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Nakanishi K, Kojima K, Sowa Y, Sudo Y. Bidirectional Optical Control of Proton Motive Force in Escherichia coli Using Microbial Rhodopsins. J Phys Chem B 2024; 128:6509-6517. [PMID: 38949422 DOI: 10.1021/acs.jpcb.4c03027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Proton (H+) motive force (PMF) serves as the energy source for the flagellar motor rotation, crucial for microbial motility. Here, to control PMF using light, we introduced light-driven inward and outward proton pump rhodopsins, RmXeR and AR3, into Escherichia coli. The motility of E. coli cells expressing RmXeR and AR3 significantly decreased and increased upon illumination, respectively. Tethered cell experiments revealed that, upon illumination, the torque of the flagellar motor decreased to nearly zero (28 pN nm) with RmXeR, while it increased to 1170 pN nm with AR3. These alterations in PMF correspond to +146 mV (RmXeR) and -140 mV (AR3), respectively. Thus, bidirectional optical control of PMF in E. coli was successfully achieved by using proton pump rhodopsins. This system holds a potential for enhancing our understanding of the roles of PMF in various biological functions.
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Affiliation(s)
- Kotaro Nakanishi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo 184-8584, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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Martinez A, Dijkstra P, Megonigal P, Hungate BA. Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions. Appl Environ Microbiol 2024; 90:e0072424. [PMID: 38771053 PMCID: PMC11218644 DOI: 10.1128/aem.00724-24] [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: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.IMPORTANCEWe observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation.
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Affiliation(s)
- Ayla Martinez
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Dijkstra
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
- Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Bruce A. Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
- Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, Arizona, USA
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Babayan A, Vassilian A, Poladyan A, Trchounian K. Role of the Escherichia coli FocA and FocB formate channels in controlling proton/potassium fluxes and hydrogen production during osmotic stress in energy-limited, stationary phase fermenting cells. Biochimie 2024; 221:91-98. [PMID: 38307245 DOI: 10.1016/j.biochi.2024.01.017] [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: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
Escherichia coli FocA and FocB formate channels export formate or import it for further disproportionation by the formate hydrogenlyase (FHL) complex to H2 and CO2. Here, we show that under pH and osmotic stress FocA and FocB play important roles in regulating proton and potassium fluxes and couple this with H2 production in stationary-phase cells. Using whole-cell assays with glucose as electron donor, a focB mutant showed a 50 % decrease in VH2, while N'N'-dicyclohexylcarbodiimide (DCCD) treatment of osmotically stressed cells underlined the role of FOF1 ATPase in H2 production. At pH 7.5 and under osmotic stress FocB contributed to the proton flux but not to the potassium flux. At pH 5.5 both formate channels contributed to the proton and potassium fluxes. Particulalry, a focA mutant had 40 % lower potassium flux whereas the proton flux increased approximately two-fold. Moreover, at pH 5.5H2 production was totally inhibited by DCCD in the focA mutant. Taken together, our results suggest that depending on external pH, the formate channels play an important role in osmoregulation by helping to balance proton/potassium fluxes and H2 production, and thus assist the proton FOF1-ATPase in maintenance of ion gradients in fermenting stationary-phase cells.
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Affiliation(s)
- A Babayan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - A Vassilian
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - A Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - K Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia.
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Cheng Y, Lu C, Gao S, Koju R, Li H, Zhu Z, Hu C, Qu J. Synchronous in-situ sludge reduction and enhanced denitrification through improving electron transfer during endogenous metabolisms with Fe(Ⅱ) addition. WATER RESEARCH 2024; 255:121472. [PMID: 38552492 DOI: 10.1016/j.watres.2024.121472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 04/24/2024]
Abstract
The creation of large amounts of excess sludge and residual nitrogen are critical issues in wastewater biotreatment. This study introduced Fe(II) into an oligotrophic anaerobic reactor (OARFe) that was implemented to modify an anoxic-oxic process to motivate in-situ sludge reduction and enhance denitrification under an effective electron shuttle among organic matter, nitrogen, and Fe. The addition of 15 mg L-1 Fe(II) resulted in a sludge reduction efficiency reached 32.0% with a decreased effluent nitrate concentration of 33.3%. This was mostly attributed to the electron transfer from Fe(II) to organic matters and nitrogen species in OARFe. The participation of Fe(II) led to the upregulation of Geothrix and Terrimonas, which caused active organic matter hydrolysis and cell lysis to stimulate the release of extracellular polymeric substances (EPS) and substance transfer between each layer of EPS. The higher utilization of released bioavailable dissolved organic matter improved endogenous denitrification, which can be combined with iron autotrophic denitrification to realize multiple electron donor-based nitrogen removal pathways, resulting in an increased nitrate removal rate of 58.2% in the absence of external carbon sources. These functional bacteria associated with the transformation of nitrogen and carbon and cycling between ferrous and ferric ions were enriched in OARFe, which contributed to efficient electron transport occurred both inside and outside the cell and increased 2,3,5-triphenyltetrazolium chloride electronic transport system activity by 46.9%. This contributed to the potential operational costs of chemical addition and sludge disposal of Fe-AO being 1.9 times lower than those of conventional A2O processes. These results imply that the addition of ferrous ions to an oligotrophic anaerobic zone for wastewater treatment has the potential for low-cost pollution control.
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Affiliation(s)
- Yu Cheng
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Chenghai Lu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujia Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Environmental Science and Engineering, Guilin University of Technology, Jiangan Road 12, Guilin, Guangxi 541004, China
| | - Rashmi Koju
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Li
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Zongqiang Zhu
- College of Environmental Science and Engineering, Guilin University of Technology, Jiangan Road 12, Guilin, Guangxi 541004, China.
| | - Chengzhi Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiuhui Qu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Gevorgyan H, Poladyan A, Trchounian K, Vassilian A. Proton conductance and regulation of proton/potassium fluxes in Escherichia coli FhlA-lacking cells during fermentation of mixed carbon sources. Arch Biochem Biophys 2024; 755:109999. [PMID: 38621444 DOI: 10.1016/j.abb.2024.109999] [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: 01/31/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Escherichia coli uptake potassium ions with the coupling of proton efflux and energy utilization via proton FOF1-ATPase. In this study contribution of formate hydrogen lyase (FHL) complexes in the proton/potassium fluxes and the formation of proton conductance (CMH+) were investigated using fhlA mutant strain. The proton flux rate (JH+) decreased in fhlA by ∼ 25 % and ∼70 % during the utilization of glucose and glycerol, respectively, at 20 h suggesting H+ transport via or through FHL complexes. The decrease in JK+ in fhlA by ∼40 % proposed the interaction between FHL and Trk secondary transport system during mixed carbon fermentation. Moreover, the usage of N,N'-dicyclohexylcarbodiimide (DCCD) demonstrated the mediation of FOF1-ATPase in this interaction. CMH+ was 13.4 nmol min-1 mV-1 in WT at 20 h, which decreased by 20 % in fhlA. Taken together, FHL complexes have a significant contribution to the modulation of H+/K+ fluxes and the CMH + for efficient energy transduction and regulation of the proton motive force during mixed carbon sources fermentation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia
| | - Anna Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia.
| | - Anait Vassilian
- Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia
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Gevorgyan H, Baghdasaryan L, Trchounian K. Regulation of metabolism and proton motive force generation during mixed carbon fermentation by an Escherichia coli strain lacking the F OF 1-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149034. [PMID: 38354879 DOI: 10.1016/j.bbabio.2024.149034] [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: 10/03/2023] [Revised: 01/15/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Proton FOF1-ATPase is the key enzyme in E. coli under fermentative conditions. In this study the role of E. coli proton ATPase in the μ and formation of metabolic pathways during the fermentation of mixture of glucose, glycerol and formate using the DK8 (lacking FOF1) mutant strain was investigated. It was shown that the contribution of FOF1-ATPase in the specific growth rate was ∼45 %. Formate was not taken up in the DK8 strain during the initial hours of the growth. The utilization rates of glucose and glycerol were unchanged in DK8, however, the production of succinate, lactate and ethanol was decreased causing a reduction of the redox state up to -450 mV. Moreover, the contribution of FOF1-ATPase in the interplay between H+ and H2 cycles was described depending on the bacterial growth phase and main utilizing substrate. Besides, the H2 production rate in the DK8 strain was decreased by ∼60 % at 20 h and was absent at 72 h. Δp was decreased from -157 ± 4.8 mV to -140 ± 4.2 mV at 20 h and from -195 ± 5.9 mV to -148 ± 4.4 mV at 72 h, compared to WT. Taken together it can be concluded that during fermentation of mixed carbon sources metabolic cross talk between FOF1-ATPase-TrkA-Hyd-Fdh-H is taking place for maintaining the cell energy balance via regulation proton motive force.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Lilit Baghdasaryan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia.
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7
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Vanyan L, Kammel M, Sawers RG, Trchounian K. Evidence for bidirectional formic acid translocation in vivo via the Escherichia coli formate channel FocA. Arch Biochem Biophys 2024; 752:109877. [PMID: 38159898 DOI: 10.1016/j.abb.2023.109877] [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: 08/08/2023] [Revised: 11/12/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Pentameric FocA permeates either formate or formic acid bidirectionally across the cytoplasmic membrane of anaerobically growing Escherichia coli. Each protomer of FocA has its own hydrophobic pore, but it is unclear whether formate or neutral formic acid is translocated in vivo. Here, we measured total and dicyclohexylcarbodiimide (DCCD)-inhibited proton flux out of resting, fermentatively grown, stationary-phase E. coli cells in dependence on FocA. Using a wild-type strain synthesizing native FocA, it was shown that using glucose as a source of formate, DCCD-independent proton efflux was ∼2.5 mmol min-1, while a mutant lacking FocA showed only DCCD-inhibited, FOF1-ATPase-dependent proton-efflux. A strain synthesizing a chromosomally-encoded FocAH209N variant that functions exclusively to translocate formic acid out of the cell, showed a further 20 % increase in FocA-dependent proton efflux relative to the parental strain. Cells synthesizing a FocAT91A variant, which is unable to translocate formic acid out of the cell, showed only DCCD-inhibited proton efflux. When exogenous formate was added, formic acid uptake was shown to be both FocA- and proton motive force-dependent. By measuring rates of H2 production, potassium ion flux and ATPase activity, these data support a role for coupling between formate, proton and K+ ion translocation in maintaining pH and ion gradient homeostasis during fermentation. FocA thus plays a key role in maintaining this homeostatic balance in fermenting cells by bidirectionally translocating formic acid.
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Affiliation(s)
- Liana Vanyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian, 0025, Yerevan, Armenia; Scientific-Research Institute of Biology Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia
| | - Michelle Kammel
- Institute for Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - R Gary Sawers
- Institute for Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian, 0025, Yerevan, Armenia; Scientific-Research Institute of Biology Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia.
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Xu J, Shi Z, Xu L, Zheng X, Zong Y, Luo G, Zhang C, Liu M, Xie L. Recovery capability of anaerobic digestion from ammonia stress: Metabolic activity, energy generation, and genome-centric metagenomics. BIORESOURCE TECHNOLOGY 2024; 394:130203. [PMID: 38109977 DOI: 10.1016/j.biortech.2023.130203] [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: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Excessive ammonia stresses anaerobic digestion (AD) significantly. Although there has been progress in understanding AD under ammonia exposure, investigations on AD liberated from ammonia exposure are limited. Here, the recovery capability of AD from ammonia stress was evaluated, by examining specific methanogenic activity, energy-conserving capability, microbial community succession, and metabolic pathway reconstruction. The findings demonstrated that ammonia stress relief resulted in < 50% methane recovery, with propionate conversion identified as the critical impediment to AD reactivation. Energy generation could not recovered either. Efforts to mitigate ammonia stress failed to restore acetoclastic methanogens, e.g., Methanothrix soehngenii, and proved futile in awakening propionate oxidizers, e.g., Desulfobulbus. Interestingly, a symbiotic metabolism emerged, prevailing in stress-relieved AD due to its energy-conserving advantage. This study underscores the importance of targeted interventions, including stimulating acetoclastic methanogenesis, propionate oxidation, and energy generation, as priorities for AD recovery following ammonia stress, rather than focusing solely on ammonia level management.
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Affiliation(s)
- Jun Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China
| | - Ling Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xiaomei Zheng
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Yang Zong
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Chen Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co., LTD., Shanghai 200092, PR China
| | - Mingxian Liu
- Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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Manutsyan T, Blbulyan S, Vassilian A, Semashko T, Kirakosyan G, Gabrielyan L, Trchounian K, Poladyan A. Gold nanoparticles activate hydrogenase synthesis and improve heterotrophic growth of Ralstonia eutropha H16. FEMS Microbiol Lett 2024; 371:fnad138. [PMID: 38167703 DOI: 10.1093/femsle/fnad138] [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: 03/09/2023] [Revised: 10/17/2023] [Accepted: 12/31/2023] [Indexed: 01/05/2024] Open
Abstract
Ralstonia eutropha is a facultative chemolithoautotrophic aerobic bacterium that grows using organic substrates or H2 and CO2. Hydrogenases (Hyds) are synthesized under lithoautotrophic, or energy-limited heterotrophic conditions and are used in enzyme fuel cells (EFC) as anodic catalysts. The effects of chemically synthesized gold nanoparticles (Au-NPs) on R. eutropha H16 growth, oxidation-reduction potential (ORP) kinetics, and H2-oxidizing Hyd activity were investigated in this study. Atomic force microscopy showed that thin, plate-shaped Au-NPs were in the nanoscale range with an average size of 5.68 nm. Compared with growth in medium without Au-NPs (control), the presence of Au-NPs stimulated growth, and resulted in a decrease in ORP to negative values. H2-oxidizing activity was not detected in the absence of Au-NPs, but activity was significantly induced (12 U/g CDW) after 24 h of growth with 18 ng/ml, increasing a further 4-fold after 72 h of growth. The results demonstrate that Au-NPs primarily influence the membrane-bound Hyd. In contrast to R. eutropha, Au-NPs had a negligible or negative effect on the growth, Hyd activity, and H2 production of Escherichia coli. The findings of this study offer new perspectives for the production of oxygen-tolerant Hyds and the development of EFCs.
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Affiliation(s)
- Tatevik Manutsyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
| | - Syuzanna Blbulyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
| | - Anait Vassilian
- Research Institute of Biology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | | | | | - Lilit Gabrielyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
- Research Institute of Biology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | - Anna Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
- Research Institute of Biology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
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10
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Babayan A, Vassilian A, Trchounian K. Osmotic stress as a factor for regulating E. coli hydrogenase activity and enhancing H 2 production during mixed carbon sources fermentation. AIMS Microbiol 2023; 9:724-737. [PMID: 38173976 PMCID: PMC10758574 DOI: 10.3934/microbiol.2023037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Abstract
Escherichia coli performs mixed-acid fermentation and produces molecular hydrogen (H2) via reversible hydrogenases (Hyd). H2 producing activity was investigated during hyper- and hypo-osmotic stress conditions when a mixture of carbon sources (glucose and glycerol) was fermented at different pHs. Hyper-osmotic stress decreased H2 production rate (VH2) ~30 % in wild type at pH 7.5 when glucose was supplemented, while addition of formate stimulated VH2 ~45% compared to hypo-stress conditions. Only in hyfG in formate assays was VH2 inhibited ~25% compared to hypo-stress conditions. In hypo-stress conditions addition of glycerol increased VH2 ~2 and 3 fold in hybC and hyfG mutants, respectively, compared to wild type. At pH 6.5 hyper-osmotic stress stimulated VH2 ~2 fold in all strains except hyaB mutant when glucose was supplemented, while in formate assays significant stimulation (~3 fold) was determined in hybC mutant. At pH 5.5 hyper-osmotic stress inhibited VH2 ~30% in wild type when glucose was supplemented, but in formate assays it was stimulated in all strains except hyfG. Taken together, it can be concluded that, depending on external pH and absence of Hyd enzymes in stationary-phase-grown osmotically stressed E. coli cells, H2 production can be stimulated significantly which can be applied in developing H2 production biotechnology.
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Affiliation(s)
- Anush Babayan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Anait Vassilian
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Department of Ecology and Nature Protection, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
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11
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Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell 2023; 186:4803-4817.e13. [PMID: 37683634 PMCID: PMC10633639 DOI: 10.1016/j.cell.2023.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.
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Affiliation(s)
- Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Pia A Andrade
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Andi Liu
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Kevin J Cutler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Jeffrey S McLean
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA
| | | | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA; Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA 98195, USA.
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12
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Gevorgyan H, Abaghyan T, Mirumyan M, Yenkoyan K, Trchounian K. Propionic and valproic acids have an impact on bacteria viability, proton flux and ATPase activity. J Bioenerg Biomembr 2023; 55:397-408. [PMID: 37700074 DOI: 10.1007/s10863-023-09983-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Short-chain fatty acids like propionic (PPA) and valproic acids (VP) can alter gut microbiota, which is suggested to play a role in development of autism spectrum disorders (ASD). In this study we investigated the role of various concentrations of PPA and VP in gut enteric gram-negative Escherichia coli K12 and gram-positive Enterococcus hirae ATCC 9790 bacteria growth properties, ATPase activity and proton flux. The specific growth rate (µ) was 0.24 h-1 and 0.82 h-1 in E. coli and E. hirae, respectively. Different concentrations of PPA reduced the value of µ similarly in both strains. PPA affects membrane permeability only in E. hirae. PPA decreased DCCD-sensitive ATPase activity in the presence of K+ ions by 20% in E. coli and 40% in E. hirae suggesting the importance of the FOF1-K+ transport system in the regulation of PPA-disrupted homeostasis. Moreover, the H+ flux during PPA consumption could be the protective mechanism for enteric bacteria. VP has a selective effect on the µ depending on bacteria. The overwhelming effect of VP was detected on the K+-promoted ATPase activity in E. hirae. Taken together it can be suggested that PPA and VP have a disruptive effect on E. coli and E. hirae growth, viability, bioenergetic and biochemical properties, which are connected with the alteration of FOF1-ATPase activity and H+ flux rate or direction.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
| | - Tamara Abaghyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Margarita Mirumyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Konstantin Yenkoyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia.
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia.
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia.
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13
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. Metabolic pathways and ΔpH regulation in Escherichia coli during the fermentation of glucose and glycerol in the presence of formate at pH 6.5: the role of FhlA transcriptional activator. FEMS Microbiol Lett 2022; 369:6825452. [PMID: 36370455 DOI: 10.1093/femsle/fnac109] [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: 03/23/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli is able to ferment mixed carbon sources and produce various fermentation end-products. In this study, the function of FhlA protein in the specific growth rate (µ), metabolism, regulation of ΔpH and proton ATPase activity was investigated. Reduced µ in fhlA mutant of ∼25% was shown, suggesting the role of FhlA in the growth process. The utilization rate of glycerol is decreased in fhlA ∼ 2 fold, depending on the oxidation-reduction potential values. Bacteria regulate the activity of hydrogenase enzymes during growth depending on the external pH, which manifests as a lack of hydrogen gas generation during glycerol utilization at pH values below 5.9. It is suggested that cells maintain ΔpH during the fermentative growth via formate-lactate-succinate exchange. The decrement of the value of pHin, but not of pHex in mutant cells, is regulating ΔpH and consequently proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Anait Vassilian
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
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14
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Vanyan L, Trchounian K. HyfF subunit of hydrogenase 4 is crucial for regulating F OF 1 dependent proton/potassium fluxes during fermentation of various concentrations of glucose. J Bioenerg Biomembr 2022; 54:69-79. [PMID: 35106641 DOI: 10.1007/s10863-022-09930-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Escherichia coli anaerobically ferment glucose and perform proton/potassium exchange at pH 7.5. The role of hyf (hydrogenase 4) subunits (HyfBDF) in sensing different concentrations of glucose (2 g L-1 or 8 g L-1) via regulating H+/K+ exchange was studied. HyfB, HyfD and HyfF part of a protein family of NADH-ubiquinone oxidoreductase ND2, ND4 and ND5 subunits is predicted to operate as proton pump. Specific growth rate was optimal in wild type and mutants grown on 2 g L-1 glucose reaching ~ 0.8 h-1. It was shown that in wild type cells proton but not potassium fluxes were stimulated ~ 1.7 fold reaching up to 1.95 mmol/min when cells were grown in the presence of 8 g L-1 glucose. Interestingly, cells grown on peptone only had similar proton/potassium fluxes as grown on 2 g L-1glucose. H+/K+ fluxes of the cells grown on 2 g L-1 but not 8 g L-1 glucose depend on externally added glucose concentration in the assays. DCCD-sensitive H+ fluxes were tripled and K+ fluxes doubled in wild type cells grown on 8 g L-1 glucose compared to 2 g L-1 when in the assays 2 g L-1glucose was added. Interestingly, in hyfF mutant when cells were grown on 2 g L-1glucose and in 2 g L-1 assays DCCD-sensitive fluxes were not determined compared to wild type while in hyfD mutant it was doubled reaching up to 0.657 mmol/min. In hyf mutants DCCD-sensitive K+ fluxes were stimulated in hyfD and hyfF mutants compared to wild type but depend on external glucose concentration. DCCD-sensitive H+/K+ ratio was equal to ~ 2 except hyfF mutant grown and assayed on 2 g L-1glucose while in 8 g L-1 conditions role of hyfB and hyfD is considered. Taken together it can be concluded that Hyd-4 subunits (HyfBDF) play key role in sensing glucose concentration for regulation of DCCD-sensitive H+/K+ fluxes for maintaining proton motive force generation.
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Affiliation(s)
- Liana Vanyan
- Department of Biochemistry, Microbiology and Biotechnology, Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia.
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia.
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15
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Targeting the ATP synthase in bacterial and fungal pathogens – beyond Mycobacterium tuberculosis. J Glob Antimicrob Resist 2022; 29:29-41. [DOI: 10.1016/j.jgar.2022.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 11/23/2022] Open
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16
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Clomburg JM, Cintolesi A, Gonzalez R. In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Microb Biotechnol 2021; 15:289-304. [PMID: 34699695 PMCID: PMC8719807 DOI: 10.1111/1751-7915.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2 , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Angela Cintolesi
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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17
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Analysis of six tonB gene homologs in Bacteroides fragilis revealed that tonB3 is essential for survival in experimental intestinal colonization and intra-abdominal infection. Infect Immun 2021; 90:e0046921. [PMID: 34662212 DOI: 10.1128/iai.00469-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic, anaerobic pathogen and commensal of the human large intestinal tract, Bacteroides fragilis strain 638R, contains six predicted TonB proteins, termed TonB1-6, four ExbBs orthologs, ExbB1-4, and five ExbDs orthologs, ExbD1-5. The inner membrane TonB/ExbB/ExbD complex harvests energy from the proton motive force (Δp) and the TonB C-terminal domain interacts with and transduces energy to outer membrane TonB-dependent transporters (TBDTs). However, TonB's role in activating nearly one hundred TBDTs for nutrient acquisition in B. fragilis during intestinal colonization and extraintestinal infection has not been established. In this study, we show that growth was abolished in the ΔtonB3 mutant when heme, vitamin B12, Fe(III)-ferrichrome, starch, mucin-glycans, or N-linked glycans were used as a substrate for growth in vitro. Genetic complementation of the ΔtonB3 mutant with the tonB3 gene restored growth on these substrates. The ΔtonB1, ΔtonB2, ΔtonB4, ΔtonB5, and ΔtonB6 single mutants did not show a growth defect. This indicates that there was no functional compensation for the lack of TonB3, and it demonstrates that TonB3, alone, drives the TBDTs involved in the transport of essential nutrients. The ΔtonB3 mutant had a severe growth defect in a mouse model of intestinal colonization compared to the parent strain. This intestinal growth defect was enhanced in the ΔtonB3 ΔtonB6 double mutant strain which completely lost its ability to colonize the mouse intestinal tract compared to the parent strain. The ΔtonB1, ΔtonB2, ΔtonB4, and ΔtonB5 mutants did not significantly affect intestinal colonization. Moreover, the survival of the ΔtonB3 mutant strain was completely eradicated in a rat model of intra-abdominal infection. Taken together, these findings show that TonB3 was essential for survival in vivo. The genetic organization of tonB1, tonB2, tonB4, tonB5, and tonB6 gene orthologs indicates that they may interact with periplasmic and nonreceptor outer membrane proteins, but the physiological relevance of this has not been defined. Because anaerobic fermentation metabolism yields a lower Δp than aerobic respiration and B. fragilis has a reduced redox state in its periplasmic space - in contrast to an oxidative environment in aerobes - it remains to be determined if the diverse system of TonB/ExbB/ExbD orthologs encoded by B. fragilis have an increased sensitivity to PMF (relative to aerobic bacteria) to allow for the harvesting of energy under anaerobic conditions.
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18
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Cheng C, Geng J, Hu H, Shi Y, Gao R, Wang X, Ren H. In-situ sludge reduction performance and mechanism in an anoxic/aerobic process coupled with alternating aerobic/anaerobic side-stream reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145856. [PMID: 33677286 DOI: 10.1016/j.scitotenv.2021.145856] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Activated sludge process with anaerobic side-stream reactors (SR) in the sludge recirculation can achieve in-situ sludge reduction, but sludge reduction efficiency is limited with the low hydraulic retention time (HRT) of SR. An anoxic/aerobic (AO) process, AO coupled with anaerobic SR and AO coupled with alternating aerobic/anaerobic side-stream reactor (AO-OASR) were operated to investigate enhancing effects of alternative aerobic and anaerobic condition (AltOA) in SR on sludge reduction and pollutants removal performance. The AltOA was firstly proposed into SR with a low HRT during the long-term continuous operation. The results showed that AO-OASR presented a lower effluent COD concentration (29.6%) with no adverse effect on nitrogen removal, compared to AO, owing to the intensified refractory carbon reuse in the mainstream aerobic tank. The sludge yield in AO-OASR (0.240 g SS/g COD) was 39.7% lower than that in AO. The OASR accelerated sludge lysis and particle organic matter hydrolysis due to the weakened network strength of flocs, leading to an enhanced increase (17.3 mg/L) of dissolved organic matter (DOM), especially for the fraction of molecular weight (MW) < 25 kDa. The OASR reduced the adenosine triphosphate (ATP) content for heterotrophic anabolism in the mainstream reactor by 42.9%, compared to the ASR. MW < 25 kDa of DOM caused the disturbance of oxidative phosphorylation with a decreasing ATP synthase activity under high-level electronic transport system, leading to ATP dissipation. The cooperation interaction of predator (norank_Chitinophagales), hydrolytic/fermentative bacteria (unclassified_Bacteroidia and Delftia), and slow grower (Trichococcus) played a key role in improving the sludge reduction and carbon reuse in AO-OASR. The results provided an efficient and cost-saving technology for sludge reduction with modified SR under low HRT, which is meaningful to overcome the present bottleneck of deficient reduction efficiency for application in wastewater treatment plants.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Jinju Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China; Yixing Environmental Protection Research Institute, Nanjing University, Nanjing 214200, Jiangsu, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Yihan Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Rongwei Gao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Xu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China; Yixing Environmental Protection Research Institute, Nanjing University, Nanjing 214200, Jiangsu, China.
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19
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Effects of fermentation with Lactiplantibacillus plantarum GDM1.191 on the umami compounds in shiitake mushrooms (Lentinus edodes). Food Chem 2021; 364:130398. [PMID: 34175630 DOI: 10.1016/j.foodchem.2021.130398] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 11/23/2022]
Abstract
Shiitake mushroom (Lentinus edodes) is the second most-widely-consumed edible fungi with strong flavor and unique taste. To study the effects of Lactiplantibacillus plantarum fermentation on umami compounds in shiitake mushrooms, the levels of taste-imparting compounds were analyzed, including organic acids, free amino acids, and 5'-nucleotides during fermentation. The contents of all umami compounds except for succinic acid and fumaric acid were improved with increasing fermentation time; broths obtained at each fermentation stage formed clear clusters upon subjecting the electronic tongue data to principal component and discriminant function analyses. Compounds that predominantly contributed to important umami were identified. Among the 30 umami compounds investigated, 11 compounds were considered to be predominantly responsible for the different taste characteristics of shiitake mushroom broths at various stages of fermentation. Taken together, L. plantarum fermentation improved the contents of umami taste compounds in shiitake mushroom.
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20
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Low-waste fermentation-derived organic acid production by bipolar membrane electrodialysis—an overview. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01720-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AbstractOrganic acids, e.g, citric acid, fumaric acid, lactic acid, malic acid, pyruvic acid and succinic acid, have important role in the food industry and are potential raw materials for the sustainable chemical industry. Their fermentative production based on renewable raw materials requires innovatively designed downstream processing to maintain low environmental impact and resource efficiency throughout the production process. The application of bipolar membranes offers clean and effective way to generate hydrogen ions required for free acid production from its salt. The water dissociation reaction inside the bipolar membrane triggered by electric field plays key role in providing hydrogen ion for the replacement of the cations in organic acid salts. Combined with monopolar ion-exchange membranes in a bipolar membrane electrodialysis process, material flow can be separated beside the product stream into additional reusable streams, thus minimizing the waste generation. This paper focuses on bipolar membrane electrodialysis applied for organic acid recovery from fermentation broth.
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21
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Karapetyan L, Mikoyan G, Vassilian A, Valle A, Bolivar J, Trchounian A, Trchounian K. Escherichia coli Dcu C 4-dicarboxylate transporters dependent proton and potassium fluxes and F OF 1-ATPase activity during glucose fermentation at pH 7.5. Bioelectrochemistry 2021; 141:107867. [PMID: 34118553 DOI: 10.1016/j.bioelechem.2021.107867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 11/27/2022]
Abstract
During fermentation in Escherichia coli succinate is transported via Dcu transporters, encoded dcuA, dcuB, dcuC and dcuD although the role of DcuD protein has not been elucidated yet. It has been shown contribution of Dcu transporters in the N,N'-dicyclohexylcarbodiimide (DCCD) sensitive proton and potassium transport through the cytoplasmic membrane and membrane-associated ATPase activity. Total H± efflux was decreased ~ 40% while K± uptake was absent in dcuD mutant. DCCD-sensitive H± flux was absent in dcuD nevertheless it was increased ~ 3 fold in dcuACB. K± uptake in dcuACB was stimulated ~ 30% compared to wild type but in DCCD assays K± ions were effluxed with the rate of 0.15 mmol/min per 109 cells/ml. In dcuACB mutant membrane potential (ΔΨ) was ~ 30 mV higher than in wild type. dcuD gene expression was increased in the dcuACB mutant respect to wild type at pH 7.5 (~120%), suggesting that an increment of DcuD activity compensates the lack of DcuA, DcuC and DcuB carriers. It can be concluded that active DcuD is important for H± efflux via the FOF1-ATPase and K± uptake at pH 7.5. In addition, DcuA, DcuB and DcuC transporters are crucial for regulating DCCD-sensitive K± transport and ΔΨ in E. coli.
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Affiliation(s)
- L Karapetyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia
| | - G Mikoyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia
| | - A Vassilian
- Scientific-Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia
| | - A Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain
| | - J Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain
| | - A Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia
| | - K Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025 Yerevan, Armenia.
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22
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. The role of Escherichia coli FhlA transcriptional activator in generation of proton motive force and F O F 1 -ATPase activity at pH 7.5. IUBMB Life 2021; 73:883-892. [PMID: 33773019 DOI: 10.1002/iub.2470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/29/2022]
Abstract
Escherichia coli is able to utilize the mixture of carbon sources and produce molecular hydrogen (H2 ) via formate hydrogen lyase (FHL) complexes. In current work role of transcriptional activator of formate regulon FhlA in generation of fermentation end products and proton motive force, N'N'-dicyclohexylcarbodiimide (DCCD)-sensitive ATPase activity at 20 and 72 hr growth during utilization of mixture of glucose, glycerol, and formate were investigated. It was shown that in fhlA mutant specific growth rate was ~1.5 fold lower compared to wt, while addition of DCCD abolished the growth in fhlA but not in wt. Formate was not utilized in fhlA mutant but wt cells simultaneously utilized formate with glucose. Glycerol utilization started earlier (from 2 hr) in fhlA than in wt. The DCCD-sensitive ATPase activity in wt cells membrane vesicles increased ~2 fold at 72 hr and was decreased 70% in fhlA. Addition of formate in the assays increased proton ATPase activity in wt and mutant strain. FhlA absence mainly affected the ΔpH but not ΔΨ component of Δp in the cells grown at 72 hr but not in 24 hr. The Δp in wt cells decreased from 24 to 72 hr of growth ~40 mV while in fhlA mutant it was stable. Taken together, it is suggested that FhlA regulates the concentration of fermentation end products and via influencing FO F1 -ATPase activity contributes to the proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia.,Laboratory of Neuroscience, Yerevan State Medical University, Yerevan, Armenia
| | - Anait Vassilian
- Department of Ecology and Nature Protection, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
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23
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Chen Z, Gao H, Wu W, Chen H, Fang X, Han Y, Mu H. Effects of fermentation with different microbial species on the umami taste of Shiitake mushroom (Lentinus edodes). Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110889] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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Poladyan A, Blbulyan S, Semashko T, Dziameshka V, Zhukouskaya L, Trchоunian A. Application of organic waste glycerol to produce crude extracts of bacterial cells and microbial hydrogenase-the anode enzymes of bio-electrochemical systems. FEMS Microbiol Lett 2021; 367:5817844. [PMID: 32267913 DOI: 10.1093/femsle/fnaa056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/26/2020] [Indexed: 01/08/2023] Open
Abstract
Glycerol is an organic waste material that can be used for the production of microbial biomass, consequently providing valuable biocatalysts promoting the generation of electrical current in microbial fuel cells (MFCs). [NiFe]-Hydrogenases (Hyds) of Escherichia coli and Ralstonia eutropha may be applied as potential anode biocatalysts in MFCs. In this study, E. coli K12 whole cells or crude extracts and R. eutropha HF649 synthesizing Strep-tagged membrane-bound Hyds (MBH) were evaluated as anode enzymes in a bioelectrochemical system. The samples were immobilized on the sensors with polyvinyl acetate support. Mediators like ferrocene and its derivatives (ferrocene-carboxy-aldehyde, ferrocene-carboxylic acid, methyl-ferrocene-methanol) were employed. The maximal level of bioelectrocatalytic activity of Hyds was demonstrated at 500 mV voltage. Depending on the mediator and biocatalyst, current strength varied from 5 to 42 μA. Introduction of ferrocene-carboxylic acid enhanced current strength; moreover, the current flow was directly correlated with H2 concentration. The maximal value (up to 150 μA) of current strength was achieved with a 2-fold hydrogen supply. It may be inferred that Hyds are efficiently produced by E. coli and R. eutropha grown on glycerol, while ferrocene derivatives act as agents mediating the electrochemical activity of Hyds.
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Affiliation(s)
- Anna Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | - Syuzanna Blbulyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | - Tatiana Semashko
- Institute of Microbiology, NAS Belarus, 2 Kuprevich Str., 220141 Minsk, Belarus
| | - Volha Dziameshka
- Institute of Microbiology, NAS Belarus, 2 Kuprevich Str., 220141 Minsk, Belarus
| | | | - Armen Trchоunian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia.,Research Institute of Biology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
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25
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Atilano-Camino MM, Luévano-Montaño CD, García-González A, Olivo-Alanis DS, Álvarez-Valencia LH, García-Reyes RB. Evaluation of dissolved and immobilized redox mediators on dark fermentation: Driving to hydrogen or solventogenic pathway. BIORESOURCE TECHNOLOGY 2020; 317:123981. [PMID: 32799081 DOI: 10.1016/j.biortech.2020.123981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
In this work, lawsone (LQ) and anthraquinone 2-sulphonate (AQS) (dissolved and covalently immobilized on activated carbon) were evaluated as redox mediators during the dark fermentation of glucose by a pretreated anaerobic sludge. Findings revealed that the use of dissolved LQ increased H2 production (10%), and dissolved AQS improved H2 production rate (11.4%). Furthermore, the total production of liquid byproducts (acetate, butyrate, ethanol, and butanol) was enhanced using dissolved (17%) and immobilized (36%) redox mediators. The established redox standard potentials of LQ and AQS suggested a possible interaction through electron transfer in cytochromes complexes for hydrogen production and the Bcd/EtfAB complex for volatile fatty acid formation.
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Affiliation(s)
- Marina M Atilano-Camino
- Universidad Autónoma de Nuevo León (UANL), Facultad de Ciencias Químicas, Av. Universidad S/N, Cd. Universitaria, C.P. 66455 San Nicolás de los Garza, Nuevo León, Mexico
| | - Cindy D Luévano-Montaño
- Universidad Autónoma de Nuevo León (UANL), Facultad de Ciencias Químicas, Av. Universidad S/N, Cd. Universitaria, C.P. 66455 San Nicolás de los Garza, Nuevo León, Mexico
| | - Alcione García-González
- Universidad Autónoma de Nuevo León (UANL), Facultad de Ciencias Químicas, Av. Universidad S/N, Cd. Universitaria, C.P. 66455 San Nicolás de los Garza, Nuevo León, Mexico
| | - Daniel S Olivo-Alanis
- Universidad Autónoma de Nuevo León (UANL), Facultad de Ciencias Químicas, Av. Universidad S/N, Cd. Universitaria, C.P. 66455 San Nicolás de los Garza, Nuevo León, Mexico
| | - Luis H Álvarez-Valencia
- Instituto Tecnológico de Sonora (ITSON), Departamento de Ciencias Agronómicas y Veterinarias, 5 de Febrero 818 Sur, C.P. 85000 Ciudad Obregón, Sonora, Mexico
| | - Refugio B García-Reyes
- Universidad Autónoma de Nuevo León (UANL), Facultad de Ciencias Químicas, Av. Universidad S/N, Cd. Universitaria, C.P. 66455 San Nicolás de los Garza, Nuevo León, Mexico.
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26
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Nath S. Molecular-level understanding of biological energy coupling and transduction: Response to "Chemiosmotic misunderstandings". Biophys Chem 2020; 268:106496. [PMID: 33160142 DOI: 10.1016/j.bpc.2020.106496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/06/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023]
Abstract
In a recent paper entitled "Chemiosmotic misunderstandings", it is claimed that "enough shortcomings in Mitchell's chemiosmotic theory have not been found and that a novel paradigm that offers at least as much explanatory power as chemiosmosis is not ready." This view is refuted by a wealth of molecular-level experimental data and strong new theoretical and computational evidence. It is shown that the chemiosmotic theory was beset with a large number of major shortcomings ever since the time when it was first proposed in the 1960s. These multiple shortcomings and flaws of chemiosmosis were repeatedly pointed out in incisive critiques by biochemical authorities of the late 20th century. All the shortcomings and flaws have been shown to be rectified by a quantitative, unified molecular-level theory that leads to a deeper and far more accurate understanding of biological energy coupling and ATP synthesis. The new theory is shown to be consistent with pioneering X-ray and cryo-EM structures and validated by state-of-the-art single-molecule techniques. Several new biochemical experimental tests are proposed and constructive ways for providing a revitalizing conceptual background and theory for integration of the available experimental information are suggested.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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27
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Zhang W, Chen X, Sun W, Nie T, Quanquin N, Sun Y. Escherichia Coli Increases its ATP Concentration in Weakly Acidic Environments Principally through the Glycolytic Pathway. Genes (Basel) 2020; 11:genes11090991. [PMID: 32854287 PMCID: PMC7563387 DOI: 10.3390/genes11090991] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.
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Affiliation(s)
- Wenbin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510640, China;
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou 510006, China;
| | - Wei Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Tao Nie
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
| | - Natalie Quanquin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA;
| | - Yirong Sun
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (W.S.); (T.N.)
- Correspondence:
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28
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Nath S. A Novel Conceptual Model for the Dual Role of FOF1-ATP Synthase in Cell Life and Cell Death. Biomol Concepts 2020; 11:143-152. [PMID: 32827389 DOI: 10.1515/bmc-2020-0014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022] Open
Abstract
The mitochondrial permeability transition (MPT) has been one of the longstanding enigmas in biology. Its cause is currently at the center of an extensive scientific debate, and several hypotheses on its molecular nature have been put forward. The present view holds that the transition arises from the opening of a high-conductance channel in the energy-transducing membrane, the permeability transition pore (PTP), also called the mitochondrial megachannel or the multiconductance channel (MMC). Here, the novel hypothesis is proposed that the aqueous access channels at the interface of the c-ring and the a-subunit of FO in the FOF1-ATP synthase are repurposed during induction of apoptosis and constitute the elusive PTP/ MMC. A unifying principle based on regulation by local potentials is advanced to rationalize the action of the myriad structurally and chemically diverse inducers and inhibitors of PTP/MMC. Experimental evidence in favor of the hypothesis and its differences from current models of PTP/MMC are summarized. The hypothesis explains in considerable detail how the binding of Ca2+ to a β-catalytic site (site 3) in the F1 portion of ATP synthase triggers the opening of the PTP/MMC. It is also shown to connect to longstanding proposals within Nath's torsional mechanism of energy transduction and ATP synthesis as to how the binding of MgADP to site 3 does not induce PTP/MMC, but instead catalyzes physiological ATP synthesis in cell life. In the author's knowledge, this is the first model that explains how Ca2+ transforms the FOF1-ATP synthase from an exquisite energy-conserving enzyme in cell life into an energy-dissipating structure that promotes cell death. This has major implications for basic as well as for clinical research, such as for the development of drugs that target the MPT, given the established role of PTP/MMC dysregulation in cancer, ischemia, cardiac hypertrophy, and various neurodegenerative diseases.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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29
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Mikoyan G, Karapetyan L, Vassilian A, Trchounian A, Trchounian K. External succinate and potassium ions influence Dcu dependent FOF1-ATPase activity and H+ flux of Escherichia coli at different pHs. J Bioenerg Biomembr 2020; 52:377-382. [DOI: 10.1007/s10863-020-09847-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/19/2020] [Indexed: 01/12/2023]
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30
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Petrosyan H, Vanyan L, Mirzoyan S, Trchounian A, Trchounian K. Roasted coffee wastes as a substrate for Escherichia coli to grow and produce hydrogen. FEMS Microbiol Lett 2020; 367:5848194. [DOI: 10.1093/femsle/fnaa088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/27/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
After brewing roasted coffee, spent coffee grounds (SCGs) are generated being one of the daily wastes emerging in dominant countries with high rate and big quantity. Escherichia coli BW25113 wild-type strain, mutants with defects in hydrogen (H2)-producing/oxidizing four hydrogenases (Hyd) (ΔhyaB ΔhybC, ΔhycE, ΔhyfG) and septuple mutant (ΔhyaB ΔhybC ΔhycA ΔfdoG ΔldhA ΔfrdC ΔaceE) were investigated by measuring change of external pH, bacterial growth and H2 production during the utilization of SCG hydrolysate. In wild type, H2 was produced with rate of 1.28 mL H2 (g sugar)−1 h−1 yielding 30.7 mL H2 (g sugar)−1 or 2.75 L (kg SCG)−1 during 24 h. In septuple mutant, H2 production yield was 72 mL H2 (g sugar)−1 with rate of 3 mL H2 (g sugar)−1 h−1. H2 generation was absent in hycE single mutant showing the main role of Hyd-3 in H2 production. During utilization of SCG wild type, specific growth rate was 0.72 ± 0.01 h−1 with biomass yield of 0.3 g L−1. Genetic modifications and control of external parameters during growth could lead to prolonged and enhanced microbiological H2 production by organic wastes, which will aid more efficiently global sustainable energy needs resulting in diversification of mobile and fixed energy sources.
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Affiliation(s)
- Hripsime Petrosyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
- Scientific Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Liana Vanyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
- Scientific Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Satenik Mirzoyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
- Scientific Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
- Scientific Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
- Scientific Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
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31
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Gevorgyan H, Trchounian A, Trchounian K. Formate and potassium ions affectEscherichia coliproton ATPase activity at low pH during mixed carbon fermentation. IUBMB Life 2020; 72:915-921. [DOI: 10.1002/iub.2219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/09/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology, Faculty of BiologyYerevan State University Yerevan Armenia
- Microbial Biotechnologies and Biofuel Innovation CenterYerevan State University Yerevan Armenia
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology, Faculty of BiologyYerevan State University Yerevan Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology, Faculty of BiologyYerevan State University Yerevan Armenia
- Microbial Biotechnologies and Biofuel Innovation CenterYerevan State University Yerevan Armenia
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32
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Karapetyan L, Pinske C, Sawers G, Trchounian A, Trchounian K. Influence ofC4‐Dcutransporters on hydrogenase and formate dehydrogenase activities in stationary phase‐grown fermentingEscherichia coli. IUBMB Life 2020; 72:1680-1685. [DOI: 10.1002/iub.2290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Lusine Karapetyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology Faculty of BiologyYerevan State University Yerevan Armenia
- Microbial Biotechnologies and Biofuel Innovation CenterYerevan State University Yerevan Armenia
| | - Constanze Pinske
- Institute of MicrobiologyMartin‐Luther University Halle‐Wittenberg Halle (Saale) Germany
| | - Gary Sawers
- Institute of MicrobiologyMartin‐Luther University Halle‐Wittenberg Halle (Saale) Germany
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology Faculty of BiologyYerevan State University Yerevan Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of BiologyYerevan State University Yerevan Armenia
- Scientific‐Research Institute of Biology Faculty of BiologyYerevan State University Yerevan Armenia
- Microbial Biotechnologies and Biofuel Innovation CenterYerevan State University Yerevan Armenia
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33
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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34
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Valk LC, Luttik MAH, de Ram C, Pabst M, van den Broek M, van Loosdrecht MCM, Pronk JT. A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway. Front Microbiol 2020; 10:3027. [PMID: 32010092 PMCID: PMC6978723 DOI: 10.3389/fmicb.2019.03027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectin-containing agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.
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Affiliation(s)
| | | | | | | | | | | | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Gabrielyan L, Trchounian A. Antibacterial activities of transient metals nanoparticles and membranous mechanisms of action. World J Microbiol Biotechnol 2019; 35:162. [PMID: 31612285 DOI: 10.1007/s11274-019-2742-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023]
Abstract
Various transient metal and metal oxide nanoparticles (NPs) have shown pronounced biological activity, including antibacterial action against different Gram-negative and Gram-positive bacteria including pathogens and drug-resistant ones. Thus, NPs can be applied in nanotechnology for controlling bacterial growth as well as in biomedicine for the treatment of various diseases. However, the mechanisms of these effects are not clear yet. This review is focused on the antibacterial effects of transient metal NPs, especially iron oxide (Fe3O4) and Ag NPs on Escherichia coli wild type and antibiotic-resistant strains. Ag NPs show more pronounced bactericidal effect than Fe3O4 NPs. Moreover, Ag NPs display more expressed antibacterial effect at low concentrations. Interestingly, kanamycin-resistant strain is more susceptible to Fe3O4 NPs than wild type strain. In order to explain the possible mechanisms of NP effects, in addition to the production of reactive oxygen species causing damage in cells, particularly, their membranes, the changes in the membrane-associated H+-translocating FOF1-ATPase activity, H+-fluxes through the bacterial membrane, redox potential and hydrogen yield by membrane-associated enzymes-hydrogenases, are discussed. We observed from the results that FOF1-ATPase could be a main target for NPs. A scheme of possible action mechanism is proposed.
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Affiliation(s)
- Lilit Gabrielyan
- Department of Medical Biochemistry and Biotechnology, Russian-Armenian University, 123 H. Emin Str., 0051, Yerevan, Armenia
- Department of Biochemistry, Microbiology and Biotechnology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025, Yerevan, Armenia
| | - Armen Trchounian
- Department of Medical Biochemistry and Biotechnology, Russian-Armenian University, 123 H. Emin Str., 0051, Yerevan, Armenia.
- Department of Biochemistry, Microbiology and Biotechnology, Biology Faculty, Yerevan State University, 1 A. Manoukian Str., 0025, Yerevan, Armenia.
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Evidence for Escherichia coli DcuD carrier dependent F OF 1-ATPase activity during fermentation of glycerol. Sci Rep 2019; 9:4279. [PMID: 30862913 PMCID: PMC6414658 DOI: 10.1038/s41598-019-41044-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/27/2019] [Indexed: 01/11/2023] Open
Abstract
During fermentation Escherichia coli excrete succinate mainly via Dcu family carriers. Current work reveals the total and N,N’-dicyclohexylcarbodiimide (DCCD) inhibited ATPase activity at pH 7.5 and 5.5 in E. coli wild type and dcu mutants upon glycerol fermentation. The overall ATPase activity was highest at pH 7.5 in dcuABCD mutant. In wild type cells 50% of the activity came from the FOF1-ATPase but in dcuD mutant it reached ~80%. K+ (100 mM) stimulate total but not DCCD inhibited ATPase activity 40% and 20% in wild type and dcuD mutant, respectively. 90% of overall ATPase activity was inhibited by DCCD at pH 5.5 only in dcuABC mutant. At pH 7.5 the H+ fluxes in E. coli wild type, dcuD and dcuABCD mutants was similar but in dcuABC triple mutant the H+ flux decreased 1.4 fold reaching 1.15 mM/min when glycerol was supplemented. In succinate assays the H+ flux was higher in the strains where DcuD is absent. No significant differences were determined in wild type and mutants specific growth rate except dcuD strain. Taken together it is suggested that during glycerol fermentation DcuD has impact on H+ fluxes, FOF1-ATPase activity and depends on potassium ions.
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