Cytochrome P450-dependent oxidation of fatty acids

Beyond Autoxidation and Lipoxygenases: Fatty Acid Oxidation Products in Plant Oils

For decades, research on oxidation of linoleic acid (LA, C18:2 n6) and α-linolenic acid (ALA, C18:3 n3) in plant oils has focused on autoxidatively formed and lipoxygenase-derived 9-hydro(pero)xy- and 13-hydro(pero)xy-LA and -ALA. Here, using a non-targeted approach, we show that other hydroxy fatty acids are more abundant in plant oils. Liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry analyses unveiled highly abundant peaks in flaxseed and rapeseed oils. Using authentic reference standards, seven of the peaks were identified as 9-, 10-, 12-, 13-, and 15-HODE as well as 9- and 13-HOTrE. Additionally, six peaks were characterized based on the retention time, the exact mass of the [M-H]- ion, and its fragment ions as 16-OH-C18:3, 18-OH-C18:3, three isomers of 12-OH-C18:2, and one of 15-OH-C18:2. 16-OH-C18:3 and 18-OH-C18:3 were tentatively identified as 16-OH-ALA and 18-OH-ALA, respectively, based on autoxidation and terminal hydroxylation of ALA using CYP4F2. Investigation of formation pathways suggests that fatty acid desaturase 3 is involved in the formation of the 12-OH-C18:2 isomers, 15-HODE, and its isomer. The dominantly occurring 12-OH-C18:2 isomer was identified as 12R,S-OH-9Z,15Z-octadecadienoic acid (densipolic acid) based on a synthetic standard. The characterized oxylipins occurred in cold-pressed flaxseed and rapeseed oils at concentrations of up to 0.1 g/100 g and thus about sixfold higher than the well-known 9-hydro(pero)xy- and 13-hydro(pero)xy-LA and -ALA. Concentrations in sunflower oil were lower but increased when oil was pressed from preheated seeds. Overall, this study provides fundamental new information about the occurrence of oxidized fatty acids in plant oils, having the potential to characterize their quality and authenticity.

Molecular and in silico cloning, identification, and preharvest period expression analysis of a putative cytochrome P450 monooxygenase gene from Camellia sinensis (L.) Kuntze (tea)

Cytochrome P450 monooxygenases are one of the largest heme-containing protein groups, and the majority of them catalyze hydroxylation reactions dependent on nicotinamide adenine dinucleotide phosphate and oxygen. Cytochrome P450 (CYP) enzymes function in a wide range of monooxygenation reactions essential in primary and secondary metabolism in plants. Camellia sinensis (L.) Kuntze is a commercially and economically valuable plant due to its medicinally important secondary metabolites and as a beloved beverage. Cytochrome P450 monooxygenases play a significant role in the biosynthesis of a variety of secondary metabolites in tea. Although the biosynthesis of secondary metabolites has been investigated in detail, there have been limited studies conducted on identifying the genetic mechanisms of CYP-catalyzed secondary metabolic pathways in the C. sinensis (tea) plant. In our study, we characterized a putative C. sinensis (L.) Kuntze cytochrome P450 monooxygenase gene (Csp450), which has 1759 bp full-length cDNA with 49 bp of 5' and 183 bp of 3' untranslated regions. eTh CDS of the gene is 1527 bp and 508 amino acids in length. BLAST results of the deduced amino acid sequence revealed a high similarity with the CYP704C1-like superfamily. Preharvest period gene expression analysis from May, July, and September did not show any difference.

Cloning, Expression in Yeast, and Functional Characterization of CYP76A4, a Novel Cytochrome P450 of Petunia That Catalyzes (ω-1)-Hydroxylation of Lauric Acid

A cDNA clone of a novel cytochrome P450, CYP76A4, was isolated from Petunia hybrida. The cDNA clone contained an open reading frame (ORF) encoding a predicted 510 amino acid polypeptide. The CYP76A4 cDNA was expressed in yeast Saccharomyces cerevisiae AH22. Recombinant yeast microsomes containing the CYP76A4 hemoprotein were found to catalyze (omega-1)-hydroxylation of lauric acid.

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

BACKGROUND

Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable "CYPomes" ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme.

RESULTS

The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson's P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database.

CONCLUSIONS

FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson's P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.

The Pseudomonas aeruginosa PsrA responds to long-chain fatty acid signals to regulate the fadBA5 beta-oxidation operon

Beta-oxidative enzymes for fatty acid degradation (Fad) of long-chain fatty acids (LCFAs) are induced in vivo during lung infection in cystic fibrosis patients, and this may contribute to nutrient acquisition and pathogenesis of Pseudomonas aeruginosa. The promoter region of one P. aeruginosa beta-oxidation operon, fadBA5 (PA3014 and PA3013), was mapped. Focusing on the transposon mutagenesis of strain PAO1 carrying the P(fadBA5)-lacZ fusion, a regulator for the fadBA5 operon was identified to be PsrA (PA3006). Transcriptome analysis of the DeltapsrA mutant indicated its importance in regulating beta-oxidative enzymes. These microarray data were confirmed by real-time RT-PCR analyses of the fadB5 and lipA (encoding a lipase) genes. Induction of the fadBA5 operon was demonstrated to respond to novel LCFA signals, and this induction required the presence of PsrA, suggesting that LCFAs bind to PsrA to derepress fadBA5. Electrophoretic mobility shift assays indicate specific binding of PsrA to the fadBA5 promoter region. This binding is disrupted by specific LCFAs (C(18:1)(Delta9), C(16:0), C(14:0) and, to a lesser extent, C(12:0)), but not by other medium- or short-chain fatty acids or the first intermediate of beta-oxidation, acyl-CoA. It is shown here that PsrA is a fadBA5 regulator that binds and responds to LCFA signals in P. aeruginosa.

Molecular definitions of fatty acid hydroxylases in Arabidopsis thaliana

Towards defining the function of Arabidopsis thaliana fatty acid hydroxylases, five members of the CYP86A subfamily have been heterologously expressed in baculovirus-infected Sf9 cells and tested for their ability to bind a range of fatty acids including unsubstituted (lauric acid (C12:0) and oleic acid (C18:1)) and oxygenated (9,10-epoxystearic acid and 9,10-dihydroxystearic acid). Comparison between these five P450s at constant P450 content over a range of concentrations for individual fatty acids indicates that binding of different fatty acids to CYP86A2 always results in a higher proportion of high spin state heme than binding titrations conducted with CYP86A1 or CYP86A4. In comparison to these three, CYP86A7 and CYP86A8 produce extremely low proportions of high spin state heme even with the most effectively bound fatty acids. In addition to their previously demonstrated lauric acid hydroxylase activities, all CYP86A proteins are capable of hydroxylating oleic acid but not oxygenated 9,10-epoxystearic acid. Homology models have been built for these five enzymes that metabolize unsubstituted fatty acids and sometimes bind oxygenated fatty acids. Comparison of the substrate binding modes and predicted substrate access channels indicate that all use channel pw2a consistent with the crystal structures and models of other fatty acid-metabolizing P450s in bacteria and mammals. Among these P450s, those that bind internally oxygenated fatty acids contain polar residues in their substrate binding cavity that help stabilize these charged/polar groups within their largely hydrophobic catalytic site.

A gene cluster for the fatty acid catabolism from Pseudonocardia autotrophica BCRC12444

Genes involved in fatty acid degradation (fad) were isolated from Pseudonocardia autotrophica BBRC12444. Six open reading frames and a bi-directional promoter region were identified by DNA sequence analyses and primer extension. The fad gene cluster included five ORFs, designated fadA, fadB, fadR, fadC, and fadD. Base on their amino acid sequence identity, the gene products were identified as acyl-CoA ligase (FadA), enoyl-CoA hydratase (FadB), transcriptional regulator (FadR), cytochrome P450 monooxygenase (FadC), and ferredoxin (FadD). Regulatory protein, FadR, could bind to an operator sequence located in the divergent promoter region between fadR and fadC genes, implicating the control of fatty acid degradation. The real-time quantitative PCR assays revealed that the expression of the fadA, fadB, fadR, and fadC genes was induced by long chain fatty acids and repressed by glucose. All results demonstrated that the fad gene cluster participated in the pathway of the fatty acid catabolism. This is the first bacterial fad gene cluster to be reported.

Differential expression and evolution of the Arabidopsis CYP86A subfamily

Some members of the Arabidopsis (Arabidopsis thaliana) CYP86A and CYP94B cytochrome P450 monooxygenase subfamilies, which share some sequence homology with the animal and fungal fatty acid hydroxylases, have been functionally defined as fatty acid omega-hydroxylases. With these activities, these and other fatty acid hydroxylases have potential roles in the synthesis of cutin, production of signaling molecules, and prevention of accumulation of toxic levels of free fatty acids. The constitutive and stress-inducible patterns of the five Arabidopsis CYP86A subfamily members have been defined in 7-d-old seedlings and 1-month-old plant tissues grown under normal conditions, and 7-d-old seedlings treated with different hormones (indole-3-acetic acid, abscisic acid, gibberellin, methyl jasmonic acid, brassinosteroid, salicylic acid), chemicals (clofibrate, 1-aminocyclopropane-1 carboxylic acid), or environmental stresses (cold, wounding, drought, mannitol, etiolation). Very distinct expression patterns exist for each of these fatty acid hydroxylases under normal growth conditions and in response to environmental and chemical stresses. Analysis of the promoter sequences for each of these genes with their expression patterns has highlighted a number of elements in current databases that potentially correlate with the responses of individual genes.

Metabolism of phytanic acid and 3-methyl-adipic acid excretion in patients with adult Refsum disease

Adult Refsum disease (ARD) is associated with defective alpha-oxidation of phytanic acid (PA). omega-Oxidation of PA to 3-methyl-adipic acid (3-MAA) occurs although its clinical significance is unclear. In a 40 day study of a new ARD patient, where the plasma half-life of PA was 22.4 days, omega-oxidation accounted for 30% initially and later all PA excretion. Plasma and adipose tissue PA and 3-MAA excretion were measured in a cross-sectional study of 11 patients. The capacity of the omega-oxidation pathway was 6.9 (2.8-19.4) mg [20.4 (8.3-57.4) micromol] PA/day. 3-MAA excretion correlated with plasma PA levels (r = 0.61; P = 0.03) but not adipose tissue PA content. omega-Oxidation during a 56 h fast was studied in five patients. 3-MAA excretion increased by 208 +/- 58% in parallel with the 158 (125-603)% rise in plasma PA. Plasma PA doubled every 29 h, while 3-MAA excretion followed second-order kinetics. Acute sequelae of ARD were noted in three patients (60%) after fasting. The omega-oxidation pathway can metabolise PA ingested by patients with ARD, but this activity is dependent on plasma PA concentration. omega-Oxidation forms a functional reserve capacity that enables patients with ARD undergoing acute stress to cope with limited increases in plasma PA levels.

Functional analysis of the LACERATA gene of Arabidopsis provides evidence for different roles of fatty acid omega -hydroxylation in development

We describe lacerata (lcr) mutants of Arabidopsis, which display various developmental abnormalities, including postgenital organ fusions, and report cloning of the LCR gene by using the maize transposon Enhancer/Suppressor-mutator (En/Spm). The pleiotropic mutant phenotype could be rescued by genetic complementation of lcr mutants with the wild-type LCR gene. The LCR gene encodes a cytochrome P450 monooxygenase, CYP86A8, which catalyzes omega-hydroxylation of fatty acids ranging from C12 to C18:1, as demonstrated by expression of the gene in yeast. Although palmitic and oleic acids were efficient substrates for LCR, 9,10-epoxystearate was not metabolized. Taken together with previous studies, our findings indicate that LCR-dependent omega-hydroxylation of fatty acids could be implicated in the biosynthesis of cutin in the epidermis and in preventing postgenital organ fusions. Strikingly, the same pathway seems to control trichome differentiation, the establishment of apical dominance, and senescence in plants.

A conservative amino acid substitution alters the regiospecificity of CYP94A2, a fatty acid hydroxylase from the plant Vicia sativa

Fatty acid omega-hydroxylation is involved in the biosynthesis of the plant cuticle, formation of plant defense signaling molecules, and possibly in the rapid catabolism of free fatty acids liberated under stress conditions. CYP94A2 is a cytochrome P450-dependent medium-chain fatty acid hydroxylase that was recently isolated from Vicia sativa. Contrary to CYP94A1 and CYP86A1, two other fatty acid hydroxylases previously characterized in V. sativa and Arabidopsis thaliana, CYP94A2 is not a strict omega-hydroxylase, but exhibits chain-length-dependent regioselectivity of oxidative attack. Sequence alignments of CYP94A2 with CYP94A1 and molecular modeling studies suggested that F494, located in SRS-6 (substrate recognition site) was involved in substrate recognition and positioning. Indeed, a conservative amino acid substitution at that position markedly altered the regiospecificity of CYP94A2. The observed shift from omega toward omega-1 hydroxylation was prominent with lauric acid as substrate and declined with increasing fatty acid chain length.

Induction and inactivation of a cytochrome P450 confering herbicide resistance in wheat seedlings

Cytochrome P450-dependent enzymes from wheat catalyze the oxidation of endogenous compounds (lauric and oleic acids) and of several herbicides (diclofop, chlortoluron, bentazon). Treatment of wheat seedlings with the safener, naphthalic anhydride and with phenobarbital increases dramatically several P450-dependent enzyme activities including diclofop and lauric acid hydroxylation. The parallel induction of lauric acid (omega-1)-hydroxylase and diclofop hydroxylase activities suggests that both compounds proceeds from the same or very similar forms of P450. To test whether either one or multiple P450 forms are involved in these oxidations, we have designed selective irreversible inhibitors of lauric acid (omega-1)-hydroxylase. Results of in vivo and in vitro experiments with acetylenic analogs of lauric acid (10- and 11-dodecynoic acids) strongly suggest that a single P450 catalyzes both laurate and diclofop hydroxylation. Treatment of wheat seedlings with these acetylenes results in a strong inhibition of the in vivo metabolism of diclofop although oxidation of chlortoluron and bentazon are not affected. Our results suggest that at least three distinct P450 forms are involved in the detoxification process of the three herbicides. Interestingly, we also demonstrate that herbicides themselves are potent inducers of the amount of total P450 and laurate/diclofop hydroxylase activies. This increased capacity of wheat to detoxify the herbicide through the induction of P450 enzymes seems to be for a large extend the mechanism which confers a tolerance on various herbicides.

Fusarium oxysporum fatty-acid subterminal hydroxylase (CYP505) is a membrane-bound eukaryotic counterpart of Bacillus megaterium cytochrome P450BM3

The gene of a fatty-acid hydroxylase of the fungus Fusarium oxysporum (P450foxy) was cloned and expressed in yeast. The putative primary structure revealed the close relationship of P450foxy to the bacterial cytochrome P450BM3, a fused protein of cytochrome P450 and its reductase from Bacillus megaterium. The amino acid sequence identities of the P450 and P450 reductase domains of P450foxy were highest (40.6 and 35.3%, respectively) to the corresponding domains of P450BM3. Recombinant P450foxy expressed in yeast was catalytically and spectrally indistinguishable from the native protein, except most of the recombinant P450foxy was recovered in the soluble fraction of the yeast cells, in marked contrast to native P450foxy, which was exclusively recovered in the membrane fraction of the fungal cells. This difference implies that a post (or co)-translational mechanism functions in the fungal cells to target and bind the protein to the membrane. These results provide conclusive evidence that P450foxy is the eukaryotic counterpart of bacterial P450BM3, which evokes interest in the evolutionary aspects concerning the P450 superfamily along with its reducing systems. P450foxy was classified in the new family, CYP505.

Fatty acid alpha-oxidation of tetradecylthioacetic acid and tetradecylthiopropionic acid in cucumber (Cucumis sativus)

Fatty acid alpha-oxidation in cucumber (Cucumis sativus) involves enzymatic conversion of long-chain Cn-fatty acids to the C(n-1)-aldehyde and CO2. However, the mechanism of this process is not well understood. In this study, the alpha-oxidation of the fatty acid analogues tetradecylthioacetic acid (TTA) and tetradecylthiopropionic acid (TTP) with a sulphur atom substituting the methylene group in positions 3 and 4, respectively, was investigated and compared to palmitic acid. Both [1-14C]TTA and [1-14C]TTP could be alpha-oxidised in the cucumber subcellular 150000xgmax fraction. [1-14C]TTP was an even better substrate compared to the natural palmitic acid, while [1-14C]TTA was alpha-oxidised to a lower extent. [2-14C]TTA revealed no 14CO2, indicating that only one cycle of alpha-oxidation occurred. TTA was an inhibitor of the palmitic acid alpha-oxidation, and the inhibitory effects were examined.

Functional expression in yeast and characterization of a clofibrate-inducible plant cytochrome P-450 (CYP94A1) involved in cutin monomers synthesis

The chemical tagging of a cytochrome P-450-dependent lauric acid omega-hydroxylase from clofibrate-treated Vicia sativa seedlings with [1-14C]11-dodecynoic acid allowed the isolation of a full-length cDNA designated CYP94A1. We describe here the functional expression of this novel P-450 in two Saccharomyces cerevisiae strains overproducing their own NADPH-cytochrome P-450 reductase or a reductase from Arabidopsis thaliana. The results show a much higher efficiency of the yeast strain overproducing the plant reductase compared with the yeast strain overproducing its own reductase for expressing CYP94A1. The methyl end of saturated (from C-10 to C-16) and unsaturated (C18:1, C18:2 and C18:3) fatty acids was mainly oxidized by CYP94A1. Both E/Z and Z/E configurations of 9, 12-octadecadienoic acids were omega-hydroxylated. Lauric, myristic and linolenic acids were oxidized with the highest turnover rate (24 min-1). The strong regioselectivity of CYP94A1 was clearly shifted with sulphur-containing substrates, since both 9- and 11-thia laurate analogues were sulphoxidized. Similar to animal omega-hydroxylases, this plant enzyme was strongly induced by clofibrate treatment. Rapid CYP94A1 transcript accumulation was detected less than 20 min after exposure of seedlings to the hypolipidaemic drug. The involvement of CYP94A1 in the synthesis of cutin monomers and fatty acid detoxification is discussed.

Cloning, expression in yeast, and functional characterization of CYP81B1, a plant cytochrome P450 that catalyzes in-chain hydroxylation of fatty acids

Several omega and in-chain fatty acid hydroxylases have been characterized in higher plants. In microsomes from Helianthus tuberosus tuber the omega-2, omega-3, and omega-4 hydroxylation of lauric acid is catalyzed by one or a few closely related aminopyrine- and MnCl2-inducible cytochrome P450(s). To isolate the cDNA and determine the sequences of the(se) enzyme(s), we used antibodies directed against a P450-enriched fraction purified from Mn2+-induced tissues. Screening of a cDNA expression library from aminopyrine-treated tubers led to the identification of a cDNA (CYP81B1) corresponding to a transcript induced by aminopyrine. CYP81B1 was expressed in yeast. A systematic exploration of its function revealed that it specifically catalyzes the hydroxylation of medium chain saturated fatty acids, capric (C10:0), lauric (C12:0), and myristic (C14:0) acids. The same metabolites were obtained with transgenic yeast and plant microsomes, a mixture of omega-1 to omega-5 monohydroxylated products. The three fatty acids were metabolized with high and similar efficiencies, the major position of attack depending on chain length. When lauric acid was the substrate, turnover was 30.7 +/- 1.4 min-1 and Km(app) 788 +/- 400 nM. No metabolism of long chain fatty acids, aromatic molecules, or herbicides was detected. This new fatty acid hydroxylase is typical from higher plants and differs from those already isolated from other living organisms.