Design of fluorescent substrates and potent inhibitors of CYP73As, P450s that catalyze 4-hydroxylation of cinnamic acid in higher plants

Cloning and functional characterization of a cinnamate 4-hydroxylase gene from the hornwort Anthoceros angustus

Hornworts, as the sister group to liverworts and mosses, comprise bryophytes, which are critical in understanding the evolution of key land plant traits. Cinnamate 4-hydroxylase (C4H) catalyzes the second step of the phenylpropanoid pathway to synthesize the precursor of numerous phenolic compounds, such as lignin and flavonoids. However, C4H in the hornwort Anthoceros angustus has not yet been cloned and functionally characterized. In this work, we screened the transcriptome database of A. angustus and identified one C4H gene, AnanC4H. AnanC4H maintained conserved cytochrome P450 domains with other typical plant C4Hs. Ultraviolet B irradiation and exogenous application of methyl jasmonate (MeJA) induced the expression of AnanC4H to varying degrees. The coding sequence of AnanC4H was expressed in yeast, and the recombinant proteins were isolated. The recombinant proteins of AnanC4H catalyzed the conversion of trans-cinnamic acid to p-coumaric acid and catalyzed the conversion of 3-hydroxycinnamic acid to caffeic acid. AnanC4H showed higher affinity for trans-cinnamic acid than for 3-hydroxycinnamic acid, but there was no significant difference in the catalytic efficiency of AnanC4H for the two substrates in vitro. Moreover, the expression of AnanC4H in Arabidopsis thaliana led to an increase in both the lignin content and the number of lignified cells in stems. However, there was no significant change in flavonoid content in transgenic Arabidopsis plants.

Promiscuity, a Driver of Plant Cytochrome P450 Evolution?

Plant cytochrome P450 monooxygenases were long considered to be highly substrate-specific, regioselective and stereoselective enzymes, in this respect differing from their animal counterparts. The functional data that have recently accumulated clearly counter this initial dogma. Highly promiscuous P450 enzymes have now been reported, mainly in terpenoid pathways with functions in plant adaptation, but also some very versatile xenobiotic/herbicide metabolizers. An overlap and predictable interference between endogenous and herbicide metabolism are starting to emerge. Both substrate preference and permissiveness vary between plant P450 families, with high promiscuity seemingly favoring retention of gene duplicates and evolutionary blooms. Yet significant promiscuity can also be observed in the families under high negative selection and with essential functions, usually enhanced after gene duplication. The strategies so far implemented, to systematically explore P450 catalytic capacity, are described and discussed.

Impact of copper nanoparticles and ionic copper exposure on wheat (Triticum aestivum L.) root morphology and antioxidant response

Copper nanoparticles (nCu) are widely used in industry and in daily life, due to their unique physical, chemical, and biological properties. Few studies have focused on nCu phytotoxicity, especially with regard to toxicity mechanisms in crop plants. The present study examined the effect of 15.6 μM nCu exposure on the root morphology, physiology, and gene transcription levels of wheat (Triticum aestivum L.), a major crop cultivated worldwide. The results obtained were compared with the effects of exposing wheat to an equivalent molar concentration of ionic Cu (Cu²⁺ released from CuSO₄) and to control plants. The relative growth rate of roots decreased to approximately 60% and the formation of lateral roots was stimulated under nCu exposure, possibly due to the enhancement of nitrogen uptake and accumulation of auxin in lateral roots. The expression of four of the genes involved in the positive regulation of cell proliferation and negative regulation of programmed cell death decreased to 50% in the Cu²⁺ treatment compared to that of the control, while only one gene was down-regulated to about half of the control in nCu treatment. This explained the decreased root cell proliferation and higher extent of induced cell death in Cu²⁺- than in nCu-exposed plants. The increased methane dicarboxylic aldehyde accumulation (2.17-fold increase compared with the control) and decreased antioxidant enzyme activities (more than 50% decrease compared with the control) observed in the Cu²⁺ treatment in relation to the nCu treatment indicated higher oxidative stress in Cu²⁺- than in nCu-exposed plants. Antioxidant (e.g., proline) synthesis was pronouncedly induced by nCu to scavenge excess reactive oxygen species, alleviating phytotoxicity to wheat exposed to this form of Cu. Overall, oxidative stress and root growth inhibition were the main causes of nCu toxicity.

The isolation and functional characterization of three liverwort genes encoding cinnamate 4-hydroxylase

The plant phenylpropanoid pathway is responsible for the synthesis of a wide variety of secondary metabolites. The second step in phenylpropanoid synthesis is carried out by the cytochrome P450 monooxygenase enzyme cinnamate 4-hydroxylase (C4H), which catalyzes the p-hydroxylation of trans-cinnamic acid to p-coumarate. Genes encoding C4H have been characterized in many vascular plant species, but as yet not in any bryophyte species. Here, a survey of the transcriptome sequences of four liverwort species was able to identify eight putative C4Hs. The three liverwort C4H genes taken forward for isolation and functional characterization were harbored by Plagiochasma appendiculatum (PaC4H) and Marchantia paleacea (MpC4H1 and MpC4H2). When the genes were heterologously expressed in yeast culture, an assay of enzyme activity indicated that PaC4H and MpC4H1 had a higher level of activity than MpC4H2. The favored substrate (trans-cinnamic acid) of all three liverwort C4Hs was the same as that of higher plant C4Hs. The co-expression of PaC4H in yeast cells harboring PaPAL (a P. appendiculatum ene encoding phenylalanine ammonia lyase) allowed the conversion of L-phenylalanine to p-coumaric acid. Furthermore, the expression level of PaC4H was enhanced after treatment with abiotic stress inducers UV irradiation or salicylic acid in the thallus of P. appendiculatum. The likelihood is that high activity C4Hs evolved in the liverworts and have remained highly conserved across the plant kingdom.

Synthesis and evaluation of naphthoic acid derivatives as fluorescent probes to screen advanced glycation end-products breakers

Advanced glycation end-products, namely AGEs, are involved in the pathogenesis of numerous diseases. If AGEs inhibitors are well-known, only few products are described as compounds able to destroy those deleterious products. In this work, we describe naphthoic acid derivatives, particularly 1-(naphthalen-1-yl)propane-1,2-dione 9, allowing the simple and rapid detection of AGEs breakers using a 96-well microplate fluorescence assay. Since the inaugurate publication about AGEs breakers whose activity was demonstrated using HPLC analysis, this work proposes the first assay suitable for automated and high throughput screening of AGEs breakers.

Discovery of 2-naphthoic acid monooxygenases by genome mining and their use as biocatalysts

The large pool of cytochrome P450 (P450) open-reading frames identified in genome sequences has attracted much attention as a resource for new oxidation biocatalysts. P450 genes were cloned from genome-sequenced bacteria and coexpressed with putidaredoxin and its reductase genes to provide the redox partners of P450 in Escherichia coli. Whole-cell assays were performed with 2-naphthoic acid as a substrate. Hydroxylated naphthoic acid products were rapidly detected with two reagents showing different colors in the presence of the products. Two P450s, CYP199A1 and CYP199A2, were found to hydroxylate the substrate to 7- and 8-hydroxy-2-naphthoic acids. The CYP199A1 whole-cell biocatalyst converted 1 mM 2-naphthoic acid to 0.27 mM 7-hydroxy-2-naphthoic acid and 0.53 mM 8-hydroxy-2-naphthoic acid. CYP199A2 exhibited similar regioselectivity to CYP199A1. Furthermore, we found that 8-hydroxy-2-naphthoic acid emits near-white fluorescence when exposed to UV light. These P450s will provide a facile and environmentally friendly synthetic approach to the hydroxynaphthoic acids.

A medium-throughput screening assay to determine catalytic activities of oxygen-consuming enzymes: a new tool for functional characterization of cytochrome P450 and other oxygenases

A challenge of the post-genomic era is to determine the functions of a plethora of orphan genes. This is a more acute problem when dealing with large gene families, such as the superfamily encoding cytochrome P450 enzymes in higher plants. We propose here a new, simple, medium-throughput methodology to screen for potential substrates of orphan P450 mono-oxygenases. The same technique can also be applied to screening for inhibitors of the oxygenases involved in the biosynthesis of compounds essential for plant development, such as growth regulators. The method is based on a commercially available microplate system, which detects the oxygen consumed by the catalytic reaction via an oxygen-sensing fluorophore. It is optimized using as a model CYP73A1, the cinnamic acid hydroxylase from Helianthus tuberosus, expressed in yeast. We show that the procedure is suitable not only for the detection and real-time monitoring, but also for the quantitative evaluation of enzyme activity. This new method has broad application for the identification of candidate substrates and inhibitors in chemical libraries, to support determination of physiological substrates, development of plant growth regulators, investigations on herbicide and pollutant metabolism, synthesis of valuable compounds and drug design. It also provides a fast-assay platform for determination of catalytic and inhibition parameters. The method applies to plant P450 enzymes, but also to cytochromes P450 from other organisms, and all types of oxygenases. The critical steps, calculation of oxygen consumption from fluorescence signal, and limits of the methods are discussed.

Non-natural cinnamic acid derivatives as substrates of cinnamate 4-hydroxylase

Cinnamate 4-hydroxylase (C4H), a monooxygenase in the plant phenylpropanoid pathway, was assayed for its ability to hydroxylate 29 substrate analogues. Nine of the tested analogues with various aromatic side chains, including 3-coumaric acid, were metabolized by C4H. Seven products from these reactive analogues were characterized using LC/MS, 1H NMR and 13C NMR spectroscopic analysis. For example, caffeic acid was the product of 3-coumaric acid. The products 4-hydroxy-2-chlorocinnamic acid and 4-hydroxy-2-ethoxycinnamic acid are novel compounds that have not been previously reported. The kinetic parameters of C4H towards these analogues were determined.

Engineering of a water-soluble plant cytochrome P450, CYP73A1, and NMR-based orientation of natural and alternate substrates in the active site

CYP73A1 catalyzes cinnamic acid hydroxylation, a reaction essential for the synthesis of lignin monomers and most phenolic compounds in higher plants. The native CYP73A1, initially isolated from Jerusalem artichoke (Helianthus tuberosus), was engineered to simplify purification from recombinant yeast and improve solublity and stability in the absence of detergent by replacing the hydrophobic N terminus with the peptitergent amphipathic sequence PD1. Optimized expression and purification procedures yielded 4 mg engineered CYP73A1 L(-1) yeast culture. This water-soluble enzyme was suitable for 1H-nuclear magnetic resonance (NMR) investigation of substrate positioning in the active site. The metabolism and interaction with the enzyme of cinnamate and four analogs were compared by UV-visible and 1H-NMR analysis. It was shown that trans-3-thienylacrylic acid, trans-2-thienylacrylic acid, and 4-vinylbenzoic acid are good ligands and substrates, whereas trans-4-fluorocinnamate is a competitive inhibitor. Paramagnetic relaxation effects of CYP73A1-Fe(III) on the 1H-NMR spectra of cinnamate and analogs indicate that their average initial orientation in the active site is parallel to the heme. Initial orientation and distances of ring protons to the iron do not explain the selective hydroxylation of cinnamate in the 4-position or the formation of single products from the thienyl compounds. Position adjustments are thus likely to occur during the later steps of the catalytic cycle.

Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis

CYP73 enzymes are highly conserved cytochromes P450 in plant species that catalyse the regiospecific 4-hydroxylation of cinnamic acid to form precursors of lignin and many other phenolic compounds. A CYP73A1 homology model based on P450 experimentally solved structures was used to identify active site residues likely to govern substrate binding and regio-specific catalysis. The functional significance of these residues was assessed using site-directed mutagenesis. Active site modelling predicted that N302 and I371 form a hydrogen bond and hydrophobic contacts with the anionic site or aromatic ring of the substrate. Modification of these residues led to a drastic decrease in substrate binding and metabolism without major perturbation of protein structure. Changes to residue K484, which is located too far in the active site model to form a direct contact with cinnamic acid in the oxidized enzyme, did not influence initial substrate binding. However, the K484M substitution led to a 50% loss in catalytic activity. K484 may affect positioning of the substrate in the reduced enzyme during the catalytic cycle, or product release. Catalytic analysis of the mutants with structural analogues of cinnamic acid, in particular indole-2-carboxylic acid that can be hydroxylated with different regioselectivities, supports the involvement of N302, I371 and K484 in substrate docking and orientation.

The biochemistry and medical significance of the flavonoids

Flavonoids are plant pigments that are synthesised from phenylalanine, generally display marvelous colors known from flower petals, mostly emit brilliant fluorescence when they are excited by UV light, and are ubiquitous to green plant cells. The flavonoids are used by botanists for taxonomical classification. They regulate plant growth by inhibition of the exocytosis of the auxin indolyl acetic acid, as well as by induction of gene expression, and they influence other biological cells in numerous ways. Flavonoids inhibit or kill many bacterial strains, inhibit important viral enzymes, such as reverse transcriptase and protease, and destroy some pathogenic protozoans. Yet, their toxicity to animal cells is low. Flavonoids are major functional components of many herbal and insect preparations for medical use, e.g., propolis (bee's glue) and honey, which have been used since ancient times. The daily intake of flavonoids with normal food, especially fruit and vegetables, is 1-2 g. Modern authorised physicians are increasing their use of pure flavonoids to treat many important common diseases, due to their proven ability to inhibit specific enzymes, to simulate some hormones and neurotransmitters, and to scavenge free radicals.

Chemical inactivation of the cinnamate 4-hydroxylase allows for the accumulation of salicylic acid in elicited cells

The cinnamate (CA) 4-hydroxylase (C4H) is a cytochrome P450 that catalyzes the second step of the main phenylpropanoid pathway, leading to the synthesis of lignin, pigments, and many defense molecules. Salicylic acid (SA) is an essential trigger of plant disease resistance. Some plant species can synthesize SA from CA by a mechanism not yet understood. A set of specific inhibitors of the C4H, including competitive, tight-binding, mechanism-based irreversible, and quasi-irreversible inhibitors have been developed with the main objective to redirect cinnamic acid to the synthesis of SA. Competitive inhibitors such as 2-hydroxy-1-naphthoic acid and the heme-coordinating compound 3-(4-pyridyl)-acrylic acid allowed strong inhibition of C4H activity in a tobacco (Nicotiana tabacum cv Bright Yellow [BY]) cell suspension culture. This inhibition was however rapidly relieved either because of substrate accumulation or because of inhibitor metabolism. Substrate analogs bearing a methylenedioxo function such as piperonylic acid (PIP) or a terminal acetylene such as 4-propynyloxybenzoic acid (4PB), 3-propynyloxybenzoic acid, and 4-propynyloxymethylbenzoic acid are potent mechanism-based inactivators of the C4H. PIP and 4PB, the best inactivators in vitro, were also efficient inhibitors of the enzyme in BY cells. Inhibition was not reversed 46 h after cell treatment. Cotreatment of BY cells with the fungal elicitor beta-megaspermin and PIP or 4PB led to a dramatic increase in SA accumulation. PIP and 4PB do not trigger SA accumulation in nonelicited cells in which the SA biosynthetic pathway is not activated. Mechanism-based C4H inactivators, thus, are promising tools for the elucidation of the CA-derived SA biosynthetic pathway and for the potentiation of plant defense.

Phytoremediation of polyaromatic hydrocarbons, anilines and phenols

Phytoremediation technologies based on the combined action of plants and the microbial communities that they support within the rhizosphere hold promise in the remediation of land and waterways contaminated with hydrocarbons but they have not yet been adopted in large-scale remediation strategies. In this review plant and microbial degradative capacities, viewed as a continuum, have been dissected in order to identify where bottle-necks and limitations exist. Phenols, anilines and polyaromatic hydrocarbons (PAHs) were selected as the target classes of molecule for consideration, in part because of their common patterns of distribution, but also because of the urgent need to develop techniques to overcome their toxicity to human health. Depending on the chemical and physical properties of the pollutant, the emerging picture suggests that plants will draw pollutants including PAHs into the plant rhizosphere to varying extents via the transpiration stream. Mycorrhizosphere-bacteria and -fungi may play a crucial role in establishing plants in degraded ecosystems. Within the rhizosphere, microbial degradative activities prevail in order to extract energy and carbon skeletons from the pollutants for microbial cell growth. There has been little systematic analysis of the changing dynamics of pollutant degradation within the rhizosphere; however, the importance of plants in supplying oxygen and nutrients to the rhizosphere via fine roots, and of the beneficial effect of microorganisms on plant root growth is stressed. In addition to their role in supporting rhizospheric degradative activities, plants may possess a limited capacity to transport some of the more mobile pollutants into roots and shoots via fine roots. In those situations where uptake does occur (i.e. only limited microbial activity in the rhizosphere) there is good evidence that the pollutant may be metabolised. However, plant uptake is frequently associated with the inhibition of plant growth and an increasing tendency to oxidant stress. Pollutant tolerance seems to correlate with the ability to deposit large quantities of pollutant metabolites in the 'bound' residue fraction of plant cell walls compared to the vacuole. In this regard, particular attention is paid to the activities of peroxidases, laccases, cytochromes P450, glucosyltransferases and ABC transporters. However, despite the seemingly large diversity of these proteins, direct proof of their participation in the metabolism of industrial aromatic pollutants is surprisingly scarce and little is known about their control in the overall metabolic scheme. Little is known about the bioavailability of bound metabolites; however, there may be a need to prevent their movement into wildlife food chains. In this regard, the application to harvested plants of composting techniques based on the degradative capacity of white-rot fungi merits attention.

CYP98A3 from Arabidopsis thaliana is a 3'-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway

The 4- and 5-hydroxylations of phenolic compounds in plants are catalyzed by cytochrome P450 enzymes. The 3-hydroxylation step leading to the formation of caffeic acid from p-coumaric acid remained elusive, however, alternatively described as a phenol oxidase, a dioxygenase, or a P450 enzyme, with no decisive evidence for the involvement of any in the reaction in planta. In this study, we show that the gene encoding CYP98A3, which was the best possible P450 candidate for a 3-hydroxylase in the Arabidopsis genome, is highly expressed in inflorescence stems and wounded tissues. Recombinant CYP98A3 expressed in yeast did not metabolize free p-coumaric acid or its glucose or CoA esters, p-coumaraldehyde, or p-coumaryl alcohol, but very actively converted the 5-O-shikimate and 5-O-d-quinate esters of trans-p-coumaric acid into the corresponding caffeic acid conjugates. The shikimate ester was converted four times faster than the quinate derivative. Antibodies directed against recombinant CYP98A3 specifically revealed differentiating vascular tissues in stem and root. Taken together, these data show that CYP98A3 catalyzes the synthesis of chlorogenic acid and very likely also the 3-hydroxylation of lignin monomers. This hydroxylation occurs on depsides, the function of which was so far not understood, revealing an additional and unexpected level of networking in lignin biosynthesis.

Flavonoid 6-hydroxylase from soybean (Glycine max L.), a novel plant P-450 monooxygenase

Cytochrome P-450-dependent hydroxylases are typical enzymes for the modification of basic flavonoid skeletons. We show in this study that CYP71D9 cDNA, previously isolated from elicitor-induced soybean (Glycine max L.) cells, codes for a protein with a novel hydroxylase activity. When heterologously expressed in yeast, this protein bound various flavonoids with high affinity (1.6 to 52 microm) and showed typical type I absorption spectra. These flavonoids were hydroxylated at position 6 of both resorcinol- and phloroglucinol-based A-rings. Flavonoid 6-hydroxylase (CYP71D9) catalyzed the conversion of flavanones more efficiently than flavones. Isoflavones were hardly hydroxylated. As soybean produces isoflavonoid constituents possessing 6,7-dihydroxy substitution patterns on ring A, the biosynthetic relationship of flavonoid 6-hydroxylase to isoflavonoid biosynthesis was investigated. Recombinant 2-hydroxyisoflavanone synthase (CYP93C1v2) efficiently used 6,7,4'-trihydroxyflavanone as substrate. For its structural identification, the chemically labile reaction product was converted to 6,7,4'-trihydroxyisoflavone by acid treatment. The structures of the final reaction products for both enzymes were confirmed by NMR and mass spectrometry. Our results strongly support the conclusion that, in soybean, the 6-hydroxylation of the A-ring occurs before the 1,2-aryl migration of the flavonoid B-ring during isoflavanone formation. This is the first identification of a flavonoid 6-hydroxylase cDNA from any plant species.

Oxidation of xenobiotics by plant microsomes, a reconstituted cytochrome P450 system and peroxidase: a comparative study

The microsomal fraction from tulip bulbs (Tulipa fosteriana, L.) contains cytochrome P450 (CYP3, EC 1.14.14.1) and peroxidase (EC 1.11.1.7.) enzymes catalyzing the NADPH--and hydrogen peroxide--dependent oxidation of the xenobiotic substrates, N-nitrosodimethylamine (NDMA), N-nitrosomethylaniline (NMA), aminopyrine and 1-phenylazo 2-hydroxynaphthalene (Sudan I), respectively. Oxidation of these model xenobiotics has also been assessed in a reconstituted electron-transport chain with a partially purified CYP fraction, phospholipid and isolated tulip NADPH:CYP reductase (EC 1.6.2.4.). Peroxidase isolated from tulip bulbs (isoenzyme C) oxidizes these xenobiotics, too. Values of kinetic parameters (Km, Vmax), requirements for cofactors (NADPH, hydrogen peroxide), the effect of inhibitors and identification of products formed from the xenobiotics by the microsomal fraction, partially purified CYP and peroxidase C were determined. These data were used to estimate the participation of the CYP preparation and peroxidase C in oxidation of two out of the four studied xenobiotics (NMA, Sudan I) in tulip microsomes. Using such detailed study, we found that the CYP-dependent enzyme system is responsible for the oxidation of these xenobiotics in the microsomal fraction of tulip bulbs. The results demonstrate the progress in resolving the role of plant CYP and peroxidase enzymes in oxidation of xenobiotics.

Cytochrome P450 monooxygenases of DIBOA biosynthesis: specificity and conservation among grasses

DIBOA and DIMBOA are secondary metabolites of grasses which function as natural pesticides. The four maize genes BX2 through BX5 encode cytochrome P450-dependent monooxygenases that catalyse four consecutive reactions in the biosynthesis of these secondary products. Although BX2-BX5 share significant sequence homology, the four enzymes have evolved into specific enzymes each catalysing predominantly only one reaction in the pathway. In addition to these natural reactions, BX3 hydroxylates 1,4-benzoxazin-3-one and BX2 shows pCMA demethylase activity. With respect to DIBOA biosynthesis, identical enzymatic reactions have been found in rye as compared to maize, indicating early evolution of the P450 enzymes in the grasses.

Piperonylic acid, a selective, mechanism-based inactivator of the trans-cinnamate 4-hydroxylase: A new tool to control the flux of metabolites in the phenylpropanoid pathway

Piperonylic acid (PA) is a natural molecule bearing a methylenedioxy function that closely mimics the structure of trans-cinnamic acid. The CYP73A subfamily of plant P450s catalyzes trans-cinnamic acid 4-hydroxylation, the second step of the general phenylpropanoid pathway. We show that when incubated in vitro with yeast-expressed CYP73A1, PA behaves as a potent mechanism-based and quasi-irreversible inactivator of trans-cinnamate 4-hydroxylase. Inactivation requires NADPH, is time dependent and saturable (KI = 17 &mgr;M, kinact = 0.064 min-1), and results from the formation of a stable metabolite-P450 complex absorbing at 427 nm. The formation of this complex is reversible with substrate or other strong ligands of the enzyme. In plant microsomes PA seems to selectively inactivate the CYP73A P450 subpopulation. It does not form detectable complexes with other recombinant plant P450 enzymes. In vivo PA induces a sharp decrease in 4-coumaric acid concomitant to cinnamic acid accumulation in an elicited tobacco (Nicotiana tabacum) cell suspension. It also strongly decreases the formation of scopoletin in tobacco leaves infected with tobacco mosaic virus.