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Qiu Y, Zhang J, Tong YW, He Y. Reverse electron transfer: Novel anaerobic methanogenesis pathway regulated through exogenous CO 2 synergized with biochar. BIORESOURCE TECHNOLOGY 2024; 401:130741. [PMID: 38670292 DOI: 10.1016/j.biortech.2024.130741] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/24/2024] [Indexed: 04/28/2024]
Abstract
Acid accumulation and carbon emission are two major challenges in anaerobic digestion. Syntrophic consortia can employ reverse electron transfer (RET) to facilitate thermodynamically unfavorable redox reactions during acetogenesis. However, the potential mechanisms and regulatory methods of RET remain unclear. This study examines the regulatory mechanisms by which exogenous CO2 affects RET and demonstrates that biochar maximizes CO2 solubility at 25.8 mmol/L to enhance effects further. CO2 synergized with biochar significantly increases cumulative methane production and propionate degradation rate. From the bioenergetic perspective, CO2 decreases energy level to a maximum of -87 kJ/mol, strengthening the thermodynamic viability. The underlying mechanism can be attributed to RET promotion, as indicated by increased formate dehydrogenase and enrichment of H2/formate-producing bacteria with their partner Methanospirillum hungatei. Moreover, the 5 % 13CH4 and methane contribution result show that CO2 accomplishes directed methanogenesis. Overall, this investigation riches the roles of CO2 and biochar in AD surrounding RET.
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Affiliation(s)
- Yang Qiu
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Yen Wah Tong
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Yiliang He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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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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Pang X, Nawrocki WJ, Cardol P, Zheng M, Jiang J, Fang Y, Yang W, Croce R, Tian L. Weak acids produced during anaerobic respiration suppress both photosynthesis and aerobic respiration. Nat Commun 2023; 14:4207. [PMID: 37452043 PMCID: PMC10349137 DOI: 10.1038/s41467-023-39898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
While photosynthesis transforms sunlight energy into sugar, aerobic and anaerobic respiration (fermentation) catabolizes sugars to fuel cellular activities. These processes take place within one cell across several compartments, however it remains largely unexplored how they interact with one another. Here we report that the weak acids produced during fermentation down-regulate both photosynthesis and aerobic respiration. This effect is mechanistically explained with an "ion trapping" model, in which the lipid bilayer selectively traps protons that effectively acidify subcellular compartments with smaller buffer capacities - such as the thylakoid lumen. Physiologically, we propose that under certain conditions, e.g., dim light at dawn, tuning down the photosynthetic light reaction could mitigate the pressure on its electron transport chains, while suppression of respiration could accelerate the net oxygen evolution, thus speeding up the recovery from hypoxia. Since we show that this effect is conserved across photosynthetic phyla, these results indicate that fermentation metabolites exert widespread feedback control over photosynthesis and aerobic respiration. This likely allows algae to better cope with changing environmental conditions.
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Affiliation(s)
- Xiaojie Pang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wojciech J Nawrocki
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR7141, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Pierre Cardol
- Génétique et Physiologie des Microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, B22, 4000, Liège, Belgium
| | - Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingjing Jiang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Yuan Fang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Roberta Croce
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation. mSystems 2020; 5:5/6/e00814-20. [PMID: 33293404 PMCID: PMC7743110 DOI: 10.1128/msystems.00814-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield. In this work, a systematic methodology was developed (based on known biochemistry, physiology, and bioenergetics) for the automated feasibility evaluation and net ATP yield quantification of large sets of pathway variants. Possible pathway variants differ in their intermediate metabolites, in which electron carriers are involved, in which steps are consuming/producing ATP, and in which steps are coupled to (and to how many) proton (or its equivalent) translocations. A pathway variant is deemed feasible, under a given set of physiological and environmental conditions, only if all pathway reaction steps have nonpositive Gibbs energy changes and if all the metabolite concentrations remain within an acceptable physiological range (10−6 to 10−2 M). The complete understanding of syntrophic propionate oxidation remains elusive due to uncertainties in pathways and the mechanisms for interspecies electron transfer (IET). Several million combinations of pathway variants and parameters/conditions were evaluated for propionate oxidation, providing unprecedented mechanistic insight into its biochemical and bioenergetic landscape. Our results show that, under a scenario of optimum environmental conditions for propionate oxidation, the Smithella pathway yields the most ATP and the methylmalonyl-coenzyme A (CoA) pathways can generate sufficient ATP for growth only under a cyclical pathway configuration with pyruvate. The results under conditions typical of methanogenic environments show that propionate oxidation via the lactate and via the hydroxypropionyl-CoA pathways yield the most ATP. IET between propionate oxidizers and methanogens can proceed either by dissolved hydrogen via the Smithella pathway or by different mechanisms (e.g., formate or direct IET) if other pathways are used. IMPORTANCE In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield. The methodology is designed to be especially relevant to hypothesize on which microbial pathway variants should be most favored in microbial ecosystems under high selective pressure for efficient metabolic energy conservation. Syntrophic microbial oxidation of propionate to acetate has an extremely small quantity of available energy and requires an extremely high metabolic efficiency to sustain life. Our results bring mechanistic insights into the optimum pathway variants, other metabolic bottlenecks, and the impact of environmental conditions on the ATP yields. Additionally, our results conclude that, as previously reported, under specific conditions, IET mechanisms other than hydrogen must exist to simultaneously sustain the growth of both propionate oxidizers and hydrogenotrophic methanogens.
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Nakanishi-Matsui M, Sekiya M, Futai M. ATP synthase from Escherichia coli : Mechanism of rotational catalysis, and inhibition with the ε subunit and phytopolyphenols. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:129-140. [DOI: 10.1016/j.bbabio.2015.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/19/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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Alam J, Yamato I, Arai S, Saijo S, Mizutani K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Kakinuma Y, Murata T. Mutant LV(476-7)AA of A-subunit of Enterococcus hirae V1-ATPase: High affinity of A3B3 complex to DF axis and low ATPase activity. SPRINGERPLUS 2014; 2:689. [PMID: 24404436 PMCID: PMC3879392 DOI: 10.1186/2193-1801-2-689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/20/2013] [Indexed: 11/22/2022]
Abstract
Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble functional domain V1 (A3B3DF) and an integral membrane domain Vo (ac), where V1 and Vo domains are connected by a central stalk, composed of D-, F-, and d-subunits; and two peripheral stalks (E- and G-subunits). We identified 120 interacting residues of A3B3 heterohexamer with D-subunit in DF heterodimer in the crystal structures of A3B3 and A3B3DF. In our previous study, we reported 10 mutants of E. hirae V1-ATPase, which showed lower binding affinities of DF with A3B3 complex leading to higher initial specific ATPase activities compared to the wild-type. In this study, we identified a mutation of A-subunit (LV476-7AA) at its C-terminal domain resulting in the A3B3 complex with higher binding affinities for wild-type or mutant DF heterodimers and lower initial ATPase activities compared to the wild-type A3B3 complex, consistent with our previous proposal of reciprocal relationship between the ATPase activity and the protein-protein binding affinity of DF axis to the A3B3 catalytic domain of E. hirae V-ATPase. These observations suggest that the binding of DF axis at the contact region of A3B3 rotary ring is relevant to its rotation activity.
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Affiliation(s)
- Jahangir Alam
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585 Japan ; Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585 Japan
| | - Satoshi Arai
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585 Japan ; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-choInage, Chiba, 263-8522 Japan
| | - Shinya Saijo
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585 Japan ; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148 Japan ; Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801 Japan
| | - Kenji Mizutani
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585 Japan ; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-choInage, Chiba, 263-8522 Japan
| | - Yoshiko Ishizuka-Katsura
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Noboru Ohsawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takaho Terada
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - So Iwata
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Department of Cell Biology, Faculty of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501 Japan
| | - Yoshimi Kakinuma
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566 Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-choInage, Chiba, 263-8522 Japan ; RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan ; JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba, 263-8522 Japan
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7
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Alam MJ, Arai S, Saijo S, Suzuki K, Mizutani K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Kakinuma Y, Yamato I, Murata T. Loose binding of the DF axis with the A3B3 complex stimulates the initial activity of Enterococcus hirae V1-ATPase. PLoS One 2013; 8:e74291. [PMID: 24058539 PMCID: PMC3772951 DOI: 10.1371/journal.pone.0074291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/30/2013] [Indexed: 11/17/2022] Open
Abstract
Vacuolar ATPases (V-ATPases) function as proton pumps in various cellular membrane systems. The hydrophilic V1 portion of the V-ATPase is a rotary motor, in which a central-axis DF complex rotates inside a hexagonally arranged catalytic A3B3 complex by using ATP hydrolysis energy. We have previously reported crystal structures of Enterococcushirae V-ATPase A3B3 and A3B3DF (V1) complexes; the result suggested that the DF axis induces structural changes in the A3B3 complex through extensive protein-protein interactions. In this study, we mutated 10 residues at the interface between A3B3 and DF complexes and examined the ATPase activities of the mutated V1 complexes as well as the binding affinities between the mutated A3B3 and DF complexes. Surprisingly, several V1 mutants showed higher initial ATPase activities than wild-type V1-ATPase, whereas these mutated A3B3 and DF complexes showed decreased binding affinities for each other. However, the high ATP hydrolysis activities of the mutants decreased faster over time than the activity of the wild-type V1 complex, suggesting that the mutants were unstable in the reaction because the mutant A3B3 and DF complexes bound each other more weakly. These findings suggest that strong interaction between the DF complex and A3B3 complex lowers ATPase activity, but also that the tight binding is responsible for the stable ATPase activity of the complex.
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Affiliation(s)
- Md Jahangir Alam
- Department of Biological Science and Technology, Tokyo University of Science, Chiba, Japan ; Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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8
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Sielaff H, Börsch M. Twisting and subunit rotation in single F(O)(F1)-ATP synthase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120024. [PMID: 23267178 DOI: 10.1098/rstb.2012.0024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
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Müller N, Worm P, Schink B, Stams AJM, Plugge CM. Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:489-99. [PMID: 23766220 DOI: 10.1111/j.1758-2229.2010.00147.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In anoxic environments such as swamps, rice fields and sludge digestors, syntrophic microbial communities are important for decomposition of organic matter to CO2 and CH4 . The most difficult step is the fermentative degradation of short-chain fatty acids such as propionate and butyrate. Conversion of these metabolites to acetate, CO2 , formate and hydrogen is endergonic under standard conditions and occurs only if methanogens keep the concentrations of these intermediate products low. Butyrate and propionate degradation pathways include oxidation steps of comparably high redox potential, i.e. oxidation of butyryl-CoA to crotonyl-CoA and of succinate to fumarate, respectively, that require investment of energy to release the electrons as hydrogen or formate. Although investigated for several decades, the biochemistry of these reactions is still not completely understood. Genome analysis of the butyrate-oxidizing Syntrophomonas wolfei and Syntrophus aciditrophicus and of the propionate-oxidizing Syntrophobacter fumaroxidans and Pelotomaculum thermopropionicum reveals the presence of energy-transforming protein complexes. Recent studies indicated that S. wolfei uses electron-transferring flavoproteins coupled to a menaquinone loop to drive butyryl-CoA oxidation, and that S. fumaroxidans uses a periplasmic formate dehydrogenase, cytochrome b:quinone oxidoreductases, a menaquinone loop and a cytoplasmic fumarate reductase to drive energy-dependent succinate oxidation. Furthermore, we propose that homologues of the Thermotoga maritima bifurcating [FeFe]-hydrogenase are involved in NADH oxidation by S. wolfei and S. fumaroxidans to form hydrogen.
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Affiliation(s)
- Nicolai Müller
- Faculty for Biology, University of Konstanz, D-78457 Konstanz, Germany. Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
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10
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Cano-Estrada A, Vázquez-Acevedo M, Villavicencio-Queijeiro A, Figueroa-Martínez F, Miranda-Astudillo H, Cordeiro Y, Mignaco JA, Foguel D, Cardol P, Lapaille M, Remacle C, Wilkens S, González-Halphen D. Subunit–subunit interactions and overall topology of the dimeric mitochondrial ATP synthase of Polytomella sp. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1439-48. [DOI: 10.1016/j.bbabio.2010.02.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 02/15/2010] [Accepted: 02/22/2010] [Indexed: 01/12/2023]
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F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1362-77. [PMID: 20193659 DOI: 10.1016/j.bbabio.2010.02.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 12/14/2022]
Abstract
This review focuses on the ATP synthases of alkaliphilic bacteria and, in particular, those that successfully overcome the bioenergetic challenges of achieving robust H+-coupled ATP synthesis at external pH values>10. At such pH values the protonmotive force, which is posited to provide the energetic driving force for ATP synthesis, is too low to account for the ATP synthesis observed. The protonmotive force is lowered at a very high pH by the need to maintain a cytoplasmic pH well below the pH outside, which results in an energetically adverse pH gradient. Several anticipated solutions to this bioenergetic conundrum have been ruled out. Although the transmembrane sodium motive force is high under alkaline conditions, respiratory alkaliphilic bacteria do not use Na+- instead of H+-coupled ATP synthases. Nor do they offset the adverse pH gradient with a compensatory increase in the transmembrane electrical potential component of the protonmotive force. Moreover, studies of ATP synthase rotors indicate that alkaliphiles cannot fully resolve the energetic problem by using an ATP synthase with a large number of c-subunits in the synthase rotor ring. Increased attention now focuses on delocalized gradients near the membrane surface and H+ transfers to ATP synthases via membrane-associated microcircuits between the H+ pumping complexes and synthases. Microcircuits likely depend upon proximity of pumps and synthases, specific membrane properties and specific adaptations of the participating enzyme complexes. ATP synthesis in alkaliphiles depends upon alkaliphile-specific adaptations of the ATP synthase and there is also evidence for alkaliphile-specific adaptations of respiratory chain components.
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Nakanishi-Matsui M, Sekiya M, Nakamoto RK, Futai M. The mechanism of rotating proton pumping ATPases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1343-52. [PMID: 20170625 DOI: 10.1016/j.bbabio.2010.02.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 11/27/2022]
Abstract
Two proton pumps, the F-ATPase (ATP synthase, FoF1) and the V-ATPase (endomembrane proton pump), have different physiological functions, but are similar in subunit structure and mechanism. They are composed of a membrane extrinsic (F1 or V1) and a membrane intrinsic (Fo or Vo) sector, and couple catalysis of ATP synthesis or hydrolysis to proton transport by a rotational mechanism. The mechanism of rotation has been extensively studied by kinetic, thermodynamic and physiological approaches. Techniques for observing subunit rotation have been developed. Observations of micron-length actin filaments, or polystyrene or gold beads attached to rotor subunits have been highly informative of the rotational behavior of ATP hydrolysis-driven rotation. Single molecule FRET experiments between fluorescent probes attached to rotor and stator subunits have been used effectively in monitoring proton motive force-driven rotation in the ATP synthesis reaction. By using small gold beads with diameters of 40-60 nm, the E. coli F1 sector was found to rotate at surprisingly high speeds (>400 rps). This experimental system was used to assess the kinetics and thermodynamics of mutant enzymes. The results revealed that the enzymatic reaction steps and the timing of the domain interactions among the beta subunits, or between the beta and gamma subunits, are coordinated in a manner that lowers the activation energy for all steps and avoids deep energy wells through the rotationally-coupled steady-state reaction. In this review, we focus on the mechanism of steady-state F1-ATPase rotation, which maximizes the coupling efficiency between catalysis and rotation.
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Affiliation(s)
- Mayumi Nakanishi-Matsui
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Iwate Medical University, Yahaba, Iwate 028-3694, Japan.
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13
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Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 2009; 7:568-77. [PMID: 19609258 DOI: 10.1038/nrmicro2166] [Citation(s) in RCA: 691] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.
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Affiliation(s)
- Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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Okano H, Yanagida T, Iriki A. Introduction. Japan: its tradition and hot topics in biological sciences. Philos Trans R Soc Lond B Biol Sci 2008; 363:2067-9. [PMID: 18339598 DOI: 10.1098/rstb.2008.2275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hideyuki Okano
- School of Medicine, Keio University, Shinjyuku-ku, Tokyo 160-8582, Japan
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