A major pathway for the mammalian oxidative degradation of phytanic acid

Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans

Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous β-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.

Untargeted mass spectrometry-based metabolomics can reveal new biochemistry, but data analysis is challenging. Here, the authors develop Metaboseek, an open-source software that facilitates metabolite discovery, and apply it to characterize fatty acid alpha-oxidation in C. elegans.

Biochemistry and genetics of inherited disorders of peroxisomal fatty acid metabolism

In humans, peroxisomes harbor a complex set of enzymes acting on various lipophilic carboxylic acids, organized in two basic pathways, alpha-oxidation and beta-oxidation; the latter pathway can also handle omega-oxidized compounds. Some oxidation products are crucial to human health (primary bile acids and polyunsaturated FAs), whereas other substrates have to be degraded in order to avoid neuropathology at a later age (very long-chain FAs and xenobiotic phytanic acid and pristanic acid). Whereas total absence of peroxisomes is lethal, single peroxisomal protein deficiencies can present with a mild or severe phenotype and are more informative to understand the pathogenic factors. The currently known single protein deficiencies equal about one-fourth of the number of proteins involved in peroxisomal FA metabolism. The biochemical properties of these proteins are highlighted, followed by an overview of the known diseases.

Fragrance material review on phytol

A toxicological and dermatologic review of phytol when used as a fragrance ingredient is presented.

Alpha-Oxidation

Phytanic acid (3,7,11,15-tetramethylhexadecanoic acid) is a branched chain fatty acid, which is a constituent of the human diet. The presence of the 3-methyl group of phytanic acid prevents degradation by beta-oxidation. Instead, the terminal carboxyl group is first removed by alpha-oxidation. The mechanism of the alpha-oxidation pathway and the enzymes involved are described in this review.

Production of a polyunsaturated isoprenoid wax ester during aerobic metabolism of squalene by Marinobacter squalenivorans sp. nov

This paper describes the production of 5,9,13-trimethyltetradeca-4E,8E,12-trienyl-5,9,13-trimethyltetradeca-4E,8E,12-trienoate during the aerobic degradation of squalene by a Marinobacter strain, 2Asq64, isolated from the marine environment. A pathway involving initial cleavage of the C(10)-C(11) or C(14)-C(15) double bonds of the squalene molecule is proposed to explain the formation of this polyunsaturated isoprenoid wax ester. The isoprenoid wax ester content reached 1.1% of the degraded squalene at the mid-exponential growth phase and then decreased during the stationary phase. The wax ester content increased by approximately threefold in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. The bacterial strain is then characterized as a member of a new species, for which we propose the name Marinobacter squalenivorans sp. nov.

Phytanic acid alpha-oxidation, new insights into an old problem: a review

Phytanic acid (3,7,10,14-tetramethylhexadecanoic acid) is a branched-chain fatty acid which is known to accumulate in a number of different genetic diseases including Refsum disease. Due to the presence of a methyl-group at the 3-position, phytanic acid and other 3-methyl fatty acids can not undergo beta-oxidation but are first subjected to fatty acid alpha-oxidation in which the terminal carboxyl-group is released as CO(2). The mechanism of alpha-oxidation has long remained obscure but has been resolved in recent years. Furthermore, peroxisomes have been found to play an indispensable role in fatty acid alpha-oxidation, and the complete alpha-oxidation machinery is probably localized in peroxisomes. This Review describes the current state of knowledge about fatty acid alpha-oxidation in mammals with particular emphasis on the mechanism involved and the enzymology of the pathway.

Photochemical oxidation and autoxidation of chlorophyll phytyl side chain in senescent phytoplanktonic cells: potential sources of several acyclic isoprenoid compounds in the marine environment

Visible light-induced degradation of the chlorophyll phytyl side chain was studied in senescent cells of two phytoplanktonic strains (Skeletonema costatum and Thalassiosira weissflogii). Particular attention was paid to the induction of autoxidation processes on the phytyl chain and its photoproducts by photochemically produced hydroperoxides. The combination of photochemical oxidation and autoxidation reactions resulted in the production of several acyclic isoprenoid compounds that have been unambiguously identified by comparison of their retention times and mass spectra with those of appropriate standards. Various mechanisms are proposed to explain the formation of these oxidation products. These processes appear to be potential sources of numerous oxidized acyclic isoprenoids that previously have been detected in lacustrine and marine environments. Some oxidation products newly described or whose presence in natural samples was never reported in the literature were then sought in particulate matter, sediment, and microbial mat samples. The results obtained supported the significance of photochemical oxidation and autoxidation of phytoplanktonic chlorophyll phytyl side chain in the marine environment.

Refsum disease, peroxisomes and phytanic acid oxidation: a review

Refsum disease was first recognized as a distinct disease entity by Sigvald Refsum in the 1940s. The discovery of markedly elevated levels of the branched-chain fatty acid phytanic acid in certain patients marked Refsum disease as a disorder of lipid metabolism. Although it was immediately recognized that the accumulation of phytanic acid is due to its deficient breakdown in Refsum disease patients, the true enzymatic defect remained mysterious until recently. A major breakthrough in this respect was the resolution of the mechanism of phytanic acid alpha-oxidation in humans. In this review we describe the many aspects of Refsum disease from the clinical signs and symptoms to the enzyme and molecular defect plus the recent identification of genetic heterogeneity in Refsum disease.

Hepatic alpha-oxidation of phytanic acid. A revised pathway

Synthetic 3-methyl-branched chain fatty acids were used to decipher the breakdown of phytanic acid. Based on results obtained in intact or permeabilized rat hepatocytes, rat liver homogenates or subcellular fractions, a revised alpha-oxidation pathway is proposed which appears to be functioning in man as well. In a first step, the 3-methyl-branched chain fatty acid is activated by an acyl-CoA synthetase. This reaction requires CoA, ATP and Mg2+. Subsequently, the acyl-CoA ester is hydroxylated at position 2 by a peroxisomal dioxygenase. This step is dependent on alpha-oxoglutarate, ascorbate (or glutathione), Fe2+ and O2. The 2-hydroxy-3-methylacyl-CoA intermediate is cleaved by a peroxisomal lyase to formyl-CoA and a 2-methyl-branched fatty aldehyde. Formyl-CoA is (partly enzymically) hydrolyzed to formate, which is then converted, most likely in the cytosol, to CO2. In the presence of NAD+, the aldehyde is dehydrogenated to a 2-methyl-branched fatty acid, presumably by a peroxisomal aldehyde dehydrogenase. This acid can--after activation--be degraded via a D-specific peroxisomal beta-oxidation system.

Biodegradation of free phytol by bacterial communities isolated from marine sediments under aerobic and denitrifying conditions

Biodegradation of (E)-phytol [3,7,11, 15-tetramethylhexadec-2(E)-en-1-ol] by two bacterial communities isolated from recent marine sediments under aerobic and denitrifying conditions was studied at 20 degrees C. This isoprenoid alcohol is metabolized efficiently by these two bacterial communities via 6,10, 14-trimethylpentadecan-2-one and (E)-phytenic acid. The first step in both aerobic and anaerobic bacterial degradation of (E)-phytol involves the transient production of (E)-phytenal, which in turn can be abiotically converted to 6,10,14-trimethylpentadecan-2-one. Most of the isoprenoid metabolites identified in vitro could be detected in a fresh sediment core collected at the same site as the sediments used for the incubations. Since (E)-phytenal is less sensitive to abiotic degradation at the temperature of the sediments (15 degrees C), the major part of (E)-phytol appeared to be biodegraded in situ via (E)-phytenic acid. (Z)- and (E)-phytenic acids are present in particularly large quantities in the upper section of the core, and their concentrations quickly decrease with depth in the core. This degradation (which takes place without significant production of phytanic acid) is attributed to the involvement of alternating beta-decarboxymethylation and beta-oxidation reaction sequences induced by denitrifiers. Despite the low nitrate concentration of marine sediments, denitrifying bacteria seem to play a significant role in the mineralization of (E)-phytol.

Production of wax esters during aerobic growth of marine bacteria on isoprenoid compounds

This paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (Acinetobacter sp. strain PHY9, Pseudomonas nautica [IP85/617], Marinobacter sp. strain CAB [DSMZ 11874], and Marinobacter hydrocarbonoclasticus [ATCC 49840]) isolated from the marine environment. Different pathways are proposed to explain the formation of these compounds. In the case of 6,10, 14-trimethylpentadecan-2-one, these esters result from the condensation of some acidic and alcoholic metabolites produced during the biodegradation, while phytol constitutes the alcohol moiety of most of the esters produced during growth on this isoprenoid alcohol. The amount of these esters formed increased considerably in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. Although conflicting evidence exists regarding the stability of these esters in sediments, it seems likely that, under some conditions, bacterial esterification can enhance the preservation potential of labile compounds such as phytol.

Comparison of fatty acid alpha-oxidation by rat hepatocytes and by liver microsomes fortified with NADPH, Fe3+ and phosphate

Rat liver microsomes, when fortified with NADPH, Fe3+ and phosphate, can catalyze the oxidative decarboxylation (alpha-oxidation) of 3-methyl-substituted fatty acids (phytanic and 3-methylheptadecanoic acids) at rates that equal 60-70% of those observed in isolated hepatocytes (Huang, S., Van Veldhoven, P.P., Vanhoutte, F., Parmentier, G., Eyssen, H.J., and Mannaerts, G.P., 1992, Arch. Biochem. Biophys. 296, 214-223). In the present study we set out to identify and compare the products and possible intermediates of alpha-oxidation formed in rat hepatocytes and by rat liver microsomes. In the presence of NADPH, Fe3+ and phosphate, microsomes decarboxylated not only 3-methyl fatty acids but also 2-methyl fatty acids and even straight chain fatty acids. The decarboxylation products of 3-methylheptadecanoic and palmitic acids were purified by high-performance liquid chromatography and identified by gas chromatography/mass spectrometry as 2-methylhexadecanoic and pentadecanoic acids, respectively. Inclusion in the incubation mixtures of glutathione plus glutathione peroxidase inhibited decarboxylation by more than 90%, suggesting that a 2-hydroperoxy fatty acid is formed as a possible intermediate. However, we have not yet been able to unequivocally identify this intermediate. Instead, several possible rearrangement metabolites were identified. In isolated rat hepatocytes incubated with 3-methylheptadecanoic acid, the formation of the decarboxylation product, 2-methylhexadecanoic acid, was demonstrated, but no accumulation of putative intermediates or rearrangement products was observed. Our data do not allow us to draw conclusions on whether the reconstituted microsomal system is representative of the cellular alpha-oxidation system.(ABSTRACT TRUNCATED AT 250 WORDS)

Phytanic acid alpha-oxidation in human cultured skin fibroblasts

We studied the oxidation of [1-14C]phytanic acid, 3-methyl substituted fatty acid, to pristanic acid and 14CO2 in human skin fibroblasts. The specific activity for alpha-oxidation of phytanic acid in peroxisomes was 29- and 124-fold higher than mitochondria and endoplasmic reticulum. This finding demonstrates for the first time the presence of fatty acid alpha-oxidation enzyme system in peroxisomes.

Evidence against alpha-hydroxyphytanic acid as an intermediate in the metabolism of phytanic acid

It was established 20 years ago that phytanic acid is degraded by an initial alpha-oxidation, and that alpha-hydroxyphytanic acid is an intermediate in the reaction. Patients with Refsum's disease, as well as those with the so-called peroxisomal disorders, have an enzymatic defect in this alpha-oxidation. The present work shows that when cultured skin fibroblasts from both groups of patients as well as from healthy controls are incubated with (1-14C)phytanic acid, the only radioactive compounds which can be detected are 14CO2 and unmetabolised phytanic acid. The degradation of (1-14C)alpha-hydroxyphytanic acid to 14CO2 takes place in the mitochondrial fraction of rat liver. Unlabelled alpha-hydroxyphytanic acid added to rat liver homogenate or mitochondria and (1-14C)phytanic acid reduced considerably the production of 14CO2. However, 14C-labelling of the alpha-hydroxyphytanic acid pool did not occur. Thus, we have been unable to confirm the previous demonstration of alpha-hydroxyphytanic acid as an intermediate in the degradation of phytanic acid.

Peroxisomal oxidation of L-2-hydroxyphytanic acid in rat kidney cortex

A previously unreported metabolite of mammalian phytanic acid catabolism, 2-oxophytanic acid, was identified by gas chromatography/mass spectrometry analysis. The formation of 2-oxophytanic acid was demonstrated to result from the oxidation of L-2-hydroxyphytanic acid, a reaction catalysed by a rat-kidney-cortex H2O2-generating oxidase. The pH optimum for the L-2-hydroxyphytanate oxidase activity was 8.5 and its apparent Km and Vm were about 0.15 mM and 0.35 mumol min-1 (g tissue)-1, respectively. L-2-Hydroxyisocaproate, a substrate of rat kidney L-alpha-hydroxyacid oxidase type B, inhibited the formation of 2-oxophytanate from L-2-hydroxyphytanic acid. Fractionation studies have indicated that 40% of L-2-hydroxyphytanate oxidase was associated with a particulate fraction and that the activity distribution of the oxidase closely paralleled that of catalase, a well known peroxisomal marker enzyme.

Tissue distribution of phytanic acid and its analogues in a kinship with Refsum's disease

Three of six kin were identified, by high performance thin layer chromatography, capillary gas chromatography and mass spectrometry, as having phytanic acid storage disease. Phytanic acid was found in triacylglycerol and, to a lesser degree, in phosphatidylcholine and free fatty acids. An unsaturated analogue of phytanic acid was additionally identified in plasma and erythrocyte triacylglycerols. In plasma, branched chain fatty acids were primarily localized in the low density lipoprotein fraction. The concentration of plasma major fatty acids was not affected by the presence of these branched chain fatty acids. In contrast to plasma, only small amounts of phytanic acid were found in cerebrospinal fluid and biopsied sural nerve. The nerve phytanate was mainly associated with triacylglycerol in epineurial and perineurial tissues. Lack of phytanate accumulation in sural endoneurium, even in cases with severe fiber degeneration, suggests that demyelination in Refsum's disease may not be due to myelin instability resulting from the incorporation of branched chain fatty acids into peripheral nerve membrane.

Presence of plasma branched-chain fatty acids in multineuronal degeneration, hepatosplenomegaly and adrenocortical insufficiency

We have previously reported a unique disorder in two brothers with multi-system neuronal degeneration, hepatosplenomegaly and adrenocortical deficiency. The clinical features were different from Refsum's disease. Biochemical analysis suggested that a metabolic defect of the omega 6 polyenoic fatty acid pathway may be involved. In the present study, were have further identified by gas chromatography-mass spectrometry two branched-chain fatty acids, phytanate and pristanate, in these two patients' plasma. This small, but unequivocally elevated elevated amount of branched-chain fatty acids were primarily localized in the triacylglycerols of plasma low density lipoprotein. Such branched-chain fatty acids were not detected in skin, liver and sural nerve samples. These two cases may represent an alternative metabolic error to that found in Refsum's disease leading to phytanate accumulation.

Heredopathia atactica polyneuritiformis (Refsum's disease): 1. Clinical features and dietary management

In a patient with Refsum's disease successful dietary control of the disease has been shown to depend on adequate energy and protein intake from phytanic acid-free sources and restriction of dietary phytanic acid to a maximum of 10 mg per day, with the provision of a generous amount of the essential fatty acid, linoleic acid. The present work gives data on the phytanic-acid content of various foodstuffs and suggests dietary manipulation of the patient. Although the role that chlorophyll-bound phytol plays in Refsum's disease is uncertain, it is advisable that this is eliminated until its role is more clearly identified.

Metabolism of long-chain isoprenoid alcohols. Incorporation of phytol and dihydrophytol into the lipids of rat brain

[U-14-C]Phytol (3,7,11,15-tetramethylhexadec-2-en-1-ol) and [U-14-C]dihydrophytol (3,7,11,15-tetramethylhexadecanol) were administered intracerebrally to 18-day-old rats and incorporation of radioactivity into brain lipids was determined after 6 and 24 h. Radioactivity from [U-14-C]phytol was found in free phytenic (3,7,11,15-tetramethylhexadec-2-enoic), phytanic (3,7,11,15-tetramethylhexadecanoic) and pristanic (2,6,10,14-tetramethylpentadecanoic) acids, in phytanic and pristanic acid moieties of neutral and polar lipids, and in esters of phytol. In addition, evidence is presented for the utilization of phytol to form 1-O-phytenyl-2-acyl glycerophosphatides. Radioactivity from [U-14-C]dihydrophytol was found in free phytanic and pristanic acids, the corresponding acyl groups of neutral and polar lipids, esters of dihydrophytol and 1-O-phytanyl-2-acyl glycerophosphatides. Incorporation of either substrate into O-alkylglycerols was very low, and labeled branched-chain alk-1-enylglycerols could not be detected.

Microbial metabolism of the isoprenoid alkane pristane

The "inert" hydrocarbon pristane (2,6,10,14-tetramethylpentadecane) can be utilized as the sole source of carbon and energy for growth of a coryneform soil isolate. Identification of the metabolites 4,8,12-trimethyltridecanoic acid and alpha-methylglutaric acid indicates that two pathways of fatty acid metabolism operate in this bacterial strain. The widespread use of pristane as a biological marker appears to be predicated on its structural similarity to phytol and its apparent stability, which may be only a reflection of the inability of microorganisms to carry out its anaerobic destruction.