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Cha M, Kim JK, Lee WH, Song H, Lee TG, Kim SK, Kim SJ. Metabolic engineering of Caldicellulosiruptor bescii for hydrogen production. Appl Microbiol Biotechnol 2024; 108:65. [PMID: 38194138 PMCID: PMC10776719 DOI: 10.1007/s00253-023-12974-7] [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: 10/07/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
Hydrogen is an alternative fuel for transportation vehicles because it is clean, sustainable, and highly flammable. However, the production of hydrogen from lignocellulosic biomass by microorganisms presents challenges. This microbial process involves multiple complex steps, including thermal, chemical, and mechanical treatment of biomass to remove hemicellulose and lignin, as well as enzymatic hydrolysis to solubilize the plant cell walls. These steps not only incur costs but also result in the production of toxic hydrolysates, which inhibit microbial growth. A hyper-thermophilic bacterium of Caldicellulosiruptor bescii can produce hydrogen by decomposing and fermenting plant biomass without the need for conventional pretreatment. It is considered as a consolidated bioprocessing (CBP) microorganism. This review summarizes the basic scientific knowledge and hydrogen-producing capacity of C. bescii. Its genetic system and metabolic engineering strategies to improve hydrogen production are also discussed. KEY POINTS: • Hydrogen is an alternative and eco-friendly fuel. • Caldicellulosiruptor bescii produces hydrogen with a high yield in nature. • Metabolic engineering can make C. bescii to improve hydrogen production.
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Affiliation(s)
- Minseok Cha
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jung Kon Kim
- Department of Animal Environment, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Won-Heong Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | | | - Tae-Gi Lee
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi, 17546, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi, 17546, Republic of Korea
| | - Soo-Jung Kim
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju, 61186, Republic of Korea.
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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2
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Xu F, Thoma CJ, Zhao W, Zhu Y, Men Y, Wackett LP. Dual feedback inhibition of ATP-dependent caffeate activation economizes ATP in caffeate-dependent electron bifurcation. Appl Environ Microbiol 2024; 90:e0060224. [PMID: 39177329 PMCID: PMC11409703 DOI: 10.1128/aem.00602-24] [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: 05/10/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
The acetogen Acetobacterium woodii couples caffeate reduction with ferredoxin reduction and NADH oxidation via electron bifurcation, providing additional reduced ferredoxin for energy conservation and cell synthesis. Caffeate is first activated by an acyl-CoA synthetase (CarB), which ligates CoA to caffeate at the expense of ATP. After caffeoyl-CoA is reduced to hydrocaffeoyl-CoA, the CoA moiety in hydrocaffeoyl-CoA could be recycled for caffeoyl-CoA synthesis by an ATP-independent CoA transferase (CarA) to save energy. However, given that CarA and CarB are co-expressed, it was not well understood how ATP could be saved when both two competitive pathways of caffeate activation are present. Here, we reported a dual feedback inhibition of the CarB-mediated caffeate activation by the intermediate hydrocaffeoyl-CoA and the end-product hydrocaffeate. As the product of CarA, hydrocaffeate inhibited CarB-mediated caffeate activation by serving as another substrate of CarB with hydrocaffeoyl-CoA produced. It effectively competed with caffeate even at a concentration much lower than caffeate. Hydrocaffeoyl-CoA formed in this process can also inhibit CarB-mediated caffeate activation. Thus, the dual feedback inhibition of CarB, together with the faster kinetics of CarA, makes the ATP-independent CarA-mediated CoA loop the major route for caffeoyl-CoA synthesis, further saving ATP in the caffeate-dependent electron-bifurcating pathway. A genetic architecture similar to carABC has been found in other anaerobic bacteria, suggesting that the feedback inhibition of acyl-CoA ligases could be a widely employed strategy for ATP conservation in those pathways requiring substrate activation by CoA. IMPORTANCE This study reports a dual feedback inhibition of caffeoyl-CoA synthetase by two downstream products, hydrocaffeate and hydrocaffeoyl-CoA. It elucidates how such dual feedback inhibition suppresses ATP-dependent caffeoyl-CoA synthesis, hence making the ATP-independent route the main pathway of caffeate activation. This newly discovered mechanism contributes to our current understanding of ATP conservation during the caffeate-dependent electron-bifurcating pathway in the ecologically important acetogen Acetobacterium woodii. Bioinformatic mining of microbial genomes revealed contiguous genes homologous to carABC within the genomes of other anaerobes from various environments, suggesting this mechanism may be widely used in other CoA-dependent electron-bifurcating pathways.
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Affiliation(s)
- Fengjun Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | - Calvin J. Thoma
- Department of Biochemistry, Molecular Biology & Biophysics, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Weiyang Zhao
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | - Yiwen Zhu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology & Biophysics, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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3
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Lachmann MT, Duan Z, Rodríguez-Maciá P, Birrell JA. The missing pieces in the catalytic cycle of [FeFe] hydrogenases. Chem Sci 2024:d4sc04041d. [PMID: 39246377 PMCID: PMC11376134 DOI: 10.1039/d4sc04041d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/02/2024] [Indexed: 09/10/2024] Open
Abstract
Hydrogen could provide a suitable means for storing energy from intermittent renewable sources for later use on demand. However, many challenges remain regarding the activity, specificity, stability and sustainability of current hydrogen production and consumption methods. The lack of efficient catalysts based on abundant and sustainable elements lies at the heart of this problem. Nature's solution led to the evolution of hydrogenase enzymes capable of reversible hydrogen conversion at high rates using iron- and nickel-based active sites. Through a detailed understanding of these enzymes, we can learn how to mimic them to engineer a new generation of highly active synthetic catalysts. Incredible progress has been made in our understanding of biological hydrogen activation over the last few years. In particular, detailed studies of the [FeFe] hydrogenase class have provided substantial insight into a sophisticated, optimised, molecular catalyst, the active site H-cluster. In this short perspective, we will summarise recent findings and highlight the missing pieces needed to complete the puzzle.
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Affiliation(s)
- Manon T Lachmann
- School of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester Leicester LE1 7RH UK
| | - Zehui Duan
- University of Oxford, Department of Chemistry, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Patricia Rodríguez-Maciá
- School of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester Leicester LE1 7RH UK
| | - James A Birrell
- School of Life Sciences, University of Essex Colchester CO4 3SQ UK
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4
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Li X, Chen R, Wen J, Ji R, Chen X, Cao Y, Yu Y, Zhao C. The mechanisms in the gut microbiota regulation and type 2 diabetes therapeutic activity of resistant starches. Int J Biol Macromol 2024; 274:133279. [PMID: 38906356 DOI: 10.1016/j.ijbiomac.2024.133279] [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: 12/08/2023] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Resistant starch (RS) can potentially prevent type 2 diabetes through the modulation of intestinal microbiota and microbial metabolites. Currently, it has been wildly noted that altering the intestinal microbial composition and short-chain fatty acids levels can achieve therapeutic effects, although the specific mechanisms were rarely elucidated. This review systematically explores the structural characteristics of different RS, analyzes the cross-feeding mechanism utilized by intestinal microbiota, and outlines the pathways and targets of butyrate, a primary microbial metabolite, for treating diabetes. Different RS types may have a unique impact on microbiota composition and their cross-feeding, thus exploring regulatory mechanisms of RS on diabetes through intestinal flora interaction and their metabolites could pave the way for more effective treatment outcomes for host health. Furthermore, by understanding the mechanisms of strain-level cross-feeding and metabolites of RS, precise dietary supplementation methods targeted at intestinal composition and metabolites can be achieved to improve T2DM.
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Affiliation(s)
- Xiaoqing Li
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Food Science and Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Ruoxin Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Food Science and Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jiahui Wen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruya Ji
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Xu Chen
- School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yigang Yu
- College of Food Science and Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chao Zhao
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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5
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Noori MT, Rossi R, Logan BE, Min B. Hydrogen production in microbial electrolysis cells with biocathodes. Trends Biotechnol 2024; 42:815-828. [PMID: 38360421 DOI: 10.1016/j.tibtech.2023.12.010] [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: 09/11/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024]
Abstract
Electroautotrophic microbes at biocathodes in microbial electrolysis cells (MECs) can catalyze the hydrogen evolution reaction with low energy demand, facilitating long-term stable performance through specific and renewable biocatalysts. However, MECs have not yet reached commercialization due to a lack of understanding of the optimal microbial strains and reactor configurations for achieving high performance. Here, we critically analyze the criteria for the inocula selection, with a focus on the effect of hydrogenase activity and microbe-electrode interactions. We also evaluate the impact of the reactor design and key parameters, such as membrane type, composition, and electrode surface area on internal resistance, mass transport, and pH imbalances within MECs. This analysis paves the way for advancements that could propel biocathode-assisted MECs toward scalable hydrogen gas production.
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Affiliation(s)
- Md Tabish Noori
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea
| | - Ruggero Rossi
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, Penn State University, Pennsylvania, PA 16801, USA
| | - Booki Min
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea.
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6
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Greening C, Cabotaje PR, Valentin Alvarado LE, Leung PM, Land H, Rodrigues-Oliveira T, Ponce-Toledo RI, Senger M, Klamke MA, Milton M, Lappan R, Mullen S, West-Roberts J, Mao J, Song J, Schoelmerich M, Stairs CW, Schleper C, Grinter R, Spang A, Banfield JF, Berggren G. Minimal and hybrid hydrogenases are active from archaea. Cell 2024; 187:3357-3372.e19. [PMID: 38866018 PMCID: PMC11216029 DOI: 10.1016/j.cell.2024.05.032] [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: 06/17/2023] [Revised: 04/12/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; SAEF: Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia.
| | - Princess R Cabotaje
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Luis E Valentin Alvarado
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; SAEF: Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia
| | - Henrik Land
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Thiago Rodrigues-Oliveira
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Moritz Senger
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Max A Klamke
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; SAEF: Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia
| | - Susan Mullen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Jacob West-Roberts
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Jie Mao
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Marie Schoelmerich
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | | | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Hoorn, the Netherlands; Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
| | - Jillian F Banfield
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA.
| | - Gustav Berggren
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden.
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7
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Hackmann TJ. The vast landscape of carbohydrate fermentation in prokaryotes. FEMS Microbiol Rev 2024; 48:fuae016. [PMID: 38821505 PMCID: PMC11187502 DOI: 10.1093/femsre/fuae016] [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: 04/05/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Science, University of California, Davis, CA 95616, United States
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8
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Nazina TN, Tourova TP, Grouzdev DS, Bidzhieva SK, Poltaraus AB. A Novel View on the Taxonomy of Sulfate-Reducing Bacterium ' Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov. Microorganisms 2024; 12:1115. [PMID: 38930497 PMCID: PMC11206085 DOI: 10.3390/microorganisms12061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | | | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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9
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Ungerfeld EM, Pitta D. Review: Biological consequences of the inhibition of rumen methanogenesis. Animal 2024:101170. [PMID: 38772773 DOI: 10.1016/j.animal.2024.101170] [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: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024] Open
Abstract
Decreasing enteric CH4 emissions from ruminants is important for containing global warming to 1.5 °C and avoid the worst consequences of climate change. However, the objective of mitigating enteric CH4 emissions is difficult to reconcile with the forecasted increase in production of ruminant meat and milk, unless CH4 production per animal and per kilogram of animal product are decreased substantially. Chemical compound 3-nitrooxypropanol and bromoform-containing red algae Asparagopsis are currently the most potent inhibitors of rumen methanogenesis, but their average efficacy would have to be increased to mitigate enteric CH4 emissions to contain global warming to 1.5 °C, if the demand for ruminant products increases as predicted. We propose that it may be possible to enhance the efficacy of inhibitors of methanogenesis through understanding the mechanisms that cause variation in their efficacy across studies. We also propose that a more thorough understanding of the effects of inhibiting methanogenesis on rumen and postabsorptive metabolism may help improve feed efficiency and cost-effectiveness as co-benefits of the methanogenesis inhibition intervention. For enhancing efficacy, we examine herein how different inhibitors of methanogenesis affect the composition of the rumen microbial community and discuss some mechanisms that may explain dissimilar sensitivities among methanogens to different types of inhibitors. For improving feed efficiency and cost-effectiveness, we discuss the consequences of inhibiting methanogenesis on rumen fermentation, and how changes in rumen fermentation can in turn affect postabsorptive metabolism and animal performance. The objectives of this review are to identify knowledge gaps of the consequences of inhibiting methanogenesis on rumen microbiology and rumen and postabsorptive metabolism, propose research to address those knowledge gaps and discuss the implications that this research can have for the efficacy and adoption of inhibitors of methanogenesis. Depending on its outcomes, research on the microbiological, biochemical, and metabolic consequences of the inhibition of rumen methanogenesis could help the adoption of feed additives inhibitors of methanogenesis to mitigate enteric CH4 emissions from ruminants to ameliorate climate change.
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Affiliation(s)
- E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Camino Cajón a Vilcún km 10, 4880000 Vilcún, La Araucanía, Chile.
| | - D Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, 19348 Kenneth Square, PA, United States
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10
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Rosenbaum FP, Müller V. A novel hexameric NADP + -reducing [FeFe] hydrogenase from Moorella thermoacetica. FEBS J 2024; 291:596-608. [PMID: 37885325 DOI: 10.1111/febs.16989] [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: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
Acetogenic bacteria such as the thermophilic anaerobic model organism Moorella thermoacetica reduce CO2 with H2 as a reductant via the Wood-Ljungdahl pathway (WLP). The enzymes of the WLP of M. thermoacetica require NADH, NADPH, and reduced ferredoxin as reductants. Whereas an electron-bifurcating ferredoxin- and NAD+ -reducing hydrogenase HydABC had been described, the enzyme that reduces NADP+ remained to be identified. A likely candidate is the HydABCDEF hydrogenase from M. thermoacetica. Genes encoding for the HydABCDEF hydrogenase are expressed during growth on glucose and dimethyl sulfoxide (DMSO), an alternative electron acceptor in M. thermoacetica, whereas expression of the genes hydABC encoding for the electron-bifurcating hydrogenase is downregulated. Therefore, we have purified the hydrogenase from cells grown on glucose and DMSO to apparent homogeneity. The enzyme had six subunits encoded by hydABCDEF and contained 58 mol of iron and 1 mol of FMN. The enzyme reduced methyl viologen with H2 as reductant and of the physiological acceptors tested, only NADP+ was reduced. Electron bifurcation with pyridine nucleotides and ferredoxin was not observed. H2 -dependent NADP+ reduction was optimal at pH 8 and 60 °C; the specific activity was 8.5 U·mg-1 and the Km for NADP+ was 0.086 mm. Cell suspensions catalyzed H2 -dependent DMSO reduction, which is in line with the hypothesis that the NADP+ -reducing hydrogenase HydABCDEF is involved in electron transfer from H2 to DMSO.
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Affiliation(s)
- Florian P Rosenbaum
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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11
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Feng X, Schut GJ, Adams MWW, Li H. Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes. Subcell Biochem 2024; 104:383-408. [PMID: 38963493 DOI: 10.1007/978-3-031-58843-3_14] [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] [Indexed: 07/05/2024]
Abstract
Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.
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Affiliation(s)
- Xiang Feng
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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12
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Ge X, Schut GJ, Tran J, Poole II FL, Niks D, Menjivar K, Hille R, Adams MWW. Characterization of the Membrane-Associated Electron-Bifurcating Flavoenzyme EtfABCX from the Hyperthermophilic Bacterium Thermotoga maritima. Biochemistry 2023; 62:3554-3567. [PMID: 38061393 PMCID: PMC10734219 DOI: 10.1021/acs.biochem.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Electron bifurcation is an energy-conservation mechanism in which a single enzyme couples an exergonic reaction with an endergonic one. Heterotetrameric EtfABCX drives the reduction of low-potential ferredoxin (E°' ∼ -450 mV) by oxidation of the midpotential NADH (E°' = -320 mV) by simultaneously coupling the reaction to reduction of the high-potential menaquinone (E°' = -74 mV). Electron bifurcation occurs at the NADH-oxidizing bifurcating-flavin adenine dinucleotide (BF-FAD) in EtfA, which has extremely crossed half-potentials and passes the first, high-potential electron to an electron-transferring FAD and via two iron-sulfur clusters eventually to menaquinone. The low-potential electron on the BF-FAD semiquinone simultaneously reduces ferredoxin. We have expressed the genes encodingThermotoga maritimaEtfABCX in E. coli and purified the EtfABCX holoenzyme and the EtfAB subcomplex. The bifurcation activity of EtfABCX was demonstrated by using electron paramagnetic resonance (EPR) to follow accumulation of reduced ferredoxin. To elucidate structural factors that impart the bifurcating ability, EPR and NADH titrations monitored by visible spectroscopy and dye-linked enzyme assays have been employed to characterize four conserved residues, R38, P239, and V242 in EtfA and R140 in EtfB, in the immediate vicinity of the BF-FAD. The R38, P239, and V242 variants showed diminished but still significant bifurcation activity. Despite still being partially reduced by NADH, the R140 variant had no bifurcation activity, and electron transfer to its two [4Fe-4S] clusters was prevented. The role of R140 is discussed in terms of the bifurcation mechanism in EtfABCX and in the other three families of bifurcating enzymes.
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Affiliation(s)
- Xiaoxuan Ge
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Gerrit J. Schut
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Jessica Tran
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Farris L. Poole II
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Dimitri Niks
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Kevin Menjivar
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Russ Hille
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
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13
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Ahmad A, Ghufran R. Microbial granules on reactors performance during organic butyrate digestion: clean production. Crit Rev Biotechnol 2023; 43:1236-1256. [PMID: 36130802 DOI: 10.1080/07388551.2022.2103641] [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: 11/13/2021] [Accepted: 06/09/2022] [Indexed: 11/03/2022]
Abstract
This critical review for anaerobic degradation of complex organic compounds like butyrate using reactors has been enormously applied for biogas production. Biogas production rate has a great impact on: reactor granulation methanogenesis, nutrient content, shear velocity, organic loading and loss of nutrients taking place in the reactor continuously. Various technologies have been applied to closed anaerobic reactors to improve biogas production and treatment efficiency. Recent reviews showed that the application of closed anaerobic reactors can accelerate the degradation of organics like volatile fatty acid-butyrate and affect microbial biofilm formation by increasing the number of methanogens and increase methane production 16.5 L-1 CH4 L-1 POME-1. The closed anaerobic reactors with stable microbial biofilm and established organic load were responsible for the improvement of the reactor and methane production. The technology mentioned in this review can be used to monitor biogas concentration, which directly correlates to organic concentrations. This review attempts to evaluate interactions among the: degradation of organics, closed anaerobic reactors system, and microbial granules. This article provides a useful picture for the improvement of the degradation of organic butyrate for COD removal, biogas and methane production in an anaerobic closed reactor.
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Affiliation(s)
- Anwar Ahmad
- Civil and Environmental Engineering Department, College of Engineering and Architecture, University of Nizwa, Nizwa, Sultanate of Oman
| | - Roomana Ghufran
- Faculty of Civil Engineering and Earth Resources, University Malaysia Pahang (UMP) Lebuhraya Tun Razak, Gambang, Malaysia
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14
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Novák LVF, Treitli SC, Pyrih J, Hałakuc P, Pipaliya SV, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V. Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria. PLoS Genet 2023; 19:e1011050. [PMID: 38060519 PMCID: PMC10703272 DOI: 10.1371/journal.pgen.1011050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.
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Affiliation(s)
- Lukáš V. F. Novák
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- Université de Bretagne Occidentale, CNRS, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Sebastian C. Treitli
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Pyrih
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Shweta V. Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vojtěch Vacek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Ondřej Brzoň
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Petr Soukal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Laura Eme
- Ecology, Systematics, and Evolution Unit, Université Paris-Saclay, CNRS, Orsay, France
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Ostrava, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
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15
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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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16
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Singh A, Schnürer A, Dolfing J, Westerholm M. Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions. THE ISME JOURNAL 2023; 17:1966-1978. [PMID: 37679429 PMCID: PMC10579422 DOI: 10.1038/s41396-023-01504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne, NE18QH, UK
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
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17
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Cha M, Kim JH, Choi HJ, Nho SB, Kim SY, Cha YL, Song H, Lee WH, Kim SK, Kim SJ. Hydrogen Production from Barley Straw and Miscanthus by the Hyperthermophilic Bacterium, Cadicellulosirupter bescii. J Microbiol Biotechnol 2023; 33:1384-1389. [PMID: 37463861 PMCID: PMC10619549 DOI: 10.4014/jmb.2305.05022] [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: 05/23/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/20/2023]
Abstract
This work aimed to evaluate the feasibility of biohydrogen production from Barley Straw and Miscanthus. The primary obstacle in plant biomass decomposition is the recalcitrance of the biomass itself. Plant cell walls consist of cellulose, hemicellulose, and lignin, which make the plant robust to decomposition. However, the hyperthermophilic bacterium, Caldicellulosiruptor bescii, can efficiently utilize lignocellulosic feedstocks (Barley Straw and Miscanthus) for energy production, and C. bescii can now be metabolically engineered or isolated to produce more hydrogen and other biochemicals. In the present study, two strains, C. bescii JWCB001 (wild-type) and JWCB018 (ΔpyrFA Δldh ΔcbeI), were tested for their ability to increase hydrogen production from Barley Straw and Miscanthus. The JWCB018 resulted in a redirection of carbon and electron (carried by NADH) flow from lactate production to acetate and hydrogen production. JWCB018 produced ~54% and 63% more acetate and hydrogen from Barley Straw, respectively than its wild-type counterpart, JWCB001. Also, 25% more hydrogen from Miscanthus was obtained by the JWCB018 strain with 33% more acetate relative to JWCB001. It was supported that the engineered C. bescii, such as the JWCB018, can be a parental strain to get more hydrogen and other biochemicals from various biomass.
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Affiliation(s)
- Minseok Cha
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jun-Ha Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyo-Jin Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo Bin Nho
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi 17546, Republic of Korea
| | - Soo-Yeon Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Republic of Korea
| | - Young-Lok Cha
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Republic of Korea
| | - Hyoungwoon Song
- Institute for Advanced Engineering, Gyeonggi 17180, Republic of Korea
| | - Won-Heong Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Biotechnology, Chung-Ang University, Gyeonggi 17546, Republic of Korea
| | - Soo-Jung Kim
- Research Center for Biological Cybernetics, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
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18
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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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19
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Kumar A, Kremp F, Roth J, Freibert SA, Müller V, Schuller JM. Molecular architecture and electron transfer pathway of the Stn family transhydrogenase. Nat Commun 2023; 14:5484. [PMID: 37673911 PMCID: PMC10482914 DOI: 10.1038/s41467-023-41212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
The challenge of endergonic reduction of NADP+ using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.
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Affiliation(s)
- Anuj Kumar
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Jennifer Roth
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Sven A Freibert
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-University of Marburg, Marburg, Germany
- Core Facility "Protein Biochemistry and Spectroscopy", Marburg, 35032, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany.
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20
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Rasmey AHM, Abd-Alla MH, Tawfik MA, Bashandy SR, Salah M, Liu R, Sun C, Hassan EA. Synergistic strategy for the enhancement of biohydrogen production from molasses through coculture of Lactobacillus brevis and Clostridium saccharobutylicum. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2023; 48:25285-25299. [DOI: 10.1016/j.ijhydene.2023.03.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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21
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Song YC, Holland SI, Lee M, Chen G, Löffler FE, Manefield MJ, Hugenholtz P, Kappler U. A comparative genome analysis of the Bacillota ( Firmicutes) class Dehalobacteriia. Microb Genom 2023; 9:mgen001039. [PMID: 37294008 PMCID: PMC10327494 DOI: 10.1099/mgen.0.001039] [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: 01/06/2023] [Accepted: 04/25/2023] [Indexed: 06/10/2023] Open
Abstract
Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.
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Affiliation(s)
- Young C. Song
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, Queensland, 4072, Australia
| | - Sophie I. Holland
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
- Present address: School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Matthew Lee
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Gao Chen
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Frank E. Löffler
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, Department of Bioengineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee, USA
| | - Michael J. Manefield
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, Queensland, 4072, Australia
| | - Ulrike Kappler
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, 4072, Australia
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22
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Terai K, Yuly JL, Zhang P, Beratan DN. Correlated particle transport enables biological free energy transduction. Biophys J 2023; 122:1762-1771. [PMID: 37056051 PMCID: PMC10209040 DOI: 10.1016/j.bpj.2023.04.009] [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: 12/21/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023] Open
Abstract
Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. We show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near-reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).
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Affiliation(s)
- Kiriko Terai
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Jonathon L Yuly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersy
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina; Department of Physics, Duke University, Durham, North Carolina; Department of Biochemistry, Duke University, Durham, North Carolina.
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23
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Leng F, Wu Y, Hu S, Jing Y, Ding M, Wei Q, Zhang Q, Wang Y. Cloning, expression, and bioinformatics analysis of heavy metal resistance-related genes fd-I and fd-II from Acidithiobacillus ferrooxidans. Lett Appl Microbiol 2023; 76:7143110. [PMID: 37115024 DOI: 10.1093/lambio/ovad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
Five heavy metals were introduced into the bacterial heavy metal resistance tests. The results showed that apparent inhibition effects of Cd2+ and Cu2+ on the growth of Acidithiobacillus ferrooxidans BYSW1 occurred at high concentrations (>0.04 mol l-1). Significant differences (P < 0.001) were both noticed in the expression of two ferredoxin-encoding genes (fd-I and fd-II) related to heavy metal resistance in the presence of Cd2+ and Cu2+ . When exposed to 0.06 mol l-1 Cd2+, the relative expression levels of fd-I and fd-II were about 11 and 13 times as much as those of the control, respectively. Similarly, exposure to 0.04 mol l-1 Cu2+ caused approximate 8 and 4 times higher than those of the control, respectively. These two genes were cloned and expressed in Escherichia coli, and the structures, functions of two corresponding target proteins, i.e. Ferredoxin-I (Fd-I) and Ferredoxin-II (Fd-II), were predicted. The recombinant cells inserted by fd-I or fd-II were more resistant to Cd2+ and Cu2+ compared with wild-type cells. This study was the first investigation regarding the contribution of fd-I and fd-II to enhancing heavy metal resistance of this bioleaching bacterium, and laid a foundation for further elucidation of heavy metal resistance mechanisms caused by Fd.
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Affiliation(s)
- Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Yamiao Wu
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Shu Hu
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Yanjun Jing
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Miao Ding
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Qingwei Wei
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Qingchun Zhang
- Agricultural Technology Extension Center of Kangxian County, 746500 Kangxian, PR China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, 730050 Lanzhou, PR China
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Kpebe A, Guendon C, Payne N, Ros J, Khelil Berbar M, Lebrun R, Baffert C, Shintu L, Brugna M. An essential role of the reversible electron-bifurcating hydrogenase Hnd for ethanol oxidation in Solidesulfovibrio fructosivorans. Front Microbiol 2023; 14:1139276. [PMID: 37051519 PMCID: PMC10084766 DOI: 10.3389/fmicb.2023.1139276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The tetrameric cytoplasmic FeFe hydrogenase Hnd from Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans) catalyses H2 oxidation and couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin by using a flavin-based electron-bifurcating mechanism. Regarding its implication in the bacterial physiology, we previously showed that Hnd, which is non-essential when bacteria grow fermentatively on pyruvate, is involved in ethanol metabolism. Under these conditions, it consumes H2 to produce reducing equivalents for ethanol production as a fermentative product. In this study, the approach implemented was to compare the two S. fructosivorans WT and the hndD deletion mutant strains when grown on ethanol as the sole carbon and energy source. Based on the determination of bacterial growth, metabolite consumption and production, gene expression followed by RT-q-PCR, and Hnd protein level followed by mass spectrometry, our results confirm the role of Hnd hydrogenase in the ethanol metabolism and furthermore uncover for the first time an essential function for a Desulfovibrio hydrogenase. Hnd is unequivocally required for S. fructosivorans growth on ethanol, and we propose that it produces H2 from NADH and reduced ferredoxin generated by an alcohol dehydrogenase and an aldehyde ferredoxin oxidoreductase catalyzing the conversion of ethanol into acetate. The produced H2 could then be recycled and used for sulfate reduction. Hnd is thus a reversible hydrogenase that operates in H2-consumption by an electron-bifurcating mechanism during pyruvate fermentation and in H2-production by an electron-confurcating mechanism when the bacterium uses ethanol as electron donor.
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Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Julien Ros
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
| | - Manel Khelil Berbar
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Régine Lebrun
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | | | - Laetitia Shintu
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- *Correspondence: Myriam Brugna,
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Katsyv A, Kumar A, Saura P, Pöverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Müller V, Schuller JM. Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. J Am Chem Soc 2023; 145:5696-5709. [PMID: 36811855 PMCID: PMC10021017 DOI: 10.1021/jacs.2c11683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H2). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P)+ and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P)+ binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P)+ reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Anuj Kumar
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany.,SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg 35032, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Maximilian C Pöverlein
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Sven A Freibert
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-University of Marburg, Marburg 35032, Germany.,Core Facility "Protein Biochemistry and Spectroscopy", Marburg 35032, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin 14195, Germany
| | - Surbhi Jain
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main 60438, Germany
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg 35032, Germany
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26
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Payne N, Kpebe A, Guendon C, Baffert C, Maillot M, Haurogné T, Tranchida F, Brugna M, Shintu L. NMR-based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation. Microbiol Res 2023; 268:127279. [PMID: 36592576 DOI: 10.1016/j.micres.2022.127279] [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: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H2) into protons and electrons. One of these, named Hnd, was demonstrated to be an electron-bifurcating hydrogenase Hnd (Kpebe et al., 2018). It couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 and whose function has been recently shown to be involved in ethanol production under pyruvate fermentation (Payne 2022). To understand further the physiological role of Hnd in S. fructosivorans, we compared the mutant deleted of part of the hnd gene with the wild-type strain grown on pyruvate without sulfate using NMR-based metabolomics. Our results confirm that Hnd is profoundly involved in ethanol metabolism, but also indirectly intervenes in global carbon metabolism and additional metabolic processes such as the biosynthesis of branched-chain amino acids. We also highlight the metabolic reprogramming induced by the deletion of hndD that leads to the upregulation of several NADP-dependent pathways.
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Affiliation(s)
- Natalie Payne
- Aix Marseille Univ, CNRS, BIP, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | | | | | | | | | - Fabrice Tranchida
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France.
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Xuan J, He L, Wen W, Feng Y. Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production. Molecules 2023; 28:molecules28031392. [PMID: 36771068 PMCID: PMC9919214 DOI: 10.3390/molecules28031392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.
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Affiliation(s)
- Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Correspondence: (J.X.); (Y.F.)
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wen Wen
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.X.); (Y.F.)
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28
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Unique H 2-utilizing lithotrophy in serpentinite-hosted systems. THE ISME JOURNAL 2023; 17:95-104. [PMID: 36207493 PMCID: PMC9751293 DOI: 10.1038/s41396-022-01197-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/08/2022]
Abstract
Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.
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29
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Simultaneous Production of Biohydrogen (bioH2) and Poly-Hydroxy-Alkanoates (PHAs) by a Photoheterotrophic Consortium Bioaugmented with Syntrophomonas wolfei. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mixed cultures represent better alternatives to ferment organic waste and dark fermentation products in anerobic conditions because the microbial associations contribute to electron transfer mechanisms and combine metabolic possibilities. The understanding of the microbial interactions in natural and synthetic consortia and the strategies to improve the performance of the processes by bioaugmentation provide insight into the physiology and ecology of the mixed cultures used for biotechnological purposes. Here, synthetic microbial communities were built from three hydrogen (bioH2) and poly-hydroxy-alkanoates (PHA) producers, Clostridium pasteurianum, Rhodopseudomonas palustris and Syntrophomonas wolfei, and a photoheterotrophic mixed consortium C4, and their performance was evaluated during photofermentation. Higher hydrogen volumetric production rates (H2VPR) were determined with the consortia (28–40 mL/Lh) as compared with individual strains (20–27 mL/Lh). The designed consortia reached the highest bioH2 and PHA productions of 44.3 mmol and 50.46% and produced both metabolites simultaneously using dark fermentation effluents composed of a mixture of lactic, butyric, acetic, and propionic acids. When the mixed culture C4 was bioaugmented with S. wolfei, the bioH2 and PHA production reached 32 mmol and 50%, respectively. Overall, the consumption of organic acids was above 50%, which accounted up to 55% of total chemical oxygen demand (COD) removed. Increased bioH2 was observed in the condition when S. wolfei was added as the bioaugmentation agent, reaching up to 562 mL of H2 produced per gram of COD. The enhanced production of bioH2 and PHA can be explained by the metabolic interaction between the three selected strains, which likely include thermodynamic equilibrium, the assimilation of organic acids via beta-oxidation, and the production of bioH2 using a proton driving force derived from reduced menaquinone or via electron bifurcation.
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Abstract
Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water-rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
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Occurrence of Capnophilic Lactic Fermentation in the Hyperthermophilic Anaerobic Bacterium Thermotoga sp. Strain RQ7. Int J Mol Sci 2022; 23:ijms231912049. [PMID: 36233345 PMCID: PMC9570489 DOI: 10.3390/ijms231912049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Capnophilic lactic fermentation (CLF) is an anaplerotic pathway exclusively identified in the anaerobic hyperthermophilic bacterium Thermotoga neapolitana, a member of the order Thermotogales. The CO2-activated pathway enables non-competitive synthesis of hydrogen and L-lactic acid at high yields, making it an economically attractive process for bioenergy production. In this work, we discovered and characterized CLF in Thermotoga sp. strain RQ7, a naturally competent strain, opening a new avenue for molecular investigation of the pathway. Evaluation of the fermentation products and expression analyses of key CLF-genes by RT-PCR revealed similar CLF-phenotypes between T. neapolitana and T. sp. strain RQ7, which were absent in the non-CLF-performing strain T. maritima. Key CLF enzymes, such as PFOR, HYD, LDH, RNF, and NFN, are up-regulated in the two CLF strains. Another important finding is the up-regulation of V-ATPase, which couples ATP hydrolysis to proton transport across the membranes, in the two CLF-performing strains. The fact that V-ATPase is absent in T. maritima suggested that this enzyme plays a key role in maintaining the necessary proton gradient to support high demand of reducing equivalents for simultaneous hydrogen and lactic acid synthesis in CLF.
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Sha C, Wang Q, Wang H, Duan Y, Xu C, Wu L, Ma K, Shao W, Jiang Y. Characterization of Thermotoga neapolitana Alcohol Dehydrogenases in the Ethanol Fermentation Pathway. BIOLOGY 2022; 11:biology11091318. [PMID: 36138797 PMCID: PMC9495900 DOI: 10.3390/biology11091318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Hyperthermophilic Thermotoga spp. are candidates for cellulosic ethanol fermentation. A bifunctional iron-acetaldehyde/alcohol dehydrogenase (Fe-AAdh) has been revealed to catalyze the acetyl-CoA (Ac-CoA) reduction to form ethanol via an acetaldehyde intermediate in Thermotoga neapolitana (T. neapolitana). In this organism, there are three additional alcohol dehydrogenases, Zn-Adh, Fe-Adh1, and Fe-Adh2, encoded by genes CTN_0257, CTN_1655, and CTN_1756, respectively. This paper reports the properties and functions of these enzymes in the fermentation pathway from Ac-CoA to ethanol. It was determined that Zn-Adh only exhibited activity when oxidizing ethanol to acetaldehyde, and no detectable activity for the reaction from acetaldehyde to ethanol. Fe-Adh1 had specific activities of approximately 0.7 and 0.4 U/mg for the forward and reverse reactions between acetaldehyde and ethanol at a pHopt of 8.5 and Topt of 95 °C. Catalyzing the reduction of acetaldehyde to produce ethanol, Fe-Adh2 exhibited the highest activity of approximately 3 U/mg at a pHopt of 7.0 and Topt of 85 °C, which were close to the optimal growth conditions. These results indicate that Fe-Adh2 and Zn-Adh are the main enzymes that catalyze ethanol formation and consumption in the hyperthermophilic bacterium, respectively.
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Affiliation(s)
- Chong Sha
- Biofuels Institute, School of the Environment, Jiangsu University, Zhenjiang 212013, China
| | - Qiang Wang
- Biofuels Institute, School of the Environment, Jiangsu University, Zhenjiang 212013, China
- School of Biological and Food Engineering, Suzhou University, Bianhe Middle Road 49, Suzhou 234000, China
| | - Hongcheng Wang
- Biofuels Institute, School of the Environment, Jiangsu University, Zhenjiang 212013, China
| | - Yilan Duan
- School of Biological and Food Engineering, Suzhou University, Bianhe Middle Road 49, Suzhou 234000, China
| | - Chongmao Xu
- Huzhou Research Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Lian Wu
- Huzhou Research Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Weilan Shao
- Shine E BioTech (Nanjing) Company, Nanjing 210023, China
- Correspondence: (W.S.); (Y.J.)
| | - Yu Jiang
- Huzhou Research Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
- Correspondence: (W.S.); (Y.J.)
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Ben Gaida L, Gannoun H, Casalot L, Davidson S, Liebgott PP. Biohydrogen production by Thermotoga maritima from a simplified medium exclusively composed of onion and natural seawater. CR CHIM 2022. [DOI: 10.5802/crchim.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Liang J, Huang H, Wang Y, Li L, Yi J, Wang S. A Cytoplasmic NAD(P)H-Dependent Polysulfide Reductase with Thiosulfate Reductase Activity from the Hyperthermophilic Bacterium Thermotoga maritima. Microbiol Spectr 2022; 10:e0043622. [PMID: 35762779 PMCID: PMC9431562 DOI: 10.1128/spectrum.00436-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/05/2022] [Indexed: 11/22/2022] Open
Abstract
Thermotoga maritima is an anaerobic hyperthermophilic bacterium that efficiently produces H2 by fermenting carbohydrates. High concentration of H2 inhibits the growth of T. maritima, and S0 could eliminate the inhibition and stimulate the growth through its reduction. The mechanism of T. maritima sulfur reduction, however, has not been fully understood. Herein, based on its similarity with archaeal NAD(P)H-dependent sulfur reductases (NSR), the ORF THEMA_RS02810 was identified and expressed in Escherichia coli, and the recombinant protein was characterized. The purified flavoprotein possessed NAD(P)H-dependent S0 reductase activity (1.3 U/mg for NADH and 0.8 U/mg for NADPH), polysulfide reductase activity (0.32 U/mg for NADH and 0.35 U/mg for NADPH), and thiosulfate reductase activity (2.3 U/mg for NADH and 2.5 U/mg for NADPH), which increased 3~4-folds by coenzyme A stimulation. Quantitative RT-PCR analysis showed that nsr was upregulated together with the mbx, yeeE, and rnf genes when the strain grew in S0- or thiosulfate-containing medium. The mechanism for sulfur reduction in T. maritima was discussed, which may affect the redox balance and energy metabolism of T. maritima. Genome search revealed that NSR homolog is widely distributed in thermophilic bacteria and archaea, implying its important role in the sulfur cycle of geothermal environments. IMPORTANCE The reduction of S0 and thiosulfate is essential in the sulfur cycle of geothermal environments, in which thermophiles play an important role. Despite previous research on some sulfur reductases of thermophilic archaea, the mechanism of sulfur reduction in thermophilic bacteria is still not clearly understood. Herein, we confirmed the presence of a cytoplasmic NAD(P)H-dependent polysulfide reductase (NSR) from the hyperthermophile T. maritima, with S0, polysulfide, and thiosulfate reduction activities, in contrast to other sulfur reductases. When grown in S0- or thiosulfate-containing medium, its expression was upregulated. And the putative membrane-bound MBX and Rnf may also play a role in the metabolism, which might influence the redox balance and energy metabolism of T. maritima. This is distinct from the mechanism of sulfur reduction in mesophiles such as Wolinella succinogenes. NSR homologs are widely distributed among heterotrophic thermophiles, suggesting that they may be vital in the sulfur cycle in geothermal environments.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Yubo Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Lexin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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Furlan C, Chongdar N, Gupta P, Lubitz W, Ogata H, Blaza JN, Birrell JA. Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase. eLife 2022; 11:79361. [PMID: 36018003 PMCID: PMC9499530 DOI: 10.7554/elife.79361] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
Electron bifurcation is a fundamental energy conservation mechanism in nature in which two electrons from an intermediate-potential electron donor are split so that one is sent along a high-potential pathway to a high-potential acceptor and the other is sent along a low-potential pathway to a low-potential acceptor. This process allows endergonic reactions to be driven by exergonic ones and is an alternative, less recognized, mechanism of energy coupling to the well-known chemiosmotic principle. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron bifurcation in HydABC remains enigmatic in spite of intense research efforts over the last few years. Structural information may provide the basis for a better understanding of spectroscopic and functional information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure shows a heterododecamer composed of two independent 'halves' each made of two strongly interacting HydABC heterotrimers connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and for proton reduction. We identified two conformations of a flexible iron-sulfur cluster domain: a 'closed bridge' and an 'open bridge' conformation, where a Zn2+ site may act as a 'hinge' allowing domain movement. Based on these structural revelations, we propose a possible mechanism of electron bifurcation in HydABC where the flavin mononucleotide serves a dual role as both the electron bifurcation center and as the NAD+ reduction/NADH oxidation site.
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Affiliation(s)
- Chris Furlan
- Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, York, United Kingdom
| | - Nipa Chongdar
- Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
| | - Pooja Gupta
- Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, York, United Kingdom
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
| | - Hideaki Ogata
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan.,Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - James N Blaza
- Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, York, United Kingdom
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
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Schut GJ, Haja DK, Feng X, Poole FL, Li H, Adams MWW. An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism. Front Microbiol 2022; 13:946711. [PMID: 35875533 PMCID: PMC9304861 DOI: 10.3389/fmicb.2022.946711] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD+ and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP+, cofactor F420, formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.
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Affiliation(s)
- Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Michael W. W. Adams, ; orcid.org/0000-0002-9796-5014
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Wang C, Wang Y, Wang Y, Liu L, Wang D, Ju F, Xia Y, Zhang T. Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters. WATER RESEARCH 2022; 219:118590. [PMID: 35597218 DOI: 10.1016/j.watres.2022.118590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Yubo Wang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Yu Xia
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
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Kayastha K, Katsyv A, Himmrich C, Welsch S, Schuller JM, Ermler U, Müller V. Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. eLife 2022; 11:77095. [PMID: 35748623 PMCID: PMC9232219 DOI: 10.7554/elife.77095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/22/2022] [Indexed: 01/22/2023] Open
Abstract
Lactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron-transferring proteins EtfA and EtfB. The electron cryo-microscopically characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle domain located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle domain contact each other thereby forming the D (dehydrogenation-connected) state. The intermediary Glu37 and Glu139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. By integrating Alphafold2 calculations a plausible novel B (bifurcation-connected) state was obtained allowing electron transfer between the EtfAB base and shuttle FADs. Kinetic analysis of enzyme variants suggests a correlation between NAD+ binding site and D-to-B-state transition implicating a 75° rotation of the EtfAB shuttle domain. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is assisted by the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was proposed.
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Affiliation(s)
- Kanwal Kayastha
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Christina Himmrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jan M Schuller
- SYNMICRO Research Center and Department of Chemistry, Philipps University, Marburg, Germany
| | - Ulrich Ermler
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation. Microbiol Spectr 2022; 10:e0101922. [PMID: 35735976 PMCID: PMC9431212 DOI: 10.1128/spectrum.01019-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus Clostridium (C. autoethanogenum, C. ljungdahlii, C. carboxidivorans, C. drakei, C. scatologenes, C. coskatii, C. ragsdalei, C. sp. AWRP) to systematically identify their intriguingly diversified hydrogenases’ repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits’ characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases. IMPORTANCE Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus Clostridium are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases’ functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases’ level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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41
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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Westerholm M, Calusinska M, Dolfing J. Syntrophic propionate-oxidizing bacteria in methanogenic systems. FEMS Microbiol Rev 2022; 46:fuab057. [PMID: 34875063 PMCID: PMC8892533 DOI: 10.1093/femsre/fuab057] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/03/2021] [Indexed: 12/04/2022] Open
Abstract
The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.
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Affiliation(s)
- Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCentre, Almas allé 5, SE-75007 Uppsala, Sweden
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, rue du Brill 41, L-4422 Belvaux, Luxembourg
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Wynne Jones 2.11, Ellison Place, Newcastle-upon-Tyne NE1 8QH, UK
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Morra S. Fantastic [FeFe]-Hydrogenases and Where to Find Them. Front Microbiol 2022; 13:853626. [PMID: 35308355 PMCID: PMC8924675 DOI: 10.3389/fmicb.2022.853626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.
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Affiliation(s)
- Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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Feng X, Schut GJ, Haja DK, Adams MWW, Li H. Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase. SCIENCE ADVANCES 2022; 8:eabm7546. [PMID: 35213221 PMCID: PMC8880783 DOI: 10.1126/sciadv.abm7546] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H2 and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H2 via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.
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Affiliation(s)
- Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
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Payne N, Kpebe A, Guendon C, Baffert C, Ros J, Lebrun R, Denis Y, Shintu L, Brugna M. The electron-bifurcating FeFe-hydrogenase Hnd is involved in ethanol metabolism in Desulfovibrio fructosovorans grown on pyruvate. Mol Microbiol 2022; 117:907-920. [PMID: 35066935 DOI: 10.1111/mmi.14881] [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: 10/17/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
Desulfovibrio fructosovorans, a sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of H2 into protons and electrons. Among them, Hnd is an electron-bifurcating hydrogenase, coupling the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 . It was previously hypothesized that its biological function involves the production of NADPH necessary for biosynthetic purposes. However, it was subsequently demonstrated that Hnd is instead a NAD+ -reducing enzyme, thus its specific function has yet to be established. To understand the physiological role of Hnd in D. fructosovorans, we compared the hnd deletion mutant with the wild-type strain grown on pyruvate. Growth, metabolites production and comsumption, and gene expression were compared under three different growth conditions. Our results indicate that hnd is strongly regulated at the transcriptional level and that its deletion has a drastic effect on the expression of genes for two enzymes, an aldehyde ferredoxin oxidoreductase and an alcohol dehydrogenase. We demonstrated here that Hnd is involved in ethanol metabolism when bacteria grow fermentatively and proposed that Hnd might oxidize part of the H2 produced during fermentation generating both NADH and reduced ferredoxin for ethanol production via its electron bifurcation mechanism.
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Affiliation(s)
| | | | | | | | - Julien Ros
- CNRS, Aix Marseille Univ, BIP, Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Univ, Plate-forme Protéomique de l'IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Yann Denis
- CNRS, Aix Marseille Univ, Plate-forme Transcriptomique, Marseille, France
| | - Laetitia Shintu
- CNRS, Aix Marseille Univ, Centrale Marseille, ISM2, Marseille, France
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46
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Wiryaman T, Toor N. Recent advances in the structural biology of encapsulin bacterial nanocompartments. J Struct Biol X 2022; 6:100062. [PMID: 35146412 PMCID: PMC8802124 DOI: 10.1016/j.yjsbx.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
Large capsid-like nanocompartments called encapsulins are common in bacteria and archaea and contain cargo proteins with diverse functions. Advances in cryo-electron microscopy have enabled structure determination of many encapsulins in recent years. Here we summarize findings from recent encapsulin structures that have significant implications for their biological roles. We also compare important features such as the E-loop, cargo-peptide binding site, and the fivefold axis channel in different structures. In addition, we describe the discovery of a flavin-binding pocket within the encapsulin shell that may reveal a role for this nanocompartment in iron metabolism.
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Affiliation(s)
| | - Navtej Toor
- University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:57-90. [DOI: 10.1007/10_2021_199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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Mostafa A, Im S, Kim J, Lim KH, Kim I, Kim DH. Electron bifurcation reactions in dark fermentation: An overview for better understanding and improvement. BIORESOURCE TECHNOLOGY 2022; 344:126327. [PMID: 34785332 DOI: 10.1016/j.biortech.2021.126327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Electron bifurcation (EB) is the most recently found mode of energy conservation, which involves both exergonic and endergonic electron transfer reactions to minimize energy loss. Several works have been devoted on EB reactions (EBRs) in anaerobic digestion but limited in dark fermentative hydrogen production (DF). Two main electron carriers in DF are ferredoxin (Fd) and reduced nicotinamide adenine dinucleotide (NADH), complicatedly involved in EB. Here, i) the importance of EB involvement in DF, ii) all EBRs possible to present in DF, as well as iii) the limitation of previous studies that tried incorporating any of EBRs in DF metabolic model, were highlighted. In addition, the concept of using metagenomic analysis for estimating the share of each EB reaction in the metabolic model, was proposed. This review is expected to initiate a new wave for studying EB, as a tool for explaining and predicting DF products.
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Affiliation(s)
- Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jimin Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Kyeong-Ho Lim
- Department of Civil and Environmental Engineering, Kongju National University, Cheonan, Chungnam 31080, Republic of Korea
| | - Ijung Kim
- Department of Civil and Environmental Engineering, Hongik University, 94 Wausan-ro, Mapo-gu, Seoul 04066, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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Affiliation(s)
- Brandon L. Greene
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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