THE METABOLISM OF PROPIONIC ACID

Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation

In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield.

In this work, a systematic methodology was developed (based on known biochemistry, physiology, and bioenergetics) for the automated feasibility evaluation and net ATP yield quantification of large sets of pathway variants. Possible pathway variants differ in their intermediate metabolites, in which electron carriers are involved, in which steps are consuming/producing ATP, and in which steps are coupled to (and to how many) proton (or its equivalent) translocations. A pathway variant is deemed feasible, under a given set of physiological and environmental conditions, only if all pathway reaction steps have nonpositive Gibbs energy changes and if all the metabolite concentrations remain within an acceptable physiological range (10⁻⁶ to 10⁻² M). The complete understanding of syntrophic propionate oxidation remains elusive due to uncertainties in pathways and the mechanisms for interspecies electron transfer (IET). Several million combinations of pathway variants and parameters/conditions were evaluated for propionate oxidation, providing unprecedented mechanistic insight into its biochemical and bioenergetic landscape. Our results show that, under a scenario of optimum environmental conditions for propionate oxidation, the Smithella pathway yields the most ATP and the methylmalonyl-coenzyme A (CoA) pathways can generate sufficient ATP for growth only under a cyclical pathway configuration with pyruvate. The results under conditions typical of methanogenic environments show that propionate oxidation via the lactate and via the hydroxypropionyl-CoA pathways yield the most ATP. IET between propionate oxidizers and methanogens can proceed either by dissolved hydrogen via the Smithella pathway or by different mechanisms (e.g., formate or direct IET) if other pathways are used.

IMPORTANCE In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield. The methodology is designed to be especially relevant to hypothesize on which microbial pathway variants should be most favored in microbial ecosystems under high selective pressure for efficient metabolic energy conservation. Syntrophic microbial oxidation of propionate to acetate has an extremely small quantity of available energy and requires an extremely high metabolic efficiency to sustain life. Our results bring mechanistic insights into the optimum pathway variants, other metabolic bottlenecks, and the impact of environmental conditions on the ATP yields. Additionally, our results conclude that, as previously reported, under specific conditions, IET mechanisms other than hydrogen must exist to simultaneously sustain the growth of both propionate oxidizers and hydrogenotrophic methanogens.

Propionate metabolism in a human pathogenic fungus: proteomic and biochemical analyses

Fungi of the complex Paracoccidioides spp. are thermodimorphic organisms that cause Paracoccidioidomycosis, one of the most prevalent mycoses in Latin America. These fungi present metabolic mechanisms that contribute to the fungal survival in host tissues. Paracoccidioides lutzii activates glycolysis and fermentation while inactivates aerobic metabolism in iron deprivation, a condition found during infection. In lungs Paracoccidioides brasiliensis face a glucose poor environment and relies on the beta-oxidation to support energy requirement. During mycelium to yeast transition P. lutzii cells up-regulate transcripts related to lipid metabolism and cell wall remodeling in order to cope with the host body temperature. Paracoccidioides spp. cells also induce transcripts/enzymes of the methylcitrate cycle (MCC), a pathway responsible for propionyl-CoA metabolism. Propionyl-CoA is a toxic compound formed during the degradation of odd-chain fatty acids, branched chain amino acids and cholesterol. Therefore, fungi require a functional MCC for full virulence and the ability to metabolize propionyl-CoA is related to the virulence traits in Paracoccidioides spp. On this way we sought to characterize the propionate metabolism in Paracoccidioides spp. The data collected showed that P. lutzii grows in propionate and activates the MCC by accumulating transcripts and proteins of methylcitrate synthase (MCS), methylcitrate dehydratase (MCD) and methylisocitrate lyase (MCL). Biochemical characterization of MCS showed that the enzyme is regulated by phosphorylation, an event not yet described. Proteomic analyses further indicate that P. lutzii yeast cells degrades lipids and amino acids to support the carbon requirement for propionate metabolism. The induction of a putative propionate kinase suggests that fungal cells use propionyl-phosphate as an intermediate in the production of toxic propionyl-CoA. Concluding, the metabolism of propionate in P. lutzii is under regulation at transcriptional and phosphorylation levels and that survival on this carbon source requires additional mechanisms other than activation of MCC.

Biosynthesis of isoxazolin-5-one and 3-nitropropanoic acid containing glucosides in juvenile Chrysomelina

Biosynthesis of isoxazolin-5-one glucoside and 3-nitropropanoate esters as hemolymph defenses in leaf beetle larvae.

Pathways of propionate degradation by enriched methanogenic cultures

A mixed methanogenic culture was highly enriched in a growth medium containing propionate as the sole organic carbon and energy source. With this culture, the pathways of propionate degradation were studied by use of C-radiotracers. Propionate was first metabolized to acetate, carbon dioxide, and hydrogen by nonmethanogenic organisms. Formate was not excreted. The carbon dioxide originated exclusively from the carboxyl group of propionate, whereas both [2-C]- and [3-C]propionate lead to the production of radioactive acetate. The methyl and carboxyl groups of the acetate produced were equally labeled, regardless of whether [2-C]- or [3-C]propionate was used. These observations suggest that in the culture, propionate was degraded through a randomizing pathway.

C nuclear magnetic resonance studies of propionate catabolism in methanogenic cocultures

Propionate catabolism was monitored in anaerobic cocultures of propionate-degrading and methanogenic bacteria. Metabolism was monitored by use of C-enriched propionate and succinate. The intermediates identified indicated that the methylmalonyl coenzyme A pathway was used in these cultures. The data also indicated that a transcarboxylation reaction between succinate and propionyl coenzyme A occurred, yielding propionate and methylmalonyl coenzyme A.

A proposed pathway for catabolism of propionate in methanogenic cocultures

A metabolic pathway for the catabolism of propionate is proposed. This pathway incorporates a transcarboxylation reaction involving propionyl coenzyme A and oxaloacetate and a carboxylation of pyruvate to regenerate oxaloacetate. Data indicated that the proposed pathway is reversible. The proposed pathway and its apparent reversibility provide a reasonable explanation of observations obtained from metabolism of labeled substrate.

Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core

Transcarboxylase from Propionibacterium shermanii is a 1.2 MDa multienzyme complex that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate, yielding propionyl-CoA and oxaloacetate. The 1.9 A resolution crystal structure of the central 12S hexameric core, which catalyzes the first carboxylation reaction, has been solved bound to its substrate methylmalonyl-CoA. Overall, the structure reveals two stacked trimers related by 2-fold symmetry, and a domain duplication in the monomer. In the active site, the labile carboxylate group of methylmalonyl-CoA is stabilized by interaction with the N-termini of two alpha-helices. The 12S domains are structurally similar to the crotonase/isomerase superfamily, although only domain 1 of each 12S monomer binds ligand. The 12S reaction is similar to that of human propionyl-CoA carboxylase, whose beta-subunit has 50% sequence identity with 12S. A homology model of the propionyl-CoA carboxylase beta-subunit, based on this 12S crystal structure, provides new insight into the propionyl-CoA carboxylase mechanism, its oligomeric structure and the molecular basis of mutations responsible for enzyme deficiency in propionic acidemia.

The suicide inactivation of ox liver short-chain acyl-CoA dehydrogenase by propionyl-CoA. Formation of an FAD adduct

Propionyl-CoA gave an unexpectedly low turnover (0.03 s-1) and high Km (153 microM) as a substrate for ox liver short-chain acyl-CoA dehydrogenase (SCAD). On addition of an excess of propionyl-CoA to SCAD the flavin A448 decreased to about 30% of its original value and the peak at 368 nm was replaced by one at 335 nm. The decrease in A448 exhibited first-order kinetics and correlated with a first-order decrease in the enzyme's catalytic activity to 22% of the initial value. The flavin, released from propionyl-CoA-treated enzyme with trichloroacetic acid, reacted with O2 to form a stable free radical. This suggests that a reduced N-5 flavin adduct is formed on the enzyme and protected from O2. The released adduct was separated from unmodified flavin and excess propionyl-CoA by h.p.l.c., and was shown by 3H-labelling to contain CoA. The incompleteness of the decrease in the enzyme's A448 and specific activity on incubation with propionyl-CoA probably reflects an equilibrium between covalently and non-covalently bound acyl-CoA, since the spectral changes could be reversed. The enzyme was also re-activated by dilution and incubation with a large molar excess of butyryl-CoA. The rate constant, approx. 2 X 10(-3) s-1, for re-activation, taken with the extrapolated rate constant for the opposing inactivation reaction, 8.9 X 10(-3) s-1, explains the 22% residual activity at equilibrium. The results suggest that propionyl-CoA is a suicide inhibitor for SCAD.

Intracellular localization of hepatic propionyl-CoA carboxylase and methylmalonyl-CoA mutase in humans and normal and vitamin B12 deficient rats

The intracellular localization of the enzymes in the vitamin B12 dependent pathway which involves the oxidation of propionate was studied in rat liver obtained from normal and vitamin B12 deficient rats as well as from man. The subcellular site of propionyl CoA carboxylase and the vitamin B12 dependent-methylmalonyl CoA mutase were determined. All of the activity of these two enzymes was demonstrated to be in the mitochondria and those enzymes were shown to be loosely bound to the inner membrane-matrix portion of the mitochondria. Vitamin B12 deficiency did not alter the subcellular localization. Finally, a rapid enzymatic assay for methylmalonyl-CoA mutase was described.

[13C]Valine metabolism in methylmalonicacidemia using nuclear magnetic resonance: propinonate as an obligate intermediate

[Alpha-13C]- and [alpha,beta-13C]valine were administered sequentially to a patient with methylmalonicacidemia to clarify the metabolic pathway of valine from methylmalonic acid semialdehyde to methylmalonyl-CoA. Methylmalonic acid was isolated from multiple urine samples, purified, and analyzed by 13C nuclear magnetic resonance spectroscopy. Contrary to the widely accepted view, the results show unequivocally that methylmalonic acid semialdehyde is decarboxylated to propionate before conversion to methylmalonyl CoA.

3-hydroxypropionate: significance of -oxidation of propionate in patients with propionic acidemia and methylmalonic acidemia

[l-(14)C]Propionate administered intravenously was metabolized to methylmalonate, to 3-hydroxypropionate, and to methylcitrate in the urine of a patient with methylmalonic acidemia. L-[U-(14)C]Isoleucine and L-[U-(14)C]valine were also converted to urinary methylmalonate and to 3-hydroxypropionate in the patient. Two patients with propionic acidemia due to a defect in propionyl-CoA carboxylase metabolized [l-(14)C]propionate to uninary methylcitrate and 3-hydroxypropionate. The appearance of radioactive 3-hydroxypropionate in the urine after the administration of these compounds indicates that beta-oxidation of propionyl-CoA through acryloyl-CoA was functioning in these patients. The conversion of valine to 3-hydroxypropionate suggests that valine is oxidized by way of propionate and propionyl-CoA in man.

The carboxyl transferase component of acetyl CoA carboxylase: structural evidence for intersubunit translocation of the biotin prosthetic group

An essential protein component of acetyl CoA carboxylase, isolated and extensively purified from cell-free extracts of Escherichia coli, has been identified as malonyl CoA: d-biotin carboxyl transferase. This enzyme, which does not contain covalently-bound biotin, catalyzes carboxyl transfer from malonyl CoA to free d-biotin, a model reaction for the second step in the carboxylation of acetyl CoA. The transcarboxylation product, after stabilization by methylation, was identified as 1'-N-carboxy-d-biotin dimethyl ester. These results indicate the presence of a biotin site on the carboxyl transferase, distinct from that on the biotin carboxylase, which carries out the first step in the overall process. In addition, the carboxyl transferase catalyzes a slower abortive decarboxylation of malonyl CoA, thus indicating that carboxyl abstraction and protonation do not require the participation of biotin. It is now evident that the half-reactions of acetyl CoA carboxylation are catalyzed by biotin carboxylase and carboxyl transferase. Both components are devoid of biotin and have specific binding sites for free d-biotin, as well as for their respective substrates; hence, the acetyl CoA carboxylation mechanism must involve intersubunit translocation of the carboxylated biotinyl group, which is bound covalently to carboxyl-carrier-protein, a noncatalytic polypeptide.

Enzymatic carboxylation of biotin: molecular and catalytic properties of a component enzyme of acetyl CoA carboxylase

The biotin carboxylase component of acetyl CoA carboxylase has been purified approximately 2000 times from Escherichia coli. This protein, which catalyzes the carboxylation of free d-biotin, is free of the biotin-containing carboxyl carrier protein, is homogeneous by polyacrylamide gel electrophoresis and analytical ultracentrifugation, and has been crystallized. Biotin carboxylase, with a molecular weight of approximately 100,000, is composed of two 50,000-dalton subunits. The catalytic capacity of biotin carboxylase is markedly enhanced by ethanol (11 times at 15% v/v), and certain other organic solvents; this may mimic an effector-mediated response. The kinetic effect is exclusively on the maximal velocity of the reaction. Activation by ethanol is reversible and not accompanied by aggregation or disaggregation of the enzyme.

The interpretation of kinetic data for enzyme-catalysed reactions involving three substrates

The analysis and interpretation of initial-rate data for reactions involving three substrates, obtained in suitably designed experiments, are discussed. Possible mechanisms for such reactions are classified, the rate equations are compared and the extent to which they can be distinguished experimentally is considered.

Identification of propionate as an endogenous CO2 acceptor in Rhodospirillum rubrum and properties of purified propionyl-coenzyme A carboxylase

A heat-stable endogenous CO(2) acceptor has been found in extracts of Rhodospirillum rubrum grown photoheterotrophically on acetate. Evidence is presented which suggests that this factor is propionic acid. Thus, paper and gas chromatographic analyses have indicated that propionic acid is present in boiled extracts prepared from R. rubrum cells. The products of (14)CO(2) fixation obtained with either the boiled extract or propionic acid as the CO(2) acceptor were identical and were identified as methylmalonic acid and succinic acid by paper chromatography. The enzyme which catalyzes the carboxylation of propionyl-coenzyme A (propionyl-CoA carboxylase) was purified from R. rubrum cells grown on acetate and its properties were studied. The enzyme is similar to propionyl-CoA carboxylases isolated from mammalian sources.

Alternate pathways of metabolism of short-chain fatty acids

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The role of biotin-dependent carboxylations in biosynthetic reactions

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Molecular characteristics of liver acetyl CoA carboxylase

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Alanine and aspartate formation during growth on valine-C14 by Pseudomonas aeruginosa

Sokatch, J. R. (University of Oklahoma School of Medicine, Oklahoma City). Alanine and aspartate formation during growth on valine-C(14) by Pseudomonas aeruginosa. J. Bacteriol. 92:72-75. 1966.-Pseudomonas aeruginosa grown with dl-valine-4,4'-C(14) synthesized alanine labeled mainly in carbons 1 and 3, indicating that the isopropyl carbons of valine were the precursors of pyruvate for alanine formation by a pathway which did not involve randomization of isotope. Alanine from cells grown on valine-1-C(14) contained isotope only in the carboxyl carbon, suggesting another route to pyruvate from valine by carbon dioxide fixation. Oxidation of valine to propionyl-coenzyme A (CoA), as it occurs in animal tissues, followed by the oxidation of propionyl-CoA to acrylyl-CoA, lactyl-CoA, and pyruvate, would account for the isotope data. Cells grown on valine oxidized valine, isobutyrate, and propionate immediately, whereas cells grown on acetate did not oxidize valine or isobutyrate and required an induction period before propionate was oxidized. P. aeruginosa grown with propionate-1-C(14) or propionate-2-C(14) formed alanine-1-C(14) and alanine-2-C(14), respectively, which agrees with the contention that at least part of the propionate is oxidized via the acrylate pathway. Aspartate formed from valine-1-C(14) was labeled only in the carboxyl carbons, whereas that formed from valine-4,4'-C(14) was labeled in all four carbons, but most heavily in carbons 1 and 3. These data suggest that the main route for the formation of the carbon skeleton of aspartate was by a C(3) plus C(1) condensation, with the C(3) unit derived from the isopropyl carbons of valine and the C(1) unit probably from carbon dioxide.