fumarates and formic-acid

The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high production and best compatibility with host physiology.

Topics: Carbon; Formates; Fumarates; Malates; Metabolic Engineering; Metabolic Networks and Pathways; Oxidation-Reduction; Propionates; Succinic Acid

Physical exercise modifies animal metabolism profoundly. Until recently, biochemical investigations related to exercise focused on a small number of biomolecules. In the present study, we used a holistic analytical approach to investigate changes in the human urine metabolome elicited by two exercise sessions differing in the duration of the rest interval between repeated efforts. Twelve men performed three sets of two 80 m maximal runs separated by either 10 s or 1 min of rest. Analysis of pre- and postexercise urine samples by (1)H NMR spectroscopy and subsequent multivariate statistical analysis revealed alterations in the levels of 22 metabolites. Urine samples were safely classified according to exercise protocol even when applying unsupervised methods of statistical analysis. Separation of pre- from postexercise samples was mainly due to lactate, pyruvate, hypoxanthine, compounds of the Krebs cycle, amino acids, and products of branched-chain amino acid (BCAA) catabolism. Separation of the two rest intervals was mainly due to lactate, pyruvate, alanine, compounds of the Krebs cycle, and 2-oxoacids of BCAA, all of which increased more with the shorter interval. Metabonomics provides a powerful methodology to gain insight in metabolic changes induced by specific training protocols and may thus advance our knowledge of exercise biochemistry.

Topics: Alanine; Citric Acid; Creatinine; Exercise; Formates; Fumarates; Histidine; Humans; Hydroxybutyrates; Hypoxanthine; Keto Acids; Lactic Acid; Magnetic Resonance Spectroscopy; Male; Metabolome; Metabolomics; Multivariate Analysis; Young Adult

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 CO

Topics: Carbon Dioxide; Catalysis; Cell Culture Techniques; Electrochemical Techniques; Formates; Fumarates; Maleates; Methylobacterium extorquens; Polymers; Succinates

The natural aminocarboxylic acid product ethylenediamine- N, N'-disuccinic acid [( S, S)-EDDS] is able to form a stable complex with metal ions, making it an attractive biodegradable alternative for the synthetic metal chelator ethylenediaminetetraacetic acid (EDTA), which is currently used on a large scale in numerous applications. Previous studies have demonstrated that biodegradation of ( S, S)-EDDS may be initiated by an EDDS lyase, converting ( S, S)-EDDS via the intermediate N-(2-aminoethyl)aspartic acid (AEAA) into ethylenediamine and two molecules of fumarate. However, current knowledge of this enzyme is limited because of the absence of structural data. Here, we describe the identification and characterization of an EDDS lyase from Chelativorans sp. BNC1, which has a broad substrate scope, accepting various mono- and diamines for addition to fumarate. We report crystal structures of the enzyme in an unliganded state and in complex with formate, succinate, fumarate, AEAA, and ( S, S)-EDDS. The structures reveal a tertiary and quaternary fold that is characteristic of the aspartase/fumarase superfamily and support a mechanism that involves general base-catalyzed, sequential two-step deamination of ( S, S)-EDDS. This work broadens our understanding of mechanistic diversity within the aspartase/fumarase superfamily and will aid in the optimization of EDDS lyase for asymmetric synthesis of valuable (metal-chelating) aminocarboxylic acids.

Topics: Bacterial Proteins; Carbon-Nitrogen Lyases; Crystallography, X-Ray; Ethylenediamines; Formates; Fumarates; Models, Molecular; Phyllobacteriaceae; Protein Conformation; Substrate Specificity; Succinates

The human gut microbiota is a crucial factor for the host's physiology with respect to health and disease. Metagenomic shotgun sequencing of microbial gut communities revealed that Prevotella copri is one of the most important players in the gastrointestinal tract of many individuals. Because of the importance of this bacterium we analyzed the growth behavior and the central metabolic pathways of P. copri. Bioinformatic data, transcriptome profiling and enzyme activity measurements indicated that the major pathways are based on glycolysis and succinate production from fumarate. In addition, pyruvate can be degraded to acetate and formate. Electron transport phosphorylation depends on fumarate respiration with NADH and reduced ferredoxin as electron donors. In contrast to Bacteroides vulgatus, P. copri showed a more pronounced dependency on the addition of CO

Topics: Acetate-CoA Ligase; Carbon Dioxide; Energy Metabolism; Formates; Fumarates; Gastrointestinal Microbiome; Gastrointestinal Tract; Glycolysis; Humans; Metabolic Networks and Pathways; Prevotella; Pyruvic Acid; Succinic Acid

Desulfitobacterium dehalogenans is able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components, and shotgun proteomics to study elements of the organohalide respiratory electron transport chain. The genome of Desulfitobacterium dehalogenans JW/IU-DC1(T) consists of a single circular chromosome of 4,321,753 bp with a GC content of 44.97%. The genome contains 4,252 genes, including six rRNA operons and six predicted reductive dehalogenases. One of the reductive dehalogenases, CprA, is encoded by a well-characterized cprTKZEBACD gene cluster. Redox active components were identified in concentrated suspensions of cells grown on formate and Cl-OHPA or formate and fumarate, using electron paramagnetic resonance (EPR), visible spectroscopy, and high-performance liquid chromatography (HPLC) analysis of membrane extracts. In cell suspensions, these components were reduced upon addition of formate and oxidized after addition of Cl-OHPA, indicating involvement in organohalide respiration. Genome analysis revealed genes that likely encode the identified components of the electron transport chain from formate to fumarate or Cl-OHPA. Data presented here suggest that the first part of the electron transport chain from formate to fumarate or Cl-OHPA is shared. Electrons are channeled from an outward-facing formate dehydrogenase via menaquinones to a fumarate reductase located at the cytoplasmic face of the membrane. When Cl-OHPA is the terminal electron acceptor, electrons are transferred from menaquinones to outward-facing CprA, via an as-yet-unidentified membrane complex, and potentially an extracellular flavoprotein acting as an electron shuttle between the quinol dehydrogenase membrane complex and CprA.

Topics: Bacterial Proteins; Desulfitobacterium; Electron Transport; Formates; Fumarates; Genome, Bacterial; Genomics; Halogens; Molecular Sequence Data; Operon; Proteomics

The adaptation capability of Desulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying Desulfovibrio alaskensis strain G20 under varying respiratory, fermentative and methanogenic coculture conditions in chemostats. Transition from lactate to pyruvate in coculture resulted in a dramatic shift in the population structure and closer interspecies cell-to-cell interactions. Lower methane production rates in coculture than predicted from pyruvate input was attributed to redirection of electron flow to fumarate reduction. Without a methanogenic partner, accumulation of H₂and formate resulted in greater succinate production. Comparative transcript and gene fitness analysis in concert with physiological data of G20 wildtype and mutants demonstrated that pyruvate fermentation involves respiration of cytoplasmically formed fumarate using cytoplasmic and membrane-bound energy-conserving complexes, Rnf, Hdr-Flox-1 and Hmc. At the low H₂/formate levels maintained in coculture, Rnf likely functions as proton-pumping ferredoxin (Fd): type-I cytochrome c oxidoreductase, which transitions to a proton-pumping Fd(red):  nicotinamide adenine dinucleotide (NAD⁺) oxidoreductase at high H₂/formate levels during fermentation in monoculture. Hdr-Flox-1 is postulated to recycle Fd(red) via a flavin-based electron bifurcation involving NADH, Fdox and the thiol/disulphide-containing DsrC. In a menaquinone (MQ)-based electron confurcation reaction, the high-molecular-weight cytochrome-c₃complex, Hmc, is proposed to then couple DsrC(red) and periplasmic H₂/formate oxidation using the MQ pool to fuel a membrane-bound fumarate reductase.

Topics: Cell Membrane; Cytoplasm; Desulfovibrio; Electron Transport; Fermentation; Formates; Fumarates; Gene Expression; Lactic Acid; Membrane Transport Proteins; Oxidation-Reduction; Oxidoreductases; Proton Pumps; Pyruvic Acid

The effect of organic acids and mannanoligosaccharide addition to the diet was assessed in pigs orally inoculated with Salmonella typhimurium. Forty-six growers were distributed among four treatments: Basal Diet (BD); BD+encapsulated organic acids; BD+free organic acids; BD+mannanoligosaccharide. Seroconversion was monitored, and feces and tissue samples were tested for Salmonella isolation. No treatment prevented the carrier state, but a tendency of lower fecal excretion was observed in the group treated with mannanoligosaccharide.

Topics: Animals; Carrier State; Citric Acid; Diet; Dietary Supplements; Feces; Formates; Fumarates; Malates; Mannans; Oligosaccharides; Phosphoric Acids; Propionates; Salmonella Infections, Animal; Salmonella typhimurium; Swine; Swine Diseases

Shewanella oneidensis MR-1 is a facultative anaerobe that derives energy by coupling organic matter oxidation to the reduction of a wide range of electron acceptors. Here, we quantitatively assessed the lactate and pyruvate metabolism of MR-1 under three distinct conditions: electron acceptor-limited growth on lactate with O(2), lactate with fumarate, and pyruvate fermentation. The latter does not support growth but provides energy for cell survival. Using physiological and genetic approaches combined with flux balance analysis, we showed that the proportion of ATP produced by substrate-level phosphorylation varied from 33% to 72.5% of that needed for growth depending on the electron acceptor nature and availability. While being indispensable for growth, the respiration of fumarate does not contribute significantly to ATP generation and likely serves to remove formate, a product of pyruvate formate-lyase-catalyzed pyruvate disproportionation. Under both tested respiratory conditions, S. oneidensis MR-1 carried out incomplete substrate oxidation, whereby the tricarboxylic acid (TCA) cycle did not contribute significantly. Pyruvate dehydrogenase was not involved in lactate metabolism under conditions of O(2) limitation but was required for anaerobic growth, likely by supplying reducing equivalents for biosynthesis. The results suggest that pyruvate fermentation by S. oneidensis MR-1 cells represents a combination of substrate-level phosphorylation and respiration, where pyruvate serves as an electron donor and an electron acceptor. Pyruvate reduction to lactate at the expense of formate oxidation is catalyzed by a recently described new type of oxidative NAD(P)H-independent d-lactate dehydrogenase (Dld-II). The results further indicate that pyruvate reduction coupled to formate oxidation may be accompanied by the generation of proton motive force.

Topics: Adenosine Triphosphate; Energy Metabolism; Fermentation; Formates; Fumarates; Lactic Acid; Oxygen; Proton-Motive Force; Pyruvic Acid; Shewanella

The fermentative metabolism of Escherichia coli was reengineered to efficiently convert glycerol to succinate under anaerobic conditions without the use of foreign genes. Formate and ethanol were the dominant fermentation products from glycerol in wild-type Escherichia coli ATCC 8739, followed by succinate and acetate. Inactivation of pyruvate formate-lyase (pflB) in the wild-type strain eliminated the production of formate and ethanol and reduced the production of acetate. However, this deletion slowed growth and decreased cell yields due to either insufficient energy production or insufficient levels of electron acceptors. Reversing the direction of the gluconeogenic phosphoenolpyruvate carboxykinase reaction offered an approach to solve both problems, conserving energy as an additional ATP and increasing the pool of electron acceptors (fumarate and malate). Recruiting this enzyme through a promoter mutation (pck*) to increase expression also increased the rate of growth, cell yield, and succinate production. Presumably, the high NADH/NAD(+) ratio served to establish the direction of carbon flow. Additional mutations were also beneficial. Glycerol dehydrogenase and the phosphotransferase-dependent dihydroxyacetone kinase are regarded as the primary route for glycerol metabolism under anaerobic conditions. However, this is not true for succinate production by engineered strains. Deletion of the ptsI gene or any other gene essential for the phosphotranferase system was found to increase succinate yield. Deletion of pflB in this background provided a further increase in the succinate yield. Together, these three core mutations (pck*, ptsI, and pflB) effectively redirected carbon flow from glycerol to succinate at 80% of the maximum theoretical yield during anaerobic fermentation in mineral salts medium.

Topics: Acetates; Anaerobiosis; Escherichia coli; Escherichia coli Proteins; Ethanol; Fermentation; Formates; Fumarates; Gene Deletion; Gene Expression; Genetic Engineering; Glycerol; Malates; Metabolic Networks and Pathways; Promoter Regions, Genetic; Succinic Acid

Deuterium-labelled compounds were prepared by (transfer) deuterogenation of unsaturated compounds using H(2) or HCO(2)H in acidic D(2)O as deuterium source with almost quantitative yields and high deuterium contents under mild reaction conditions via heterolytic cleavage of H(2) (or decomposition of HCO(2)H) and rapid H(+)/D(+) exchange using iridium catalysts with 4,4'-dihydroxy-2,2'-bipyridine.

Topics: 2,2'-Dipyridyl; Catalysis; Deuterium; Deuterium Oxide; Formates; Fumarates; Hydrogen; Iridium; Maleates; Succinates

A soluble ferric reductase, SfrAB, which catalysed the NADPH-dependent reduction of chelated Fe(III), was previously purified from the dissimilatory Fe(III)-reducing micro-organism Geobacter sulfurreducens, suggesting that reduction of chelated forms of Fe(III) might be cytoplasmic. However, metabolically active spheroplast suspensions could not catalyse acetate-dependent Fe(III) citrate reduction, indicating that periplasmic and/or outer-membrane components were required for Fe(III) citrate reduction. Furthermore, phenotypic analysis of an SfrAB knockout mutant suggested that SfrAB was involved in acetate metabolism rather than respiration-linked Fe(III) reduction. The mutant could not grow via the reduction of either Fe(III) citrate or fumarate when acetate was the electron donor but could grow with either acceptor if either hydrogen or formate served as the electron donor. Following prolonged incubation in acetate : fumarate medium in the absence of hydrogen and formate, an 'acetate-adapted' SfrAB-null strain was isolated that was capable of growth on acetate : fumarate medium but not acetate : Fe(III) citrate medium. Comparison of gene expression in this strain with that of the wild-type revealed upregulation of a potential NADPH-dependent ferredoxin oxidoreductase as well as genes involved in energy generation and amino acid uptake, suggesting that NADPH homeostasis and the tricarboxylic acid (TCA) cycle were perturbed in the 'acetate-adapted' SfrAB-null strain. Membrane and soluble fractions prepared from the 'acetate-adapted' strain were depleted of NADPH-dependent Fe(III), viologen and quinone reductase activities. These results indicate that cytoplasmic, respiration-linked reduction of Fe(III) by SfrAB in vivo is unlikely and suggest that deleting SfrAB may interfere with growth via acetate oxidation by interfering with NADP regeneration.

Topics: Acetates; Amino Acid Transport Systems; Bacterial Proteins; Cell Membrane; Citric Acid Cycle; Cytoplasm; Energy Metabolism; Ferric Compounds; Formates; Fumarates; Gene Deletion; Gene Expression Profiling; Geobacter; Hydrogen; NADH, NADPH Oxidoreductases; Oligonucleotide Array Sequence Analysis

Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed.

Topics: Acetic Acid; Arctic Regions; Bacterial Typing Techniques; Deltaproteobacteria; Fatty Acids; Ferric Compounds; Formates; Fumarates; Genes, rRNA; Geologic Sediments; Hydrogen; Lactic Acid; Manganese; Microscopy, Electron; Molecular Sequence Data; Movement; Oxidation-Reduction; Phylogeny; Propionates; RNA, Bacterial; RNA, Ribosomal, 16S; Soil Microbiology; Sulfur

Sulfurospirillum multivorans is a dehalorespiring organism, which is able to utilize tetrachloroethene as terminal electron acceptor in an anaerobic respiratory chain. The localization of the tetrachloroethene reductive dehalogenase in dependence on different growth substrates was studied using the freeze-fracture replica immunogold labeling technique. When the cells were grown with pyruvate plus fumarate, a major part of the enzyme was either localized in the cytoplasm or membrane associated facing the cytoplasm. In cells grown on pyruvate or formate as electron donors and tetrachloroethene as electron acceptor, most of the enzyme was detected at the periplasmic side of the cytoplasmic membrane. These results were confirmed by immunoblots of the enzyme with and without the twin arginine leader peptide. Trichloroethene exhibited the same effect on the enzyme localization as tetrachloroethene. The data indicated that the localization of the enzyme was dependent on the electron acceptor utilized.

Topics: Bacterial Proteins; Cell Membrane; Cytoplasm; Epsilonproteobacteria; Formates; Fumarates; Immunoblotting; Microscopy, Immunoelectron; Models, Biological; Oxidoreductases; Pyruvic Acid

To compare fermentation pattern in cultures of Bacteroides caccae supplied with pectin and glucose, and identify enzymes involved in metabolism of pectin.. A strain KWN isolated from the rabbit caecum was used. Fermentation pattern, changes of viscosity and enzyme reactions products were determined. Cultures grown on pectin produced significantly more acetate and less formate, lactate, fumarate and succinate than cultures grown on glucose. Production of cell dry matter and protein per gram of substrate used was the same in pectin- and glucose-grown cultures. The principal enzymes that participated in the metabolism of pectin were extracellular exopectate hydrolase (EC 3.2.1.67), extracellular endopectate lyase (EC 4.2.2.2) and cell-associated 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14). The latter enzyme is unique to the Entner-Doudoroff pathway. Activities of pectinolytic enzymes in cultures grown on glucose were low. Activity of KDPG aldolase was similar in pectin- and glucose-grown cells.. Metabolites and activities of pectin-degrading enzymes differed in cultures of B. caccae KWN grown on pectin and glucose. Yields of dry matter and protein were the same on both substrates.. Information on metabolism of pectin in animal strains of Bacteroides is incomplete. This study extends the knowledge on metabolism in bacteria from the rabbit caecum.

Topics: Acetates; Aldehyde-Lyases; Animals; Bacterial Proteins; Bacteroides; Biomass; Cecum; Fermentation; Formates; Fumarates; Glucose; Lactic Acid; Pectins; Polygalacturonase; Polysaccharide-Lyases; Rabbits; Succinic Acid

Dinoflagellate algae of the genus Symbiodinium in symbiosis with marine animals release much of their photosynthetic carbon to the animal host. The compounds translocated to the host ('mobile compounds') were investigated by metabolite comparison as follows: a substrate was identified as a candidate mobile compound when comparable profiles of metabolites were generated from host metabolism of this substrate (supplied exogenously) and the endogenous mobile compounds. When the sea anemone Anemonia viridis was incubated with NaH14CO2 under photosynthesizing conditions, most of the radioactivity in the animal tissue was recovered from the low-molecular-mass fraction and distributed in the ratio 1:2:1 between the neutral, acidic and basic sub-fractions. Prominent 14C-labelled compounds included glucose, malate and glucose-6-phosphate. When the symbiosis was incubated with 14C-labelled glucose plus succinate or fumarate (but none of eight other substrate combinations tested), the 14C-labelled metabolites closely matched those obtained with NaH14CO2. These data suggest that glucose and succinate/fumarate (or metabolically allied compounds) may be important photosynthetic compounds transferred from the Symbiodinium cells to the tissues of A. viridis. Metabolite comparisons can be applied to study nutritional interactions in symbioses involving photosynthetic algae and, with appropriate modification, other associations between microorganisms and plants or animals.

Topics: Animals; Carbon Radioisotopes; Dinoflagellida; Formates; Fumarates; Glucose; Photosynthesis; Sea Anemones; Succinic Acid; Symbiosis; Wales

The cell homogenate and the soluble cell fraction of Wolinella succinogenes grown with formate and fumarate catalyzed the oxidation of benzyl viologen radical by methacrylate [apparent Km=0.23 mM, Vmax=1.0 U (mg cell protein) -1] or acrylate [apparent Km=0.50 mM, Vmax=0.77 U (mg cell protein) -1]. Crotonate did not serve as an oxidant. A mutant of W. succinogenes lacking the fccABC operon was unable to catalyze methacrylate or acrylate reduction. In contrast, the inactivation of fccC alone had no effect on these activities. Methacrylate reduction by benzyl viologen radical was not catalyzed by fumarate reductase isolated from the membrane of W. succinogenes. Cells grown with formate and fumarate did not catalyze methacrylate reduction by formate, and W. succinogenes did not grow with formate and methacrylate as catabolic substrates. The results suggest that the reduction of methacrylate or acrylate by benzyl viologen radical is most likely catalyzed either by the periplasmic flavoprotein FccA or by a complex consisting of FccA and the predicted c-type cytochrome FccB. The metabolic function of the fccABC operon remains unknown.

Topics: Cell Membrane; Cytochrome c Group; Formates; Fumarates; Methacrylates; Periplasm; Restriction Mapping; Succinate Dehydrogenase; Wolinella

The catalysts for many microbially mediated environmental processes such as the dechlorination of polychlorinated biphenyls (PCBs) have been difficult to identify by traditional isolation techniques. Numerous, as yet unsuccessful, attempts have been made to isolate and culture the dechlorinating species. To overcome this limitation, amplified rDNA restriction analysis (ARDRA) of a clone library, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP) were used concurrently to compare their effectiveness for characterizing an enriched microbial community. These methods were applied to enrichment cultures that selectively dechlorinated double-flanked chlorines in the PCB congener 2,3,4,5 chlorinated biphenyl. The methods have different biases, which were apparent from discrepancies in the relative clone frequencies (ARDRA), band intensities (DGGE) or peak heights (TRFLP) from the same enrichment culture. However, each method was effectively qualitative and identified the same organisms: a low G + C Gram-positive eubacterium, an organism most similar to the green non-sulphur bacteria, an Aminobacterium sp. and a Desulfovibrio sp. Overall, in community fingerprinting and preliminary identification, DGGE proved to be the most rapid and effective tool for the monitoring of microorganisms within a highly enriched culture. TRFLP results corroborated DGGE fingerprint analysis; however, identification required the additional step of creating a clone library. ARDRA provided an in-depth analysis of the community and this technique detected slight intraspecies sequence variation in 16S rDNA. These molecular methods are common in environmental microbiology, but rarely are they compared with the same sample site or culture. In general, all three methods detected similar community profiles, but inherent biases resulted in different detection limits for individual OTUs (operational taxonomic units).

Topics: Ampicillin; Anti-Bacterial Agents; Anticarcinogenic Agents; Bacteria; Chlorine; DNA, Bacterial; DNA, Ribosomal; Electrophoresis; Formates; Fumarates; Molecular Sequence Data; Penicillins; Phylogeny; Polychlorinated Biphenyls; Polymorphism, Restriction Fragment Length; Vancomycin

Eight barrows (Yorkshire x [Finnish Landrace x Dutch Landrace]), initially 30 kg BW, were fitted with ileal cannulas to evaluate the effects of supplementing Ca benzoate (2.4%) and organic acids (OA) in the amount of 300 mEq acid/kg feed on dietary buffering capacity (BC), apparent digestibility and retention of nutrients, and manure characteristics. Swine were allotted in a 2 x 4 factorial arrangement of treatments according to a cyclic (8 x 5) changeover design. Two tapioca-corn-soybean meal-based diets were formulated without and with acidogenic Ca benzoate. Each diet was fed in combination with OA (none, formic, fumaric, or n-butyric acid). Daily rations were equal to 2.8 x maintenance requirement (418 kJ ME/BW(.75)) and were given in two portions. Chromic oxide (.25 g/kg) was used as a marker. On average, Ca benzoate lowered BC by 54 mEq/kg feed. This salt enhanced (P < .05) the ileal digestibility (ID) of DM, OM, arginine, isoleucine, leucine, phenylalanine, alanine, aspartic acid, and tyrosine (by up to 2.4 percentage units). Also, the total tract digestibility (TD) of DM, ash, Ca and GE, and Ca retention (percentage of intake) was greater (P < .05) in swine fed Ca benzoate, whereas N retention remained unaffected. Addition of all OA (formic and n-butyric acid, in particular) exerted a positive effect (P < .05) on the ID of amino acids (except for arginine, methionine, and cysteine). A similar effect (P < .05) was found for the TD of DM, OM, CP, Ca and total P and for the retention of N and Ca. In swine fed Ca benzoate, urinary pH decreased by 1.6 units (P < .001). In conclusion, dietary OA have a beneficial effect on the apparent ileal/total tract nutrient digestibilities, and Ca benzoate increased urine acidity, which could be effective against a rapid ammonia emission from manure of swine.

Topics: Animal Feed; Animals; Buffers; Butyrates; Calcium; Dietary Supplements; Digestion; Feces; Formates; Fumarates; Hydrogen-Ion Concentration; Male; Random Allocation; Swine

During growth with fumarate as the terminal electron transport acceptor and either formate or sulfide as the electron donor, Wolinella succinogenes induced a peri-plasmic protein (54 kDa) that reacted with an antiserum raised against the periplasmic fumarate reductase (Fcc) of Shewanella putrefaciens. However, the periplasmic cell fraction of W. succinogenes did not catalyze fumarate reduction with viologen radicals. W. succinogenes grown with polysulfide instead of fumarate contained much less (< 10%) of the 54-kDa antigen, and the antigen was not detectable in nitrate-grown bacteria. The antigen was most likely encoded by the fccA gene of W. succinogenes. The antigen was absent from a DeltafccABC mutant, and its size is close to that of the protein predicted by fccA. The fccA gene probably encodes a pre-protein carrying an N-terminal signal peptide. The sequence of the mature FccA (481 residues, 52.4 kDa) is similar (31% identity) to that of the C-terminal part (450 residues) of S. putrefaciens fumarate reductase. As indicated by Northern blot analysis, fccA is cotranscribed with fccB and fccC. The proteins predicted from the fccB and fccC gene sequences represent tetraheme cytochromes c. FccB is similar to the N-terminal part (150 residues) of S. putrefaciens fumarate reductase, while FccC resembles the tetraheme cytochromes c of the NirT/NapC family. The DeltafccABC mutant of W. succinogenes grew with fumarate and formate or sulfide, suggesting that the deleted proteins were not required for fumarate respiration with either electron donor.

Topics: Amino Acid Sequence; Cell Membrane; Cytochrome c Group; Formates; Fumarates; Genes, Bacterial; Gram-Negative Facultatively Anaerobic Rods; Molecular Sequence Data; Molecular Weight; Periplasm; Restriction Mapping; RNA, Bacterial; RNA, Messenger; Sequence Deletion; Sequence Homology, Amino Acid; Succinate Dehydrogenase; Sulfides; Wolinella

The metabolism of fumarate by Helicobacter pylori was investigated employing one- and two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy. Metabolically competent cells generated malate and succinate from fumarate as the sole substrate indicating the presence of fumarase and fumarate reductase activities in the bacterium. In incubations of fumarate with cell lysates accumulation of lactate, acetate, formate and alanine was observed after the initial production of malate and succinate. The results indicate the existence of active fumarate catabolism in H. pylori and suggest the possibility of an ATP generating mechanism which may play an important role in the bioenergetics of the bacterium.

Topics: Acetates; Alanine; Energy Metabolism; Formates; Fumarates; Helicobacter pylori; Kinetics; Lactates; Lactic Acid; Magnetic Resonance Spectroscopy; Malates; Succinates; Succinic Acid

Bacteroides gracilis is a gram-negative anaerobic bacillus which requires formate and fumarate for growth; it has been implicated in periodontal disease and serious infections of the head and neck. In this study, Bacteroides ureolyticus (NTU) medium was tested for its ability to allow the growth of B. gracilis and other formate-fumarate requiring gram-negative anaerobes and to enable the recovery of these organisms from clinical specimens. All reference strains grew on NTU medium with the exception of Wolinella recta and formate-fumarate requiring organisms were isolated from 18 of 20 samples of subgingival dental plaque from patients with chronic periodontitis. B. gracilis was the commonest species isolated (14 of the 29 isolates); B. ureolyticus was not found.

Topics: Bacteroides; Culture Media; Formates; Fumarates; Humans; Periodontitis

Experimental data showed a significant improvement of growth rate and efficiency of feed utilization of young animals (piglets) by the dietary inclusion of organic acids. These ergotropic effects were mainly observed with citric acid, fumaric acid and formic acid as well as with Ca and Na formate. The merely dietary pH lowering with an inorganic acid (ortho-phosphoric acid) failed to show a nutritive efficacy. Studies on the mode of action of organic acids indicated a higher protein and energy digestibility, a lower stomach pH and reduced levels of NH3 and lactic acid in the stomach and duodenal digesta. Furthermore, the duodenum mainly contained a significant lower bacterial population for E. coli and enterococci. By this way the burden of metabolism of the host may be reduced which results in a higher overall performance.

Topics: Animal Feed; Animals; Carboxylic Acids; Citrates; Citric Acid; Dietary Proteins; Digestion; Duodenum; Energy Metabolism; Formates; Fumarates; Gastric Mucosa; Hydrogen-Ion Concentration; Phosphoric Acids; Swine

Topics: Bacteroides; Campylobacter; Culture Media; Eikenella corrodens; Formates; Fumarates; Vibrio

The Mu dl (ApR lac) bacteriophage was used to generate mutants of Escherichia coli which were defective in formate hydrogenlyase. Three mutants were chosen for further analysis: they lacked hydrogenase (hydrogen: benzyl viologen oxidoreductase) activity, but produced normal levels of fumarate reductase activity and two- to three-fold reduced levels of benzyl viologen (BV)-dependent formate dehydrogenase activity. Two of them (hydC) were shown to contain about 4-fold reduced amounts of formate hydrogenlyase and fumarate-dependent H2 uptake activities. The third one (hydD) was totally devoid of both activities. Their insertion sites were located at 77 min on the E. coli map. Subdivision of these mutants into two classes was subsequently based on the restoration capacity of hydrogenase activity with high concentration of nickel in the growth media. Addition of 500 microM NiCl2 led to a complete recovery of hydrogenase activity, and to the concomitant restoration of normal BV-linked formate dehydrogenase, formate hydrogenlyase and fumarate-dependent H2 uptake activities in the hydC mutants. The hydD mutant was insensitive to the effect of nickel. Expression of the lac operon in hydC and hydD mutants was induced by anaerobiosis. It was not increased by the addition of formate under anaerobic conditions. The presence of nitrate resulted in slightly reduced beta-galactosidase activities in the hydC mutants, whereas those found in the hydD mutant reached only one third of the level obtained in its absence. Fumarate had no effect on both classes. Moreover, in contrast to the hydD locus, the hydC::Mu dl fusions were found to be dependent upon the positive control exerted by the nirR gene product and were totally repressed by an excess of nickel. In addition, the low levels of overall hydrogenase-dependent activities found in a nirR strain were also relieved by the presence of nickel. Our results strongly suggest that the pleiotropic regulatory gene nirR is essential for the expression of a gene (hydC) involved in either transport or processing of nickel in the cell, whose alteration leads to a loss of hydrogenase activity.

Topics: Alleles; Benzyl Viologen; beta-Galactosidase; Conjugation, Genetic; Escherichia coli; Formate Dehydrogenases; Formates; Fumarates; Gene Expression Regulation; Genes, Bacterial; Hydrogen; Hydrogenase; Mutation; Nickel; Transcription, Genetic; Transduction, Genetic

The electron-transport chain catalyzing fumarate reduction by formate has recently been reconstituted from the formate dehydrogenase complex and the fumarate reductase complex from Vibrio succinogenes, in a liposomal preparation containing vitamin K-1 (Unden, G. and Kröger, A. (1982) Biochim. Biophys. Acta 682, 258-263). We have now investigated the structural properties of this preparation. The preparation was found to consist of a homogeneous population of unilamellar proteoliposomes with an average diameter of about 100 nm and an internal volume of 2-4 ml/g phospholipid. The buoyant density (1.07 g/ml) was consistent with the protein/phospholipid ratio (0.2 g/g) of the preparation. Leakage of glucose from the internal spaces of the proteoliposomes was negligibly slow. Proteoliposomes prepared with either of the enzyme complexes showed peripheral projections mainly on the outer surface, when examined by electron microscopy after negative staining. The size, orientation and surface density of the projections were consistent with those of the enzymes. Most of the substrate and dye-reactive sites (70-90%) of the enzymes in the proteoliposomes were accessible to external non-permeant substrates. The proteoliposomes catalyzing electron transport were formed by freeze-thawing a mixture of liposomes and protein-phospholipid complexes which did not perform electron transport from formate to fumarate. Nearly the entire amount of the enzymes supplied (0.2 g protein/g phospholipid) was incorporated into the liposomes by this procedure. The transformation of liposomes into proteoliposomes was accompanied by exchange of the internal solutes with the external medium.

Topics: Aldehyde Oxidoreductases; Electron Transport; Formate Dehydrogenases; Formates; Fumarates; Kinetics; Liposomes; Microscopy, Electron; Multienzyme Complexes; Proteolipids; Succinate Dehydrogenase; Vibrio

1. With fumarate as the terminal electron acceptor and either H2 or formate as donor, Vibrio succinogenes could grow anaerobically in a mineral medium using fumarate as the sole carbon source. Both the growth rate and the cell yield were increased when glutamate was also present in the medium. 2. Glutamate was incorporated only into the amino acids of the glutamate family (glutamate, glutamine, proline and arginine) of the protein. The residual cell constituents were synthesized from fumarate. 3. Pyruvate and phosphoenolpyruvate, as the central intermediates of most of the cell constituents, were formed through the action of malic enzyme and phosphoenolpyruvate synthetase. Fructose-1,6-bisphosphate aldolase was present in the bacterium suggesting that this enzyme is involved in carbohydrate synthesis. 4. In the absence of added glutamate the amino acids of the glutamate family were synthesized from fumarate via citrate. The enzymes involved in glutamate synthesis were present. 5. During growth in the presence of glutamate, net reducing equivalents were needed for cell synthesis. Glutamate and not H2 or formate was used as the source of these reducing equivalents. For this purpose part of the glutamate was oxidized to yield succinate and CO2. 6. The alpha-ketoglutarate dehydrogenase involved in this reaction was found to use ferredoxin as the electron acceptor. The ferredoxin of the bacterium was reoxidized by means of a NADP-ferredoxin oxidoreductase. Enzymes catalyzing the reduction of NAD, NADP or ferredoxin by H2 or formate were not detected in the bacterium.

Topics: Electron Transport; Formates; Fumarates; Glutamates; Kinetics; Vibrio

Vibrio succinogenes which gains all the ATP by anaerobic electron transport phosphorylation, was grown in continuous culture on a defined medium with formate and fumarate as sole energy sources. The growth yield at infinite dilution rate (Ymax) was obtained by extrapolation from the growth yields measured at various dilution rates. With formate as the growth limiting substrate, Ymax was found as 14 g dry cells/mol formate. Under these conditions growth was limited by the rate of energy supply, because formate is used only as a catabolic substrate (Bronder et al. 1982). The YmaxATP calculated from the ATP requirement for cell synthesis was 18 g dry cells/mol ATP. This gives an ATP/2e ratio of 0.8. The ATP/2e ratio in vitro had been measured as 1 (Kröger and Winkler 1981). It is concluded that growing V. succinogenes gain at least 80% the stoichiometrically possible amount of ATP, when growth is limited by energy supply.

Topics: Adenosine Triphosphate; Anaerobiosis; Electron Transport; Formates; Fumarates; Kinetics; Vibrio

Deibel, R. H. (American Meat Institute Foundation, Chicago, Ill.), and M. J. Kvetkas. Fumarate reduction and its role in the diversion of glucose fermentation by Streptococcus faecalis. J. Bacteriol. 88:858-864. 1964.-Fumarate diverts the normal fermentation of glucose by Streptococcus faecalis FB82, as shown by the production of increased amounts of CO(2), formate, acetate, and acetoin, and decreased formation of lactate and ethanol. Experiments with d-glucose-1-C(14), in which low levels of labeled CO(2) were recovered, indicated that C-1 cleavage of the glucose molecule was not involved. The presence of fumarate afforded consistently larger cell crops in growth studies with glucose and other energy sources. On a molar growth-yield basis, anaerobically grown, glucose-fumarate cultures were equivalent to aerobically grown, glucose cultures. The reduction of fumarate by cell suspensions indicated that glucose, gluconate, and, to a lesser extent, glycerol and mannitol could serve as hydrogen donors. Several common metabolic inhibitors had no effect upon the fumarate reductase system in cell suspensions, although some sensitivity to acidic pH was noted. Significant levels of succinate oxidation activity were not detected. Fumarate reductase activity was demonstrated in all five S. faecalis strains tested. Distribution of this ability in S. faecium strains was variable, ranging from activity comparable with that of S. faecalis to total inactivity. The observations support the conclusion that fumarate functions as an alternate hydrogen acceptor, thus allowing pyruvate to participate in the energy-yielding phosphoroclastic and dismutation pathways.

Topics: Acetates; Carbohydrate Metabolism; Enterococcus faecalis; Ethanol; Fermentation; Formates; Fumarates; Gluconates; Glucose; Glycerol; Hydrogen; Lactates; Mannitol; Oxidation-Reduction; Oxidoreductases; Pyruvates; Pyruvic Acid; Research; Succinates