Identification of a Unique Germacrene A Oxidase from <i>Xanthium strumarium</i>

8,12-sesquiterpene lactones (STLs) are an important class of natural products with unique pharmaceutical activities. For years the pathway leading to 8,12-STLs remains an enigma. Xanthium strumarium accumulates abundant 8,12-STLs, and xanthatin is a characteristic 8,12-STL in it. Xanthatin has been previously postulated to be derived from germacrene A, but the steps from germacrene A to xanthatin are unknown. As part of an effort to understand the xanthatin biosynthetic pathway. This study reports the characterization of a unique germacrene A oxidase (XsGAO) from X. strumarium. Unlike a classical GAO enzyme, which is known to catalyze a three-step oxidation of germarene A to yield germacrene A acid (GAA), surprisingly, XsGAO catalyzed only one-step conversion of germacrene A to germacrene A alcohol. We discussed that GAO may be pressured to acquire a novel activity during the evolutionary path for the biosynthesis of 8,12-STLs.     

Reconstitution of the costunolide biosynthetic pathway in yeast and Nicotiana benthamiana

The sesquiterpene costunolide has a broad range of biological activities and is the parent compound for many other biologically active sesquiterpenes such as parthenolide. Two enzymes of the pathway leading to costunolide have been previously characterized: germacrene A synthase (GAS) and germacrene A oxidase (GAO), which together catalyse the biosynthesis of germacra-1(10),4,11(13)-trien-12-oic acid. However, the gene responsible for the last step toward costunolide has not been characterized until now. Here we show that chicory costunolide synthase (CiCOS), CYP71BL3, can catalyse the oxidation of germacra-1(10),4,11(13)-trien-12-oic acid to yield costunolide. Co-expression of feverfew GAS (TpGAS), chicory GAO (CiGAO), and chicory COS (CiCOS) in yeast resulted in the biosynthesis of costunolide. The catalytic activity of TpGAS, CiGAO and CiCOS was also verified in planta by transient expression in Nicotiana benthamiana. Mitochondrial targeting of TpGAS resulted in a significant increase in the production of germacrene A compared with the native cytosolic targeting. When the N. benthamiana leaves were co-infiltrated with TpGAS and CiGAO, germacrene A almost completely disappeared as a result of the presence of CiGAO. Transient expression of TpGAS, CiGAO and CiCOS in N. benthamiana leaves resulted in costunolide production of up to 60 ng.g(-1) FW. In addition, two new compounds were formed that were identified as costunolide-glutathione and costunolide-cysteine conjugates.     

Comparison of acetate and propionate uptake by polyphosphate accumulating organisms and glycogen accumulating organisms

Enhanced biological phosphorus removal (EBPR) performance is directly affected by the competition between polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). This study investigates the effects of carbon source on PAO and GAO metabolism. Enriched PAO and GAO cultures were tested with the two most commonly found volatile fatty acids (VFAs) in wastewater systems, acetate and propionate. Four sequencing batch reactors (SBRs) were operated under similar conditions and influent compositions with either acetate or propionate as the sole carbon source. The stimulus for selection of the PAO and GAO phenotypes was provided only through variation of the phosphorus concentration in the feed. The abundance of PAOs and GAOs was quantified using fluorescence in situ hybridisation (FISH). In the acetate fed PAO and GAO reactors, "Candidatus Accumulibacter phosphatis" (a known PAO) and "Candidatus Competibacter phosphatis" (a known GAO) were present in abundance. A novel GAO, likely belonging to the group of Alphaproteobacteria, was found to dominate the propionate fed GAO reactor. The results clearly show that there are some very distinctive differences between PAOs and GAOs in their ability to take up acetate and propionate. PAOs enriched with acetate as the sole carbon source were immediately able to take up propionate, likely at a similar rate as acetate. However, an enrichment of GAOs with acetate as the sole carbon source took up propionate at a much slower rate (only about 5% of the rate of acetate uptake on a COD basis) during a short-term switch in carbon source. A GAO enrichment with propionate as the sole carbon source took up acetate at a rate that was less than half of the propionate uptake rate on a COD basis. These results, along with literature reports showing that PAOs fed with propionate (also dominated by Accumulibacter) can immediately switch to acetate, suggesting that PAOs are more adaptable to changes in carbon source as compared to GAOs. This study suggests that the PAO and GAO competition could be influenced in favour of PAOs through the provision of propionate in the feed or even by regularly switching the dominant VFA species in the wastewater. Further study is necessary in order to provide greater support for these hypotheses.     

Molecular weights of glycollate oxidase from C3 and C4 plants determined during early stages of purification

The M_rs of glycollate oxidase (EC 1.1.3.1) (GAO) determined soon after extraction from the leaves of several C₃ and C₄ plants are reported. The enzyme isolated from the C₃ plants wheat, barley, spinach, pea and tobacco has M_r in the range 160–180 000 and is probably a homotetramer. GAO purified from pea was previously reported as a dimer and as an octamer from spinach leaves. Therefore the quaternary structure of these GAOs soon after extraction differs from that of the purified proteins. The enzymes from the C₄ plants maize and sugar cane have M_rs ca twice this value in the range 290–310 000, whilst that of the C₄ grass Panicum maximum has an M_r of 162 000. An improved spectrophotometric assay for GAO, using a non-carcinogenic dye, is described.     

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges.     

Phylogenetic analysis and evolutionary studies of plant carotenoid cleavage dioxygenase gene

The oxidative breakdown of carotenoid evidences the formation of apocarotenoids through carotenoid cleavage dioxygenases (CCDs). Numerous CCDs and apocarotenoids have been identified and characterized in plants. Using available sequence data, a study was performed to investigate the phylogenetic relationship among CCD genes and to statistically estimate the sequence conservation and functional divergence. In total, 77 genes were identified from 39 species belonging to 21 families. Our result of phylogenetic analysis indicated the existence of well-conserved subfamilies. Moreover, comparative genomic analysis showed that the gene structures of the CCDs were highly conserved across some different lineage species. Through functional divergence analysis, a substantial divergence was found between CCD subfamilies. In addition, examination of the site-specific profile revealed the critical amino acid residues accounting for functional divergence. This study mainly focused on the evolution of CCD genes and their functional divergence which may deliver an initial step for further experimental verifications.     

Evolution of dimorphisms of the proteasome subunit beta type 8 gene (PSMB8) in basal ray-finned fish

The proteasome subunit beta type 8 (PSMB8) gene encodes a catalytic subunit of immunoproteasome that plays a central role in the processing of antigenic peptides presented by major histocompatibility complex class I molecules. The A- and F-type alleles defined by the 31st amino acid residue determining cleaving specificity have been identified from ray-finned fish, amphibia, and reptiles. These two types show extremely long-term trans-species polymorphism in Polypteriformes, Cypriniformes, and Salmoniformes, suggesting the presence of very ancient lineages termed A and F. To elucidate the evolution of the PSMB8 dimorphism in basal ray-finned fish, we analyzed Pantodon buchholzi (Osteoglossiformes), seven species of Anguilliformes, and Hypomesus nipponensis (Osmeriformes). Both A and F lineage sequences were identified from P. buchholzi and H. nipponensis, confirming that these two lineages have been conserved by basal ray-finned fish. However, both the A- and F-type alleles found in Anguilliformes species belonged to the F lineage irrespective of their types. This apparently suggests that the A lineage was lost in the common ancestor of Anguilliformes, and recovery of the A type within the F lineage occurred in Anguilliformes. The apparent loss of the F lineage and recovery of the F type within the A lineage have already been reported from tetrapods and higher teleosts. However, this is the first report on the reverse situation and reveals the dynamic evolution of the PSMB8 dimorphism.     

Determination of glutamic acid decarboxylase activity and inhibition by an H2O2-sensing glutamic acid oxidase biosensor.

The catalytic activity of the enzyme L-glutamic acid decarboxylase (GAD) is determined by an amperometric method based on a recently developed glutamate-selective biosensor. The biosensor is composed of an amperometric H2O2 electrode and a biocatalytic membrane containing the enzyme glutamic acid oxidase (GAO). The biosensor allows the direct and continuous measurement of GA levels by monitoring the H2O2 produced at the electrode interface as a coproduct of the GAO-catalyzed GA oxidation to alpha-ketoglutaric acid. Since GA is transformed to gamma-aminobutyric acid and CO2 under the catalytic activity of GAD, the rate of GA consumption in solution, monitored by the GAO biosensor, represents a reliable measure of GAD catalytic activity. Additional experiments performed in the presence of different concentrations of the GAD inhibitor valproic acid have shown the suitability of the proposed approach for the study of GAD inhibitors also. Discussion of the main experimental characteristics of this new analytical method is given in terms of sensitivity, reproducibility, and reliability of the experimental results and ease, time, and cost of operation.     

A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity

In Archaea, splicing endonuclease (EndA) recognizes and cleaves precursor RNAs to remove introns. Currently, EndAs are classified into three families according to their subunit structures: homotetramer, homodimer, and heterotetramer. The crenarchaeal heterotetrameric EndAs can be further classified into two subfamilies based on the size of the structural subunit. Subfamily A possesses a structural subunit similar in size to the catalytic subunit, whereas subfamily B possesses a structural subunit significantly smaller than the catalytic subunit. Previously, we solved the crystal structure of an EndA from Pyrobaculum aerophilum. The endonuclease was classified into subfamily B, and the structure revealed that the enzyme lacks an N-terminal subdomain in the structural subunit. However, no structural information is available for crenarchaeal heterotetrameric EndAs that are predicted to belong to subfamily A. Here, we report the crystal structure of the EndA from Aeropyrum pernix, which is predicted to belong to subfamily A. The enzyme possesses the N-terminal subdomain in the structural subunit, revealing that the two subfamilies of heterotetrameric EndAs are structurally distinct. EndA from A. pernix also possesses an extra loop region that is characteristic of crenarchaeal EndAs. Our mutational study revealed that the conserved lysine residue in the loop is important for endonuclease activity. Furthermore, the sequence characteristics of the loops and the positions towards the substrate RNA according to a docking model prompted us to propose that crenarchaea-specific loops and an extra amino acid sequence at the catalytic loop of nanoarchaeal EndA are derived by independent convergent evolution and function for recognizing noncanonical bulge-helix-bulge motif RNAs as substrates.     

Biotechnological approaches for cultivation and enhancement of secondary metabolites in Arnica montana L.

Arnica montana L. (Asteraceae) is a valuable medicinal plant with anti-inflammatory and cicatrizing properties attributed to the sesquiterpene lactones, flavonoids and essential oil produced in the flower heads. In many European countries, the populations of A. montana are close to extinction in their natural habitats because of uncontrolled eradication and indiscriminate collection of the plants. Various approaches for in vitro propagation of the species and also, biosynthesis of secondary metabolites in tissue and cell cultures are assessed in the current review. Special attention is paid to the biological activity and chemical composition of compounds produced by the species as well as the opportunities of in vitro methods to isolate high-productive clones. The influence of different factors on the micropropagation, callusogenesis, genetic transformation and identification of certain biologically active substances is discussed in detail. By the reference to the available issues we concluded that biotechnology applied to A. montana cultivation may improved the plant preservation and increased the production of sesquiterpene lactones and other secondary metabolites.     

Molecular characterization of the mitochondrial cytochrome oxidase I gene of Oestridae species causing obligate myiasis

A 688-bp region of the mitochondrial cytochrome oxidase I gene was sequenced from larvae of 18 species of Oestridae causing obligate myiasis. Larvae belonged to the four Oestridae subfamilies (Cuterebrinae, Gasterophilinae, Hypodermatinae and Oestrinae), which are commonly found throughout the world. Analysis of both nucleotide and amino acid data was performed. Nucleotide sequences included 385 conserved sites and 303 variable sites; mean nucleotide variation between all species was 18.1% and variation within each subfamily ranged from 5.3% to 13.34%. Intraspecific pairwise divergences ranged from 0.14% to 1.59%, and interspecific variation ranged from 0.7% to 27%. Of the 229 amino acids, 76 were variable (60 of which were phylogenetically informative), with some highly conserved residues identified within each subfamily. Phylogenetic analysis showed a strong divergence among the four subfamilies, concordant with classical taxonomy based on morphological and biological features. This study provides the first molecular data set for myiasis-causing Oestridae species, providing an essential database for the molecular identification of these parasites and the assessment of phylogenetic relationships within family Oestridae.     

Variation of sesquiterpene lactones in Lactuca aculeata natural populations from Israel,Jordan and Turkey

A comparative phytochemical study of seven sesquiterpene lactones in natural populations of the wild lettuce Lactuca aculeata Boiss. (Asteraceae) was performed, based on 23 accessions derived from eight, two, and single localities from Israel, Jordan, and Turkey, respectively. The compounds were profiled and quantified in leaves and roots of the plants, grown from achenes (cypselas) in a greenhouse under controlled conditions, using reverse phase HPLC with on-line photodiode array detector. In the present study, L. aculeata was confirmed as a taxon strongly characterized by four dominant sesquiterpene lactones: 8-deoxylactucin, jacquinelin, crepidiaside B and lactuside A. An analysis of quantitative results of these four constituents led to the following conclusions: (i) the sesquiterpene lactone contents varied significantly, mainly within the populations; however, for two variables (crepidiaside B and lactuside A in root samples) the contents varied mostly between populations, (ii) these differences are likely to be genetically controlled since all accessions were grown under standardized glasshouse conditions. Accessions containing high levels of some sesquiterpene lactones were found in several populations. These traits should be conserved in situ and ex situ and utilized in further research and lettuce improvement.     

A comprehensive generic-level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae

The sunflower family (Asteraceae) is the largest and the most diverse flowering plant family, comprising 24 000–30 000 species and 1600–1700 genera. In China, Asteraceae are also the largest family, with approximately 2336 indigenous species in 248 genera. In the past two decades, molecular phylogenetic analyses has contributed greatly to our understanding of the systematics of Asteraceae. Nevertheless, the large-scale analyses and knowledge about the relationships of Chinese Asteraceae at the generic level as a whole are far from complete due to difficulties in sampling. In this study, we presented a three-marker (rbcL, ndhF, and matK) phylogeny of Asteraceae, including 506 genera (i.e., approximately one-third of Asteraceae genera). The study sampled 200 Chinese genera (i.e., approximately 80% of Chinese Asteraceae genera). The backbones of the new phylogeny were largely congruent with earlier studies, with 13 subfamilies and 45 tribes recognized. Chinese Asteraceae were distributed in 7 subfamilies (Mutisioideae, Wunderlichioideae, Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, and Asteroideae) and 22 tribes (Mutiseae, Hyalideae, Cardueae, Pertyeae, Gymnarrheneae, Vernonieae, Cichorieae, Doroniceae, Senecioneae, Astereae, Anthemideae, Gnaphalieae, Calenduleae, Inuleae, Athroismeae, Helenieae, Coreopsideae, Neurolaeneae, Tageteae, Millieae, Eupatorieae, and Heliantheae). Chinese Asteraceae lacked 6 basal subfamilies and 23 tribes. Several previously ambiguous relationships were clarified. Our analyses also resolved some unplaced genera within Chinese Asteraceae. Finally, our phylogenetic tree was used to revise the classification for all genera of Chinese Asteraceae. In total, 255 genera, 22 tribes, and 7 subfamilies in China are recognized.     

QSAR models of quail dietary toxicity based on the graph of atomic orbitals

Graphs of atomic orbitals (GAOs) have been used to represent molecular structures. We describe rules to convert the labelled hydrogen-filled graphs (LHFGs) into GAOs. The GAO is one possible way of taking account of the structure of atoms (i.e., atomic orbitals, such as 1s(1), 2p(2) and 3d(10)) for QSPR/QSAR analyses. Optimization of correlation weights of local invariants (OCWLI) of the LHFGs and the GAOs was used to obtain a method of quail dietary toxicity modelling. Statistical characteristics of the models based on the OCWLI of GAO are better than those based on the OCWLI of the LHFGs.     

Identification and Characterization of γ-Glutamylamine Cyclotransferase,an Enzyme Responsible for γ-Glutamyl-?-lysine Catabolism

γ-Glutamylamine cyclotransferase (GGACT) is an enzyme that converts γ-glutamylamines to free amines and 5-oxoproline. GGACT shows high activity toward γ-glutamyl-ϵ-lysine, derived from the breakdown of fibrin and other proteins cross-linked by transglutaminases. The enzyme adopts the newly identified cyclotransferase fold, observed in γ-glutamylcyclotransferase (GGCT), an enzyme with activity toward γ-glutamyl-α-amino acids (Oakley, A. J., Yamada, T., Liu, D., Coggan, M., Clark, A. G., and Board, P. G. (2008) J. Biol. Chem. 283, 22031–22042). Despite the absence of significant sequence identity, several residues are conserved in the active sites of GGCT and GGACT, including a putative catalytic acid/base residue (GGACT Glu⁸²). The structure of GGACT in complex with the reaction product 5-oxoproline provides evidence for a common catalytic mechanism in both enzymes. The proposed mechanism, combined with the three-dimensional structures, also explains the different substrate specificities of these enzymes. Despite significant sequence divergence, there are at least three subfamilies in prokaryotes and eukaryotes that have conserved the GGCT fold and GGCT enzymatic activity.     

Biosynthesis of costunolide,dihydrocostunolide, and leucodin. Demonstration of cytochrome p450-catalyzed formation of the lactone ring present in sesquiterpene lactones of chicory

Chicory (Cichorium intybus) is known to contain guaianolides, eudesmanolides, and germacranolides. These sesquiterpene lactones are postulated to originate from a common germacranolide, namely (+)-costunolide. Whereas a pathway for the formation of germacra-1(10),4,11(13)-trien-12-oic acid from farnesyl diphosphate had previously been established, we now report the isolation of an enzyme activity from chicory roots that converts the germacrene acid into (+)-costunolide. This (+)-costunolide synthase catalyzes the last step in the formation of the lactone ring present in sesquiterpene lactones and is dependent on NADPH and molecular oxygen. Incubation of the germacrene acid in the presence of 18O2 resulted in the incorporation of one atom of 18O into (+)-costunolide. The label was situated at the ring oxygen atom. Hence, formation of the lactone ring most likely occurs via C6-hydroxylation of the germacrene acid and subsequent attack of this hydroxyl group at the C12-atom of the carboxyl group. Blue light-reversible CO inhibition and experiments with cytochrome P450 inhibitors demonstrated that the (+)-costunolide synthase is a cytochrome P450 enzyme. In addition, enzymatic conversion of (+)-costunolide into 11(S),13-dihydrocostunolide and leucodin, a guaianolide, was detected. The first-mentioned reaction involves an enoate reductase, whereas the formation of leucodin from (+)-costunolide probably involves more than one enzyme, including a cytochrome P450 enzyme.     

Purification and identification of antimicrobial sesquiterpene lactones from yacon (Smallanthus sonchifolius) leaves

The extraction of yacon [Smallanthus sonchifolius (Poepp. and Endl.) H. Robinson; Asteraceae] leaves and chromatographic separation yielded two new antibacterial melampolide-type sesquiterpene lactones, 8beta-tigloyloxymelampolid-14-oic acid methyl ester and 8beta-methacryloyloxymelampolid-14-oic acid methyl ester, as well as the four known melampolides, sonchifolin, uvedalin, enhydrin and fluctuanin. The newly identified compound, 8beta-methacryloyloxymelampolid-14-oic acid methyl ester, exhibited potent antimicrobial activity against Bacillus subtilis and Pyricularia oryzae, while 8beta-tigloyloxymelampolid-14-oic acid methyl ester showed lower activity. Fluctuanin exhibited the strongest antibacterial activity against B. subtilis among these six sesquiterpene lactones.     

Echinate fossil pollen of Asteraceae from the Late Oligocene of Patagonia: an assessment of its botanical affinity

The Late Oligocene Mutisiapollis telleriae, which is the oldest echinate fossil pollen of Asteraceae from Patagonia, was tentatively related to the subfamily Mutisioideae. A detailed comparison of M. telleriae with extant asteraceous pollen indicates strong similarities with both Mutisioideae (in particular the Gongylolepis type) and Carduoideae (some genera of Carduinae) subfamilies. This morphotype, as an example of the exceptional diversity of fossil pollen of Asteraceae found in Patagonia, contributes to the knowledge of the early history of the family.