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Tejedor‐Sanz S, Song YE, Sundstrom ER. Utilization of formic acid by extremely thermoacidophilic archaea species. Microb Biotechnol 2024; 17:e70003. [PMID: 39215388 PMCID: PMC11364514 DOI: 10.1111/1751-7915.70003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.
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Affiliation(s)
- Sara Tejedor‐Sanz
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
| | - Young Eun Song
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
| | - Eric R. Sundstrom
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National LaboratoryEmeryvilleCaliforniaUSA
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2
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Bourgade B, Islam MA. Progresses and challenges of engineering thermophilic acetogenic cell factories. Front Microbiol 2024; 15:1476253. [PMID: 39282569 PMCID: PMC11392765 DOI: 10.3389/fmicb.2024.1476253] [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: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
Thermophilic acetogens are gaining recognition as potent microbial cell factories, leveraging their unique metabolic capabilities to drive the development of sustainable biotechnological processes. These microorganisms, thriving at elevated temperatures, exhibit robust carbon fixation abilities via the linear Wood-Ljungdahl pathway to efficiently convert C1 substrates, including syngas (CO, CO2 and H2) from industrial waste gasses, into acetate and biomass via the central metabolite acetyl-CoA. This review summarizes recent advancements in metabolic engineering and synthetic biology efforts that have expanded the range of products derived from thermophilic acetogens after briefly discussing their autotrophic metabolic diversity. These discussions highlight their potential in the sustainable bioproduction of industrially relevant compounds. We further review the remaining challenges for implementing efficient and complex strain engineering strategies in thermophilic acetogens, significantly limiting their use in an industrial context.
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Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
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3
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Baum C, Zeldes B, Poehlein A, Daniel R, Müller V, Basen M. The energy-converting hydrogenase Ech2 is important for the growth of the thermophilic acetogen Thermoanaerobacter kivui on ferredoxin-dependent substrates. Microbiol Spectr 2024; 12:e0338023. [PMID: 38385688 PMCID: PMC10986591 DOI: 10.1128/spectrum.03380-23] [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: 09/15/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Thermoanaerobacter kivui is the thermophilic acetogenic bacterium with the highest temperature optimum (66°C) and with high growth rates on hydrogen (H2) plus carbon dioxide (CO2). The bioenergetic model suggests that its redox and energy metabolism depends on energy-converting hydrogenases (Ech). Its genome encodes two Echs, Ech1 and Ech2, as sole coupling sites for energy conservation during growth on H2 + CO2. During growth on other substrates, its redox activity, the (proton-gradient-coupled) oxidation of H2 may be essential to provide reduced ferredoxin (Fd) to the cell. While Ech activity has been demonstrated biochemically, the physiological function of both Ech's is unclear. Toward that, we deleted the complete gene cluster encoding Ech2. Surprisingly, the ech2 mutant grew as fast as the wild type on sugar substrates and H2 + CO2. Hence, Ech1 may be the essential enzyme for energy conservation, and either Ech1 or another enzyme may substitute for H2-dependent Fd reduction during growth on sugar substrates, putatively the H2-dependent CO2 reductase (HDCR). Growth on pyruvate and CO, substrates that are oxidized by Fd-dependent enzymes, was significantly impaired, but to a different extent. While ∆ech2 grew well on pyruvate after four transfers, ∆ech2 did not adapt to CO. Cell suspensions of ∆ech2 converted pyruvate to acetate, but no acetate was produced from CO. We analyzed the genome of five T. kivui strains adapted to CO. Strikingly, all strains carried mutations in the hycB3 subunit of HDCR. These mutations are obviously essential for the growth on CO but may inhibit its ability to utilize Fd as substrate. IMPORTANCE Acetogens thrive by converting H2+CO2 to acetate. Under environmental conditions, this allows for only very little energy to be conserved (∆G'<-20 kJ mol-1). CO2 serves as a terminal electron acceptor in the ancient Wood-Ljungdahl pathway (WLP). Since the WLP is ATP neutral, energy conservation during growth on H2 + CO2 is dependent on the redox metabolism. Two types of acetogens can be distinguished, Rnf- and Ech-type. The function of both membrane-bound enzyme complexes is twofold-energy conversion and redox balancing. Ech couples the Fd-dependent reduction of protons to H2 to the formation of a proton gradient in the thermophilic bacterium Thermoanaerobacter kivui. This bacterium may be utilized in gas fermentation at high temperatures, due to very high conversion rates and the availability of genetic tools. The physiological function of an Ech hydrogenase in T. kivui was studied to contribute an understanding of its energy and redox metabolism, a prerequisite for future industrial applications.
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Affiliation(s)
- Christoph Baum
- Microbiology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Benjamin Zeldes
- Microbiology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Mirko Basen
- Microbiology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
- Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
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Nissen LS, Moon J, Hitschler L, Basen M. A Versatile Aldehyde: Ferredoxin Oxidoreductase from the Organic Acid Reducing Thermoanaerobacter sp. Strain X514. Int J Mol Sci 2024; 25:1077. [PMID: 38256150 PMCID: PMC10816221 DOI: 10.3390/ijms25021077] [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: 11/17/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Aldehyde:ferredoxin oxidoreductases (AORs) have been isolated and biochemically-characterized from a handful of anaerobic or facultative aerobic archaea and bacteria. They catalyze the ferredoxin (Fd)-dependent oxidation of aldehydes to acids. Recently, the involvement of AOR in the reduction of organic acids to alcohols with electrons derived from sugar or synthesis gas was demonstrated, with alcohol dehydrogenases (ADHs) carrying out the reduction of the aldehyde to the alcohol (AOR-ADH pathway). Here, we describe the biochemical characterization of an AOR of the thermophilic fermentative bacterium Thermoanaerobacter sp. strain X514 (AORX514). The putative aor gene (Teth514_1380) including a 6x-His-tag was introduced into the genome of the genetically-accessible, related species Thermoanaerobacter kivui. The protein was purified to apparent homogeneity, and indeed revealed AOR activity, as measured by acetaldehyde-dependent ferredoxin reduction. AORX514 was active over a wide temperature (10 to 95 °C) and pH (5.5 to 11.5) range, utilized a wide variety of aldehydes (short and branched-chained, aliphatic, aromatic) and resembles archaeal sensu stricto AORs, as the protein is active in a homodimeric form. The successful, recombinant production of AORX514 in a related, well-characterized and likewise strict anaerobe paves the road towards structure-function analyses of this enzyme and possibly similar oxygen-sensitive or W/Mo-dependent proteins in the future.
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Affiliation(s)
- Laura Sofie Nissen
- Microbiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany;
| | - Jimyung Moon
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
| | - Lisa Hitschler
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany;
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
- Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
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Lehmann M, Prohaska C, Zeldes B, Poehlein A, Daniel R, Basen M. Adaptive laboratory evolution of a thermophile toward a reduced growth temperature optimum. Front Microbiol 2023; 14:1265216. [PMID: 37901835 PMCID: PMC10601643 DOI: 10.3389/fmicb.2023.1265216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023] Open
Abstract
Thermophily is an ancient trait among microorganisms. The molecular principles to sustain high temperatures, however, are often described as adaptations, somewhat implying that they evolved from a non-thermophilic background and that thermophiles, i.e., organisms with growth temperature optima (TOPT) above 45°C, evolved from mesophilic organisms (TOPT 25-45°C). On the contrary, it has also been argued that LUCA, the last universal common ancestor of Bacteria and Archaea, may have been a thermophile, and mesophily is the derived trait. In this study, we took an experimental approach toward the evolution of a mesophile from a thermophile. We selected the acetogenic bacterium T. kivui (TOPT 66°C) since acetogenesis is considered ancient physiology and cultivated it at suboptimal low temperatures. We found that the lowest possible growth temperature (TMIN) under the chosen conditions was 39°C. The bacterium was subsequently subjected to adaptive laboratory evolution (ALE) by serial transfer at 45°C. Interestingly, after 67 transfers (approximately 180 generations), the adapted strain Adpt45_67 did not grow better at 45°C, but a shift in the TOPT to 60°C was observed. Growth at 45°C was accompanied by a change in the morphology as shorter, thicker cells were observed that partially occurred in chains. While the proportion of short-chain fatty acids increased at 50°C vs. 66°C in both strains, Adpt45_67 also showed a significantly increased proportion of plasmalogens. The genome analysis revealed 67 SNPs compared to the type strain, among these mutations in transcriptional regulators and in the cAMP binding protein. Ultimately, the molecular basis of the adaptation of T. kivui to a lower TOPT remains to be elucidated. The observed change in phenotype is the first experimental step toward the evolution of thermophiles growing at colder temperatures and toward a better understanding of the cold adaptation of thermophiles on early Earth.
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Affiliation(s)
- Maria Lehmann
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Christoph Prohaska
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Benjamin Zeldes
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Mirko Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
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6
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Moon J, Schubert A, Poehlein A, Daniel R, Müller V. A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:339-351. [PMID: 37150590 PMCID: PMC10472528 DOI: 10.1111/1758-2229.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Schubert
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
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7
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Katsyv A, Essig M, Bedendi G, Sahin S, Milton RD, Müller V. Characterization of ferredoxins from the thermophilic, acetogenic bacterium Thermoanaerobacter kivui. FEBS J 2023; 290:4107-4125. [PMID: 37074156 DOI: 10.1111/febs.16801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 04/19/2023] [Indexed: 04/20/2023]
Abstract
A major electron carrier involved in energy and carbon metabolism in the acetogenic model organism Thermoanaerobacter kivui is ferredoxin, an iron-sulfur-containing, electron-transferring protein. Here, we show that the genome of T. kivui encodes four putative ferredoxin-like proteins (TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530). All four genes were cloned, a His-tag encoding sequence was added and the proteins were produced from a plasmid in T. kivui. The purified proteins had an absorption peak at 430 nm typical for ferredoxins. The determined iron-sulfur content is consistent with the presence of two predicted [4Fe4S] clusters in TKV_c09620 and TKV_c19530 or one predicted [4Fe4S] cluster in TKV_c16450 and TKV_c10420 respectively. The reduction potential (Em ) for TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530 was determined to be -386 ± 4 mV, -386 ± 2 mV, -559 ± 10 mV and -557 ± 3 mV, respectively. TKV_c09620 and TKV_c16450 served as electron carriers for different oxidoreductases from T. kivui. Deletion of the ferredoxin genes led to only a slight reduction of growth on pyruvate or autotrophically on H2 + CO2 . Transcriptional analysis revealed that TKV_c09620 was upregulated in a ΔTKV_c16450 mutant and vice versa TKV_c16450 in a ΔTKV_c09620 mutant, indicating that TKV_c09620 and TKV_c16450 can replace each other. In sum, our data are consistent with the hypothesis that TKV_c09620 and TKV_c16450 are ferredoxins involved in autotrophic and heterotrophic metabolism of T. kivui.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Melanie Essig
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Giada Bedendi
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Selmihan Sahin
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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Hocq R, Bottone S, Gautier A, Pflügl S. A fluorescent reporter system for anaerobic thermophiles. Front Bioeng Biotechnol 2023; 11:1226889. [PMID: 37476481 PMCID: PMC10355840 DOI: 10.3389/fbioe.2023.1226889] [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: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Owing to their inherent capacity to make invisible biological processes visible and quantifiable, fluorescent reporter systems have numerous applications in biotechnology. For classical fluorescent protein systems (i.e., GFP and derivatives), chromophore maturation is O2-dependent, restricting their applications to aerobic organisms. In this work, we pioneered the use of the oxygen-independent system FAST (Fluorescence Activating and absorption Shifting tag) in the thermophilic anaerobe Thermoanaerobacter kivui. We developed a modular cloning system that was used to easily clone a library of FAST expression cassettes in an E. coli-Thermoanaerobacter shuttle plasmid. FAST-mediated fluorescence was then assessed in vivo in T. kivui, and we observed bright green and red fluorescence for cells grown at 55°C. Next, we took advantage of this functional reporter system to characterize a set of homologous and heterologous promoters by quantifying gene expression, expanding the T. kivui genetic toolbox. Low fluorescence at 66°C (Topt for T. kivui) was subsequently investigated at the single-cell level using flow cytometry and attributed to plasmid instability at higher temperatures. Adaptive laboratory evolution circumvented this issue and drastically enhanced fluorescence at 66°C. Whole plasmid sequencing revealed the evolved strain carried functional plasmids truncated at the Gram-positive origin of replication, that could however not be linked to the increased fluorescence displayed by the evolved strain. Collectively, our work demonstrates the applicability of the FAST fluorescent reporter systems to T. kivui, paving the way for further applications in thermophilic anaerobes.
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Affiliation(s)
- Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sara Bottone
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Arnaud Gautier
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
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9
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [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: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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10
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Moon J, Schubert A, Waschinger LM, Müller V. Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis. THE ISME JOURNAL 2023:10.1038/s41396-023-01411-2. [PMID: 37061584 DOI: 10.1038/s41396-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Methyl groups are abundant in anoxic environments and their utilization as carbon and energy sources by microorganisms involves oxidation of the methyl groups to CO2, followed by transfer of the electrons to an acceptor. In acetogenic bacteria, the electron acceptor is CO2 that is reduced to enzyme bound carbon monoxide, the precursor of the carboxyl group in acetate. Here, we describe the generation of a mutant of the acetogen Acetobacterium woodii in which the last step in methyl group oxidation, formate oxidation to CO2 catalyzed by the HDCR enzyme, has been genetically deleted. The mutant grew on glycine betaine as methyl group donor, and in contrast to the wild type, formed formate alongside acetate, in a 1:2 ratio, demonstrating that methyl group oxidation stopped at the level of formate and reduced electron carriers were reoxidized by CO2 reduction to acetate. In the presence of the alternative electron acceptor caffeate, CO2 was no longer reduced to acetate, formate was the only product and all the carbon went to formate. Apparently, acetogenesis was not required to sustain formatogenic growth. This is the first demonstration of a genetic reprogramming of an acetogen into a formatogen that grows by homoformatogenesis from methyl groups. Formate production from methyl groups is not only of biotechnological interest but also for the mechanism of electron transfer in syntrophic interactions in anoxic environments.
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Affiliation(s)
- Jimyung Moon
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Schubert
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany.
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Yao Y, Fu B, Han D, Zhang Y, Wei Z, Liu H. Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:129-141. [PMID: 36779246 PMCID: PMC10103890 DOI: 10.1111/1758-2229.13129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/23/2022] [Indexed: 05/20/2023]
Abstract
Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO2 and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO2 reduction to formate as the first step of methyl branch of WLP may have evolved independently.
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Affiliation(s)
- Ye Yao
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Dongfei Han
- School of Environmental Science and EngineeringSuzhou University of Science and TechnologySuzhouPeople's Republic of China
- Institute of Environment and Sustainable Development in AgricultureChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Zhang
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Zhiyuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of MedicineJiangnan UniversityWuxiJiangsuChina
| | - He Liu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
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12
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Ceron-Chafla P, de Vrieze J, Rabaey K, van Lier JB, Lindeboom REF. Steering the product spectrum in high-pressure anaerobic processes: CO 2 partial pressure as a novel tool in biorefinery concepts. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:27. [PMID: 36803622 PMCID: PMC9938588 DOI: 10.1186/s13068-023-02262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/05/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor. RESULTS Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided. CONCLUSIONS Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands.
| | - Jo de Vrieze
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Korneel Rabaey
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium ,grid.510907.aCenter for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Coupure Links 653, 9000 Ghent, Belgium
| | - Jules B. van Lier
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Ralph E. F. Lindeboom
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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13
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Zeldes B, Poehlein A, Jain S, Baum C, Daniel R, Müller V, Basen M. DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component. ISME COMMUNICATIONS 2023; 3:2. [PMID: 37938748 PMCID: PMC9834392 DOI: 10.1038/s43705-022-00211-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.
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Affiliation(s)
- Benjamin Zeldes
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Surbhi Jain
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Christoph Baum
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany.
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14
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Burger Y, Schwarz FM, Müller V. Formate-driven H2 production by whole cells of Thermoanaerobacter kivui. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:48. [PMID: 35545791 PMCID: PMC9097184 DOI: 10.1186/s13068-022-02147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/26/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.
Results
In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.
Conclusions
The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.
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15
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Brazelton WJ, McGonigle JM, Motamedi S, Pendleton HL, Twing KI, Miller BC, Lowe WJ, Hoffman AM, Prator CA, Chadwick GL, Anderson RE, Thomas E, Butterfield DA, Aquino KA, Früh-Green GL, Schrenk MO, Lang SQ. Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field. Appl Environ Microbiol 2022; 88:e0092922. [PMID: 35950875 PMCID: PMC9469722 DOI: 10.1128/aem.00929-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022] Open
Abstract
Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth's mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.
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Affiliation(s)
| | - Julia M. McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Shahrzad Motamedi
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Katrina I. Twing
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - William J. Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Cecilia A. Prator
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - Elaina Thomas
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USA
| | | | | | - Matthew O. Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
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16
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Membrane-anchored HDCR nanowires drive hydrogen-powered CO 2 fixation. Nature 2022; 607:823-830. [PMID: 35859174 DOI: 10.1038/s41586-022-04971-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 06/13/2022] [Indexed: 01/11/2023]
Abstract
Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive1. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO2 fixation-hydrogen-dependent CO2 reductase (HDCR)2,3-which directly converts H2 and CO2 into formic acid. HDCR reduces CO2 with a higher activity than any other known biological or chemical catalyst4,5, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO2. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
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Trischler R, Roth J, Sorbara MT, Schlegel X, Müller V. A functional Wood-Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae, Blautia luti and beyond. Environ Microbiol 2022; 24:3111-3123. [PMID: 35466558 DOI: 10.1111/1462-2920.16029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Species of the genus Blautia are typical inhabitants of the human gut and considered as beneficial gut microbes. However, their role in the gut microbiome and their metabolic features are poorly understood. Blautia schinkii was described as an acetogenic bacterium, characterized by a functional Wood-Ljungdahl pathway (WLP) of acetogenesis from H2 + CO2 . Here we report that two relatives, Blautia luti and Blautia wexlerae do not grow on H2 + CO2 . Inspection of the genome sequence revealed all genes of the WLP except genes encoding a formate dehydrogenase and an electron-bifurcating hydrogenase. Enzyme assays confirmed this prediction. Accordingly, resting cells neither converted H2 + CO2 nor H2 + HCOOH + CO2 to acetate. Carbon monoxide is an intermediate of the WLP and substrate for many acetogens. B. luti and B. wexlerae had an active CO dehydrogenase and resting cells performed acetogenesis from HCOOH + CO2 + CO, demonstrating a functional WLP. Bioinformatic analyses revealed that many Blautia strains as well as other gut acetogens lack formate dehydrogenases and hydrogenases. Thus, the use of formate instead of H2 + CO2 as an interspecies hydrogen and electron carrier seems to be more common in the gut microbiome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Jennifer Roth
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Matthew T Sorbara
- Department Molecular and Cellular Biology, University of Guelph, Ontario, N1G 2W1, Canada
| | - Xenia Schlegel
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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18
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Chatzipanagiotou KR, Jourdin L, Bitter H, Strik D. Concentration-dependent effects of nickel doping on activated carbon biocathodes. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02151f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In microbial electrosynthesis (MES), microorganisms grow on a cathode electrode as biofilm, or in the catholyte as planktonic biomass, and utilize CO2 for their growth and metabolism. Modification of the...
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19
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Jain S, Katsyv A, Basen M, Müller V. The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide. Extremophiles 2021; 26:4. [PMID: 34919167 PMCID: PMC8683389 DOI: 10.1007/s00792-021-01251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.
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Affiliation(s)
- Surbhi Jain
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, 18059, Rostock, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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20
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Electron carriers involved in autotrophic and heterotrophic acetogenesis in the thermophilic bacterium Thermoanaerobacter kivui. Extremophiles 2021; 25:513-526. [PMID: 34647163 PMCID: PMC8578170 DOI: 10.1007/s00792-021-01247-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022]
Abstract
Thermoanaerobacter kivui is an acetogenic model organism that reduces CO2 with electrons derived from H2 or CO, or from organic substrates in the Wood–Ljugdahl pathway (WLP). For the calculation of ATP yields, it is necessary to know the electron carriers involved in coupling of the oxidative and reductive parts of metabolism. Analyses of key catabolic oxidoreductases in cell-free extract (CFE) or with purified enzymes revealed the physiological electron carriers involved. The glyceraldehyde-3-phosphate dehydrogenase (GA3P-DH) assayed in CFE was NAD+-specific, NADP+ was used with less than 4% and ferredoxin (Fd) was not used. The methylene-THF dehydrogenase was NADP+-specific, NAD+ or Fd were not used. A Nfn-type transhydrogenase that catalyzes reduced Fd-dependent reduction of NADP+ with NADH as electron donor was also identified in CFE. The electron carriers used by the potential electron-bifurcating hydrogenase (HydABC) could not be unambiguously determined in CFE for technical reasons. Therefore, the enzyme was produced homologously in T. kivui and purified by affinity chromatography. HydABC contained 33.9 ± 4.5 mol Fe/mol of protein and FMN; it reduced NADP+ but not NAD+. The methylene-THF reductase (MetFV) was also produced homologously in T. kivui and purified by affinity chromatography. MetFV contained 7.2 ± 0.4 mol Fe/mol of protein and FMN; the complex did neither use NADPH nor NADH as reductant but only reduced Fd. In sum, these analysis allowed us to propose a scheme for entire electron flow and bioenergetics in T. kivui.
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Bourgade B, Minton NP, Islam MA. Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. FEMS Microbiol Rev 2021; 45:fuab008. [PMID: 33595667 PMCID: PMC8351756 DOI: 10.1093/femsre/fuab008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.
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Affiliation(s)
- Barbara Bourgade
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, University of Nottingham, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
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Formate-Dependent Acetogenic Utilization of Glucose by the Fecal Acetogen Clostridium bovifaecis. Appl Environ Microbiol 2020; 86:AEM.01870-20. [PMID: 32948524 DOI: 10.1128/aem.01870-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/12/2020] [Indexed: 11/20/2022] Open
Abstract
Acetogenic bacteria are a diverse group of anaerobes that use the reductive acetyl coenzyme A (acetyl-CoA) (Wood-Ljungdahl) pathway for CO2 fixation and energy conservation. The conversion of 2 mol CO2 into acetyl-CoA by using the Wood-Ljungdahl pathway as the terminal electron accepting process is the most prominent metabolic feature for these microorganisms. However, here, we describe that the fecal acetogen Clostridium bovifaecis strain BXX displayed poor metabolic capabilities of autotrophic acetogenesis, and acetogenic utilization of glucose occurred only with the supplementation of formate. Genome analysis of Clostridium bovifaecis revealed that it contains almost the complete genes of the Wood-Ljungdahl pathway but lacks the gene encoding formate dehydrogenase, which catalyzes the reduction of CO2 to formate as the first step of the methyl branch of the Wood-Ljungdahl pathway. The lack of a gene encoding formate dehydrogenase was verified by PCR, reverse transcription-PCR analysis, enzyme activity assay, and its formate-dependent acetogenic utilization of glucose on DNA, RNA, protein, and phenotype level, respectively. The lack of a formate dehydrogenase gene may be associated with the adaption to a formate-rich intestinal environment, considering the isolating source of strain BXX. The formate-dependent acetogenic growth of Clostridium bovifaecis provides insight into a unique metabolic feature of fecal acetogens.IMPORTANCE The acetyl-CoA pathway is an ancient pathway of CO2 fixation, which converts 2 mol of CO2 into acetyl-CoA. Autotrophic growth with H2 and CO2 via the acetyl-CoA pathway as the terminal electron accepting process is the most unique feature of acetogenic bacteria. However, the fecal acetogen Clostridium bovifaecis strain BXX displayed poor metabolic capabilities of autotrophic acetogenesis, and acetogenic utilization of glucose occurred only with the supplementation of formate. The formate-dependent acetogenic growth of Clostridium bovifaecis was associated with its lack of a gene encoding formate dehydrogenase, which may result from adaption to a formate-rich intestinal environment. This study gave insight into a unique metabolic feature of fecal acetogens. Because of the requirement of formate for the acetogenic growth of certain acetogens, the ecological impact of acetogens could be more complex and important in the formate-rich environment due to their trophic interactions with other microbes.
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23
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Schwarz FM, Ciurus S, Jain S, Baum C, Wiechmann A, Basen M, Müller V. Revealing formate production from carbon monoxide in wild type and mutants of Rnf- and Ech-containing acetogens, Acetobacterium woodii and Thermoanaerobacter kivui. Microb Biotechnol 2020; 13:2044-2056. [PMID: 32959527 PMCID: PMC7533326 DOI: 10.1111/1751-7915.13663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023] Open
Abstract
Acetogenic bacteria have gained much attraction in recent years as they can produce different biofuels and biochemicals from H2 plus CO2 or even CO alone, therefore opening a promising alternative route for the production of biofuels from renewable sources compared to existing sugar-based routes. However, CO metabolism still raises questions concerning the biochemistry and bioenergetics in many acetogens. In this study, we focused on the two acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui which, so far, are the only identified acetogens harbouring a H2 -dependent CO2 reductase and furthermore belong to different classes of 'Rnf'- and 'Ech-acetogens'. Both strains catalysed the conversion of CO into the bulk chemical acetate and formate. Formate production was stimulated by uncoupling the energy metabolism from the Wood-Ljungdahl pathway, and specific rates of 1.44 and 1.34 mmol g-1 h-1 for A. woodii ∆rnf and T. kivui wild type were reached. The demonstrated CO-based formate production rates are, to the best of our knowledge, among the highest rates ever reported. Using mutants of ∆hdcr, ∆cooS, ∆hydBA, ∆rnf and ∆ech2 with deficiencies in key enzyme activities of the central metabolism enabled us to postulate two different CO utilization pathways in these two model organisms.
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Affiliation(s)
- Fabian M. Schwarz
- Molecular Microbiology and BioenergeticsInstitute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Sarah Ciurus
- Molecular Microbiology and BioenergeticsInstitute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Surbhi Jain
- Molecular Microbiology and BioenergeticsInstitute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Christoph Baum
- MicrobiologyInstitute of Biological SciencesUniversity RostockRostockGermany
| | - Anja Wiechmann
- Molecular Microbiology and BioenergeticsInstitute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Mirko Basen
- MicrobiologyInstitute of Biological SciencesUniversity RostockRostockGermany
| | - Volker Müller
- Molecular Microbiology and BioenergeticsInstitute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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Moon J, Jain S, Müller V, Basen M. Homoacetogenic Conversion of Mannitol by the Thermophilic Acetogenic Bacterium Thermoanaerobacter kivui Requires External CO 2. Front Microbiol 2020; 11:571736. [PMID: 33042077 PMCID: PMC7522397 DOI: 10.3389/fmicb.2020.571736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/24/2020] [Indexed: 01/12/2023] Open
Abstract
Acetogenic microorganisms utilize organic substrates such as sugars in addition to hydrogen (H2) + carbon dioxide (CO2). Recently, we reported that the thermophilic acetogenic microorganism Thermoanaerobacter kivui is among the few acetogens that utilize the sugar alcohol mannitol, dependent on a gene cluster encoding mannitol uptake, phosphorylation and oxidation of mannitol-1-phosphate to fructose-6-phosphate. Here, we studied mannitol metabolism with resting cells of T. kivui; and found that mannitol was "fermented" in a homoacetogenic manner, i.e., acetate was the sole product if HCO3 - was present. We found an acetate:mannitol ratio higher than 3, indicating the requirement of external CO2, and the involvement of the WLP as terminal electron accepting pathway. In the absence of CO2 (or bicarbonate, HCO3 -), however, the cells still converted mannitol to acetate, but slowly and with stoichiometric amounts of H2 formed in addition, resulting in a "mixed" fermentation. This showed that-in addition to the WLP-the cells used an additional electron sink-protons, making up for the "missing" CO2 as electron sink. Growth was 2.5-fold slower in the absence of external CO2, while the addition of formate completely restored the growth rate. A model for mannitol metabolism is presented, involving the major three hydrogenases, to explain how [H] make their way from glycolysis into the products acetate or acetate + H2.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Surbhi Jain
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
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