ABSTRACT
The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while ß-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.
Subject(s)
Feces , Formates , Gastrointestinal Microbiome , Humans , Female , Feces/microbiology , Male , Formates/metabolism , Middle Aged , Aged , Neoplasms/metabolism , Neoplasms/microbiology , Adult , Dysbiosis/microbiology , Metabolomics/methods , Metabolome , Gas Chromatography-Mass Spectrometry , Metagenomics/methodsABSTRACT
Nitrogenases are the only known enzymes that reduce molecular nitrogen (N2) to ammonia. Recent findings have demonstrated that nitrogenases also reduce the greenhouse gas carbon dioxide (CO2), suggesting CO2 to be a competitor of N2. However, the impact of omnipresent CO2 on N2 fixation has not been investigated to date. Here, we study the competing reduction of CO2 and N2 by the two nitrogenases of Rhodobacter capsulatus, the molybdenum and the iron nitrogenase. The iron nitrogenase is almost threefold more efficient in CO2 reduction and profoundly less selective for N2 than the molybdenum isoform under mixtures of N2 and CO2. Correspondingly, the growth rate of diazotrophically grown R. capsulatus strains relying on the iron nitrogenase notably decreased after adding CO2. The in vivo CO2 activity of the iron nitrogenase facilitates the light-driven extracellular accumulation of formate and methane, one-carbon substrates for other microbes, and feedstock chemicals for a circular economy.
Subject(s)
Carbon Dioxide , Formates , Methane , Nitrogen , Nitrogenase , Carbon Dioxide/metabolism , Methane/metabolism , Nitrogenase/metabolism , Formates/metabolism , Nitrogen/metabolism , Rhodobacter capsulatus/metabolism , Nitrogen Fixation , Oxidation-ReductionABSTRACT
We have recently demonstrated the ability of a C18 stationary phase with a positively charged surface (PCS-C18) to provide superior chromatographic separation of peptides using mobile phase acidified with a mere 0.01 % formic acid, significantly improving MS sensitivity. Here, we examined three columns packed with different PCS-C18 phases using the MS-favorable mobile phase acidified with low formic acid concentrations to establish the impact of separation performance and better MS sensitivity on peptide identifications. The surface charge interaction was evaluated using the retention of nitrate. The highest interaction was observed for the AdvanceBio Peptide Plus column. A surface charge-dependent shift in the retention time of peptides was confirmed with a change in formic acid concentration in the mobile phase. The separation performance of the columns with MS-favorable mobile phase acidified with low concentrations of formic acid was evaluated using well-characterized peptides. The loading capacity was assessed using a basic peptide with three lysine residues. Good chromatographic peak shapes and high loading capacity were observed for the Acquity Premier CSH C18 column, even when using a mobile phase acidified with 0.01 % formic acid. The extent of improvement in peptide identification when using reduced formic acid concentration was evaluated by analyzing the tryptic digest of trastuzumab and tryptic digest of whole bacteria cell lysate. Each column provided improved MS signal intensity and peptide identification when using the mobile phase with 0.01 % formic acid. The ability of the Acquity Premier CSH C18 column to provide better separation of peptides, even with a reduced formic acid concentration in the mobile phase, boosted MS signal intensity by 65 % and increased the number of identified peptides from the bacterial sample by 19 %. Our study confirms that significant improvement in the proteomic outputs can be achieved without additional costs only by tailoring the chemistry of the stationary phase to the composition of the mobile phase. Our results can help researchers understand the retention mechanism of peptides on the PCS-C18 stationary phases using low-ionic strength mobile phases and, more importantly, select the best-suited stationary phases for their LC-MS proteomic applications.
Subject(s)
Formates , Proteomics , Formates/chemistry , Proteomics/methods , Chromatography, Liquid/methods , Peptides/chemistry , Peptides/analysis , Peptides/isolation & purification , Trastuzumab/chemistry , Tandem Mass Spectrometry/methods , Liquid Chromatography-Mass SpectrometryABSTRACT
This article employs six organic acids to selectively dissolve Mo, Ni and V from spent catalysts, and the most effective acid is identified. Then, the effects of key leaching parameters, including acid concentration, temperature, and S/L ratio, on metal leaching are systematically explored to determine the leaching mechanism. The results demonstrate that the leaching ability of organic acids followed the order: oxalic acid > citric acid > tartaric acid > malonic acid > acetic acid > formic acid. The leaching process of metals was jointly influenced by acidolysis and complexolysis. Among them, more than 93.07 % of Mo, 86.64 % of V, and 74.21 % of Ni were selectively leached with oxalic acid at the optimum condition: S/l: 1/20, oxalic acid: 1.0 mol/L, temp: 60 °C. From the correlation coefficients, the resulting activation energies, and n values, it was demonstrated that Mo and V followed the Avrami dissolution reaction model, V leaching was controlled by the diffusion mode, and Mo leaching was controlled by a mixed mode of chemical reaction and diffusion. The dissolution behavior of both metals consistently adhered to the linear trend of the Avrami kinetic model under varying S/L ratios and oxalic acid concentrations.
Subject(s)
Molybdenum , Nickel , Oxalic Acid , Kinetics , Nickel/chemistry , Catalysis , Oxalic Acid/chemistry , Molybdenum/chemistry , Tartrates/chemistry , Citric Acid/chemistry , Formates/chemistry , Acetic Acid/chemistry , MalonatesABSTRACT
It is desirable but challenging to develop highly-efficient catalysts for the direct synthesis of dimethyl carbonate (DMC) from methanol and CO2. The vacancy-mediated incorporation of heteroatom into surface reconstruction is an efficient method of defect engineering for enhancing the catalytic properties. In this work, manganese-doped cerium oxide porous nanoribbons (Mn/CeO2-BTC) were prepared derived from a Ce-BTC by a sacrificial template approach. It is found that the catalytic activity of Mn/CeO2-BTC catalysts can be readily controlled by varying the amount of Mn dopants and the as-synthesized 0.1-Mn/CeO2-BTC exhibited an outstanding activity for the synthesis of DMC from CO2 and methanol, which reached a high DMC yield (6.53 mmolDMC/gcat.) without any dehydrating agents. Based on characterization results, the enhanced performance may be attributed to the defective structures caused by Mn doping and the porous nanoribbons of the CeO2 crystals, which provide more surface oxygen vacancies and acidic-basic sites, favoring adsorption and activation of CO2 and methanol.
Subject(s)
Carbon Dioxide , Cerium , Formates , Manganese , Methanol , Methanol/chemistry , Cerium/chemistry , Catalysis , Formates/chemistry , Carbon Dioxide/chemistry , Porosity , Manganese/chemistry , Adsorption , Nanotubes, Carbon/chemistryABSTRACT
OBJECTIVES: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS (biomerieux), but the performance of fungi identification on new EXS2600 (Zybio) is still unknow. Our study aims to evaluate the new EXS2600 system's (Zybio) ability to rapidly identify filamentous fungi and determine its effect on turnaround time (TAT) in our laboratory. METHODS: We tested 117 filamentous fungi using two pretreatment methods: the formic acid sandwich (FA-sandwich) and a commercial mold extraction kit (MEK, Zybio). All isolates were confirmed via sequence analysis. Laboratory data were extracted from our laboratory information system over two 9-month periods: pre-EXS (April to December 2022) and post-EXS (April to December 2023), respectively. RESULTS: The total correct identification (at the species, genus, or complex/group level) rate of fungi was high, FA-sandwich (95.73%, 112/117), followed by MEK (94.02%, 110/117). Excluding 6 isolates not in the database, species-level identification accuracy was 92.79% (103/111) for FA-sandwich and 91.89% (102/111) for MEK; genus-level accuracy was 97.29% (108/111) and 96.39% (107/111), respectively. Both methods attained a 100% correct identification rate for Aspergillus, Lichtheimia, Rhizopus Mucor and Talaromyces species, and were able to differentiate between Fusarium verticillioides and Fusarium proliferatum within the Fusarium fujikuroi species complex. Notably, high confidence was observed in the species-level identification of uncommon fungi such as Trichothecium roseum and Geotrichum candidum. The TAT for all positive cultures decreased from pre EXS2600 to post (108.379 VS 102.438, P < 0.05), and the TAT for tissue decreased most (451.538 VS 222.304, P < 0.001). CONCLUSIONS: The FA-sandwich method is more efficient and accurate for identifying filamentous fungi with EXS2600 than the MEK. Our study firstly evaluated the performance of fungi identification on EXS2600 and showed it is suitable for clinical microbiology laboratories use.
Subject(s)
Formates , Fungi , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Fungi/classification , Fungi/isolation & purification , Fungi/chemistry , Fungi/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Formates/chemistryABSTRACT
Extracellular iodate reduction by Shewanella spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether Shewanella spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of Shewanella oneidensis MR-1 were created to investigate the roles of dmsEFABGH, mtrCAB, and so4357-so4362 operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H2 as the sole electron donors, respectively. In the absence of single-dms gene, iodate reduction efficiency of the mutants was only 12.9%-84.0% with lactate at 24 hours, 22.1%-85.9% with formate at 20 hours, and 19.6%-57.7% with H2 at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the dms homolog from the so4357-so4362 operon was deleted in the single-dms gene mutants. This result revealed complementation of dmsEFABGH by so4357-so4362 at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by dmsEFABGH operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H2O2 were detected for ΔmtrCAB. Collectively, these results demonstrated that the dmsEFABGH operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in S. oneidensis MR-1. The mtrCAB operon was involved in H2O2 elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.IMPORTANCEIodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain Shewanella oneidensis MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the dmsEFABGH operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H2. The so4357-so4362 operon was first demonstrated to be capable of complementing the function of dmsEFABGH at single-gene level.
Subject(s)
Bacterial Proteins , Iodates , Operon , Oxidation-Reduction , Shewanella , Shewanella/genetics , Shewanella/metabolism , Electron Transport , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Iodates/metabolism , Formates/metabolism , Gene DeletionABSTRACT
Electrocatalytic CO2 reduction to CO and formate can be coupled to gas fermentation with anaerobic microorganisms. In combination with a competing hydrogen evolution reaction in the cathode in aqueous medium, the in situ, electrocatalytic produced syngas components can be converted by an acetogenic bacterium, such as Clostridium ragsdalei, into acetate, ethanol, and 2,3-butanediol. In order to study the simultaneous conversion of CO, CO2, and formate together with H2 with C. ragsdalei, fed-batch processes were conducted with continuous gassing using a fully controlled stirred tank bioreactor. Formate was added continuously, and various initial CO partial pressures (pCO0) were applied. C. ragsdalei utilized CO as the favored substrate for growth and product formation, but below a partial pressure of 30 mbar CO in the bioreactor, a simultaneous CO2/H2 conversion was observed. Formate supplementation enabled 20-50% higher growth rates independent of the partial pressure of CO and improved the acetate and 2,3-butanediol production. Finally, the reaction conditions were identified, allowing the parallel CO, CO2, formate, and H2 consumption with C. ragsdalei at a limiting CO partial pressure below 30 mbar, pH 5.5, n = 1200 min-1, and T = 32 °C. Thus, improved carbon and electron conversion is possible to establish efficient and sustainable processes with acetogenic bacteria, as shown in the example of C. ragsdalei.
Subject(s)
Bioreactors , Butylene Glycols , Carbon Dioxide , Carbon Monoxide , Clostridium , Fermentation , Formates , Hydrogen , Formates/metabolism , Formates/chemistry , Clostridium/metabolism , Clostridium/growth & development , Carbon Monoxide/metabolism , Hydrogen/metabolism , Carbon Dioxide/metabolism , Butylene Glycols/metabolism , Butylene Glycols/chemistry , Gases/metabolism , Gases/chemistry , Ethanol/metabolismABSTRACT
Anaerobic, acetogenic bacteria are well known for their ability to convert various one-carbon compounds, promising feedstocks for a future, sustainable biotechnology, to products such as acetate and biofuels. The model acetogen Acetobacterium woodii can grow on CO2, formate or methanol, but not on carbon monoxide, an important industrial waste product. Since hydrogenases are targets of CO inhibition, here, we genetically delete the two [FeFe] hydrogenases HydA2 and HydBA in A. woodii. We show that the ∆hydBA/hydA2 mutant indeed grows on CO and produces acetate, but only after a long adaptation period. SNP analyzes of CO-adapted cells reveal a mutation in the HycB2 subunit of the HydA2/HydB2/HydB3/Fdh-containing hydrogen-dependent CO2 reductase (HDCR). We observe an increase in ferredoxin-dependent CO2 reduction and vice versa by the HDCR in the absence of the HydA2 module and speculate that this is caused by the mutation in HycB2. In addition, the CO-adapted ∆hydBA/hydA2 mutant growing on formate has a final biomass twice of that of the wild type.
Subject(s)
Acetobacterium , Bacterial Proteins , Carbon Monoxide , Formates , Acetobacterium/genetics , Acetobacterium/metabolism , Acetobacterium/growth & development , Formates/metabolism , Carbon Monoxide/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Hydrogenase/metabolism , Hydrogenase/genetics , Mutation , Carbon Dioxide/metabolism , Electron Transport , Biomass , Acetates/metabolism , Polymorphism, Single NucleotideABSTRACT
Formate is an important environmental pollutant, and meanwhile its concentration change is associated with a variety of diseases. Thus, rapid and sensitive detection of formate is critical for the biochemical analysis of complex samples and clinical diagnosis of multiple diseases. Herein, a colorimetric biosensor was constructed based on the cascade catalysis of formate oxidase (FOx) and horseradish peroxidase (HRP). These two enzymes were co-immobilized in Cu3(PO4)2-based hybrid nanoflower with spatial localization, in which FOx and HRP were located in the shell and core of nanoflower, respectively (FOx@HRP). In this system, FOx could catalyze the oxidation of formate to generate H2O2, which was then utilized by HRP to oxidize 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid to yield blue product. Ideal linear correlation could be obtained between the absorbance at 420 nm and formate concentration. Meanwhile, FOx@HRP exhibited excellent detection performance with low limit of detection (6 µM), wide linear detection range (10-900 µM), and favorable specificity, stability and reusability. Moreover, it could be applied in the detection of formate in environmental, food and biological samples with high accuracy. Collectively, FOx@HRP provides a useful strategy for the simple and sensitive detection of formate and is potentially to be used in biochemical analysis and clinical diagnosis.
Subject(s)
Colorimetry , Enzymes, Immobilized , Formates , Horseradish Peroxidase , Colorimetry/methods , Formates/chemistry , Horseradish Peroxidase/chemistry , Horseradish Peroxidase/metabolism , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism , Biosensing Techniques/methods , Limit of Detection , Nanostructures/chemistry , Particle Size , Surface PropertiesABSTRACT
Synthetic biology is contributing to the advancement of the global net-negative carbon economy, with emphasis on formate as a member of the one-carbon substrate garnering substantial attention. In this study, we employed base editing tools to facilitate adaptive evolution, achieving a formate tolerance of Yarrowia lipolytica to 1 M within 2 months. This effort resulted in two mutant strains, designated as M25-70 and M25-14, both exhibiting significantly enhanced formate utilization capabilities. Transcriptomic analysis revealed the upregulation of nine endogenous genes encoding formate dehydrogenases when cultivated utilizing formate as the sole carbon source. Furthermore, we uncovered the pivotal role of the glyoxylate and threonine-based serine pathway in enhancing glycine supply to promote formate assimilation. The full potential of Y. lipolytica to tolerate and utilize formate establishing the foundation for pyruvate carboxylase-based carbon sequestration pathways. Importantly, this study highlights the existence of a natural formate metabolic pathway in Y. lipolytica.
Subject(s)
Formates , Yarrowia , Yarrowia/genetics , Yarrowia/metabolism , Formates/metabolism , Metabolic Engineering/methods , Metabolic Networks and Pathways/genetics , Formate Dehydrogenases/genetics , Formate Dehydrogenases/metabolism , Directed Molecular Evolution , Glyoxylates/metabolism , Gene EditingABSTRACT
The development of synthetic microorganisms that could use one-carbon compounds, such as carbon dioxide, methanol, or formate, has received considerable interest. In this study, we engineered Pichia pastoris and Saccharomyces cerevisiae to both synthetic methylotrophy and formatotrophy, enabling them to co-utilize methanol or formate with CO2 fixation through a synthetic C1-compound assimilation pathway (MFORG pathway). This pathway consisted of a methanol-formate oxidation module and the reductive glycine pathway. We first assembled the MFORG pathway in P. pastoris using endogenous enzymes, followed by blocking the native methanol assimilation pathway, modularly engineering genes of MFORG pathway, and compartmentalizing the methanol oxidation module. These modifications successfully enabled the methylotrophic yeast P. pastoris to utilize both methanol and formate. We then introduced the MFORG pathway from P. pastoris into the model yeast S. cerevisiae, establishing the synthetic methylotrophy and formatotrophy in this organism. The resulting strain could also successfully utilize both methanol and formate with consumption rates of 20 mg/L/h and 36.5 mg/L/h, respectively. The ability of the engineered P. pastoris and S. cerevisiae to co-assimilate CO2 with methanol or formate through the MFORG pathway was also confirmed by 13C-tracer analysis. Finally, production of 5-aminolevulinic acid and lactic acid by co-assimilating methanol and CO2 was demonstrated in the engineered P. pastoris and S. cerevisiae. This work indicates the potential of the MFORG pathway in developing different hosts to use various one-carbon compounds for chemical production.
Subject(s)
Carbon Dioxide , Formates , Metabolic Engineering , Methanol , Saccharomyces cerevisiae , Formates/metabolism , Methanol/metabolism , Carbon Dioxide/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomycetales/metabolism , Saccharomycetales/geneticsABSTRACT
In order to obtain the best mass spectrometry identification results for using the most appropriate methods in clinical practice, we explore the optimal pretreatment methods for different species and morphologies of filamentous fungi. 98 fungal strains were treated with formic acid sandwich method, dispersion method, extraction method, and other methods using a medium element mass spectrometer (EXS3000) as a platform. Each strain had three targets, and the identification rates and confidence differences under different pre-treatment methods were compared to evaluate the identification effects of these methods. The mass spectrometry identification rates of 98 filamentous fungi obtained after pre-treatment with formic acid sandwich method, dispersion method, and extraction method were 85.71%, 82.65%, and 75.51%, respectively. The identification rate of the formic acid sandwich method was significantly higher than the other two methods (P < 0 005) has the best identification ability and the obtained confidence is also higher than the other two methods. The use of formic acid sandwich method for mass spectrometry identification of filamentous fungi can achieve ideal identification results, which is suitable for mass spectrometry identification of filamentous fungi in conventional laboratories.
Subject(s)
Fungi , Mass Spectrometry , Fungi/isolation & purification , Fungi/classification , Mass Spectrometry/methods , Formates/chemistry , Formates/analysis , Mycoses/microbiology , Mycoses/diagnosis , HumansABSTRACT
Despite the use of various integrated pest management strategies to control the honey bee mite, Varroa destructor, varroosis remains the most important threat to honey bee colony health in many countries. In Canada, ineffective varroa control is linked to high winter colony losses and new treatment options, such as a summer treatment, are greatly needed. In this study, a total of 135 colonies located in 6 apiaries were submitted to one of these 3 varroa treatment strategies: (i) an Apivar® fall treatment followed by an oxalic acid (OA) treatment by dripping method; (ii) same as in (i) with a summer treatment consisting of formic acid (Formic Pro™); and (iii) same as in (i) with a summer treatment consisting of slow-release OA/glycerin pads (total of 27 g of OA/colony). Treatment efficacy and their effects on colony performance, mortality, varroa population, and the abundance of 6 viruses (acute bee paralysis virus [ABPV], black queen cell virus [BQCV], deformed wing virus variant A [DWV-A], deformed wing virus variant B [DWV-B], Israeli acute paralysis virus [IAPV], and Kashmir bee virus [KBV]) were assessed. We show that a strategy with a Formic Pro summer treatment tended to reduce the varroa infestation rate to below the economic fall threshold of 15 daily varroa drop, which reduced colony mortality significantly but did not reduce the prevalence or viral load of the 6 tested viruses at the colony level. A strategy with glycerin/OA pads reduced hive weight gain and the varroa infestation rate, but not below the fall threshold. A high prevalence of DWV-B was measured in all groups, which could be related to colony mortality.
Subject(s)
Beekeeping , Seasons , Varroidae , Viral Load , Animals , Varroidae/physiology , Bees/parasitology , Bees/virology , Beekeeping/methods , Acaricides , Formates/pharmacology , CanadaABSTRACT
Formate as an ideal mediator between the physicochemical and biological realms can be obtained from electrochemical reduction of CO2 and used to produce bio-chemicals. Yet, limitations arise when employing natural formate-utilizing microorganisms due to restricted product range and low biomass yield. This study presents a breakthrough: engineered Corynebacterium glutamicum strains (L2-L4) through modular engineering. L2 incorporates the formate-tetrahydrofolate cycle and reverse glycine cleavage pathway, L3 enhances NAD(P)H regeneration, and L4 reinforces metabolic flux. Metabolic modeling elucidates C1 assimilation, guiding strain optimization for co-fermentation of formate and glucose. Strain L4 achieves an OD600 of 0.5 and produces 0.6 g/L succinic acid. 13C-labeled formate confirms C1 assimilation, and further laboratory evolution yields 1.3 g/L succinic acid. This study showcases a successful model for biologically assimilating formate in C. glutamicum that could be applied in C1-based biotechnological production, ultimately forming a formate-based bioeconomy.
Subject(s)
Biomass , Corynebacterium glutamicum , Formates , Metabolic Engineering , Succinic Acid , Corynebacterium glutamicum/metabolism , Formates/metabolism , Metabolic Engineering/methods , Succinic Acid/metabolism , Fermentation , Models, Biological , Glucose/metabolismABSTRACT
Nucleotides perform important metabolic functions, carrying energy and feeding nucleic acid synthesis. Here, we use isotope tracing-mass spectrometry to quantitate contributions to purine nucleotides from salvage versus de novo synthesis. We further explore the impact of augmenting a key precursor for purine synthesis, one-carbon (1C) units. We show that tumors and tumor-infiltrating T cells (relative to splenic or lymph node T cells) synthesize purines de novo. Shortage of 1C units for T cell purine synthesis is accordingly a potential bottleneck for anti-tumor immunity. Supplementing 1C units by infusing formate drives formate assimilation into purines in tumor-infiltrating T cells. Orally administered methanol functions as a formate pro-drug, with deuteration enabling kinetic control of formate production. Safe doses of methanol raise formate levels and augment anti-PD-1 checkpoint blockade in MC38 tumors, tripling durable regressions. Thus, 1C deficiency can gate antitumor immunity and this metabolic checkpoint can be overcome with pharmacological 1C supplementation.
Subject(s)
Carbon , Mice, Inbred C57BL , Purines , Animals , Mice , Purines/chemistry , Purines/pharmacology , Carbon/chemistry , Carbon/metabolism , Immune Checkpoint Inhibitors/pharmacology , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Lymphocytes, Tumor-Infiltrating/drug effects , T-Lymphocytes/metabolism , T-Lymphocytes/immunology , T-Lymphocytes/drug effects , Formates/chemistry , Formates/metabolism , Formates/pharmacology , Methanol/chemistry , Methanol/pharmacology , Female , Humans , Cell Line, TumorABSTRACT
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation.
Subject(s)
Desulfovibrio vulgaris , Formate Dehydrogenases , Desulfovibrio vulgaris/enzymology , Desulfovibrio vulgaris/genetics , Formate Dehydrogenases/chemistry , Formate Dehydrogenases/genetics , Formate Dehydrogenases/metabolism , Catalytic Domain , Crystallography, X-Ray , Oxidation-Reduction , Models, Molecular , Formates/metabolism , Formates/chemistry , Carbon Dioxide/metabolism , Carbon Dioxide/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolismABSTRACT
Formic acid (HCOOH) and dihydrogen (H2) are characteristic products of enterobacterial mixed-acid fermentation, with H2 generation increasing in conjunction with a decrease in extracellular pH. Formate and acetyl-CoA are generated by radical-based and coenzyme A-dependent cleavage of pyruvate catalysed by pyruvate formate-lyase (PflB). Formate is also the source of H2, which is generated along with carbon dioxide through the action of the membrane-associated, cytoplasmically-oriented formate hydrogenlyase (FHL-1) complex. Synthesis of the FHL-1 complex is completely dependent on the cytoplasmic accumulation of formate. Consequently, formate determines its own disproportionation into H2 and CO2 by the FHL-1 complex. Cytoplasmic formate levels are controlled by FocA, a pentameric channel that translocates formic acid/formate bidirectionally between the cytoplasm and periplasm. Each protomer of FocA has a narrow hydrophobic pore through which neutral formic acid can pass. Two conserved amino acid residues, a histidine and a threonine, at the center of the pore control directionality of translocation. The histidine residue is essential for pH-dependent influx of formic acid. Studies with the formate analogue hypophosphite and amino acid variants of FocA suggest that the mechanisms of formic acid efflux and influx differ. Indeed, current data suggest, depending on extracellular formate levels, two separate uptake mechanisms exist, both likely contributing to maintain pH homeostasis. Bidirectional formate/formic acid translocation is dependent on PflB and influx requires an active FHL-1 complex. This review describes the coupling of formate and H2 production in enterobacteria.
Subject(s)
Enterobacteriaceae , Fermentation , Formates , Hydrogen , Formates/metabolism , Hydrogen/metabolism , Enterobacteriaceae/metabolism , Enterobacteriaceae/genetics , Enterobacteriaceae/enzymology , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Formate Dehydrogenases , Hydrogenase , Multienzyme ComplexesABSTRACT
Metabolic changes contribute to cancer initiation and progression through effects on cancer cells, the tumor microenvironment and whole-body metabolism. Alterations in serine metabolism and the control of one-carbon cycles have emerged as critical for the development of many tumor types. In this Review, we focus on the mitochondrial folate cycle. We discuss recent evidence that, in addition to supporting nucleotide synthesis, mitochondrial folate metabolism also contributes to metastasis through support of antioxidant defense, mitochondrial protein synthesis and the overflow of excess formate. These observations offer potential therapeutic opportunities, including the modulation of formate metabolism through dietary interventions and the use of circulating folate cycle metabolites as biomarkers for cancer detection.
Subject(s)
Folic Acid , Mitochondria , Neoplasms , Humans , Folic Acid/metabolism , Neoplasms/metabolism , Mitochondria/metabolism , Animals , Formates/metabolism , Tumor Microenvironment , Neoplasm MetastasisABSTRACT
Formic acid is a viable product of CO2 utilization. Here, we present a protocol for designing and operating a pilot-scale formic acid production plant with a 10 kg/day capacity produced via CO2 hydrogenation. We describe the essential process specifications required for successful operation, including prevention of corrosion and formic acid decomposition. We then detail procedures for steady-state operation of the individual units. This protocol provides the necessary information for further scale-up and commercialization of the CO2 hydrogenation process. For complete details on the use and execution of this protocol, please refer to Kim et al.1.