Genomic structure, cloning and expression of two phospholipase D isoenzymes from white cabbage

The wide world of non-mammalian phospholipase D enzymes

Phospholipase D (PLD) hydrolyses phosphatidylcholine (PtdCho) to produce free choline and the critically important lipid signaling molecule phosphatidic acid (PtdOH). Since the initial discovery of PLD activities in plants and bacteria, PLDs have been identified in a diverse range of organisms spanning the taxa. While widespread interest in these proteins grew following the discovery of mammalian isoforms, research into the PLDs of non-mammalian organisms has revealed a fascinating array of functions ranging from roles in microbial pathogenesis, to the stress responses of plants and the developmental patterning of flies. Furthermore, studies in non-mammalian model systems have aided our understanding of the entire PLD superfamily, with translational relevance to human biology and health. Increasingly, the promise for utilization of non-mammalian PLDs in biotechnology is also being recognized, with widespread potential applications ranging from roles in lipid synthesis, to their exploitation for agricultural and pharmaceutical applications.

Expression and Purification of Recombinant Vigna unguiculata Phospholipase D in Pichia pastoris for Structural Studies

The production of pure enzymes in high quantities is a proven strategy to study the catalytic mechanism as well as the solving of structure at the atomic scale for therapeutic or industrial purposes. Phospholipase D (PLD, EC 3.1.4.4) is found in a wide majority of living organisms and has been shown to be involved in signal transduction, vesicle trafficking, and membrane metabolism processes. Located at the membrane-cytoplasm interface, plant PLDs are soluble but also bear an evident hydrophobic aspect making challenging its expression and its purification in large quantity. So far there is no high-resolution three-dimensional structure for a eukaryotic PLD. The protocols herein describe the cloning of the eukaryotic recombinant PLDα of Vigna unguiculata (cowpea) into the yeast expression system Pichia pastoris and its two-step purification process. This allowed us to purify to homogeneity hundreds of micrograms of highly pure protein to conduct in fine structural studies.

Metal ions and phosphatidylinositol 4,5-bisphosphate as interacting effectors of α-type plant phospholipase D

Plant phospholipases D (PLD) are typically characterized by a C2 domain with at least two Ca²⁺ binding sites. In vitro, the predominantly expressed α-type PLDs need 20-100 mM CaCl₂ for optimum activity, whereas the essential activator of β- or γ-type PLDs, phosphatidylinositol 4,5-bisphosphate (PIP₂), plays a secondary role. In the present paper, we have studied the interplay between PIP₂ and metal ion activation of the well-known α-type PLD from cabbage (PLDα). With mixed micelles containing phosphatidyl-p-nitrophenol as substrate, PIP₂-concentrations in the nanomolar range are able to activate the enzyme in addition to the essential Ca²⁺ activation. Mg²⁺ ions are able to replace Ca²⁺ ions but they do not activate PLDα. Rather, they abolish the activation of the enzyme by Ca²⁺ ions in the absence, but not in the presence, of PIP₂. The presence of PIP₂ causes a shift in the pH optimum of PLDα activity to the acidic range. Employing fluorescence measurements and replacing Ca²⁺ by Tb³⁺ ions, confirmed the presence of two metal ion-binding sites, in which the one of lower affinity proved crucial for PLD activation. Moreover, we have generated a homology model of the C2 domain of this enzyme, which was used for Molecular Dynamics (MD) simulations and docking studies. As is common for C2 domains, it shows two antiparallel β-sheets consisting of four β-strands each and loop regions that harbor two Ca²⁺ binding sites. Based on the findings of the MD simulation, one of the bound Ca²⁺ ions is coordinated by five amino acid residues. The second Ca²⁺ ion induces a loop movement upon its binding to three amino acid residues. Docking studies with PIP₂ reveal, in addition to the previously postulated PIP₂-binding site in the middle of the β-sheet structure, another PIP₂-binding site near the two Ca²⁺ ions, which is in accordance with the experimental interplay of PIP₂, Ca²⁺ and Mg²⁺ ions.

Functional Characterization of the N-Terminal C2 Domain from Arabidopsis thaliana Phospholipase Dα and Dβ

Most of plant phospholipases D (PLD) exhibit a C2-lipid binding domain of around 130 amino acid residues at their N-terminal region, involved in their Ca²⁺-dependent membrane binding. In this study, we expressed and partially purified catalytically active PLDα from Arabidopsis thaliana (AtPLDα) in the yeast Pichia pastoris. The N-terminal amino acid sequence of the recombinant AtPLDα was found to be NVEETIGV and thus to lack the first 35 amino acid belonging to the C2 domain, as found in other recombinant or plant purified PLDs. To investigate the impact of such a cleavage on the functionality of C2 domains, we expressed, in E. coli, purified, and refolded the mature-like form of the C2 domain of the AtPLDα along with its equivalent C2 domain of the AtPLDβ, for the sake of comparison. Using Förster Resonance Energy Transfer and dot-blot assays, both C2 domains were shown to bind phosphatidylglycerol in a Ca²⁺-independent manner while phosphatidic acid and phosphatidylserine binding were found to be enhanced in the presence of Ca²⁺. Amino acid sequence alignment and molecular modeling of both C2 domains with known C2 domain structures revealed the presence of a novel Ca²⁺-binding site within the C2 domain of AtPLDα.

Purification, sequencing and characterization of phospholipase D from Indian mustard seeds

Phospholipase D (PLD; E.C. 3.1.4.4) is widespread in plants where it fulfills diverse functions in growth and in the response to stresses. The enzyme occurs in multiple forms that differ in their biochemical properties. In the present paper PLD from medicinally relevant Indian mustard seeds was purified by Ca(2+)-mediated hydrophobic interaction and anion exchange chromatography to electrophoretic homogeneity. Based on mass-spectrometric sequence analysis of tryptic protein fragments, oligonucleotide primers for cloning genomic DNA fragments that encoded the enzyme were designed and used to derive the complete amino acid sequence of this PLD. The sequence data, as well as the molecular properties (molecular mass of 92.0 kDa, pI 5.39, maximum activity at pH 5.5-6.0 and Ca(2+) ion concentrations ⩾60 mM), allowed the assignment of this enzyme to the class of α-type PLDs. The apparent kinetic parameters Vmax and Km, determined for the hydrolysis of phosphatidylcholine (PC) in an aqueous mixed-micellar system were 356±15 μmol min(-1) mg(-1) and 1.84±0.17 mM, respectively. Phosphate analogs such as NaAlF4 and Na3VO4 displayed strong inhibition of the enzyme. Phosphatidylinositol 4,5-bisphosphate had a strong activating effect at 2-10 mM CaCl2. PLD was inactivated at temperatures >45 °C. The enzyme exhibited the highest activity toward PC followed by phosphatidylethanolamine and phosphatidylglycerol. PCs with short-chain fatty acids were better substrates than PCs with long fatty acid chains. Lyso-PC was not accepted as substrate.

Fe(III)-resorcylate as a spectrophotometric probe for phospholipid-cation interactions

A simple spectrophotometric microplate assay that allows quantification of the interaction between phospholipids and metal ions or other small cationic compounds has been developed. The assay is based on the competition of the phospholipids for the Fe(3+) ion in the purple-colored Fe(III)-γ-resorcylate complex and for other cations. To compare the binding affinities of several cation-phospholipid interactions, K0.5 values were derived from binding curves constructed by determination of the absorbance of the Fe(III)-γ-resorcylate at 490 nm as a function of the cation concentration. The assay was used to analyze the binding of lanthanide ions, calcium ions, and amines (hydrochlorides of ethanolamine, spermidine, and hexyltrimethylammonium chloride) to small unilamellar vesicles (SUVs) and mixed micelles containing anionic lipids such as phosphatidic acid and phosphatidyl-p-nitrophenol. The method was evaluated by fluorescence measurements with Eu(3+) ions as tracer. Lanthanide ions such as La(3+) and Ce(3+) ions showed K0.5 values smaller by one to two orders of magnitude compared with Ca(2+) ions. In the presence of increasing amounts of detergents such as Triton X-100, the method also reflected transitions from SUVs to micelles. The binding capacity for metal ions was higher for phospholipid-containing micelles than for the corresponding SUVs.

Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering

Phospholipase D (PLD) is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids (PLs). Many reports exist on PLD-mediated synthesis of natural and tailor-made PLs with functional head groups, from easily available lecithin or phosphatidylcholine. Early studies on PLD-mediated synthesis mainly employed enzymes of plant origin, which were later supplanted by ones from microorganisms, especially actinomycetes. Many PLDs are members of the PLD superfamily, having one or two copies of a signature sequence, HxKxxxxD or HKD motif, in the primary structures. PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism. The catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base. PLD is being engineered to improve its activity and stability, alter head group specificity and further identify catalytically important residues. Since the knowledge on PLD enzymology is constantly expanding, this review focuses on recent advances in the field, regarding PLD-catalyzed synthesis of bioactive PLs, deeper understanding of substrate recognition and binding mechanism, altering substrate specificity, and improving thermostability. We introduced some of our recent results in combination with existing facts to further deepen the story on the nature of this useful enzyme.

Spectrophotometric determination of phosphatidic acid via iron(III) complexation for assaying phospholipase D activity

The ability of negatively charged phosphatidates to form complexes with Fe(3+) ions was used to design a simple spectrophotometric assay for the quantitative determination of phosphatidic acid (PA). In the reaction with the purple iron(III)-salicylate, PA extracts Fe(3+) ions and decreases the absorbance at 490 nm. Lower competition with salicylate for Fe(3+) ions was observed with single negatively charged phosphatidates such as phosphatidylglycerol (PG), whereas neutral phosphatidates such as phosphatidylcholine (PC) and phosphatidylethanolamine (PE) showed no influence on the absorbance of the iron(III) complex. The detection limit of the method on a microplate scale was 10 microM PA. Based on these results, an assay for determining the activity of phospholipase D (PLD) toward natural phospholipids such as PC, PE, and PG was developed. In contrast to other spectroscopic PLD assays, this method is able to determine PLD activity toward different lipids or even lipid mixtures.

Substrate specificity in phospholipid transformations by plant phospholipase D isoenzymes

Phospholipase D (PLD) catalyzes the hydrolysis and transesterification of glycerophospholipids at the terminal phosphodiester bond. In many plants, several isoforms of PLD have been identified without knowing their functional differences. In this paper, the specificities of two PLD isoenzymes from white cabbage (Brassica oleracea var. capitata) and two ones from opium poppy (Papaver somniferum L.), which were recombinantly produced in Escherichia coli, were compared in the hydrolysis of phospholipids with different head groups and in the transphosphatidylation of phosphatiylcholine with several acceptor alcohols. In a biphasic reaction system, consisting of buffer and diethyl ether, the highly homologous isoenzymes are able to hydrolyze phosphatidylcholine, -glycerol, -ethanolamine, -inositol and - with one exception - also phosphatidylserine but with different individual reaction rates. In transphosphatidylation of phosphatidylcholine, they show significant differences in the rates of head group exchange but with the same trend in the preference of acceptor alcohols (ethanolamine>glycerol>>l-serine). For l- and d-serine a stereoselectivity of PLD was observed. The results suggest a physiological relevance of the different hydrolytic and transphosphatidylation activities in plant PLD isoenzymes.

Calcium-induced membrane microdomains trigger plant phospholipase D activity

Plant alpha-type phospholipase D proteins are calcium-dependent, lipolytic enzymes. The morphology of the aggregates of their phospholipid substrate fundamentally defines the interaction between the enzyme and the surface. Here we demonstrate that the Ca(2+)-induced generation of membrane microdomains dramatically activates alpha-type phospholipase D from white cabbage. 500-fold stimulation was observed upon incorporation of 10 mol % 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate (POPA) into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) vesicles in the presence of Ca(2+) ions. Enhanced association of PLDalpha2 with phospholipid surfaces containing anionic components was indicated by lag phase analysis and film balance measurements. Differential scanning calorimetry showed that the POPA-specific activation correlates with the phase behavior of the POPC/POPA vesicles in the presence of Ca(2+) ions. We conclude from the results that the Ca(2+)-induced formation of POPA microdomains is the crucial parameter that facilitates the binding of PLD to the phospholipid surface and suggest that this effect serves as a cellular switch for controlling PLD activity.

Insights into the structure of plant α-type phospholipase D

Phospholipases D play an important role in the regulation of cellular processes in plants and mammals. Moreover, they are an essential tool in the synthesis of phospholipids and phospholipid analogs. Knowledge of phospholipase D structures, however, is widely restricted to sequence data. The only known tertiary structure of a microbial phospholipase D cannot be generalized to eukaryotic phospholipases D. In this study, the isoenzyme form of phospholipase D from white cabbage (PLDalpha2), which is the most widely used plant phospholipase D in biocatalytic applications, has been characterized by small-angle X-ray scattering, UV-absorption, CD and fluorescence spectroscopy to yield the first insights into its secondary and tertiary structure. The structural model derived from small-angle X-ray scattering measurements reveals a barrel-shaped monomer with loosely structured tops. The far-UV CD-spectroscopic data indicate the presence of alpha-helical as well as beta-structural elements, with the latter being dominant. The fluorescence and near-UV CD spectra point to tight packing of the aromatic residues in the core of the protein. From the near-UV CD signals and activity data as a function of the calcium ion concentration, two binding events characterized by dissociation constants in the ranges of 0.1 mm and 10-20 mm can be confirmed. The stability of PLDalpha2 proved to be substantially reduced in the presence of calcium ions, with salt-induced aggregation being the main reason for irreversible inactivation.

Identification and partial characterization of a highly active and stable phospholipase D from Brassica juncea seeds

Phospholipase D (PLD) activity has been identified in some new plant sources i.e. Brassica juncea (mustard) seeds, Zingibar officinale (ginger) rhizomes and Azadirachta indica (neem) leaves with the aim of identifying PLDs that possess high catalytic activity and stability. PLD from mustard seeds (PLD(ms)) exhibited the highest PLD specific activity, which was highly pH and temperature tolerant. PLD(ms) unlike many plant PLDs exhibited high thermal stability. The activity of PLD(ms) is optimum in the millimolar concentration of calcium ions and is independent of phosphatidylinositol-4,5-bisphosphate (PIP2). An active and stable enzyme like PLD(ms) may be utilized in the lipid industry.

Two highly homologous phospholipase D isoenzymes from Papaver somniferum L. with different transphosphatidylation potential

The genes of two phospholipase D (PLD) isoenzymes, PLD1 and PLD2, from poppy seedlings (2829 and 2828 bp) were completely sequenced. The two genes have 96.9% identity in the encoding region and can be assigned to the alpha-type of plant PLDs. The corresponding amino acid sequences do not contain any signal sequences. One Asn-glycosylation site, six and two phosphorylation sites for protein kinase C and tyrosine kinase, respectively, and two phosphatidylinositol-4,5-bisphosphate binding motifs could be identified. Like in most plant PLDs, two HKD motifs and one C2 domain are present. PLD1 and PLD2 have ten and nine cysteine residues. The two enzymes were expressed in E. coli and purified to homogeneity by Ca2+ ion-mediated hydrophobic interaction chromatography. The Ca2+ ion concentration needed for carrier binding of the two enzymes in chromatography as well as for optimum activity was found to be considerably higher (>100 mM) than with other alpha-type plant PLDs. Although PLD1 and PLD2 differ in eleven amino acids only, they showed remarkable differences in their transphosphatidylation activity. Two amino acid exchanges within and near the first HKD motif contribute to this difference as shown by the A349E/E352Q-variant of PLD2.

Phospholipase D and its application in biocatalysis

Phospholipase D (PLD) from plants or microorganisms is used as biocatalyst in the transformation of phospholipids and phospholipid analogs in both laboratory and industrial scale. In recent years the elucidation of the primary structure of many PLDs from several sources, as well as the resolution of the first crystal structure of a microbial PLD, have yielded new insights into the structural basis and the catalytic mechanism of this catalyst. This review summarizes some new results of PLD research in the light of application.

Asymmetric in vitro synthesis of diastereomeric phosphatidylglycerols from phosphatidylcholine and glycerol by bacterial phospholipase D

Using chiral-phase HPLC, we determined the stereochemical configuration of the phosphatidylglycerols (PtdGro) synthesized in vitro from 1,2-diacyl-sn-glycero-3-phosphocholine (PtdCho, R configuration) or 1,2-diacyl-sn-glycero-3-phosphoethanolamine (PtdEtn, R configuration) and glycerol by transphosphatidylation with bacterial phospholipase D (PLD). The results obtained with PLD preparations from three Streptomyces strains (S. septatus TH-2, S. halstedii K5, and S. halstedii subsp. scabies K6) and one Actinomadura species were compared with those obtained using cabbage and peanut PLD. The reaction was carried out at 30 degrees C in a biphasic system consisting of diethyl ether and acetate buffer. The resulting PtdGro were then converted into bis(3,5-dinitrophenylurethane) derivatives, which were separated on an (R)-1-(1-naphthyl)ethylamine polymer. In contrast to the cabbage and peanut PLD, which gave equimolar mixtures of the R,S and R,R diastereomers, as previously established, the bacterial PLD yielded diastereomixtures of 30-40% 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol (R,S configuration) and 60-70% 1,2-diacyl-sn-glycero-3-phospho-3'-sn-glycerol (R,R configuration). The highest disproportionation was found for the Streptomyces K6 species. The present study demonstrates that bacterial PLD-catalyzed transphosphatidylation proceeds to a considerable extent stereoselectively to produce PtdGro from PtdCho or PtdEtn and prochiral glycerol, indicating a preference for the sn-3' position of the glycerol molecule.