Pseudopterosin biosynthesis in Symbiodinium sp., the dinoflagellate symbiont of Pseudopterogorgia elisabethae

Investigations are reported that identify the biosynthetic source and origins of the pseudopterosins, pharmacologically important diterpene glycosides, in the gorgonian coral Pseudopterogorgia elisabethae. We report here the isolation of physiologically significant levels of endogenous pseudopterosins A, B, C, and D from purified symbionts identified as the dinoflagellate Symbiodinium sp. Biosynthetic studies in photosynthesizing symbiont isolates utilizing 14C-labeled inorganic carbon and the tritiated intermediate geranylgeranyl diphosphate yielded radiochemically pure pseudopterosins A through D and the first committed intermediate, elisabethatriene. The 14CO(2) uptake into the pseudopterosin pathway occurred at low levels compared to the 14CO(2) uptake into total lipids, suggesting a large reserve pool of the compounds. These results reveal for the first time that pseudopterosin biosynthesis is occurring within the algal symbiont and suggests the physiological implications of this biosynthesis.     

Comparison by PAM fluorometry of photosynthetic activity of nine marine phytoplankton grown under identical conditions

The photosynthetic activity of marine phytoplankton from five algal classes (Phaeodactylum tricornutum, Skeletonema costatum, Thalassiosira oceanica, Thalassiosira weissflogii, Dunaliella tertiolecta, Mantoniella squamata, Emiliania huxleyi, Pavlova lutheri and Heterosigma akashiwo) was investigated under identical growth conditions to determine interspecies differences. Primary photochemistry and electron transport capacity of individual species were examined by pulse amplitude-modulated (PAM) fluorescence. Although few differences were found in maximal photosystem II (PSII) photochemical efficiency between various species, large differences were noticed in their PSII-photosystem I (PSI) electron transport activity. We found that species such as T. oceanica and M. squamata have much lower photochemical activity than H. akashiwo. It appeared that processes involved in electron transport activity were more susceptible to change during algal evolution compared with the primary photochemical act close to PSII. Large variations in the nonphotochemical energy dissipation event among species were also observed. Light energy required to saturate photosynthesis was very different between species. We have shown that M. squamata and H. akashiwo required higher light energy (>1300 micromol m(-2) s(-1)) to saturate photosynthesis compared with S. costatum and E. huxleyi (ca 280 micromol m(-2) s(-1)). These differences were interpreted to be the result of variations in the size of light-harvesting complexes associated with PSII. These disparities in photosynthetic activity might modulate algal community structure in the natural environment where light energy is highly variable. Our results suggest that for an accurate evaluation of primary productivity from fluorescence measurements, it is essential to know the species composition of the algal community and the individual photosynthetic capacity related to the major phytoplankton species present in the natural phytoplankton assemblage.     

Reassessment of the structural composition of the alkenone distributions in natural environments using an improved method for double bond location based on GC-MS analysis of cyclopropylimines

The usefulness of n-propyl-, iso-propyl-, and cyclopropylamines for the location of double bonds positions in C37-C40 alkenones after formation of imino derivatives has been evaluated. Cyclopropylamine is the best reagent for its high reaction yields, GC retention time difference between derivatives and precursor compounds, and absence of generation of byproducts. The use of this C3 amine involves higher sensitivity and ease of application than previously reported C5 amines. Examination of a large group of alkenones from cultures of Emiliania huxleyi, water particles, and recent and ancient sediments with cyclopropylamine derivatization shows that, in all cases, the double bonds were located at the same carbon atom distance from the carbonyl group, and spaced in intervals of five methylene groups either from the carbonyl or between them, e.g., at sites 7, 14, 21, and 28. This result represents a correction from previous assumptions in which double-bond positions were situated by reference to the methyl end. 4,4-Dimethyloxazoline derivatization of hexatriacontenoates showed that these compounds have also their unsaturations with seven carbon atom spacing and counting by reference to the carboxyl group. The concurrence of both series of isomers in compounds of different oxygen functionalities indicates that the precursor haptophycean algal species have a major biosynthetic pathway leading to the formation of these lipids. The data presented in this work unify the structures of the known alkenones in the present and the recent past under a common metabolic pathway.     

Identification of critical residues in loop E in the 5-HT3ASR binding site

Background  

The serotonin type 3 receptor (5-HT₃R) is a member of a superfamily of ligand gated ion channels. All members of this family share a large degree of sequence homology and presumably significant structural similarity. A large number of studies have explored the structure-function relationships of members of this family, particularly the nicotinic and GABA receptors. This information can be utilized to gain additional insights into specific structural and functional features of other receptors in this family.     

Landornamides: Antiviral Ornithine‐Containing Ribosomal Peptides Discovered through Genome Mining

Proteusins are a family of bacterial ribosomal peptides that largely remain hypothetical genome‐predicted metabolites. The only known members are the polytheonamide‐type cytotoxins, which have complex structures due to numerous unusual posttranslational modifications (PTMs). Cyanobacteria contain large numbers of putative proteusin loci. To investigate their chemical and pharmacological potential beyond polytheonamide‐type compounds, we characterized landornamide A, the product of the silent osp gene cluster from Kamptonema sp. PCC 6506. Pathway reconstruction in E. coli revealed a peptide combining lanthionines, d ‐residues, and, unusually, two ornithines introduced by the arginase‐like enzyme OspR. Landornamide A inhibited lymphocytic choriomeningitis virus infection in mouse cells, thus making it one of the few known anti‐arenaviral compounds. These data support proteusins as a rich resource of chemical scaffolds, new maturation enzymes, and bioactivities.     

Landornamides: Antiviral Ornithine-Containing Ribosomal Peptides Discovered through Genome Mining

Proteusins are a family of bacterial ribosomal peptides that largely remain hypothetical genome-predicted metabolites. The only known members are the polytheonamide-type cytotoxins, which have complex structures due to numerous unusual posttranslational modifications (PTMs). Cyanobacteria contain large numbers of putative proteusin loci. To investigate their chemical and pharmacological potential beyond polytheonamide-type compounds, we characterized landornamide A, the product of the silent osp gene cluster from Kamptonema sp. PCC 6506. Pathway reconstruction in E. coli revealed a peptide combining lanthionines, d -residues, and, unusually, two ornithines introduced by the arginase-like enzyme OspR. Landornamide A inhibited lymphocytic choriomeningitis virus infection in mouse cells, thus making it one of the few known anti-arenaviral compounds. These data support proteusins as a rich resource of chemical scaffolds, new maturation enzymes, and bioactivities.     

Dimericbiscognienynes B and C: New diisoprenyl-cyclohexene-type meroterpenoid dimers from Biscogniauxia sp.

Till now, only three diisoprenyl-cyclohexene/ane-type meroterpenoid dimers have been identified. The isolation of two new diisoprenyl-cyclohexene-type meroterpenoid dimers (dimericbiscognienynes B and C) from Biscogniauxia sp. 71-10-1-1 added new members to this family.     

Macrocycle Embrace: Encapsulation of Fluoroarenes by m‐Phenylene Ethynylene Host

We report structural characterization of a new member of m‐phenylene ethynylene ring family. This shape‐persistent macrocycle also co‐crystallizes with hexafluoro‐, 1,2,4,5‐tetrafluoro‐, 1,3,5‐trifluoro, and 1,4‐difluorobenzene. The four complexes are almost isostructural, and all show the fluoroarene included into the central cavity of the macrocycle. Characterized by multiple short C?H???F?C contacts, these inclusion complexes further dimerize in the solid state into a 2+2 assembly, in which the two macrocycles embrace each other by their large hydrophobic groups that are rotated by 60° relative to one another.     

Optimization of DNA extraction from a scleractinian coral for the detection of thymine dimers by immunoassay

Ultraviolet (UV)-B is known to cause DNA damage, principally by the formation of thymine dimers, but little research has been conducted in coral reef environments where UV doses are high. The majority of tropical reef-dwelling corals form a mutualistic symbiosis with the dinoflagellate Symbiodinium but few studies have been conducted on in situ DNA damage in corals and none have investigated the symbiotic components separately. The aim of this research was to quantify DNA damage in both the coral host and the dinoflagellate symbiont. The first step in this investigation was to optimize the extraction of DNA from the host, Porites astreoides, as well as the symbiont. The optimization was divided into a series of steps: the preservation of the samples, separation of the coral tissue from the skeleton, separation of the host tissue from the algal cells to prevent cross contamination as well as the extraction and purification of genomic DNA from the algae that are located intracellularly within the invertebrate animal tissue. The best preservation method was freezing at low temperatures without ethanol. After scraping with a razor blade, the coral tissue can be divided into host and algal components and the DNA extracted using modifications of published techniques yielding DNA suitable for the quantification of thymine dimer formation using antibodies. Preliminary data suggest that in P. astreoides collected from 1 m depth, thymine dimers form approximately 2.8 times more frequently in the host DNA than in the DNA of its symbionts.     

Several new electrofocusing techniques

The segregation and analysis of low-abundance proteins from complex biological fluids requires serial application of separation techniques that can simultaneously fractionate and concentrate solutes. In general, these techniques belong either to the family of displacement methods, e.g., ITP, or to the gradient methods, e.g., gradient-elution HPLC. IEF is a member of the subset of the gradient methods referred to as equilibrium gradient methods (EGM) and has the important property that, starting from an arbitrarily distributed initial state, evolves over time to a self-sharpening, stationary steady state. Until the introduction of counteracting chromatographic electrophoresis by O'Farrell in 1985, IEF was the only known electrokinetic technique with this property. Today, the sub-family of electrokinetic EGMs has at least half a dozen members and is slowly growing. This review describes some of the essential properties of the displacement methods, the EGMs and the non-EGMs, showing how they can be applied in microelectromechanical systems platforms, how their performance can be predicted and how new members with orthogonal properties may be added to the EGM family.     

Convergent, stereoselective syntheses of the glycosidase inhibitors broussonetines C, O and P

The first syntheses of the polyhydroxylated alkaloids (iminosugars) broussonetines O and P, glycosidase inhibitors of the pyrrolidine class, have been performed in a convergent, stereocontrolled way from d-serine as the chiral starting material. The synthesis of broussonetin C, a further member of this compound family, is also reported. A cross-metathesis step was one key feature of the synthesis. The versatility of the synthetic concept chosen permits the access to many members of this compound family, both natural ones and analogues thereof.     

Total synthesis of (-)-tirandamycin C

Tirandamycin C is a newly isolated member of the tetramic acid family natural products. We described herein the first enantioselective synthesis of natural (-)-tirandamycin C, the postulated biosynthetic precursor of other members of this family. The highly stereoselective (>15:1) mismatched double asymmetric γ-stannylcrotylboration reaction of aldehyde 8 with crotylborane reagent (R)-E-9 was utilized to access the key anti,anti-stereotriad 18.     

bryA: an unusual modular polyketide synthase gene from the uncultivated bacterial symbiont of the marine bryozoan Bugula neritina

"Candidatus Endobugula sertula," the uncultivated bacterial symbiont of Bugula neritina, is the proposed source of the bryostatin family of anticancer compounds. We cloned a large modular polyketide synthase (PKS) gene complex from "Candidatus Endobugula sertula" and characterized one gene, bryA, which we propose is responsible for the initial steps of bryostatin biosynthesis. Typical PKS domains are present. However, acyltransferase domains are lacking in bryA, and beta-ketoacyl synthase domains of bryA cluster with those of PKSs with discrete, rather than integral, acyltransferases. We propose a model for biosynthesis of the bryostatin D-lactate starter unit by the bryA loading module, utilizing atypical domains homologous to FkbH, KR, and DH. The bryA gene product is proposed to synthesize a portion of the pharmacologically active part of bryostatin and may be useful in semisynthesis of clinically useful bryostatin analogs.     

Predicting microRNA biological functions based on genes discriminant analysis

Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into their corresponding families will be helpful for their further functional analysis. In this study, we initially built a vector space by characterizing the features from miRNA sequences and structures according to their miRBase family organizations. Then we further assigned miRNAs into its specific miRNA families by developing a novel genes discriminant analysis (GDA) approach in this study. As can be seen from the results of new families from GDA, in each of these new families, there was a high degree of similarity among all members of nucleotide sequences. At the same time, we employed 10-fold cross-validation machine learning to achieve the accuracy rates of 68.68%, 80.74%, and 83.65% respectively for the original miRNA families with no less than two, three, and four members. The encouraging results suggested that the proposed GDA could not only provide a support in identifying new miRNAs’ families, but also contributing to predicting their biological functions.     

Cloning of BNIP3h, a member of proapoptotic BNIP3 family genes

Apoptosis is regulated by interaction of antiapoptotic Bcl-2 family proteins with various proapoptotic proteins, several of which are also members of the Bcl-2 family. BNIP3 (formerly NIP3) is a proapoptotic mitochondrial protein classified in the Bcl-2 family based on limited sequence homology-3 (BH3) domain and COOH-terminal transmembrane domain. Sequence comparison of BNIP3 has indicated that there are several BNIP3 human homologs of this protein, like BNIP3L, Nix and BNIP3. We have cloned a new member of BNIP3 family from the cDNA library prepared from human dermal papilla cells and designated as BNIP3h. BNIP3h shows substantial homology with other BNIP3 family proteins. BNIP3h induced apoptosis from 24 hours after transfection in MCF7 cell lines and its apoptosis inducing activity is extended until 72 hours after transfection.     

Evolution of class C β-lactamases: factors influencing their hydrolysis and recognition mechanisms

The most common bacterial resistance mechanism to β-lactam antibiotics is the production of β-lactamases. So far, β-lactamases have been classified into four different classes, three of them (A, C and D) have a serine in the active site as the nucleophilic group, which attacks to lactam antibiotic. Despite the large number of kinetic and theoretical studies and many native and complexed β-lactamases crystal structures, the mechanism by which they act is not well understood. The aim of this review is to show the different hypotheses which have been proposed to explain the hydrolysis mechanisms for class A and C lactamases and to cast light onto the interactions between the antibiotic and the Enterobacter cloacae P99 (a class C β-lactamase) in the Henry-Michaelis complex formed previous to the serine attack. Knowledge of these crucial points is essential for obtaining new β-lactam antibiotics not vulnerable to β-lactamases in order to minimize bacterial resistance.     

Assembling OX40 aptamers on a molecular scaffold to create a receptor-activating aptamer

We show that a molecular scaffold can be utilized to convert a receptor binding aptamer into a receptor agonist. Many receptors (including tumor necrosis receptor family members) are activated when they are multimerized on the cell surface. Molecular scaffolds have been utilized to assemble multiple receptor binding peptide ligands to generate activators of such receptors. We demonstrate that an RNA aptamer that recognizes OX40, a member of the tumor necrosis factor receptor superfamily, can be converted into a receptor-activating aptamer by assembling two copies on an olignucleotide-based scaffold. The OX40 receptor-activating aptamer is able to induce nuclear localization of nuclear factor-kappaB, cytokine production, and cell proliferation, as well as enhance the potency of dendritic cell-based tumor vaccines when systemically delivered to mice.