Characterization of the activity of fatty-acid epoxide hydrolase in seeds of castor bean (Ricinus communis L.)

Epoxide hydrolase (EC 3.3.2.3) activity was measured with [1-¹⁴C]cis-9,10-epoxystearic acid as the substrate. Homogenates were prepared from the endosperm tissue of germinating seeds of castor bean (Ricinus communis L. zanzibariensis). The activity of fatty-acid epoxide hydrolase was characterized with respect to dependence on time, amount of protein, pH and temperature. Analyses of enzyme distribution in endosperm, cotyledons, root and hypocotyl showed the highest total activity in the endosperm, less in the cotyledons and low activity in the root and hypocotyl. The specific activity was similar for cotyledons and endosperm. Analysis of the temporal expression of the enzyme in the endosperm during germination revealed high activity already in the imbibed seed. Activity was maximal between days four to six and then decreased at the end of one week. Subcellular fractionation of endosperm revealed a dual distribution of activity between the glyoxysomal and the cytosolic fractions.     

Domain Evolution in the α-Amylase Family

The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (β/α)₈-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (β/α)₈-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family. Received: 4 December 1996 / Accepted: 13 March 1997     

Further studies on the subcellular localization of lipid-degrading enzymes

Further work on the subcellular localization of two lipid-degrading enzymes, lipolytic acyl hydrolase (LAH) and lipoxygenase (LOX) has been carried out on brassica florets, potato shoots and pea roots. In all cases, the LAH profile on sucrose and Ficoll density gradients was coincident with ‘lysosomal’ acid phosphatase activity. However, the localization of LOX activity was different for each tissue. In pea roots the activity of LOX was localized in the ‘lysosomal’ fraction, whereas with brassica florets (cauliflower and calabrese) it was present in a heavy body with a similar density to plastids and in potato shoots LOX gave only low particulate recoveries.     

Properties of acyl hydrolase enzymes from Phaseolus multiflorus leaves

The properties of acyl hydrolase enzymes purified from the leaves of Phaseolus multiflorus have been studied. Hydrolase I which deacylates phosphatidylcholine and oleoylglycerol had a pH optimum towards phosphatidylcholine of 5.3. Hydrolase II which deacylates glycosylglycerides and oleoylglycerol showed pH optima of 7.3 (monogalactosyldiglyceride, MGDG) and 4.3 (sulphoquinovosyldiglyceride, SQDG). Both enzymes showed activity peaks towards oleoylglycerol at pH 6.8 and 8.8. Unesterified fatty acids and Triton X-100 inhibited the rate of SQDG hydrolysis while bovine serum albumin increased activity. An apparent K_m for SQDG of 0.15 mM was found. Hydrolase II catalysed transmethylation of liberated fatty acids during the hydrolysis of oleoylglycerol when methanol was included in the assay system. A number of salts inhibited SQDG hydrolysis but their effect on oleoylglycerol was less consistent. The position of ester cleavage of oleoylglycerol was determined by the use of H₂¹⁸O. Cell-free extracts from P. multiflorus leaves degraded SQDG as far as sulphoquinovose.     

Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations

Ram2 from Pediococcus acidilactici is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of −34.4 and −30.6 kJ mol⁻¹ respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol⁻¹. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated residues in the active site (Asp217, Asp222, Trp226, Asp229 and Glu488) and quantifies the importance of individual residues for the binding. The most important amino acids are Asp229 and Phe339 which are involved in many interactions during the simulations. While Phe339 was observed in more simulations, Asp229 was involved in more persistent interactions (forming an average of at least 2 hydrogen bonds during the simulation). These analyses directly suggest mutations that could be used in a further experimental characterization of the enzyme. This study shows once more the strength of computer simulations to rationalize and guide experiments at an atomic level.     

Preparation and evaluation of soluble epoxide hydrolase inhibitors with improved physical properties and potencies for treating diabetic neuropathic pain

Soluble epoxide hydrolase (sEH), a novel therapeutic target for neuropathic pain, is a largely cytosolic enzyme that degrades epoxy-fatty acids (EpFAs), an important class of lipid signaling molecules. Many inhibitors of sEH have been reported, and to date, the 1,3-disubstituted urea has the highest affinity reported for the sEH among the central pharmacophores evaluated. An earlier somewhat water soluble sEH inhibitor taken to the clinic for blood pressure control had mediocre potency (both affinity and kinetics) and a short in vivo half-life. We undertook a study to overcome these difficulties, but the sEH inhibitors carrying a 1,3-disubstituted urea often suffer poor physical properties that hinder their formulation. In this report, we described new strategies to improve the physical properties of sEH inhibitors with a 1,3-disubstituted urea while maintaining their potency and drug-target residence time (a complementary in vitro parameter) against sEH. To our surprise, we identified two structural modifications that substantially improve the potency and physical properties of sEH inhibitors carrying a 1,3-disubstituted urea pharmacophore. Such improvements will greatly facilitate the movement of sEH inhibitors to the clinic.     

天麻栽培用蜜环菌的遗传多样性、生长和水解酶

蜜环菌Armillaria是一种广泛分布的担子菌,是栽培中药天麻所必须的共生菌。为揭示我国天麻栽培用和鄂西地区部分野生蜜环菌资源的遗传多样性和生物学特性,本文收集了9个省市EF-1-α的19个蜜环菌商品菌株和鄂西地区20株野生蜜环菌菌株,以IGS、ITS和elongation factor-1-alpha（EF-1-α）为分子标记对这些菌株进行系统发育与遗传多样性分析,并对影响与天麻共生的生物学特性（菌索发育和胞外水解酶活性）进行对比研究。结果表明,这19株蜜环菌商品菌株分别归属于2个clade。其中,有18个菌株聚在cladeⅢ,说明不同来源的蜜环菌商品菌株之间系统发育关系很近;通过对蜜环菌的系统发育、菌索生长以及胞外水解酶活性的研究,总体上商品种优于鄂西的野生蜜环菌生物种。从鄂西野生蜜环菌中筛选出4个具有潜在栽培价值的菌株。本研究为天麻栽培生产中蜜环菌菌种的选择提供参考。     

戴云山黄山松林土壤碳组分的海拔变化特征及影响因素

海拔梯度可能通过多种环境因子影响土壤有机质,土壤有机碳库是土壤有机质的重要组成部分,其微小变化将会产生极其重要的影响。因此海拔差异可能导致海拔间土壤碳库差异。土壤有机碳是反映土壤肥力的重要指标,可能受土壤理化性质和微生物等多种因素的影响。黄山松是高山地绿化和用材的优良树种,近年来戴云山自然保护区内高海拔地区的黄山松群落呈现衰退趋势。研究戴云山黄山松林土壤有机碳组分沿海拔梯度的变化情况,不仅可以为该区域碳库估算提供科学依据,而且有助于揭示影响黄山松生长变化的机理。因此,选取戴云山不同海拔[1300 m (L)、1450 m (M)和1600 m (H)]梯度的黄山松林,对其土壤基本理化性质、有机碳组分及微生物特征进行测定和分析。研究发现,海拔梯度下土壤养分含量呈先升高后降低的变化趋势,土壤碳组分含量与其变化一致,且微生物生物量碳和微生物生物量氮均在M海拔处最高,海拔梯度对碳水解酶没有显著影响。冗余分析表明,总氮是影响土壤有机碳变化的最主要因素,其次是碳氮比。因此在海拔跨度不大的情况下,土壤有机碳动态可能主要受氮素而非温度的影响。高海拔地区土壤惰性碳占比高,未来可能会持续加剧该地区黄山松的生长困境,使该区域碳库受到影响。     

Enzymatic characterization of ancestral/group-IV clade xyloglucan endotransglycosylase/hydrolase enzymes reveals broad substrate specificities

Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes play important roles in cell wall remodelling. Although previous studies have shown a pathway of evolution for XTH genes from bacterial licheninases, through plant endoglucanases (EG16), the order of development within the phylogenetic clades of true XTHs is yet to be elucidated. In addition, recent studies have revealed interesting and potentially useful patterns of transglycosylation beyond the standard xyloglucan–xyloglucan donor/acceptor substrate activities. To study evolutionary relationships and to search for enzymes with useful broad substrate specificities, genes from the ‘ancestral’ XTH clade of two monocots, Brachypodium distachyon and Triticum aestivum, and two eudicots, Arabidopsis thaliana and Populus tremula, were investigated. Specific activities of the heterologously produced enzymes showed remarkably broad substrate specificities. All the enzymes studied had high activity with the cellulose analogue HEC (hydroxyethyl cellulose) as well as with mixed-link β-glucan as donor substrates, when compared with the standard xyloglucan. Even more surprising was the wide range of acceptor substrates that these enzymes were able to catalyse reactions with, opening a broad range of possible roles for these enzymes, both within plants and in industrial, pharmaceutical and medical fields. Genome screening and expression analyses unexpectedly revealed that genes from this clade were found only in angiosperm genomes and were predominantly or solely expressed in reproductive tissues. We therefore posit that this phylogenetic group is significantly different and should be renamed as the group-IV clade.