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Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2315568121. [PMID: 38530900 PMCID: PMC10998594 DOI: 10.1073/pnas.2315568121] [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: 09/13/2023] [Accepted: 02/24/2024] [Indexed: 03/28/2024] Open
Abstract
Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by N 5-methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na+ transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B12 derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG)3 composed of the central Mtr(ABFG)3 stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na+ were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na+ transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B12, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na+ flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na+ outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B12-carrying domain.
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Affiliation(s)
- Iram Aziz
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Kanwal Kayastha
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Susann Kaltwasser
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Janet Vonck
- Structural Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Bonnie J. Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Di Wu
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, BremenD-28359, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Ulrich Ermler
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
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Patra AK, Puchala R. Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways. Biotechnol Adv 2023; 69:108268. [PMID: 37793598 DOI: 10.1016/j.biotechadv.2023.108268] [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: 05/11/2023] [Revised: 09/20/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.
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Affiliation(s)
- Amlan Kumar Patra
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA.
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; Applied Physiology Unit, Military Institute of Hygiene and Epidemiology, Kozielska 4, Warsaw, Poland
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Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME COMMUNICATIONS 2022; 2:86. [PMID: 37938354 PMCID: PMC9723716 DOI: 10.1038/s43705-022-00175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2023]
Abstract
Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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Fuchs ACD, Ammelburg M, Martin J, Schmitz RA, Hartmann MD, Lupas AN. Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits. Proc Natl Acad Sci U S A 2021; 118:e2017871118. [PMID: 33688044 PMCID: PMC7980362 DOI: 10.1073/pnas.2017871118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Sequence-specific protein ligations are widely used to produce customized proteins "on demand." Such chimeric, immobilized, fluorophore-conjugated or segmentally labeled proteins are generated using a range of chemical, (split) intein, split domain, or enzymatic methods. Where short ligation motifs and good chemoselectivity are required, ligase enzymes are often chosen, although they have a number of disadvantages, for example poor catalytic efficiency, low substrate specificity, and side reactions. Here, we describe a sequence-specific protein ligase with more favorable characteristics. This ligase, Connectase, is a monomeric homolog of 20S proteasome subunits in methanogenic archaea. In pulldown experiments with Methanosarcina mazei cell extract, we identify a physiological substrate in methyltransferase A (MtrA), a key enzyme of archaeal methanogenesis. Using microscale thermophoresis and X-ray crystallography, we show that only a short sequence of about 20 residues derived from MtrA and containing a highly conserved KDPGA motif is required for this high-affinity interaction. Finally, in quantitative activity assays, we demonstrate that this recognition tag can be repurposed to allow the ligation of two unrelated proteins. Connectase catalyzes such ligations at substantially higher rates, with higher yields, but without detectable side reactions when compared with a reference enzyme. It thus presents an attractive tool for the development of new methods, for example in the preparation of selectively labeled proteins for NMR, the covalent and geometrically defined attachment of proteins on surfaces for cryo-electron microscopy, or the generation of multispecific antibodies.
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Affiliation(s)
- Adrian C D Fuchs
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Moritz Ammelburg
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrecht University of Kiel, 24118 Kiel, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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Watanabe T, Shima S. MvhB-type Polyferredoxin as an Electron-transfer Chain in Putative Redox-enzyme Complexes. CHEM LETT 2021. [DOI: 10.1246/cl.200774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Shima S, Huang G, Wagner T, Ermler U. Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 2020; 74:713-733. [DOI: 10.1146/annurev-micro-011720-122807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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Speth DR, Orphan VJ. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 2018; 6:e5614. [PMID: 30245936 PMCID: PMC6147122 DOI: 10.7717/peerj.5614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/21/2018] [Indexed: 01/24/2023] Open
Abstract
Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
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Affiliation(s)
- Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
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Bai L, Fujishiro T, Huang G, Koch J, Takabayashi A, Yokono M, Tanaka A, Xu T, Hu X, Ermler U, Shima S. Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase. Faraday Discuss 2017; 198:37-58. [DOI: 10.1039/c6fd00209a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H2 activation at the active site. FeII of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.
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Affiliation(s)
- Liping Bai
- Max-Planck-Institut für terrestrische Mikrobiologie
- 35043 Marburg
- Germany
| | - Takashi Fujishiro
- Max-Planck-Institut für terrestrische Mikrobiologie
- 35043 Marburg
- Germany
| | - Gangfeng Huang
- Max-Planck-Institut für terrestrische Mikrobiologie
- 35043 Marburg
- Germany
| | - Jürgen Koch
- Max-Planck-Institut für terrestrische Mikrobiologie
- 35043 Marburg
- Germany
| | - Atsushi Takabayashi
- The Institute of Low Temperature Science
- Hokkaido University
- Sapporo 060-0819
- Japan
| | - Makio Yokono
- The Institute of Low Temperature Science
- Hokkaido University
- Sapporo 060-0819
- Japan
| | - Ayumi Tanaka
- The Institute of Low Temperature Science
- Hokkaido University
- Sapporo 060-0819
- Japan
| | - Tao Xu
- Institute of Chemical Science and Engineering
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Xile Hu
- Institute of Chemical Science and Engineering
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik
- 60438 Frankfurt/Main
- Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie
- 35043 Marburg
- Germany
- PRESTO
- Japan, Science and Technology Agency (JST)
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