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Molecular Metabolism Mar 2020Formate is a one-carbon molecule at the crossroad between cellular and whole body metabolism, between host and microbiome metabolism, and between nutrition and... (Review)
Review
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.
Topics: Diet; Female; Formates; Gastrointestinal Microbiome; Host-Pathogen Interactions; Humans; Obesity
PubMed: 31402327
DOI: 10.1016/j.molmet.2019.05.012 -
Current Issues in Molecular Biology 2019One-carbon (C1) feedstocks can provide a vital link between cheap and sustainable abiotic resources and microbial bioproduction. Soluble C1 substrates, methanol and... (Review)
Review
One-carbon (C1) feedstocks can provide a vital link between cheap and sustainable abiotic resources and microbial bioproduction. Soluble C1 substrates, methanol and formate, could prove more suitable than gaseous feedstocks as they avoid mass transfer barriers. However, microorganisms that naturally assimilate methanol and formate are limited by a narrow product spectrum and a restricted genetic toolbox. Engineering biotechnological organisms to assimilate these soluble C1 substrates has therefore become an attractive goal. Here, we discuss the use of a step-wise, modular engineering approach for the implementation of C1-pathways. In this strategy, pathways are divided into metabolic modules, the activities of which are selected for in dedicated gene-deletion strains whose growth directly depends on module activity. This provides an easy way to identify and resolve metabolic barriers hampering pathway performance. Optimization of gene expression levels and adaptive laboratory evolution can be used to establish the desired activity if direct selection fails. We exemplify this approach using several pathways, focusing especially on the ribulose monophosphate cycle for methanol assimilation and the reductive glycine pathway for formate assimilation. We argue that such modular engineering and selection strategies will prove essential for rewiring microbial metabolism towards new growth phenotypes and sustainable bioproduction.
Topics: Biotransformation; Directed Molecular Evolution; Formates; Glycine; Metabolic Engineering; Metabolic Networks and Pathways; Methanol; Organisms, Genetically Modified; Oxidation-Reduction; Selection, Genetic; Synthetic Biology
PubMed: 31166196
DOI: 10.21775/cimb.033.237 -
Microbiology (Reading, England) Oct 2022During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In , especially at low pH,... (Review)
Review
During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In , especially at low pH, formate is then disproportionated to CO and H by the cytoplasmically oriented, membrane-associated formate hydrogenlyase (FHL) complex. If electron acceptors are available, however, formate is oxidized by periplasmically oriented, respiratory formate dehydrogenases. Formate translocation across the cytoplasmic membrane is controlled by the formate channel, FocA, a member of the formate-nitrite transporter (FNT) family of homopentameric anion channels. This review highlights recent advances in our understanding of how FocA helps to maintain intracellular formate and pH homeostasis during fermentation. Efflux and influx of formate/formic acid are distinct processes performed by FocA and both are controlled through protein interaction between FocA's N-terminal domain with PflB. Formic acid efflux by FocA helps to maintain cytoplasmic pH balance during exponential-phase growth. Uptake of formate against the electrochemical gradient (inside negative) is energetically and mechanistically challenging for a fermenting bacterium unless coupled with proton/cation symport. Translocation of formate/formic acid into the cytoplasm necessitates an active FHL complex, whose synthesis also depends on formate. Thus, FocA, FHL and PflB function together to govern formate homeostasis. We explain how FocA achieves efflux of formic acid and propose mechanisms for pH-dependent uptake of formate both with and without proton symport. We propose that FocA displays both channel- and transporter-like behaviour. Whether this translocation behaviour is shared by other members of the FNT family is also discussed.
Topics: Anions; Carbon Dioxide; Enterobacteriaceae; Escherichia coli; Escherichia coli Proteins; Formate Dehydrogenases; Formates; Homeostasis; Hydrogen-Ion Concentration; Hydrogenase; Membrane Transport Proteins; Nitrites; Protons; Pyruvates
PubMed: 36197793
DOI: 10.1099/mic.0.001253 -
ACS Applied Bio Materials Oct 2023A formate (HCOO) bioanode was developed by utilizing a phenothiazine-based electropolymerized layer deposited on sucrose-derived carbon. The electrode modified with...
A formate (HCOO) bioanode was developed by utilizing a phenothiazine-based electropolymerized layer deposited on sucrose-derived carbon. The electrode modified with NAD-dependent formate dehydrogenase and the electropolymerized layer synergistically catalyzed the oxidation of the coenzyme (NADH) and fuel (HCOO) to achieve efficient electron transfer. Further, the replacement of carbon nanotubes with water-dispersible sucrose-derived carbon used as the electrode base allowed the fabrication of a surfactant-free bioanode delivering a maximum current density of 1.96 mA cm in the fuel solution. Finally, a separator- and surfactant-free HCOO/O biofuel cell featuring the above bioanode and a gas-diffusion biocathode modified with bilirubin oxidase and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) was fabricated, delivering a maximum power density of 70 μW cm (at 0.24 V) and an open-circuit voltage of 0.59 V. Thus, this study demonstrates the potential of formic acid as a fuel and possibilities for the application of carbon materials in bioanodes.
Topics: Surface-Active Agents; Bioelectric Energy Sources; Nanotubes, Carbon; Formates; Phenothiazines; Sucrose
PubMed: 37750824
DOI: 10.1021/acsabm.3c00502 -
International Journal of Molecular... Feb 2021The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods,... (Review)
Review
The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.
Topics: Biocatalysis; Carbon; Carbon Dioxide; Carbon Monoxide; Carboxy-Lyases; Chemistry Techniques, Synthetic; Formaldehyde; Formates; Ligases; Synthetic Biology
PubMed: 33672882
DOI: 10.3390/ijms22041890 -
Applied and Environmental Microbiology Dec 2022The complete remineralization of organic matter in anoxic environments relies on communities of microorganisms that ferment organic acids and alcohols to CH. This is...
The complete remineralization of organic matter in anoxic environments relies on communities of microorganisms that ferment organic acids and alcohols to CH. This is accomplished through syntrophic association of H or formate producing bacteria and methanogenic archaea, where exchange of these intermediates enables growth of both organisms. While these communities are essential to Earth's carbon cycle, our understanding of the dynamics of H or formate exchanged is limited. Here, we establish a model partnership between Syntrophotalea carbinolica and Methanococcus maripaludis. Through sequencing a transposon mutant library of M. maripaludis grown with ethanol oxidizing S. carbinolica, we found that genes encoding the F-dependent formate dehydrogenase (Fdh) and F-dependent methylene-tetrahydromethanopterin dehydrogenase (Mtd) are important for growth. Competitive growth of M. maripaludis mutants defective in either H or formate metabolism verified that, across multiple substrates, interspecies formate exchange was dominant in these communities. Agitation of these cultures to facilitate diffusive loss of H to the culture headspace resulted in an even greater competitive advantage for M. maripaludis strains capable of oxidizing formate. Finally, we verified that an M. maripaludis mutant had a defect during syntrophic growth. Together, these results highlight the importance of formate exchange for the growth of methanogens under syntrophic conditions. In the environment, methane is typically generated by fermentative bacteria and methanogenic archaea working together in a process called syntrophy. Efficient exchange of small molecules like H or formate is essential for growth of both organisms. However, difficulties in determining the relative contribution of these intermediates to methanogenesis often hamper efforts to understand syntrophic interactions. Here, we establish a model syntrophic coculture composed of S. carbinolica and the genetically tractable methanogen M. maripaludis. Using mutant strains of M. maripaludis that are defective for either H or formate metabolism, we determined that interspecies formate exchange drives syntrophic growth of these organisms. Together, these results advance our understanding of the degradation of organic matter in anoxic environments.
Topics: Methanococcus; Formates; Formate Dehydrogenases; Methane; Hydrogen
PubMed: 36374033
DOI: 10.1128/aem.01159-22 -
International Journal of Molecular... Mar 2022Bioethanol from lignocellulosic biomass is a promising and sustainable strategy to meet the energy demand and to be carbon neutral. Nevertheless, the damage of...
Bioethanol from lignocellulosic biomass is a promising and sustainable strategy to meet the energy demand and to be carbon neutral. Nevertheless, the damage of lignocellulose-derived inhibitors to microorganisms is still the main bottleneck. Developing robust strains is critical for lignocellulosic ethanol production. An evolved strain with a stronger tolerance to formate and acetate was obtained after adaptive laboratory evolution (ALE) in the formate. Transcriptional analysis was conducted to reveal the possible resistance mechanisms to weak acids, and coding for formate dehydrogenase was selected as the target to verify whether it was related to resistance enhancement in F3. Engineered FA with overexpression exhibited boosted tolerance to both formate and acetate, but the resistance mechanism to formate and acetate was different. When formate exists, it breaks down by formate dehydrogenase into carbon dioxide (CO) to relieve its inhibition. When there was acetate without formate, FDH1 converted CO from glucose fermentation to formate and ATP and enhanced cell viability. Together, overexpression alone can improve the tolerance to both formate and acetate with a higher cell viability and ATP, which provides a novel strategy for robustness strain construction to produce lignocellulosic ethanol.
Topics: Acetic Acid; Adenosine Triphosphate; Carbon Dioxide; Ethanol; Fermentation; Formate Dehydrogenases; Formates; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 35328826
DOI: 10.3390/ijms23063406 -
Clinical Chemistry and Laboratory... Mar 2013Plasma and urinary formate concentrations were recently found to be elevated during vitamin B12 and folate deficiencies. It was proposed that formate may be a valuable... (Review)
Review
Plasma and urinary formate concentrations were recently found to be elevated during vitamin B12 and folate deficiencies. It was proposed that formate may be a valuable biomarker of impaired one-carbon metabolism. Formate is an essential intermediary metabolite in folate-mediated one-carbon metabolism and, despite its importance, our knowledge of its metabolism is limited. Formate can be produced from several substrates (e.g., methanol, branched chain fatty acids, amino acids), some reactions being folate-dependent while others are not. Formate removal proceeds via two pathways; the major one being folate-dependent. Formate is a potentially toxic molecule and we suggest that formate may play a role in some of the pathologies associated with defective one-carbon metabolism.
Topics: Animals; Biomarkers; Carbon; Folic Acid; Folic Acid Deficiency; Formates; Humans; Vitamin B Deficiency
PubMed: 23241677
DOI: 10.1515/cclm-2012-0552 -
FEMS Microbiology Ecology Feb 2022Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some...
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8, or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Increasing formate concentrations delayed the onsets of growth and sulfate reduction of D. multivorans, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
Topics: Desulfovibrio; Formates; Microbiota; Oxidation-Reduction; Sulfates
PubMed: 35040992
DOI: 10.1093/femsec/fiac003 -
Biochimica Et Biophysica Acta.... Jan 2023Formate hydrogenlyase-1 (FHL-1) is a complex-I-like enzyme that is commonly found in gram-negative bacteria. The enzyme comprises a peripheral arm and a membrane arm but... (Review)
Review
Formate hydrogenlyase-1 (FHL-1) is a complex-I-like enzyme that is commonly found in gram-negative bacteria. The enzyme comprises a peripheral arm and a membrane arm but is not involved in quinone reduction. Instead, FHL-1 couples formate oxidation to the reduction of protons to molecular hydrogen (H). Escherichia coli produces FHL-1 under fermentative conditions where it serves to detoxify formic acid in the environment. The membrane biology and bioenergetics surrounding E. coli FHL-1 have long held fascination. Here, we review recent work on understanding the molecular basis of formic acid efflux and influx. We also consider the structure and function of E. coli FHL-1, its relationship with formate transport, and pay particular attention to the molecular interface between the peripheral arm and the membrane arm. Finally, we highlight the interesting phenotype of genetic mutation of the ND1 Loop, which is located at that interface.
Topics: Escherichia coli; Fermentation; Formate Dehydrogenases; Formates; Hydrogen
PubMed: 36152681
DOI: 10.1016/j.bbabio.2022.148919