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Li W, Feng Q, Li Z, Jin T, Zhang Y, Southam G. Inhibition of iron oxidation in Acidithiobacillus ferrooxidans by low-molecular-weight organic acids: Evaluation of performance and elucidation of mechanisms. Sci Total Environ 2024; 927:171919. [PMID: 38554963 DOI: 10.1016/j.scitotenv.2024.171919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
The catalytic role of Acidithiobacillus ferrooxidans (A. ferrooxidans) in iron biooxidation is pivotal in the formation of Acid Mine Drainage (AMD), which poses a significant threat to the environment. To control AMD generation, treatments with low-molecular-weight organic acids are being studied, yet their exact mechanisms are unclear. In this study, AMD materials, organic acids, and molecular methods were employed to gain a deeper understanding of the inhibitory effects of low-molecular-weight organic acids on the biooxidation of iron by A. ferrooxidans. The inhibition experiments of A. ferrooxidans on the oxidation of Fe2+ showed that to attain a 90 % inhibition efficacy within 72 h, the minimum concentrations required for formic acid, acetic acid, propionic acid, and lactic acid are 0.5, 6, 4, and 10 mmol/L, respectively. Bacterial imaging illustrated the detrimental effects of these organic acids on the cell envelope structure. This includes severe damage to the outer membrane, particularly from formic and acetic acids, which also caused cell wall damage. Coupled with alterations in the types and quantities of protein, carbohydrate, and nucleic acid content in extracellular polymeric substances (EPS), indicate the mechanisms underlying these inhibitory treatments. Transcriptomic analysis revealed interference of these organic acids with crucial metabolic pathways, particularly those related to energy metabolism. These findings establish a comprehensive theoretical basis for understanding the inhibition of A. ferrooxidans' biooxidation by low-molecular-weight organic acids, offering a novel opportunity to effectively mitigate the generation of AMD at its source.
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Affiliation(s)
- Wenbo Li
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China; School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Qiyan Feng
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ze Li
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China
| | - Tao Jin
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China
| | - Yun Zhang
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, Xuzhou 221116, China
| | - Gordon Southam
- School of the Environment, The University of Queensland, Brisbane 4072, Australia; The Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
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Wani SR, Jain V. Deciphering the molecular mechanism and regulation of formaldehyde detoxification in Mycobacterium smegmatis. Appl Environ Microbiol 2024; 90:e0203923. [PMID: 38259108 PMCID: PMC10880627 DOI: 10.1128/aem.02039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
The build-up of formaldehyde, a highly reactive molecule is cytotoxic and must be eliminated for the organism's survival. Formaldehyde detoxification system is found in nearly all organisms including both pathogenic and non-pathogenic mycobacteria. MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis (Msm), is an indispensable part of this system and forms a bicistronic operon with its downstream uncharacterized gene, fmh. We here show that Fmh, a putative metallo-beta-lactamase, is essential in tolerating higher amounts of formaldehyde when co-overexpressed with mscR in vivo. Our NMR studies indicate that MscR, along with Fmh, enhances formate production through a mycothiol (MSH)-dependent pathway, emphasizing the importance of Fmh in detoxifying formaldehyde. Although another aldehyde dehydrogenase, MSMEG_1543, induces upon formaldehyde addition, it is not involved in its detoxification. We also show that the expression of the mscR operon is constitutive and remains unchanged upon formaldehyde addition, as displayed by the promoter activity of PmscR and by the transcript and protein levels of MscR. Furthermore, we establish the role of a thiol-responsive sigma factor SigH in formaldehyde detoxification. We show that SigH, and not SigE, is crucial for formaldehyde detoxification, even though it does not directly regulate mscR operon expression. In addition, sensitivity to formaldehyde in sigH-knockout could be alleviated by overexpression of mscR. Taken together, our data demonstrate the importance of MSH-dependent pathways in detoxifying formaldehyde in a mycobacterial system. An absence of such MSH-dependent proteins in eukaryotes and its complete conservation in M. tuberculosis, the causative agent of tuberculosis, further unravel new drug targets for this pathogen.IMPORTANCEExtensive research has been done on formaldehyde detoxification in different bacteria. However, our current understanding of the mechanisms underlying this process in mycobacteria remains exceedingly little. We previously showed that MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis, plays a pivotal role in this detoxification pathway. Here, we present a potential S-formyl-mycothiol hydrolase named Fmh, thought to be a metallo-beta-lactamase, which functions along with mycothiol (MSH) and MscR to enhance formate production within this detoxification pathway. Co-expression of Fmh with MscR significantly enhances the efficiency of formaldehyde detoxification in M. smegmatis. Our experiments establish that Fmh catalyzes the final step of this detoxification pathway. Although an alternative sigma factor SigH was found to be involved in formaldehyde detoxification, it did not directly regulate the expression of mscR. Since formaldehyde detoxification is essential for bacterial survival, we envisage this process to be a potential drug target for M. tuberculosis eradication.
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Affiliation(s)
- Saloni Rajesh Wani
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
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Bordel S, Martín-González D, Börner T, Muñoz R, Santos-Beneit F. Genome-scale metabolic model of the versatile bacterium Paracoccus denitrificans Pd1222. mSystems 2024; 9:e0107723. [PMID: 38180324 PMCID: PMC10878069 DOI: 10.1128/msystems.01077-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/26/2023] [Indexed: 01/06/2024] Open
Abstract
A genome scale metabolic model of the bacterium Paracoccus denitrificans has been constructed. The model containing 972 metabolic genes, 1,371 reactions, and 1,388 unique metabolites has been reconstructed. The model was used to carry out quantitative predictions of biomass yields on 10 different carbon sources under aerobic conditions. Yields on C1 compounds suggest that formate is oxidized by a formate dehydrogenase O, which uses ubiquinone as redox co-factor. The model also predicted the threshold methanol/mannitol uptake ratio, above which ribulose biphosphate carboxylase has to be expressed in order to optimize biomass yields. Biomass yields on acetate, formate, and succinate, when NO3- is used as electron acceptor, were also predicted correctly. The model reconstruction revealed the capability of P. denitrificans to grow on several non-conventional substrates such as adipic acid, 1,4-butanediol, 1,3-butanediol, and ethylene glycol. The capacity to grow on these substrates was tested experimentally, and the experimental biomass yields on these substrates were accurately predicted by the model.IMPORTANCEParacoccus denitrificans has been broadly used as a model denitrifying organism. It grows on a large portfolio of carbon sources, under aerobic and anoxic conditions. These characteristics, together with its amenability to genetic manipulations, make P. denitrificans a promising cell factory for industrial biotechnology. This paper presents and validates the first functional genome-scale metabolic model for P. denitrificans, which is a key tool to enable P. denitrificans as a platform for metabolic engineering and industrial biotechnology. Optimization of the biomass yield led to accurate predictions in a broad scope of substrates.
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Affiliation(s)
- Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Diego Martín-González
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Tim Börner
- HES-SO Valais/Wallis, School of Engineering, Institute of Life Technologies, Sion, Switzerland
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Fernando Santos-Beneit
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
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Cheon H, Kim JH, Kim JS, Park JB. Valorization of single-carbon chemicals by using carboligases as key enzymes. Curr Opin Biotechnol 2024; 85:103047. [PMID: 38128199 DOI: 10.1016/j.copbio.2023.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.
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Affiliation(s)
- Huijin Cheon
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Jin-Byung Park
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea.
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5
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Ohnuki J, Jaunet-Lahary T, Yamashita A, Okazaki KI. Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT. J Phys Chem Lett 2024; 15:725-732. [PMID: 38215403 DOI: 10.1021/acs.jpclett.3c03052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Transporter proteins change their conformations to carry their substrate across the cell membrane. The conformational dynamics is vital to understanding the transport function. We have studied the oxalate transporter (OxlT), an oxalate:formate antiporter from Oxalobacter formigenes, significant in avoiding kidney stone formation. The atomic structure of OxlT has been recently solved in the outward-open and occluded states. However, the inward-open conformation is still missing, hindering a complete understanding of the transporter. Here, we performed a Gaussian accelerated molecular dynamics simulation to sample the extensive conformational space of OxlT and successfully predicted the inward-open conformation where cytoplasmic substrate formate binding was preferred over oxalate binding. We also identified critical interactions for the inward-open conformation. The results were complemented by an AlphaFold2 structure prediction. Although AlphaFold2 solely predicted OxlT in the outward-open conformation, mutation of the identified critical residues made it partly predict the inward-open conformation, identifying possible state-shifting mutations.
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Affiliation(s)
- Jun Ohnuki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Titouan Jaunet-Lahary
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Kei-Ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
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6
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Lim JK. Theoretical hypothesis in a direct electron transfer between non-interacting Fe-S proteins within an artificial fusion. FEMS Microbiol Lett 2024; 371:fnad137. [PMID: 38196139 PMCID: PMC10795574 DOI: 10.1093/femsle/fnad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
Reduction of CO2 to formate utilizing formate dehydrogenases (FDHs) has been attempted biologically and electrochemically. However, the conversion efficiency is very low due to the low energy potential of electron donors and/or electron competition with other electron acceptors. To overcome such a low conversion efficiency, I focused on a direct electron transfer between two unrelated redox enzymes for the efficient reduction of CO2 and utilized the quantum mechanical magnetic properties of the [Fe-S] ([iron-sulfur]) cluster to develop a novel electron path. Using this electron path, we connected non-interacting carbon monoxide dehydrogenase and FDH, constructing a synthetic carbon monoxide:formate oxidoreductase as a single functional enzyme complex in the previous study. Here, a theoretical hypothesis that can explain the direct electron transfer phenomenon based on the magnetic properties of the [Fe-S] cluster is proposed.
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Affiliation(s)
- Jae Kyu Lim
- Korea Institute of Ocean Science and Technology (KIOST), Jeju Bio Research Center, Jeju 63349, Republic of Korea
- University of Science and Technology (UST), KIOST School, Daejeon 34113, Republic of Korea
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7
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Bysani VR, Alam AS, Bar-Even A, Machens F. Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO 2 assimilation. Metab Eng 2024; 81:167-181. [PMID: 38040111 DOI: 10.1016/j.ymben.2023.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
Using captured CO2 and C1-feedstocks like formate and methanol derived from electrochemical activation of CO2 are key solutions for transforming industrial processes towards a circular carbon economy. Engineering formate and CO2-based growth in the biotechnologically relevant yeast Saccharomyces cerevisiae could boost the emergence of a formate-mediated circular bio-economy. This study adopts a growth-coupled selection scheme for modular implementation of the Reductive Glycine Pathway (RGP) and subsequent Adaptive Laboratory Evolution (ALE) to enable formate and CO2 assimilation for biomass formation in yeast. We first constructed a serine biosensor strain and then implemented the serine synthesis module of the RGP into yeast, establishing glycine and serine synthesis from formate and CO2. ALE improved the RGP-dependent growth by 8-fold. 13C-labeling experiments reveal glycine, serine, and pyruvate synthesis via the RGP, demonstrating the complete pathway activity. Further, we re-established formate and CO2-dependent growth in non-evolved biosensor strains via reverse-engineering a mutation in GDH1 identified from ALE. This mutation led to significantly more 13C-formate assimilation than in WT without any selection or overexpression of the RGP. Overall, we demonstrated the activity of the complete RGP, showing evidence for carbon transfer from formate to pyruvate coupled with CO2 assimilation.
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Affiliation(s)
- Viswanada R Bysani
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Ayesha S Alam
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fabian Machens
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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8
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Abdul Halim MF, Fonseca DR, Niehaus TD, Costa KC. Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J Biol Chem 2024; 300:105550. [PMID: 38072055 PMCID: PMC10805699 DOI: 10.1016/j.jbc.2023.105550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/02/2024] Open
Abstract
Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2 as an electron donor to reduce CO2 to CH4, but in the absence of H2 many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for the reduction of coenzyme F420 or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is unknown. Using Methanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420 at similar rates. F420 reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1 mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in the loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth, and the metal content of the proteins suggested that isoforms are dependent on either molybdenum or tungsten for activity. These data suggest that both isoforms of Fdh are functionally redundant, but their activities in vivo may be limited by gene regulation or metal availability under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.
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Affiliation(s)
- Mohd Farid Abdul Halim
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Dallas R Fonseca
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA.
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9
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Leggieri PA, Blair EM, Lankiewicz TS, O'Malley MA. Continuous culture of anaerobic fungi enables growth and metabolic flux tuning without use of genetic tools. Bioresour Technol 2024; 391:129854. [PMID: 37863334 DOI: 10.1016/j.biortech.2023.129854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
Abstract
Anaerobic gut fungi (AGF) have potential to valorize lignocellulosic biomass owing to their diverse repertoire of carbohydrate-active enzymes (CAZymes). However, AGF metabolism is poorly understood, and no stable genetic tools are available to manipulate growth and metabolic flux to enhance production of specific targets, e.g., cells, CAZymes, or metabolites. Herein, a cost-effective, Arduino-based, continuous-flow anaerobic bioreactor with online optical density control is presented to probe metabolism and predictably tune fluxes in Caecomyces churrovis. Varying the C. churrovis turbidostat setpoint titer reliably controlled growth rate (from 0.04 to 0.20 h-1), metabolic flux, and production rates of acetate, formate, lactate, and ethanol. Bioreactor setpoints to maximize production of each product were identified, and all continuous production rates significantly exceed batch rates. Formate spike-ins increased lactate flux and decreased acetate, ethanol, and formate fluxes. The bioreactor and turbidostat culture schemes demonstrated here offer tools to tailor AGF fermentations to application-specific hydrolysate product profiles.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Thomas S Lankiewicz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA; Biological Engineering Program, University of California, Santa Barbara, CA 93106, USA.
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10
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McDaniel EA, Scarborough M, Mulat DG, Lin X, Sampara PS, Olson HM, Young RP, Eder EK, Attah IK, Markillie LM, Hoyt DW, Lipton MS, Hallam SJ, Ziels RM. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. ISME J 2023; 17:2326-2339. [PMID: 37880541 PMCID: PMC10689502 DOI: 10.1038/s41396-023-01542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, USA
| | - Daniel Girma Mulat
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Xuan Lin
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Pranav S Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M Olson
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert P Young
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Elizabeth K Eder
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Isaac K Attah
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lye Meng Markillie
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David W Hoyt
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, The University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, The University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada.
- Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.
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11
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Moniruzzaman M, Khac Nguyen H, Kiyasu Y, Hirose T, Handa Y, Koide T, Ogo S, Yoon KS. H 2-driven reduction of CO 2 to formate using bacterial plasma membranes. Bioresour Technol 2023; 390:129921. [PMID: 37884095 DOI: 10.1016/j.biortech.2023.129921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Bacterial membranes shield the intracellular compartment by selectively allowing unwanted substances to enter in, which in turn reduces overall catalytic efficiency. This report presents a model system using the isolated plasma membranes of Citrobacter sp. S-77 that harbor oxygen-stable [NiFe]hydrogenase and [Mo]formate dehydrogenase, which are integrated into a natural catalytic nanodevice through an electron transfer relay. This naturally occurring nanodevice exhibited selectivity and efficiency in catalyzing the H2-driven conversion of CO2 to formate with the rate of 817 mmol·L-1·gprotein-1·h-1 under mild conditions of 30 °C, pH 7.0, and 0.1 MPa. When the isolated plasma membranes of Citrobacter sp. S-77 was immobilized with multi-walled carbon nanotubes and encapsulated in hydrogel beads of gellan-gum cross-linked with calcium ions, the catalyst for formate production remained stable over 10 repeated uses. This paper reports the first case of efficient and selective formate production from H2 and CO2 using bacterial plasma membranes.
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Affiliation(s)
- Mohammad Moniruzzaman
- Mitsui Chemicals, Inc.-Carbon Neutral Research Center (MCI-CNRC), Kyushu University, Japan; International Institute for Carbon-Neutral Energy Research (I2CNER), Kyushu University, Japan.
| | - Hung Khac Nguyen
- International Institute for Carbon-Neutral Energy Research (I2CNER), Kyushu University, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Yu Kiyasu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Takumi Hirose
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Yuya Handa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Taro Koide
- International Institute for Carbon-Neutral Energy Research (I2CNER), Kyushu University, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (I2CNER), Kyushu University, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
| | - Ki-Seok Yoon
- Mitsui Chemicals, Inc.-Carbon Neutral Research Center (MCI-CNRC), Kyushu University, Japan; International Institute for Carbon-Neutral Energy Research (I2CNER), Kyushu University, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Japan.
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12
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Mitic BM, Troyer C, Lutz L, Baumschabl M, Hann S, Mattanovich D. The oxygen-tolerant reductive glycine pathway assimilates methanol, formate and CO 2 in the yeast Komagataella phaffii. Nat Commun 2023; 14:7754. [PMID: 38012236 PMCID: PMC10682033 DOI: 10.1038/s41467-023-43610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
The current climatic change is predominantly driven by excessive anthropogenic CO2 emissions. As industrial bioprocesses primarily depend on food-competing organic feedstocks or fossil raw materials, CO2 co-assimilation or the use of CO2-derived methanol or formate as carbon sources are considered pathbreaking contributions to solving this global problem. The number of industrially-relevant microorganisms that can use these two carbon sources is limited, and even fewer can concurrently co-assimilate CO2. Here, we search for alternative native methanol and formate assimilation pathways that co-assimilate CO2 in the industrially-relevant methylotrophic yeast Komagataella phaffii (Pichia pastoris). Using 13C-tracer-based metabolomic techniques and metabolic engineering approaches, we discover and confirm a growth supporting pathway based on native enzymes that can perform all three assimilations: namely, the oxygen-tolerant reductive glycine pathway. This finding paves the way towards metabolic engineering of formate and CO2 utilisation to produce proteins, biomass, or chemicals in yeast.
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Affiliation(s)
- Bernd M Mitic
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Christina Troyer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Lisa Lutz
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Michael Baumschabl
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Stephan Hann
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Diethard Mattanovich
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
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13
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Tian J, Deng W, Zhang Z, Xu J, Yang G, Zhao G, Yang S, Jiang W, Gu Y. Discovery and remodeling of Vibrio natriegens as a microbial platform for efficient formic acid biorefinery. Nat Commun 2023; 14:7758. [PMID: 38012202 PMCID: PMC10682008 DOI: 10.1038/s41467-023-43631-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Formic acid (FA) has emerged as a promising one-carbon feedstock for biorefinery. However, developing efficient microbial hosts for economically competitive FA utilization remains a grand challenge. Here, we discover that the bacterium Vibrio natriegens has exceptional FA tolerance and metabolic capacity natively. This bacterium is remodeled by rewiring the serine cycle and the TCA cycle, resulting in a non-native closed loop (S-TCA) which as a powerful metabolic sink, in combination with laboratory evolution, enables rapid emergence of synthetic strains with significantly improved FA-utilizing ability. Further introduction of a foreign indigoidine-forming pathway into the synthetic V. natriegens strain leads to the production of 29.0 g · L-1 indigoidine and consumption of 165.3 g · L-1 formate within 72 h, achieving a formate consumption rate of 2.3 g · L-1 · h-1. This work provides an important microbial chassis as well as design rules to develop industrially viable microorganisms for FA biorefinery.
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Affiliation(s)
- Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Xianghu Laboratory, Hangzhou, 311231, China.
| | - Wangshuying Deng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwen Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Xu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311215, China
| | | | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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14
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Sahin S, Lemaire ON, Belhamri M, Kurth JM, Welte CU, Wagner T, Milton RD. Bioelectrocatalytic CO 2 Reduction by Mo-Dependent Formylmethanofuran Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202311981. [PMID: 37712590 DOI: 10.1002/anie.202311981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
Massive efforts are invested in developing innovative CO2 -sequestration strategies to counter climate change and transform CO2 into higher-value products. CO2 -capture by reduction is a chemical challenge, and attention is turned toward biological systems that selectively and efficiently catalyse this reaction under mild conditions and in aqueous solvents. While a few reports have evaluated the effectiveness of isolated bacterial formate dehydrogenases as catalysts for the reversible electrochemical reduction of CO2 , it is imperative to explore other enzymes among the natural reservoir of potential models that might exhibit higher turnover rates or preferential directionality for the reductive reaction. Here, we present electroenzymatic catalysis of formylmethanofuran dehydrogenase, a CO2 -reducing-and-fixing biomachinery isolated from a thermophilic methanogen, which was deposited on a graphite rod electrode to enable direct electron transfer for electroenzymatic CO2 reduction. The gas is reduced with a high Faradaic efficiency (109±1 %), where a low affinity for formate prevents its electrochemical reoxidation and favours formate accumulation. These properties make the enzyme an excellent tool for electroenzymatic CO2 -fixation and inspiration for protein engineering that would be beneficial for biotechnological purposes to convert the greenhouse gas into stable formate that can subsequently be safely stored, transported, and used for power generation without energy loss.
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Affiliation(s)
- Selmihan Sahin
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
- Department of Chemistry, Faculty of Arts and Sciences, Suleyman Demirel University, Cunur, 32260, Isparta, Turkiye
| | - Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mélissa Belhamri
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
- Microcosm Earth Center - Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Ross D Milton
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
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15
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Treece TR, Pattanayak S, Matson MM, Cepeda MM, Berben LA, Atsumi S. Electrical-biological hybrid system for carbon efficient isobutanol production. Metab Eng 2023; 80:142-150. [PMID: 37739158 DOI: 10.1016/j.ymben.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
We have developed an electrical-biological hybrid system wherein an engineered microorganism consumes electrocatalytically produced formate from CO2 to supplement the bioproduction of isobutanol, a valuable fuel chemical. Biological CO2 sequestration is notoriously slow compared to electrochemical CO2 reduction, while electrochemical methods struggle to generate carbon-carbon bonds which readily form in biological systems. A hybrid system provides a promising method for combining the benefits of both biology and electrochemistry. Previously, Escherichia coli was engineered to assimilate formate and CO2 in central metabolism using the reductive glycine pathway. In this work, we have shown that chemical production in E. coli can benefit from single carbon substrates when equipped with the RGP. By installing the RGP and the isobutanol biosynthetic pathway into E. coli and by further genetic modifications, we have generated a strain of E. coli that can consume formate and produce isobutanol at a yield of >100% of theoretical maximum from glucose. Our results demonstrate that carbon produced from electrocatalytically reduced CO2 can bolster chemical production in E. coli. This study shows that E. coli can be engineered towards carbon efficient methods of chemical production.
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Affiliation(s)
- Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Santanu Pattanayak
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Morgan M Matson
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Mateo M Cepeda
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Louise A Berben
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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16
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Singh A, Schnürer A, Dolfing J, Westerholm M. Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions. ISME J 2023; 17:1966-1978. [PMID: 37679429 PMCID: PMC10579422 DOI: 10.1038/s41396-023-01504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne, NE18QH, UK
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
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17
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Li Y, Luo Q, Su J, Dong G, Cao M, Wang Y. Metabolic regulation of Shewanella oneidensis for microbial electrosynthesis: From extracellular to intracellular. Metab Eng 2023; 80:1-11. [PMID: 37673324 DOI: 10.1016/j.ymben.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023]
Abstract
Shewanella oneidensis MR-1 (S. oneidensis MR-1) has been shown to benefit from microbial electrosynthesis (MES) due to its exceptional electron transfer efficiency. In this study, genes involved in both extracellular electron uptake (EEU) and intracellular CO2 conversion processes were examined and regulated to enhance MES performance. The key genes identified for MES in the EEU process were mtrB, mtrC, mtrD, mtrE, omcA and cctA. Overexpression of these genes resulted in 1.5-2.1 times higher formate productivity than that of the wild-type strains (0.63 mmol/(L·μg protein)), as 0.94-1.61 mmol/(L·μg protein). In the intracellular CO2 conversion process, overexpression of the nadE, nadD, nadR, nadV, pncC and petC genes increased formate productivity 1.3-fold-3.4-fold. Moreover, overexpression of the formate dehydrogenase genes fdhA1, fdhB1 and fdhX1 in modified strains led to a 2.3-fold-3.1-fold increase in formate productivity compared to wild-type strains. The co-overexpression of cctA, fdhA1 and nadV in the mutant strain resulted in 5.59 times (3.50 mmol/(L·μg protein)) higher formate productivity than that of the wild-type strains. These findings revealed that electrons of MES derived from the electrode were utilized in the energy module for synthesizing ATP and NADH, followed by the synthesis of formate in formate dehydrogenase by the combinatorial effects of ATP, NADH, electrons and CO2. The results provide new insights into the mechanism of MES in S. oneidensis MR-1 and pave the way for genetic improvements that could facilitate the further application of MES.
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Affiliation(s)
- Yixin Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China
| | - Qingliu Luo
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Jiaying Su
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China; School of Resource and Chemical Engineering, Sanming University, Sanming, 365004, China
| | - Guowen Dong
- School of Resource and Chemical Engineering, Sanming University, Sanming, 365004, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China.
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China.
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18
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Shi HL, Yuan SW, Xi XQ, Xie YL, Yue C, Zhang YJ, Yao LG, Xue C, Tang CD. Engineering of formate dehydrogenase for improving conversion potential of carbon dioxide to formate. World J Microbiol Biotechnol 2023; 39:352. [PMID: 37864750 DOI: 10.1007/s11274-023-03739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 10/23/2023]
Abstract
Formate dehydrogenase (FDH) is a D-2-hydroxy acid dehydrogenase, which can reversibly reduce CO2 to formate and thus act as non-photosynthetic CO2 reductase. In order to increase catalytic efficiency of formate dehydrogenase for CO2 reduction, two mutants V328I/F285W and V354G/F285W were obtained of which reduction activity was about two times more than the parent CbFDHM2, and the formate production from CO2 catalyzed by mutants were 2.9 and 2.7-fold higher than that of the parent CbFDHM2. The mutants had greater potential in CO2 reduction. The optimal temperature for V328I/F285W and V354G/F285W was 55 °C, and they showed increasement of relative activity under 45 °C to 55 °C compared with parent. The optimal pH for the mutants was 9.0, and they showed excellent stability in pH 4.0-11.5. The kcat/Km values of mutants were 1.75 times higher than that of the parent. Then the molecular basis for its improvement of biochemical characteristics were preliminarily elucidated by computer-aided methods. All of these results further established a solid foundation for molecular modification of formate dehydrogenase and CO2 reduction.
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Affiliation(s)
- Hong-Ling Shi
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, Liaoning, People's Republic of China
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Shu-Wei Yuan
- School of Chemistry and Chemical Engineering, Henan Normal University, 46 Jianshe East Road, Xinxiang, 453007, Henan, People's Republic of China
| | - Xiao-Qi Xi
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Yu-Li Xie
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Chao Yue
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Ying-Jun Zhang
- Henan Engineering Technology Research Center for Mushroom-based Foods, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, Liaoning, People's Republic of China.
| | - Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
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19
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Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
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Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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20
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Partipilo M, Whittaker JJ, Pontillo N, Coenradij J, Herrmann A, Guskov A, Slotboom DJ. Biochemical and structural insight into the chemical resistance and cofactor specificity of the formate dehydrogenase from Starkeya novella. FEBS J 2023; 290:4238-4255. [PMID: 37213112 DOI: 10.1111/febs.16871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
Formate dehydrogenases (Fdhs) mediate the oxidation of formate to carbon dioxide and concomitant reduction of nicotinamide adenine dinucleotide (NAD+ ). The low cost of the substrate formate and importance of the product NADH as a cellular source of reducing power make this reaction attractive for biotechnological applications. However, the majority of Fdhs are sensitive to inactivation by thiol-modifying reagents. In this study, we report a chemically resistant Fdh (FdhSNO ) from the soil bacterium Starkeya novella strictly specific for NAD+ . We present its recombinant overproduction, purification and biochemical characterization. The mechanistic basis of chemical resistance was found to be a valine in position 255 (rather than a cysteine as in other Fdhs) preventing the inactivation by thiol-modifying compounds. To further improve the usefulness of FdhSNO as for generating reducing power, we rationally engineered the protein to reduce the coenzyme nicotinamide adenine dinucleotide phosphate (NADP+ ) with better catalytic efficiency than NAD+ . The single mutation D221Q enabled the reduction of NADP+ with a catalytic efficiency kCAT /KM of 0.4 s-1 ·mm-1 at 200 mm formate, while a quadruple mutant (A198G/D221Q/H379K/S380V) resulted in a fivefold increase in catalytic efficiency for NADP+ compared with the single mutant. We determined the cofactor-bound structure of the quadruple mutant to gain mechanistic evidence behind the improved specificity for NADP+ . Our efforts to unravel the key residues for the chemical resistance and cofactor specificity of FdhSNO may lead to wider use of this enzymatic group in a more sustainable (bio)manufacture of value-added chemicals, as for instance the biosynthesis of chiral compounds.
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Affiliation(s)
- Michele Partipilo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Jacob J Whittaker
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Nicola Pontillo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
| | - Jelmer Coenradij
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Andreas Herrmann
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Germany
| | - Albert Guskov
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
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21
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Winter MG, Hughes ER, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Gillis CC, McClelland M, Andrews-Polymenis H, Winter SE. Formate oxidation in the intestinal mucus layer enhances fitness of Salmonella enterica serovar Typhimurium. mBio 2023; 14:e0092123. [PMID: 37498116 PMCID: PMC10470504 DOI: 10.1128/mbio.00921-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/12/2023] [Indexed: 07/28/2023] Open
Abstract
Salmonella enterica serovar Typhimurium induces intestinal inflammation to create a niche that fosters the outgrowth of the pathogen over the gut microbiota. Under inflammatory conditions, Salmonella utilizes terminal electron acceptors generated as byproducts of intestinal inflammation to generate cellular energy through respiration. However, the electron donating reactions in these electron transport chains are poorly understood. Here, we investigated how formate utilization through the respiratory formate dehydrogenase-N (FdnGHI) and formate dehydrogenase-O (FdoGHI) contribute to gut colonization of Salmonella. Both enzymes fulfilled redundant roles in enhancing fitness in a mouse model of Salmonella-induced colitis, and coupled to tetrathionate, nitrate, and oxygen respiration. The formic acid utilized by Salmonella during infection was generated by its own pyruvate-formate lyase as well as the gut microbiota. Transcription of formate dehydrogenases and pyruvate-formate lyase was significantly higher in bacteria residing in the mucus layer compared to the lumen. Furthermore, formate utilization conferred a more pronounced fitness advantage in the mucus, indicating that formate production and degradation occurred predominantly in the mucus layer. Our results provide new insights into how Salmonella adapts its energy metabolism to the local microenvironment in the gut. IMPORTANCE Bacterial pathogens must not only evade immune responses but also adapt their metabolism to successfully colonize their host. The microenvironments encountered by enteric pathogens differ based on anatomical location, such as small versus large intestine, spatial stratification by host factors, such as mucus layer and antimicrobial peptides, and distinct commensal microbial communities that inhabit these microenvironments. Our understanding of how Salmonella populations adapt its metabolism to different environments in the gut is incomplete. In the current study, we discovered that Salmonella utilizes formate as an electron donor to support respiration, and that formate oxidation predominantly occurs in the mucus layer. Our experiments suggest that spatially distinct Salmonella populations in the mucus layer and the lumen differ in their energy metabolism. Our findings enhance our understanding of the spatial nature of microbial metabolism and may have implications for other enteric pathogens as well as commensal host-associated microbial communities.
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Affiliation(s)
- Maria G. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Elizabeth R. Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Matthew K. Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Angel G. Jimenez
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rachael B. Chanin
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Caroline C. Gillis
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, UC Irvine, Irvine, California, USA
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, Texas A&M College of Medicine, College Station, Texas, USA
| | - Sebastian E. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
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22
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Hennequart M, Pilley SE, Labuschagne CF, Coomes J, Mervant L, Driscoll PC, Legrave NM, Lee Y, Kreuzaler P, Macintyre B, Panina Y, Blagih J, Stevenson D, Strathdee D, Schneider-Luftman D, Grönroos E, Cheung EC, Yuneva M, Swanton C, Vousden KH. ALDH1L2 regulation of formate, formyl-methionine, and ROS controls cancer cell migration and metastasis. Cell Rep 2023; 42:112562. [PMID: 37245210 DOI: 10.1016/j.celrep.2023.112562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 05/09/2023] [Indexed: 05/30/2023] Open
Abstract
Mitochondrial 10-formyltetrahydrofolate (10-formyl-THF) is utilized by three mitochondrial enzymes to produce formate for nucleotide synthesis, NADPH for antioxidant defense, and formyl-methionine (fMet) to initiate mitochondrial mRNA translation. One of these enzymes-aldehyde dehydrogenase 1 family member 2 (ALDH1L2)-produces NADPH by catabolizing 10-formyl-THF into CO2 and THF. Using breast cancer cell lines, we show that reduction of ALDH1L2 expression increases ROS levels and the production of both formate and fMet. Both depletion of ALDH1L2 and direct exposure to formate result in enhanced cancer cell migration that is dependent on the expression of the formyl-peptide receptor (FPR). In various tumor models, increased ALDH1L2 expression lowers formate and fMet accumulation and limits metastatic capacity, while human breast cancer samples show a consistent reduction of ALDH1L2 expression in metastases. Together, our data suggest that loss of ALDH1L2 can support metastatic progression by promoting formate and fMet production, resulting in enhanced FPR-dependent signaling.
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Affiliation(s)
- Marc Hennequart
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steven E Pilley
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christiaan F Labuschagne
- Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), 11 Hoffman Street, Potchesfstoom 2531, South Africa
| | - Jack Coomes
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Loic Mervant
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul C Driscoll
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Younghwan Lee
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Kreuzaler
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Yulia Panina
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Julianna Blagih
- Department of Obstetrics-Gynaecology, University of Montreal, Maisonneuve-Rosemont Hospital Research Centre, 5414 Assomption Blvd, Montreal, QC H1T 2M4, Canada
| | | | | | | | - Eva Grönroos
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eric C Cheung
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariia Yuneva
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Karen H Vousden
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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23
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Wang KC, Lerche MH, Ardenkjær-Larsen JH, Jensen PR. Formate Metabolism in Shigella flexneri and Its Effect on HeLa Cells at Different Stages during the Infectious Process. Microbiol Spectr 2023; 11:e0063122. [PMID: 37042762 PMCID: PMC10269805 DOI: 10.1128/spectrum.00631-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
Shigellosis caused by Shigella is one of the most important foodborne illnesses in global health, but little is known about the metabolic cross talk between this bacterial pathogen and its host cells during the different stages of the infection process. A detailed understanding of the metabolism can potentially lead to new drug targets remedying the pressing problem of antibiotic resistance. Here, we use stable isotope-resolved metabolomics as an unbiased and fast method to investigate how Shigella metabolizes 13C-glucose in three different environments: inside the host cells, adhering to the host cells, and alone in suspension. We find that especially formate metabolism by bacteria is sensitive to these different environments. The role of formate in pathogen metabolism is sparsely described in the literature compared to the roles of acetate and butyrate. However, its metabolic pathway is regarded as a potential drug target due to its production in microorganisms and its absence in humans. Our study provides new knowledge about the regulatory effect of formate. Bacterial metabolism of formate is pH dependent when studied alone in culture medium, whereas this effect is less pronounced when the bacteria adhere to the host cells. Once the bacteria are inside the host cells, we find that formate accumulation is reduced. Formate also affects the host cells resulting in a reduced infection rate. This was correlated to an increased immune response. Thus, intriguingly formate plays a double role in pathogenesis by increasing the virulence of Shigella and at the same time stimulating the immune response of the host. IMPORTANCE Bacterial infection is a pressing societal concern due to development of resistance toward known antibiotics. Central carbon metabolism has been suggested as a potential new target for drug development, but metabolic changes upon infection remain incompletely understood. Here, we used a cellular infection model to study how the bacterial pathogen Shigella adapts its metabolism depending on the environment starting from the extracellular medium until Shigella successfully invaded and proliferated inside host cells. The mixed-acid fermentation of Shigella was the major metabolic pathway during the infectious process, and the glucose-derived metabolite formate surprisingly played a divergent role in the pathogen and in the host cell. Our data show reduced infection rate when both host cells and bacteria were treated with formate, which correlated with an upregulated immune response in the host cells. The formate metabolism in Shigella thus potentially provides a route toward alternative treatment strategies for Shigella prevention.
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Affiliation(s)
- Ke-Chuan Wang
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathilde Hauge Lerche
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jan Henrik Ardenkjær-Larsen
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pernille Rose Jensen
- Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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24
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da Silva RR, Zaiter MA, Boscolo M, da Silva R, Gomes E. Xylose consumption and ethanol production by Pichia guilliermondii and Candida oleophila in the presence of furans, phenolic compounds, and organic acids commonly produced during the pre-treatment of plant biomass. Braz J Microbiol 2023; 54:753-759. [PMID: 36826705 PMCID: PMC10234969 DOI: 10.1007/s42770-023-00937-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
For 2G ethanol production, pentose fermentation and yeast tolerance to lignocellulosic hydrolyzate components are essential to improve biorefinery yields. Generally, physicochemical pre-treatment methodologies are used to facilitate access to cellulose and hemicellulose in plant material, which consequently can generate microbial growth inhibitory compounds, such as furans, weak acids, and phenolic compounds. Because of the unsatisfactory yield of wild-type Saccharomyces cerevisiae during pentose fermentation, the search for xylose-fermenting yeasts tolerant to microbial growth inhibitors has gained attention. In this study, we investigated the ability of the yeasts Pichia guilliermondii G1.2 and Candida oleophila G10.1 to produce ethanol from xylose and tolerate the inhibitors furfural, 5-hydroxymethylfurfural (HMF), acetic acid, formic acid, ferulic acid, and vanillin. We demonstrated that both yeasts were able to grow and consume xylose in the presence of all single inhibitors, with greater growth limitation in media containing furfural, acetic acid, and vanillin. In saline medium containing a mixture of these inhibitors (2.5-3.5 mM furfural and HMF, 1 mM ferulic acid, 1-1.5 mM vanillin, 10-13 mM acetic acid, and 5-7 mM formic acid), both yeasts were able to produce ethanol from xylose, similar to that detected in the control medium (without inhibitors). In future studies, the proteins involved in the transport of pentose and tolerance to these inhibitors need to be investigated.
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Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil.
| | - Mohammed Anas Zaiter
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Maurício Boscolo
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Roberto da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Eleni Gomes
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
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25
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Yao Y, Fu B, Han D, Zhang Y, Wei Z, Liu H. Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats. Environ Microbiol Rep 2023; 15:129-141. [PMID: 36779246 PMCID: PMC10103890 DOI: 10.1111/1758-2229.13129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/23/2022] [Indexed: 05/20/2023]
Abstract
Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO2 and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO2 reduction to formate as the first step of methyl branch of WLP may have evolved independently.
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Affiliation(s)
- Ye Yao
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Dongfei Han
- School of Environmental Science and EngineeringSuzhou University of Science and TechnologySuzhouPeople's Republic of China
- Institute of Environment and Sustainable Development in AgricultureChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Zhang
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
| | - Zhiyuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of MedicineJiangnan UniversityWuxiJiangsuChina
| | - He Liu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxiChina
- Jiangsu Collaborative Innovation Center of Technology and Material of Water TreatmentSuzhouChina
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26
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He Q, Jin J, Li P, Zhu H, Wang Z, Fan W, Yang JL. Involvement of SlSTOP1 regulated SlFDH expression in aluminum tolerance by reducing NAD + to NADH in the tomato root apex. Plant J 2023; 113:387-401. [PMID: 36471650 DOI: 10.1111/tpj.16054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Formate dehydrogenase (FDH; EC 1.2.1.2.) has been implicated in plant responses to a variety of stresses, including aluminum (Al) stress in acidic soils. However, the role of this enzyme in Al tolerance is not yet fully understood, and how FDH gene expression is regulated is unknown. Here, we report the identification and functional characterization of the tomato (Solanum lycopersicum) SlFDH gene. SlFDH encodes a mitochondria-localized FDH with Km values of 2.087 mm formate and 29.1 μm NAD+ . Al induced the expression of SlFDH in tomato root tips, but other metals did not, as determined by quantitative reverse transcriptase-polymerase chain reaction. CRISPR/Cas9-generated SlFDH knockout lines were more sensitive to Al stress and formate than wild-type plants. Formate failed to induce SlFDH expression in the tomato root apex, but NAD+ accumulated in response to Al stress. Co-expression network analysis and interaction analysis between genomic DNA and transcription factors (TFs) using PlantRegMap identified seven TFs that might regulate SlFDH expression. One of these TFs, SlSTOP1, positively regulated SlFDH expression by directly binding to its promoter, as demonstrated by a dual-luciferase reporter assay and electrophoretic mobility shift assay. The Al-induced expression of SlFDH was completely abolished in Slstop1 mutants, indicating that SlSTOP1 is a core regulator of SlFDH expression under Al stress. Taken together, our findings demonstrate that SlFDH plays a role in Al tolerance and reveal the transcriptional regulatory mechanism of SlFDH expression in response to Al stress in tomato.
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Affiliation(s)
- Qiyu He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianfeng Jin
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Pengfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Wei Fan
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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27
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Tomita R, Yoshida N, Meng L. Formate: A promising electron donor to enhance trichloroethene-to-ethene dechlorination in Dehalococcoides-augmented groundwater ecosystems with minimal bacterial growth. Chemosphere 2022; 307:136080. [PMID: 35988762 DOI: 10.1016/j.chemosphere.2022.136080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Various substrates have been used to stimulate habitat microbes in chloroethene-contaminated groundwater, however, the specific efficiency and minimum growth of microbes have rarely been studied. This study investigated the effects of seven substrates on trichloroethene (TCE) dechlorination by augmentation of groundwater with Dehalococcoides mccartyi NIT01 and its contribution to the microbial community. Three out of eight test groups completed dechlorination of 1 mM TCE-to-ethene in varying durations; groundwater supplemented with formate (FOR) required 78 days, whereas the microcosms with lactate (LAC) and citrate (CIT) required approximately twice as long (143 days). The calculated efficiency of how much produced H2 was used in dechlorination indicated a higher efficiency in FOR (36%) compared with LAC (1.9%) or CIT (2.9%). FOR showed lower microbial growth (3.4 × 105 copies/mL) than LAC (1.5 × 106) or CIT (4.4 × 106), and maintained a higher Shannon diversity index (5.65) than LAC (4.97) and CIT (4.30). The rapid and higher H2 transfer efficiency with lower bacterial growth by using formate was attributed to the slightly positive Gibbs free energy identified in H2 production requiring a H2-utilizer, lower carbon in the molecule, and adaptation to metabolic potential of the original groundwater microbiome. Formate is, therefore, a promising electron donor for rapid Dehalococcoides-augmented remediation with minimum bacterial growth. Sequential transferring of the FOR culture successfully maintained TCE-to-ethene dechlorination activity and enriched the members of genera Dehalococcoides (33%), Methanosphaerula (23%), Rectinema (13%), and Desulfitobacterium (5.6%). This suggests that formate is transferred to H2 and acetate, and provided to Dehalococcoides.
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Affiliation(s)
- Ryuya Tomita
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan.
| | - Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan
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28
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Chen X, Tang K, Zhang M, Liu S, Chen M, Zhan P, Fan W, Chen CTA, Zhang Y. Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents. Microbiome 2022; 10:170. [PMID: 36242065 PMCID: PMC9563475 DOI: 10.1186/s40168-022-01351-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems. RESULTS Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera. CONCLUSIONS The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Shujing Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Peiwen Zhan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, China
| | - Chen-Tung Arthur Chen
- Institute of Marine Geology and Chemistry, National Sun Yat-Sen University, Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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29
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Gu W, Müller AL, Deutzmann JS, Williamson JR, Spormann AM. Growth rate-dependent coordination of catabolism and anabolism in the archaeon Methanococcus maripaludis under phosphate limitation. ISME J 2022; 16:2313-2319. [PMID: 35780255 PMCID: PMC9478154 DOI: 10.1038/s41396-022-01278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Catabolic and anabolic processes are finely coordinated in microorganisms to provide optimized fitness under varying environmental conditions. Understanding this coordination and the resulting physiological traits reveals fundamental strategies of microbial acclimation. Here, we characterized the system-level physiology of Methanococcus maripaludis, a niche-specialized methanogenic archaeon, at different dilution rates ranging from 0.09 to 0.003 h-1 in chemostat experiments under phosphate (i.e., anabolic) limitation. Phosphate was supplied as the limiting nutrient, while formate was supplied in excess as the catabolic substrate and carbon source. We observed a decoupling of catabolism and anabolism resulting in lower biomass yield relative to catabolically limited cells at the same dilution rates. In addition, the mass abundance of several coarse-grained proteome sectors (i.e., combined abundance of proteins grouped based on their function) exhibited a linear relationship with growth rate, mostly ribosomes and their biogenesis. Accordingly, cellular RNA content also correlated with growth rate. Although the methanogenesis proteome sector was invariant, the metabolic capacity for methanogenesis, measured as methane production rates immediately after transfer to batch culture, correlated with growth rate suggesting translationally independent regulation that allows cells to only increase catabolic activity under growth-permissible conditions. These observations are in stark contrast to the physiology of M. maripaludis under formate (i.e., catabolic) limitation, where cells keep an invariant proteome including ribosomal content and a high methanogenesis capacity across a wide range of growth rates. Our findings reveal that M. maripaludis employs fundamentally different strategies to coordinate global physiology during anabolic phosphate and catabolic formate limitation.
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Affiliation(s)
- Wenyu Gu
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Albert L Müller
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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Molinero N, Conti E, Walker AW, Margolles A, Duncan SH, Delgado S. Survival Strategies and Metabolic Interactions between Ruminococcus gauvreauii and Ruminococcoides bili, Isolated from Human Bile. Microbiol Spectr 2022; 10:e0277621. [PMID: 35863028 PMCID: PMC9431564 DOI: 10.1128/spectrum.02776-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/05/2022] [Indexed: 11/26/2022] Open
Abstract
Little is known about the bacteria that reside in the human gallbladder and the mechanisms that allow them to survive within this harsh environment. Here we describe interactions between two strains from a human bile sample, one Ruminococcus gauvreauii (IPLA60001), belonging to the Lachnospiraceae family, and the other, designated as Ruminococcoides bili (IPLA60002T; DSM 110008) most closely related to Ruminococcus bromii within the family Ruminococcaceae. We provide evidence for bile salt resistance and sporulation for these new strains. Both differed markedly in their carbohydrate metabolism. The R. bili strain mainly metabolized resistant starches to form formate, lactate and acetate. R. gauvreauii mainly metabolized sugar alcohols, including inositol and also utilized formate to generate acetate employing the Wood Ljungdahl pathway. Amino acid and vitamin biosynthesis genomic profiles also differed markedly between the two isolates, likely contributing to their synergistic interactions, as revealed by transcriptomic analysis of cocultures. Transcriptome analysis also revealed that R. gauvreauii IPLA60001 is able to grow using the end-products of starch metabolism formed by the R. bili strain such as formate, and potentially other compounds (such as ethanolamine and inositol) possibly provided by the autolytic behavior of R. bili. IMPORTANCE Unique insights into metabolic interaction between two isolates; Ruminococcus gauvreauii IPLA60001 and Ruminococcoides bili IPLA60002, from the human gallbladder, are presented here. The R. bili strain metabolized resistant starches while R. gauvreauii failed to do so but grew well on sugar alcohols. Transcriptomic analysis of cocultures of these strains, provides new data on the physiology and ecology of two bacteria from human bile, with a particular focus on cross-feeding mechanisms. Both biliary strains displayed marked resistance to bile and possess many efflux transporters, potentially involved in bile export. However, they differ markedly in their amino acid catabolism and vitamin synthesis capabilities, a feature that is therefore likely to contribute to the strong synergistic interactions between these strains. This is therefore the first study that provides evidence for syntrophic metabolic cooperation between bacterial strains isolated from human bile.
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Affiliation(s)
- Natalia Molinero
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Elena Conti
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Alan W. Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Abelardo Margolles
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Sylvia H. Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Susana Delgado
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
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31
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Zeng L, Si Z, Zhao X, Feng P, Huang J, Long X, Yi Y. Metabolome analysis of the response and tolerance mechanisms of Saccharomyces cerevisiae to formic acid stress. Int J Biochem Cell Biol 2022; 148:106236. [PMID: 35688405 DOI: 10.1016/j.biocel.2022.106236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 11/18/2022]
Abstract
Various inhibitors are produced during the hydrolysis of lignocellulosic biomass that can interfere with the growth of yeast cells and the production of bioethanol. Formic acid is a common weak acid inhibitor present in lignocellulosic hydrolysate that has toxic effects on yeast cells. However, the mechanism of the response of Saccharomyces cerevisiae to formic acid is not fully understood. In this study, liquid chromatography-mass spectrometry (LC-MS) was used to investigate the effects of formic acid treatment on cell metabolites of S. cerevisiae. Treatment with different concentrations of formic acid significantly inhibited the growth of yeast cells, reduced the yield of ethanol, prolonged the cell fermentation cycle, and increased the content of malondialdehyde. Principal component analysis and orthogonal partial least squares discriminant analysis showed that 55 metabolites were significantly altered in S. cerevisiae after formic acid treatment. The metabolic relevance of these compounds in the response of S. cerevisiae to formic acid stress was investigated. Formic acid can cause oxidative stress, inhibit protein synthesis, and damage DNA in S. cerevisiae, and these are possible reasons for the inhibition of S. cerevisiae cell growth. In addition, the levels of several aromatic amino acids identified in the cells of formic acid-treated yeast were increased; the biosynthesis of nucleotides was slowed, and energy consumption was reduced. These mechanisms may help to improve the tolerance of yeast cells to formic acid. The results described herein highlight our current understanding of the molecular mechanism of the response of S. cerevisiae to formic acid. The study will provide a theoretical basis for research on the tolerance mechanisms of S. cerevisiae.
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Affiliation(s)
- Lingjie Zeng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zaiyong Si
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Xuemei Zhao
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Pixue Feng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Jinxiang Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Xiufeng Long
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Yi Yi
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China.
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Peng MZ, Shao YX, Li XZ, Zhang KD, Cai YN, Lin YT, Jiang MY, Liu ZC, Su XY, Zhang W, Jiang XL, Liu L. Mitochondrial FAD shortage in SLC25A32 deficiency affects folate-mediated one-carbon metabolism. Cell Mol Life Sci 2022; 79:375. [PMID: 35727412 DOI: 10.1007/s00018-022-04404-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022]
Abstract
The SLC25A32 dysfunction is associated with neural tube defects (NTDs) and exercise intolerance, but very little is known about disease-specific mechanisms due to a paucity of animal models. Here, we generated homozygous (Slc25a32Y174C/Y174C and Slc25a32K235R/K235R) and compound heterozygous (Slc25a32Y174C/K235R) knock-in mice by mimicking the missense mutations identified from our patient. A homozygous knock-out (Slc25a32-/-) mouse was also generated. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice presented with mild motor impairment and recapitulated the biochemical disturbances of the patient. While Slc25a32-/- mice die in utero with NTDs. None of the Slc25a32 mutations hindered the mitochondrial uptake of folate. Instead, the mitochondrial uptake of flavin adenine dinucleotide (FAD) was specifically blocked by Slc25a32Y174C/K235R, Slc25a32K235R/K235R, and Slc25a32-/- mutations. A positive correlation between SLC25A32 dysfunction and flavoenzyme deficiency was observed. Besides the flavoenzymes involved in fatty acid β-oxidation and amino acid metabolism being impaired, Slc25a32-/- embryos also had a subunit of glycine cleavage system-dihydrolipoamide dehydrogenase damaged, resulting in glycine accumulation and glycine derived-formate reduction, which further disturbed folate-mediated one-carbon metabolism, leading to 5-methyltetrahydrofolate shortage and other folate intermediates accumulation. Maternal formate supplementation increased the 5-methyltetrahydrofolate levels and ameliorated the NTDs in Slc25a32-/- embryos. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice had no glycine accumulation, but had another formate donor-dimethylglycine accumulated and formate deficiency. Meanwhile, they suffered from the absence of all folate intermediates in mitochondria. Formate supplementation increased the folate amounts, but this effect was not restricted to the Slc25a32 mutant mice only. In summary, we established novel animal models, which enabled us to understand the function of SLC25A32 better and to elucidate the role of SLC25A32 dysfunction in human disease development and progression.
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Affiliation(s)
- Min-Zhi Peng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yong-Xian Shao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Xiu-Zhen Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Kang-Di Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yan-Na Cai
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yun-Ting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Min-Yan Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Zong-Cai Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Xue-Ying Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Wen Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
| | - Xiao-Ling Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
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Min K, Moon M, Park GW, Lee JP, Kim SJ, Lee JS. Newly explored formate dehydrogenases from Clostridium species catalyze carbon dioxide to formate. Bioresour Technol 2022; 348:126832. [PMID: 35149183 DOI: 10.1016/j.biortech.2022.126832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
With concerns over global warming and climate change, many efforts have been devoted to mitigate atmospheric CO2 level. As a CO2 utilization strategy, formate dehydrogenase (FDH) from Clostridium species were explored to discover O2-tolerant and efficient FDHs that can catalyze CO2 to formate (i.e. CO2 reductase). With FDH from Clostridium ljungdahlii (ClFDH) that plays as a CO2 reductase previously reported as the reference, FDH from C.autoethanogenum (CaFDH), C. coskatii (CcFDH), and C. ragsdalei (CrFDH) were newly discovered via genome-mining. The FDHs were expressed in Escherichia coli and the recombinant FDHs successfully catalyzed CO2 reduction with a specific activity of 15 U g-1-CaFDH, 17 U g-1-CcFDH, and 8.7 U g-1-CrFDH. Interestingly, all FDHs newly discovered retain their catalytic activity under aerobic condition, although Clostridium species are strict anaerobe. The results discussed herein can contribute to biocatalytic CO2 utilization.
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Affiliation(s)
- Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
| | - Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Seon Jeong Kim
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
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Abstract
During mixed-acid fermentation, Escherichia coli initially translocates formate out of the cell, but re-imports it at lower pH. This is performed by FocA, the archetype of the formate-nitrite transporter (FNT) family of pentameric anion channels. Each protomer of FocA has a hydrophobic pore through which formate/formic acid is bidirectionally translocated. It is not understood how the direction of formate/formic acid passage through FocA is controlled by pH. A conserved histidine residue (H209) is located within the translocation pore, suggesting that protonation/deprotonation might be linked to the direction of formate translocation. Using a formate-responsive lacZ-based reporter system we monitored changes in formate levels in vivo when H209 in FocA was exchanged for either of the non-protonatable amino acids asparagine or glutamine, which occur naturally in some FNTs. These FocA variants (with N or Q) functioned as highly efficient formate efflux channels and the bacteria could neither accumulate formate nor produce hydrogen gas. Therefore, the data in this study suggest that this central histidine residue within the FocA pore is required for pH-dependent formate uptake into E. coli cells. We also address why H209 is evolutionarily conserved and provide a physiological rationale for the natural occurrence of N/Q variants of FNT channels.
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Affiliation(s)
- Michelle Kammel
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Oliver Trebbin
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
- Present address: IMD Laboratory Oderland GmbH, Am Kleistpark 1, Frankfurt (Oder), Germany
| | - Constanze Pinske
- 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
- *Correspondence: R. Gary Sawers,
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35
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Newman AC, Falcone M, Huerta Uribe A, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK. Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells. Mol Cell 2021; 81:2290-2302.e7. [PMID: 33831358 PMCID: PMC8189438 DOI: 10.1016/j.molcel.2021.03.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/31/2022]
Abstract
Cancer cells adapt their metabolism to support elevated energetic and anabolic demands of proliferation. Folate-dependent one-carbon metabolism is a critical metabolic process underpinning cellular proliferation supplying carbons for the synthesis of nucleotides incorporated into DNA and RNA. Recent research has focused on the nutrients that supply one-carbons to the folate cycle, particularly serine. Tryptophan is a theoretical source of one-carbon units through metabolism by IDO1, an enzyme intensively investigated in the context of tumor immune evasion. Using in vitro and in vivo pancreatic cancer models, we show that IDO1 expression is highly context dependent, influenced by attachment-independent growth and the canonical activator IFNγ. In IDO1-expressing cancer cells, tryptophan is a bona fide one-carbon donor for purine nucleotide synthesis in vitro and in vivo. Furthermore, we show that cancer cells release tryptophan-derived formate, which can be used by pancreatic stellate cells to support purine nucleotide synthesis.
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MESH Headings
- Allografts
- Animals
- Antineoplastic Agents/pharmacology
- Carbon/immunology
- Carbon/metabolism
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/mortality
- Cell Line, Tumor
- Formates/immunology
- Formates/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Indoleamine-Pyrrole 2,3,-Dioxygenase/immunology
- Interferon-gamma/genetics
- Interferon-gamma/immunology
- Metabolic Networks and Pathways/drug effects
- Metabolic Networks and Pathways/genetics
- Mice
- Mice, Inbred C57BL
- Mice, Nude
- Oximes/pharmacology
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/mortality
- Pancreatic Stellate Cells/drug effects
- Pancreatic Stellate Cells/immunology
- Pancreatic Stellate Cells/metabolism
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/immunology
- Serine/immunology
- Serine/metabolism
- Serine/pharmacology
- Signal Transduction
- Sulfonamides/pharmacology
- Tryptophan/immunology
- Tryptophan/metabolism
- Tryptophan/pharmacology
- Tumor Escape/drug effects
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/immunology
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Affiliation(s)
- Alice Clare Newman
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Mattia Falcone
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Alejandro Huerta Uribe
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Tong Zhang
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Dimitris Athineos
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
| | - Matthias Pietzke
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
| | - Alexei Vazquez
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK; Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
| | - Karen Blyth
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK; Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
| | - Oliver David Kenneth Maddocks
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK.
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36
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Huang F, Sardari RRR, Jasilionis A, Böök O, Öste R, Rascón A, Heyman‐Lindén L, Holst O, Karlsson EN. Cultivation of the gut bacterium Prevotella copri DSM 18205 T using glucose and xylose as carbon sources. Microbiologyopen 2021; 10:e1213. [PMID: 34180602 PMCID: PMC8236902 DOI: 10.1002/mbo3.1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Prevotella copri DSM18205T is a human gut bacterium, suggested as a next-generation probiotic. To utilize it as such, it is, however, necessary to grow the species in a reproducible manner. Prevotella copri has previously been reported to be highly sensitive to oxygen, and hence difficult to isolate and cultivate. This study presents successful batch cultivation strategies for viable strain inoculations and growth in both serum bottles and a stirred tank bioreactor (STR), without the use of an anaerobic chamber, as long as the cells were kept in the exponential growth phase. A low headspace volume in the STR was important to reach high cell density. P. copri utilized xylose cultivated in Peptone Yeast Xylose medium (PYX medium), resulting in a comparable growth rate and metabolite production as in Peptone Yeast Glucose medium (PYG medium) in batch cultivations at pH 7.2.Up to 5 g/L of the carbon source was consumed, leading to the production of succinic acid, acetic acid, and formic acid, and cell densities (OD620 nm ) in the range 6-7.5. The highest yield of produced succinic acid was 0.63 ± 0.05 g/g glucose in PYG medium cultivations and 0.88 ± 0.06 g/g xylose in PYX medium cultivations.
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Affiliation(s)
- Fang Huang
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
- Aventure ABLundSweden
| | - Roya R. R. Sardari
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
| | - Andrius Jasilionis
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
| | | | | | - Ana Rascón
- Department of Food Technology, Engineering and NutritionLund UniversityLundSweden
| | | | - Olle Holst
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
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37
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Rork AM, Xu S, Attygalle A, Renner T. Primary Metabolism co-Opted for Defensive Chemical Production in the Carabid Beetle, Harpalus pensylvanicus. J Chem Ecol 2021; 47:334-349. [PMID: 33689113 DOI: 10.1007/s10886-021-01253-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 11/25/2022]
Abstract
Of the approximately one million described insect species, ground beetles (Coleoptera: Carabidae) have long captivated the attention of evolutionary biologists due to the diversity of defensive compounds they synthesize. Produced using defensive glands in the abdomen, ground beetle chemicals represent over 250 compounds including predator-deterring formic acid, which has evolved as a defensive strategy at least three times across Insecta. Despite being a widespread method of defense, formic acid biosynthesis is poorly understood in insects. Previous studies have suggested that the folate cycle of one-carbon (C1) metabolism, a pathway involved in nucleotide biosynthesis, may play a key role in defensive-grade formic acid production in ants. Here, we report on the defensive gland transcriptome of the formic acid-producing ground beetle Harpalus pensylvanicus. The full suite of genes involved in the folate cycle of C1 metabolism are significantly differentially expressed in the defensive glands of H. pensylvanicus when compared to gene expression profiles in the rest of the body. We also find support for two additional pathways potentially involved in the biosynthesis of defensive-grade formic acid, the kynurenine pathway and the methionine salvage cycle. Additionally, we have found an array of differentially expressed genes in the secretory lobes involved in the biosynthesis and transport of cofactors necessary for formic acid biosynthesis, as well as genes presumably involved in the detoxification of secondary metabolites including formic acid. We also provide insight into the evolution of the predominant gene family involved in the folate cycle (MTHFD) and suggest that high expression of folate cycle genes rather than gene duplication and/or neofunctionalization may be more important for defensive-grade formic acid biosynthesis in H. pensylvanicus. This provides the first evidence in Coleoptera and one of a few examples in Insecta of a primary metabolic process being co-opted for defensive chemical biosynthesis. Our results shed light on potential mechanisms of formic acid biosynthesis in the defensive glands of a ground beetle and provide a foundation for further studies into the evolution of formic acid-based chemical defense strategies in insects.
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Affiliation(s)
- Adam M Rork
- Department of Entomology, The Pennsylvania State University, 501 ASI Building, University Park, PA, 16802, USA.
| | - Sihang Xu
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Athula Attygalle
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, 501 ASI Building, University Park, PA, 16802, USA
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38
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Agne M, Appel L, Seelmann C, Boll M. Enoyl-Coenzyme A Respiration via Formate Cycling in Syntrophic Bacteria. mBio 2021; 13:e0374021. [PMID: 35100874 PMCID: PMC8805022 DOI: 10.1128/mbio.03740-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 11/23/2022] Open
Abstract
Syntrophic bacteria play a key role in the anaerobic conversion of biological matter to methane. They convert short-chain fatty acids or alcohols to H2, formate, and acetate that serve as substrates for methanogenic archaea. Many syntrophic bacteria can also grow with unsaturated fatty acids such as crotonate without a syntrophic partner, and the reducing equivalents derived from the oxidation of one crotonate to two acetate are regenerated by the reduction of a second crotonate. However, it has remained unresolved how the oxidative and reductive catabolic branches are interconnected and how energy may be conserved in the reductive branch. Here, we provide evidence that during axenic growth of the syntrophic model organism Syntrophus aciditrophicus with crotonate, the NAD+-dependent oxidation of 3-hydroxybutyryl-CoA to acetoacetyl-CoA is coupled to the reduction of crotonyl-CoA via formate cycling. In this process, the intracellular formate generated by a NAD+-regenerating CO2 reductase is taken up by a periplasmic, membrane-bound formate dehydrogenase that in concert with a membrane-bound electron-transferring flavoprotein (ETF):methylmenaquinone oxidoreductase, ETF, and an acyl-CoA dehydrogenase reduces intracellular enoyl-CoA to acyl-CoA. This novel type of energy metabolism, referred to as enoyl-CoA respiration, generates a proton motive force via a methylmenaquinone-dependent redox-loop. As a result, the beneficial syntrophic cooperation of fermenting bacteria and methanogenic archaea during growth with saturated fatty acids appears to turn into a competition for formate and/or H2 during growth with unsaturated fatty acids. IMPORTANCE The syntrophic interaction of fermenting bacteria and methanogenic archaea is important for the global carbon cycle. As an example, it accomplishes the conversion of biomass-derived saturated fatty acid fermentation intermediates into methane. In contrast, unsaturated fatty acid intermediates such as crotonate may serve as growth substrate for the fermenting partner alone. Thereby, the reducing equivalents generated during the oxidation of one crotonate to two acetate are regenerated by reduction of a second crotonate to butyrate. Here, we show that the oxidative and reductive branches of this pathway are connected via formate cycling involving an energy-conserving redox-loop. We refer to this previously unknown type of energy metabolism as to enoyl-CoA respiration with acyl-CoA dehydrogenases serving as cytoplasmic terminal reductases.
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Affiliation(s)
- Michael Agne
- Faculty of Biology–Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Lena Appel
- Faculty of Biology–Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Carola Seelmann
- Faculty of Biology–Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Matthias Boll
- Faculty of Biology–Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
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Sou NL, Huang YH, Chen DY, Chen YM, Tang FY, Ko HA, Fan YH, Lin YY, Wang YC, Chih HM, Shane B, Huang WN, Chiang EPI. Folinate Supplementation Ameliorates Methotrexate Induced Mitochondrial Formate Depletion In Vitro and In Vivo. Int J Mol Sci 2021; 22:1350. [PMID: 33572934 PMCID: PMC7866403 DOI: 10.3390/ijms22031350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Antifolate methotrexate (MTX) is the most common disease-modifying antirheumatic drug (DMARD) for treating human rheumatoid arthritis (RA). The mitochondrial-produced formate is essential for folate-mediated one carbon (1C) metabolism. The impacts of MTX on formate homeostasis in unknown, and rigorously controlled kinetic studies can greatly help in this regard. (2) Methods: Combining animal model (8-week old female C57BL/6JNarl mice, n = 18), cell models, stable isotopic tracer studies with gas chromatography/mass spectrometry (GC/MS) platforms, we systematically investigated how MTX interferes with the partitioning of mitochondrial and cytosolic formate metabolism. (3) Results: MTX significantly reduced de novo deoxythymidylate (dTMP) and methionine biosyntheses from mitochondrial-derived formate in cells, mouse liver, and bone marrow, supporting our postulation that MTX depletes mitochondrial 1C supply. Furthermore, MTX inhibited formate generation from mitochondria glycine cleavage system (GCS) both in vitro and in vivo. Folinate selectively rescued 1C metabolic pathways in a tissue-, cellular compartment-, and pathway-specific manner: folinate effectively reversed the inhibition of mitochondrial formate-dependent 1C metabolism in mouse bone marrow (dTMP, methionine, and GCS) and cells (dTMP and GCS) but not methionine synthesis in liver/liver-derived cells. Folinate failed to fully recover hepatic mitochondrial-formate utilization for methionine synthesis, suggesting that the efficacy of clinical folinate rescue in MTX therapy on hepatic methionine metabolism is poor. (4) Conclusion: Conducting studies in mouse and cell models, we demonstrate novel findings that MTX specifically depletes mitochondrial 1C supply that can be ameliorated by folinate supplementation except for hepatic transmethylation. These results imply that clinical use of low-dose MTX may particularly impede 1C metabolism via depletion of mitochondrial formate. The MTX induced systematic and tissue-specific formate depletion needs to be addressed more carefully, and the efficacy of folinate with respect to protecting against such depletion deserves to be evaluated in medical practice.
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Grants
- 108-2321-B-005-004 Ministry of Science and Technology, Taiwan
- 107-2320-B005-003-MY3 Ministry of Science and Technology, Taiwan
- 107-2621-M005-008-MY3 Ministry of Science and Technology, Taiwan
- 107-2321-B-005-009 Ministry of Science and Technology, Taiwan
- 108-2321-B-005 -004 Ministry of Science and Technology, Taiwan
- 107-2320-B039-008-MY3 Ministry of Science and Technology, Taiwan
- 104-2320-B-039-041-MY3 Ministry of Science and Technology, Taiwan
- CMU103-ASIA-20 China Medical University, Taiwan
- CMU103-S-46 China Medical University, Taiwan
- CMU104-S-32 China Medical University, Taiwan
- 997608 Taipei Veterans General Hospital
- 1077602 Taipei Veterans General Hospital
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Affiliation(s)
- Nga-Lai Sou
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - Yu-Hsuan Huang
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - Der-Yuan Chen
- Allergy Immunology Rheumatology, Taichung Veterans General Hospital (TVGH), Taichung 402, Taiwan; (D.-Y.C.); (Y.-M.C.); (W.-N.H.)
- Allergy Immunology Rheumatology, China Medical University Hospital, Taichung 402, Taiwan
| | - Yi-Ming Chen
- Allergy Immunology Rheumatology, Taichung Veterans General Hospital (TVGH), Taichung 402, Taiwan; (D.-Y.C.); (Y.-M.C.); (W.-N.H.)
| | - Feng-Yao Tang
- Department of Nutrition, China Medical University, Taichung 402, Taiwan;
| | - Hsin-An Ko
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
| | - Yi-Hsuan Fan
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
| | - Yi-Ying Lin
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
| | - Yi-Cheng Wang
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
| | - Hui-Ming Chih
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
- Department of Nursing and Pediatrics, Taichung Veterans General Hospital (TVGH), Taichung 402, Taiwan
| | - Barry Shane
- Nutritional Sciences and Toxicology, UC Berkeley, Berkeley, CA 94701, USA;
| | - Wen-Nan Huang
- Allergy Immunology Rheumatology, Taichung Veterans General Hospital (TVGH), Taichung 402, Taiwan; (D.-Y.C.); (Y.-M.C.); (W.-N.H.)
| | - En-Pei Isabel Chiang
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (N.-L.S.); (Y.-H.H.); (H.-A.K.); (Y.-H.F.); (Y.-Y.L.); (Y.-C.W.); (H.-M.C.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
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Tan YL, Sou NL, Tang FY, Ko HA, Yeh WT, Peng JH, Chiang EPI. Tracing Metabolic Fate of Mitochondrial Glycine Cleavage System Derived Formate In Vitro and In Vivo. Int J Mol Sci 2020; 21:ijms21228808. [PMID: 33233834 PMCID: PMC7699879 DOI: 10.3390/ijms21228808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Folate-mediated one-carbon (1C) metabolism is a major target of many therapies in human diseases. Studies have focused on the metabolism of serine 3-carbon as it serves as a major source for 1C units. The serine 3-carbon enters the mitochondria transferred by folate cofactors and eventually converted to formate and serves as a major building block for cytosolic 1C metabolism. Abnormal glycine metabolism has been reported in many human pathological conditions. The mitochondrial glycine cleavage system (GCS) catalyzes glycine degradation to CO2 and ammonium, while tetrahydrofolate (THF) is converted into 5,10-methylene-THF. GCS accounts for a substantial proportion of whole-body glycine flux in humans, yet the particular metabolic route of glycine 2-carbon recycled from GCS during mitochondria glycine decarboxylation in hepatic or bone marrow 1C metabolism is not fully investigated, due to the limited accessibility of human tissues. Labeled glycine at 2-carbon was given to humans and primary cells in previous studies for investigating its incorporations into purines, its interconversion with serine, or the CO2 production in the mitochondria. Less is known on the metabolic fate of the glycine 2-carbon recycled from the GCS; hence, a model system tracing its metabolic fate would help in this regard. We took the direct approach of isotopic labeling to further explore the in vitro and in vivo metabolic fate of the 2-carbon from [2-13C]glycine and [2-13C]serine. As the 2-carbon of glycine and serine is decarboxylated and catabolized via the GCS, the original 13C-labeled 2-carbon is transferred to THF and yield methyleneTHF in the mitochondria. In human hepatoma cell-lines, 2-carbon from glycine was found to be incorporated into deoxythymidine (dTMP, dT + 1), M + 3 species of purines (deoxyadenine, dA and deoxyguanine, dG), and methionine (Met + 1). In healthy mice, incorporation of GCS-derived formate from glycine 2-carbon was found in serine (Ser + 2 via cytosolic serine hydroxy methyl transferase), methionine, dTMP, and methylcytosine (mC + 1) in bone marrow DNA. In these experiments, labeled glycine 2-carbon directly incorporates into Ser + 1, A + 2, and G + 2 (at C2 and C8 of purine) in the cytosol. It is noteworthy that since the serine 3-carbon is unlabeled in these experiments, the isotopic enrichments in dT + 1, Ser + 2, dA + 3, dG + 3, and Met + 1 solely come from the 2-carbon of glycine/serine recycled from GCS, re-enters the cytosolic 1C metabolism as formate, and then being used for cytosolic syntheses of serine, dTMP, purine (M + 3) and methionine. Taken together, we established model systems and successfully traced the metabolic fate of mitochondrial GCS-derived formate from glycine 2-carbon in vitro and in vivo. Nutritional supply significantly alters formate generation from GCS. More GCS-derived formate was used in hepatic serine and methionine syntheses, whereas more GCS-derived formate was used in dTMP synthesis in the bone marrow, indicating that the utilization and partitioning of GCS-derived 1C unit are tissue-specific. These approaches enable better understanding concerning the utilization of 1C moiety generated from mitochondrial GCS that can help to further elucidate the role of GCS in human disease development and progression in future applications. More studies on GCS using these approaches are underway.
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Affiliation(s)
- Yee-Ling Tan
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Nga-Lai Sou
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - Feng-Yao Tang
- Department of Nutrition, China Medical University, Taichung 402, Taiwan;
| | - Hsin-An Ko
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Wei-Ting Yeh
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Jian-Hau Peng
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
- Microbial Genomics Ph.D. Graduate Program, National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - En-Pei Isabel Chiang
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Department of Nutrition, China Medical University, Taichung 402, Taiwan;
- Microbial Genomics Ph.D. Graduate Program, National Chung Hsing University (NCHU), Taichung 402, Taiwan
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Correspondence: ; Tel.: +886-4-22853049; Fax: +886-4-22876211
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Hegner R, Neubert K, Kroner C, Holtmann D, Harnisch F. Coupled Electrochemical and Microbial Catalysis for the Production of Polymer Bricks. ChemSusChem 2020; 13:5295-5300. [PMID: 32658366 PMCID: PMC7590143 DOI: 10.1002/cssc.202001272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Power-to-X technologies have the potential to pave the way towards a future resource-secure bioeconomy as they enable the exploitation of renewable resources and CO2 . Herein, the coupled electrocatalytic and microbial catalysis of the C5 -polymer precursors mesaconate and 2S-methylsuccinate from CO2 and electric energy by in situ coupling electrochemical and microbial catalysis at 1 L-scale was developed. In the first phase, 6.1±2.5 mm formate was produced by electrochemical CO2 reduction. In the second phase, formate served as the substrate for microbial catalysis by an engineered strain of Methylobacterium extorquens AM-1 producing 7±2 μm and 10±5 μm of mesaconate and 2S-methylsuccinate, respectively. The proof of concept showed an overall conversion efficiency of 0.2 % being 0.4 % of the theoretical maximum.
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Affiliation(s)
- Richard Hegner
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
| | - Katharina Neubert
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
| | - Cora Kroner
- DECHEMA Research InstituteIndustrial BiotechnologyTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Dirk Holtmann
- DECHEMA Research InstituteIndustrial BiotechnologyTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
- Technische Hochschule MittelhessenInstitute of Bioprocess Engineering and Pharmaceutical TechnologyWiesenstraße 1435390GießenGermany
| | - Falk Harnisch
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
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Tian Y, Zhou Y, Zong Y, Li J, Yang N, Zhang M, Guo Z, Song H. Construction of Functionally Compartmental Inorganic Photocatalyst-Enzyme System via Imitating Chloroplast for Efficient Photoreduction of CO 2 to Formic Acid. ACS Appl Mater Interfaces 2020; 12:34795-34805. [PMID: 32805792 DOI: 10.1021/acsami.0c06684] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Inorganic photocatalyst-enzyme systems are a prominent platform for the photoreduction of CO2 to value-added chemicals and fuels. However, poor electron transfer kinetics and enzyme deactivation by reactive oxygen species in the photoexcitation process severely limit catalytic efficiency. In chloroplast, enzymatic CO2 reduction and photoexcitation are compartmentalized by the thylakoid membrane, which protects enzymes from photodamage, while the tightly integrated photosystem facilitates electron transfer, promoting photocatalysis. By mimicking this strategy, we constructed a novel functionally compartmental inorganic photocatalyst-enzyme system for CO2 reduction to formate. To accomplish efficient electron transfer, we first synthesized an integrated artificial photosystem by conjugation of the cocatalyst (a Rh complex) onto thiophene-modified C3N4 (TPE-C3N4), demonstrating an NADH regeneration rate of 9.33 μM·min-1, 2.33 times higher than that of a homogeneous counterpart. The enhanced NADH regeneration activity was caused by the tightly conjugated structure of the artificial photosystem, enabling rapid electron transfer from TPE-C3N4 to the Rh complex. To protect formate dehydrogenase (FDH) from photoinduced deactivation, FDH was encapsulated into MAF-7, a metal-organic framework (MOF) material, to compartmentalize FDH from the toxic photoexcitation process, similar to the function of the thylakoid membrane. Moreover, the triazole linkers of MAF-7 possess both hydrophilicity and pH-buffering capacity providing a stable microenvironment for FDH, which could enhance enzyme stability in photosynthesis. The synergy between the enhanced electron transfer of TPE-C3N4 for NADH cofactor regeneration and MOF-protection of the redox enzyme enables the construction of a functionally compartmental inorganic photocatalyst-enzyme association system, promoting CO2 photoconversion to formic acid with a yield of 16.75 mM after 9 h of illumination, 3.24 times greater than that of the homogeneous reaction counterpart.
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Affiliation(s)
- Yao Tian
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yinuo Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yongchao Zong
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jiansheng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Nan Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhiqi Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 2020; 8:111. [PMID: 32709258 PMCID: PMC7382037 DOI: 10.1186/s40168-020-00885-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored. RESULTS To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate. CONCLUSION Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
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Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, HK Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, UK
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
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Adhikari P, Yadav S, Cosby DE, Cox NA, Jendza JA, Kim WK. Research Note: Effect of organic acid mixture on growth performance and Salmonella Typhimurium colonization in broiler chickens. Poult Sci 2020; 99:2645-2649. [PMID: 32359600 PMCID: PMC7597380 DOI: 10.1016/j.psj.2019.12.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 12/17/2022] Open
Abstract
Feed additives can be alternatives to antibiotics for routinely encountered pathogens in the poultry production. The objective of this study was to understand effects of organic acid mixture on growth parameters and Salmonella Typhimurium (ST) colonization in broilers. Organic acid mixture is a feed-grade buffered formic acid and sodium formate mixture (Amasil NA). A total of 800 1-day-old Cobb500 males were fed one of the five dietary treatments: a negative control diet without ST challenge (NC), positive control diet with ST challenge (PC), 0.3% organic acid mixture with ST, 0.6% organic acid mixture with ST, and 0.9% organic acid mixture with ST. Treatments were assigned to 20 pens with 40 chicks/pen and 4 replicates of each treatment. Chickens were challenged with 107 CFU/mL of nalidixic acid-resistant ST (STNAR) 4-D posthatch. In the grower phase, feed conversion rate was significantly reduced in the 9% organic acid mixture compared with the PC. The body weight and body weight gain (BWG) were not affected either in the starter or grower phases. However, in the finisher phase, the nonchallenged NC had higher BWG than the PC (P < 0.05), whereas there were no differences in BWG among the NC and organic acid mixture fed groups. In addition, there was a significant effect of organic acid mixture on the colonization of cecal STNAR. At 9 dpi, cecal STNAR was 3.28 log10 in the PC that was reduced to 2.65 log10 at 0.3%, 1.40 log10 at 0.6%, and 0.84 log10 in 0.9% organic acid mixture. At 24 dpi, cecal STNAR recovery was 0.81, 0.99, 0.53, and 0.33 log10 in the PC and 0.3, 0.6, and 0.9% organic acid mixture, respectively. Similarly, at 38 dpi, cecal STNAR was 0.26, 0.11, 0.33, and 0 log10 in the PC, 0.3, 0.6, and 0.9%, respectively. These results show that organic acid mixture can be one dietary strategy to control ST infection and maintain efficient growth performance.
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Affiliation(s)
- Pratima Adhikari
- Department of Poultry Science, Mississippi State University, Starkville, MS, USA
| | - Sudhir Yadav
- Department of Poultry Science, University of Georgia, Athens, GA, USA
| | - Douglas E Cosby
- USDA, ARS, The U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Nelson A Cox
- USDA, ARS, The U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | | | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA, USA.
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Abstract
BACKGROUND Formate is a one-carbon molecule at the crossroad between cellular and whole body metabolism, between host and microbiome metabolism, and between nutrition and toxicology. This centrality confers formate with a key role in human physiology and disease that is currently unappreciated. SCOPE OF REVIEW Here we review the scientific literature on formate metabolism, highlighting cellular pathways, whole body metabolism, and interactions with the diet and the gut microbiome. We will discuss the relevance of formate metabolism in the context of embryonic development, cancer, obesity, immunometabolism, and neurodegeneration. MAJOR CONCLUSIONS We will conclude with an outlook of some open questions bringing formate metabolism into the spotlight.
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Affiliation(s)
| | - Johannes Meiser
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Alexei Vazquez
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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Singh V, Mishra VN, Prajapati GD, Ampapathi RS, Thakur MK. Quantitative metabolic biomarker analysis of mild cognitive impairment in eastern U.P. and Bihar population. J Pharm Biomed Anal 2020; 180:113033. [PMID: 31841796 DOI: 10.1016/j.jpba.2019.113033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Mild cognitive impairment (MCI) is a transition phase between healthy individuals and Alzheimer's disease (AD). Therefore, diagnosis of MCI at early stage will help to delay or prevent its progression to disease. In the present study, we aim to identify the metabolic biomarkers, which can help in the diagnosis of MCI. We have screened 2000 elderly individuals from north India, out of which 200 were identified as MCI. We continued our study on 10 MCI individuals who regularly participated in the follow-up. The age and gender matched 10 healthy individuals were taken as control. These control and MCI individuals were subjected to neuropsychological examination such as Hindi mental state examination (HMSE) and Montreal cognitive assessment (MOCA) followed by 1H Nuclear Magnetic Resonance (NMR) analysis. Remarkable changes were noted between control and MCI individuals at metabolic level. In silico study showed the involvement of eight metabolites in MCI. We found higher level of lactate, N-acetyl aspartate, histidine and lower level of formate, choline, alanine, creatinine and glucose in blood plasma of MCI individuals compared to control. Further, In silico study showed that choline might be directly associated with MCI or AD. Such In silico study with quantitative metabolite analysis of plasma could be used as diagnostic biomarkers for the identification of MCI.
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Affiliation(s)
- Vineeta Singh
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Vijaya Nath Mishra
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Guru Dayal Prajapati
- NMR Division, Sophisticated Analytical Instrument Facility, CSIR- Central Drug Research Institute, Lucknow, 226301, UP, India.
| | - Ravi Shankar Ampapathi
- NMR Division, Sophisticated Analytical Instrument Facility, CSIR- Central Drug Research Institute, Lucknow, 226301, UP, India.
| | - M K Thakur
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India.
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Abstract
PURPOSE OF REVIEW The aim of this report is to examine critical relationships between amino acid and formate metabolism with particular reference to the production of formate, and to review novel functions of formate. RECENT FINDINGS In addition to well established mechanisms in one-carbon metabolism, formate may play an important role in early pregnancy by preventing the onset of neural tube defects in sensitive strains of mice, including mice with deficiencies in MTHFD1L, the glycine cleavage system and the mitochondrial folate transporter. Markedly elevated, circulating levels of formate are found in late pregnancy, including in cord blood, as well as elevated levels of amino acid precursors. These are consistent with specific roles for formate in late pregnancy. Serine metabolism may reduce NADP to NADPH and permit the use of NADPH in reductive reactions. Novel, noncanonical functions of formate include high rates of formate production from serine in cells and in cancers. SUMMARY Novel, noncanonical functions of formate continue to be discovered. Integrating their functions with well established elements of one-carbon metabolism remains an important future objective.
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Affiliation(s)
- John T Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Vyrides I, Rivett DW, Bruce KD, Lilley AK. Selection and assembly of indigenous bacteria and methanogens from spent metalworking fluids and their potential as a starting culture in a fluidized bed reactor. Microb Biotechnol 2019; 12:1302-1312. [PMID: 31328378 PMCID: PMC6801153 DOI: 10.1111/1751-7915.13448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/28/2022] Open
Abstract
Waste metalworking fluids (MWFs) are highly biocidal resulting in real difficulties in the, otherwise favoured, bioremediation of these high chemical oxygen deman (COD) wastes anaerobically in bioreactors. We have shown, as a proof of concept, that it is possible to establish an anaerobic starter culture using strains isolated from spent MWFs which are capable of reducing COD or, most significantly, methanogenesis in this biocidal waste stream. Bacterial strains (n = 99) and archaeal methanogens (n = 28) were isolated from spent MWFs. The most common bacterial strains were Clostridium species (n = 45). All methanogens were identified as Methanosarcina mazei. Using a random partitions design (RPD) mesocosm experiment, we found that bacterial diversity and species-species interactions had significant effects on COD reduction but that bacterial composition did not. The RPD study showed similar effects on methanogenesis, except that composition was also significant. We identified bacterial species with positive and negative effects on methane production. A consortium of 16 bacterial species and three methanogens was used to initiate a fluidized bed bioreactor (FBR), in batch mode. COD reduction and methane production were variable, and the reactor was oscillated between continuous and batch feeds. In both microcosm and FBR experiments, periodic inconsistencies in bacterial reduction in fermentative products to formic and acetic acids were identified as a key issue.
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Affiliation(s)
- Ioannis Vyrides
- Molecular Microbiology Research LaboratoryPharmaceutical Science Research DivisionKing's College London150 Stamford Street, Franklin‐Wilkins BuildingLondonSE1 9NHUK
- Present address:
Department of Environmental Science and TechnologyCyprus University of Technology30 Archbishop Kyprianos3036LemesosCyprus
| | - Damian W. Rivett
- Division of Biology and Conservation EcologySchool of Science and the EnvironmentManchester Metropolitan UniversityManchesterUK
| | - Kenneth D. Bruce
- Molecular Microbiology Research LaboratoryPharmaceutical Science Research DivisionKing's College London150 Stamford Street, Franklin‐Wilkins BuildingLondonSE1 9NHUK
| | - Andrew K. Lilley
- Molecular Microbiology Research LaboratoryPharmaceutical Science Research DivisionKing's College London150 Stamford Street, Franklin‐Wilkins BuildingLondonSE1 9NHUK
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Dussourd DE, Van Valkenburg M, Rajan K, Wagner DL. A notodontid novelty: Theroa zethus caterpillars use behavior and anti-predator weaponry to disarm host plants. PLoS One 2019; 14:e0218994. [PMID: 31291279 PMCID: PMC6619741 DOI: 10.1371/journal.pone.0218994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/13/2019] [Indexed: 11/19/2022] Open
Abstract
Unlike most notodontids, Theroa zethus larvae feed on plants that emit copious latex when damaged. To determine how the larvae overcome this defense, we filmed final instars on poinsettia, Euphorbia pulcherrima, then simulated their behaviors and tested how the behaviors individually and combined affect latex exudation. Larvae initially scraped the stem, petiole, or midrib with their mandibles, then secreted acid from their ventral eversible gland (VEG) onto the abraded surface. Scraping facilitated acid penetration by disrupting the waxy cuticle. As the acid softened tissues, the larvae used their mandibles to compress the plant repeatedly, thereby rupturing the latex canals. Scraping, acid application, and compression created withered furrows that greatly diminished latex exudation distal to the furrows where the larvae invariably fed. The VEG in notodontids ordinarily serves to deter predators; when attacked, larvae spray acid aimed directly at the assailant. Using HPLC, we documented that the VEG secretion of T. zethus contains 30% formic acid (6.53M) with small amounts of butyric acid (0.05M). When applied to poinsettia petioles, the acids caused a similar reduction in latex outflow as VEG secretion milked from larvae. VEG acid could disrupt latex canals in part by stimulating the normal acid-growth mechanism employed by plants to loosen walls for cell elongation. Histological examination of cross sections in poinsettia midribs confirmed that cell walls within furrows were often highly distorted as expected if VEG acids weaken walls. Theroa zethus is the only notodontid caterpillar known to use mandibular scraping and VEG acid to disable plant defenses. However, we document that mandibular constriction of petioles occurs also in other notodontids including species that feed on hardwood trees. This capability may represent a pre-adaptation that facilitated the host shift in the Theroa lineage onto latex-bearing plants by enabling larvae to deactivate laticifers with minimal latex contact.
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Affiliation(s)
- David E. Dussourd
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
- * E-mail:
| | - Madalyn Van Valkenburg
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Kalavathy Rajan
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - David L. Wagner
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
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Lindenstrauß U, Pinske C. Dissection of the Hydrogen Metabolism of the Enterobacterium Trabulsiella guamensis: Identification of a Formate-Dependent and Essential Formate Hydrogenlyase Complex Exhibiting Phylogenetic Similarity to Complex I. J Bacteriol 2019; 201:e00160-19. [PMID: 30962355 PMCID: PMC6531613 DOI: 10.1128/jb.00160-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/29/2019] [Indexed: 01/06/2023] Open
Abstract
Trabulsiella guamensis is a nonpathogenic enterobacterium that was isolated from a vacuum cleaner on the island of Guam. It has one H2-oxidizing Hyd-2-type hydrogenase (Hyd) and encodes an H2-evolving Hyd that is most similar to the uncharacterized Escherichia coli formate hydrogenlyase (FHL-2 Ec ) complex. The T. guamensis FHL-2 (FHL-2 Tg ) complex is predicted to have 5 membrane-integral and between 4 and 5 cytoplasmic subunits. We showed that the FHL-2 Tg complex catalyzes the disproportionation of formate to CO2 and H2 FHL-2 Tg has activity similar to that of the E. coli FHL-1 Ec complex in H2 evolution from formate, but the complex appears to be more labile upon cell lysis. Cloning of the entire 13-kbp FHL-2 Tg operon in the heterologous E. coli host has now enabled us to unambiguously prove FHL-2 Tg activity, and it allowed us to characterize the FHL-2 Tg complex biochemically. Although the formate dehydrogenase (FdhH) gene fdhF is not contained in the operon, the FdhH is part of the complex, and FHL-2 Tg activity was dependent on the presence of E. coli FdhH. Also, in contrast to E. coli, T. guamensis can ferment the alternative carbon source cellobiose, and we further investigated the participation of both the H2-oxidizing Hyd-2 Tg and the H2-forming FHL-2 Tg under these conditions.IMPORTANCE Biological H2 production presents an attractive alternative for fossil fuels. However, in order to compete with conventional H2 production methods, the process requires our understanding on a molecular level. FHL complexes are efficient H2 producers, and the prototype FHL-1 Ec complex in E. coli is well studied. This paper presents the first biochemical characterization of an FHL-2-type complex. The data presented here will enable us to solve the long-standing mystery of the FHL-2 Ec complex, allow a first biochemical characterization of T. guamensis's fermentative metabolism, and establish this enterobacterium as a model organism for FHL-dependent energy conservation.
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Affiliation(s)
- Ute Lindenstrauß
- Department of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Constanze Pinske
- Department of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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