt J, Shima S. Isolation of an H 2-dependent electron-bifurcating CO 2-reducing megacomplex with MvhB polyferredoxin from Methanothermobacter marburgensis. FEBS J 2024; 291:2449-2460. [PMID: 38468562 DOI: 10.1111/febs.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) catalyzes the formation of formylmethanofuran through reducing CO2. Heterodisulfide reductase (Hdr) provides two low potential electrons for the Fmd reaction using a flavin-based electron-bifurcating mechanism. [NiFe]-hydrogenase (Mvh) or formate dehydrogenase (Fdh) complexes with Hdr and provides electrons to Hdr from H2 and formate, or the reduced form of F420, respectively. Recently, an Fdh-Hdr complex was purified as a 3-MDa megacomplex that contained Fmd, and its three-dimensional structure was elucidated by cryo-electron microscopy. In contrast, the Mvh-Hdr complex has been characterized only as a complex without Fmd. Here, we report the isolation and characterization of a 1-MDa Mvh-Hdr-Fmd megacomplex from Methanothermobacter marburgensis. After anion-exchange and hydrophobic chromatography was performed, the proteins with Hdr activity eluted in the 1- and 0.5-MDa fractions during size exclusion chromatography. Considering the apparent molecular mass and the protein profile in the fractions, the 1-MDa megacomplex was determined to be a dimeric Mvh-Hdr-Fmd complex. The megacomplex fraction contained a polyferredoxin subunit MvhB, which contains 12 [4Fe-4S]-clusters. MvhB polyferredoxin has never been identified in the previously purified Mvh-Hdr and Fmd preparations, suggesting that MvhB polyferredoxin is stabilized by the binding between Mvh-Hdr and Fmd in the Mvh-Hdr-Fmd complex. The purified Mvh-Hdr-Fmd megacomplex catalyzed electron-bifurcating reduction of [13C]-CO2 to form [13C]-formylmethanofuran in the absence of extrinsic ferredoxin. These results demonstrated that the subunits in the Mvh-Hdr-Fmd megacomplex are electronically connected for the reduction of CO2, which likely involves MvhB polyferredoxin as an electron relay.
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Affiliation(s)
- Shunsuke Nomura
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Yao S, Swanson CS, Cheng Z, He Q, Yuan H. Alternating polarity as a novel strategy for building synthetic microbial communities capable of robust Electro-Methanogenesis. BIORESOURCE TECHNOLOGY 2024; 395:130374. [PMID: 38280409 DOI: 10.1016/j.biortech.2024.130374] [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: 12/11/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Electro-methanogenic microbial communities can produce biogas with high efficiency and have attracted extensive research interest. In this study an alternating polarity strategy was developed to build electro-methanogenic communities. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4th enrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities assembled under alternating polarity were electroactive and structurally different from those assembled under other conditions. One Methanobacterium population and two Geobacter populations were consistently abundant and active in the communities. Their 16S rRNA was up-regulated by electrode potentials. Bayesian networks inferred close associations between these populations. Overall, electro-methanogenic communities have been successfully assembled with alternating polarity.
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Affiliation(s)
- Shiyun Yao
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA 19122, United States
| | - Clifford S Swanson
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Zhang Cheng
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA 19122, United States
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States.
| | - Heyang Yuan
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA 19122, United States.
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Kimura ZI, Kuriyama H, Iwasaki Y. Exploring Acetogenesis in Firmicutes: From Phylogenetic Analysis to Solid Medium Cultivation with Solid-Phase Electrochemical Isolation Equipments. Microorganisms 2023; 11:2976. [PMID: 38138120 PMCID: PMC10746088 DOI: 10.3390/microorganisms11122976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
This study introduces a groundbreaking approach for the exploration and utilization of electrotrophic acetogens, essential for advancing microbial electrosynthesis systems (MES). Our initial focus was the development of Solid-Phase Electrochemical Isolation Equipment (SPECIEs), a novel cultivation method for isolating electrotrophic acetogens directly from environmental samples on a solid medium. SPECIEs uses electrotrophy as a selection pressure, successfully overcoming the traditional cultivation method limitations and enabling the cultivation of diverse microbial communities with enhanced specificity towards acetogens. Following the establishment of SPECIEs, we conducted a genome-based phylogenetic analysis using the Genome Taxonomy Database (GTDB) to identify potential electrotrophic acetogens within the Firmicutes phylum and its related lineages. Subsequently, we validated the electrotrophic capabilities of selected strains under electrode-oxidizing conditions in a liquid medium. This sequential approach, integrating innovative cultivation techniques with detailed phylogenetic analysis, paves the way for further advances in microbial cultivation and the identification of new biocatalysts for sustainable energy applications.
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Affiliation(s)
- Zen-ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506, Japan; (H.K.); (Y.I.)
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Mathlouthi NEH, Belguith I, Yengui M, Oumarou Hama H, Lagier JC, Ammar Keskes L, Grine G, Gdoura R. The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures. Microorganisms 2023; 11:2742. [PMID: 38004753 PMCID: PMC10673094 DOI: 10.3390/microorganisms11112742] [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: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND AND AIMS Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea's role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC. METHODS We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions. RESULTS Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype. CONCLUSIONS The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea's role in CRC dynamics.
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Affiliation(s)
- Nour El Houda Mathlouthi
- Laboratoire de Recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Faculté des Sciences de Sfax, University of Sfax, Sfax 3000, Tunisia; (N.E.H.M.); (M.Y.)
| | - Imen Belguith
- Laboratoire de Recherche de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, University of Sfax, Avenue Majida BOULILA, Sfax 3029, Tunisia; (I.B.); (L.A.K.)
| | - Mariem Yengui
- Laboratoire de Recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Faculté des Sciences de Sfax, University of Sfax, Sfax 3000, Tunisia; (N.E.H.M.); (M.Y.)
| | - Hamadou Oumarou Hama
- IHU Méditerranée Infection, l’unité de Recherche Microbes, Evolution, Phylogénie et Infection (MEPHI), 19-21, Bd. Jean Moulin, 13005 Marseille, France; (H.O.H.); (J.-C.L.); (G.G.)
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, l’unité de Recherche Microbes, Evolution, Phylogénie et Infection (MEPHI), 19-21, Bd. Jean Moulin, 13005 Marseille, France; (H.O.H.); (J.-C.L.); (G.G.)
| | - Leila Ammar Keskes
- Laboratoire de Recherche de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, University of Sfax, Avenue Majida BOULILA, Sfax 3029, Tunisia; (I.B.); (L.A.K.)
| | - Ghiles Grine
- IHU Méditerranée Infection, l’unité de Recherche Microbes, Evolution, Phylogénie et Infection (MEPHI), 19-21, Bd. Jean Moulin, 13005 Marseille, France; (H.O.H.); (J.-C.L.); (G.G.)
- Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, IHU Méditerranée Infection, l’unité de Recherche Microbes, Evolution, Phylogénie et Infection (MEPHI), 13005 Marseille, France
| | - Radhouane Gdoura
- Laboratoire de Recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Faculté des Sciences de Sfax, University of Sfax, Sfax 3000, Tunisia; (N.E.H.M.); (M.Y.)
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Gilep A, Varaksa T, Bukhdruker S, Kavaleuski A, Ryzhykau Y, Smolskaya S, Sushko T, Tsumoto K, Grabovec I, Kapranov I, Okhrimenko I, Marin E, Shevtsov M, Mishin A, Kovalev K, Kuklin A, Gordeliy V, Kaluzhskiy L, Gnedenko O, Yablokov E, Ivanov A, Borshchevskiy V, Strushkevich N. Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450. Front Mol Biosci 2023; 9:1100032. [PMID: 36699703 PMCID: PMC9868604 DOI: 10.3389/fmolb.2022.1100032] [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: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Ferredoxins are small iron-sulfur proteins and key players in essential metabolic pathways. Among all types, 3Fe-4S ferredoxins are less studied mostly due to anaerobic requirements. Their complexes with cytochrome P450 redox partners have not been structurally characterized. In the present work, we solved the structures of both 3Fe-4S ferredoxins from M. tuberculosis-Fdx alone and the fusion FdxE-CYP143. Our SPR analysis demonstrated a high-affinity binding of FdxE to CYP143. According to SAXS data, the same complex is present in solution. The structure reveals extended multipoint interactions and the shape/charge complementarity of redox partners. Furthermore, FdxE binding induced conformational changes in CYP143 as evident from the solved CYP143 structure alone. The comparison of FdxE-CYP143 and modeled Fdx-CYP51 complexes further revealed the specificity of ferredoxins. Our results illuminate the diversity of electron transfer complexes for the production of different secondary metabolites.
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Affiliation(s)
- Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus,Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Sviatlana Smolskaya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatsiana Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- European Molecular Biology Laboratory, Hamburg Unit C/O DESY, Hamburg, Germany
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin Gordeliy
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Oksana Gnedenko
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Evgeniy Yablokov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
| | - Natallia Strushkevich
- Skolkovo Institute of Science and Technology, Moscow, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
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