THE INFLUENCE OF CHOLESTEROL AND CHARGE ON THE MEMBRANE DOMAINS OF ALKYLPHOSPHOLIPID LIPOSOMES AS STUDIED BY EPR

ABSTRACT

Alkylphospholipids are physiologically active derivatives of lipids effective in the treatment of breast cancer. Among them, octadecyl-(1,1-dimethyl-4-piperidino-4-yl)-phosphate (OPP) was demonstrated recently to have the strongest antitumor effect in micellar as well as in sterically stabilised liposome suspension with a low cholesterol content. In this work electron paramagnetic resonance (EPR) was used to study the influence of cholesterol, charge, and sterical stabilisation by PEG₂₀₀₀DSPE on the domain structure and fluidity characteristics of the membrane of OPP liposomes. As a spin probe 5-doxylpalmitoyl methyl ester was used. By computer simulation of the EPR spectra it was found that the experimental spectra are composed of three spectral components, which were attributed to three types of domains with different fluidity characteristics. The EPR parameters as well as the proportions of the individual domains were found to be mainly dependent on the amount of cholesterol, and only to a minor degree on charge and sterical stabilisation. There was a pronounced increase in the proportion of membrane domains with low order parameter, when the molar ratio of cholesterol to OPP was decreased below 1. At the same time the order parameters of all domains decreased, pointing to a transition from a less to a more fluid membrane organisation. These results coincide with an improved therapeutic activity of formulations with a low molar ratio of cholesterol to OPP and indicates that the fluidity characteristics of the membrane may be important for the effectiveness of liposomal alkylphospholipids against breast cancer cells.     

Chemical and Physicochemical Properties of Phytase from Aspergillus terreus

Some chemical and physicochemical properties of the purified phytase preparation produced by Asp. terreus were investigated. From the results of the examination of amino acid analysis, it was suggested that there existed some components other than amino acids in the purified enzyme. Examination of the neutral sugar analysis, therefore, was made by gaschromatography, and it was found that the purified enzyme preparation contained mannose, galactose and a small amount of inositol.

The molecular weight of the enzyme was found to be 214,000 by the Archibald method, and 2.2~2.3×10⁵ by gel-filtration on a Sephadex G–200 column. It was found that by guanidine hydrochloride or by urea, the purified enzyme preparation was dissociated into only one kind of subunit. The native enzyme was supposed to be a homohexamer of the subunits whose molecular weight is 37,000.     

Decarboxylation of Oxalic Acid during Ripening of Banana Fruit (Musa sapientum L.)

ABSTRACT

Japanese apricot, Prunus mume Sieb. et Zucc., biosynthesizes the l-phenylalanine-derived cyanogenic glucosides prunasin and amygdalin. Prunasin has biological properties such as anti-inflammation, but plant extraction and chemical synthesis are impractical. In this study, we identified and characterized UGT85A47 from Japanese apricot. Further, UGT85A47 was utilized for prunasin microbial production. Full-length cDNA encoding UGT85A47 was isolated from Japanese apricot after 5?- and 3?-RACE. Recombinant UGT85A47 stoichiometrically catalyzed UDP-glucose consumption and synthesis of prunasin and UDP from mandelonitrile. Escherichia coli C41(DE3) cells expressing UGT85A47 produced prunasin (0.64 g/L) from racemic mandelonitrile and glucose. In addition, co-expression of genes encoding UDP-glucose biosynthetic enzymes (phosphoglucomutase and UTP-glucose 1-phosphate uridiltransferase) and polyphosphate kinase clearly improved prunasin production up to 2.3 g/L. These results showed that our whole-cell biocatalytic system is significantly more efficient than the existing prunasin production systems, such as chemical synthesis.     

Introduction of New Tools for Chemical Biology Research on Microbial Metabolites

Recently, high-throughput screening (HTS) has become the mainstream technique for drug discovery. Compounds that are synthesized by combinatorial chemistry might be more suitable than natural products to apply to HTS, because the purification procedure is a drawback of using natural products. Nevertheless, natural products remain an extremely important source of drugs. To overcome the demerits of natural products, we are constructing the RIKEN Natural Products Depository (NPDepo) that is focused primarily on microbial metabolites. In this review, I describe (i) engineering pathways for biosynthetic gene clusters of microbial metabolites, (ii) construction of fraction libraries of microbial metabolites, and (iii) the development of a new screening system using a chemical array and a protein library produced by GLORIA.     

Domain organization of membrane‐bound factor VIII

Factor VIII (FVIII) is the blood coagulation protein which when defective or deficient causes for hemophilia A, a severe hereditary bleeding disorder. Activated FVIII (FVIIIa) is the cofactor to the serine protease factor IXa (FIXa) within the membrane‐bound Tenase complex, responsible for amplifying its proteolytic activity more than 100,000 times, necessary for normal clot formation. FVIII is composed of two noncovalently linked peptide chains: a light chain (LC) holding the membrane interaction sites and a heavy chain (HC) holding the main FIXa interaction sites. The interplay between the light and heavy chains (HCs) in the membrane‐bound state is critical for the biological efficiency of FVIII. Here, we present our cryo‐electron microscopy (EM) and structure analysis studies of human FVIII‐LC, when helically assembled onto negatively charged single lipid bilayer nanotubes. The resolved FVIII‐LC membrane‐bound structure supports aspects of our previously proposed FVIII structure from membrane‐bound two‐dimensional (2D) crystals, such as only the C2 domain interacts directly with the membrane. The LC is oriented differently in the FVIII membrane‐bound helical and 2D crystal structures based on EM data, and the existing X‐ray structures. This flexibility of the FVIII‐LC domain organization in different states is discussed in the light of the FVIIIa–FIXa complex assembly and function. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 448–459, 2013.     

Microhabitat Variation Explains Local‐scale Distribution of Terrestrial Amazonian Lizards in Rondônia,Western Brazil

We investigate the role of ecology and phylogeny in the association between lizard abundance and microhabitat variables in an Amazon rain forest site. Using pitfall trap arrays, we collected data from 349 individuals belonging to 23 lizard species. After accounting for spatial autocorrelation and using a canonical correspondence analysis (CCA), we found that lizard captures were significantly associated with microhabitat variables, which accounted for 48 percent of the observed variation. Furthermore, a canonical phylogenetic ordination (CPO) indicated that microhabitat variables are more important in determining the distribution of lizard species than phylogenetic relationships among species. Termite nests, canopy openness, and tree circumference were strongly associated with the number of captures of certain lizard species. Our results confirm autecology studies of individual lizard species for which data are available. We suggest that maintaining heterogeneous forested microhabitats should be a central goal for sustaining a high lizard biodiversity in Amazon rain forests.     

Edaphic Factors are a More Important Control on Surface Fine Roots than Stand Age in Secondary Tropical Dry Forests

Although there are generalized conceptual models that predict how above and belowground biomass increase during secondary succession after abandonment from agriculture, there are few data to test these models for fine roots (defined as ≤2 mm diameter) in tropical forests. We measured live and dead fine roots (0–10 cm depth) in 18 plots of regenerating tropical dry forest in Costa Rica that varied in age from 5 to 60 yrs, as well as in soil properties. We predicted that both stand age and soil fertility would affect fine roots, with greater values in older forests on low fertility soils. Across two sampling dates and locations, live fine roots varied from 0.35 to 3.53 Mg/ha and dead roots varied from 0.15 to 0.93 Mg/ha. Surprisingly, there was little evidence that surface fine roots varied between sampling dates or in relation to stand age. By contrast, total, live, and dead fine roots averaged across sampling dates within plots were negatively correlated with a multivariate index of soil fertility (Pearson correlations coefficients were ?0.64, ?0.58, and ?0.68, respectively; P < 0.01) and other individual edaphic variables including pH, silt, calcium, magnesium, nitrogen, and phosphorus. These results suggest that soil fertility is a more important determinant of fine roots than forest age in tropical dry forests in Costa Rica, and that one‐way these plant communities respond to low soil fertility is by increasing fine roots. Thus, simple conceptual models of forest responses to abandonment from agriculture may not be appropriate for surface fine roots.     

Biofilm model calibration and microbial diversity study using Monte Carlo simulations

Mathematical models are useful tools for studying and exploring biological conversion processes as well as microbial competition in biological treatment processes. A single‐species biofilm model was used to describe biofilm reactor operation at three different hydraulic retention times (HRT). The single‐species biofilm model was calibrated with sparse experimental data using the Monte Carlo filtering method. This calibrated single‐species biofilm model was then extended to a multi‐species model considering 10 different heterotrophic bacteria. The aim was to study microbial diversity in bulk phase biomass and biofilm, as well as the competition between suspended and attached biomass. At steady state and independently of the HRT, Monte Carlo simulations resulted only in one unique dominating bacterial species for suspended and attached biomass. The dominating bacterial species was determined by the highest specific substrate affinity (ratio of µ/K_S). At a short HRT of 20 min, the structure of the microbial community in the bulk liquid was determined by biomass detached from the biofilm. At a long HRT of 8 h, both biofilm detachment and microbial growth in the bulk liquid influenced the microbial community distribution. Biotechnol. Bioeng. 2013; 110: 1323–1332. © 2012 Wiley Periodicals, Inc.     

The translation initiation factor 3 subunit eIF3K interacts with PML and associates with PML nuclear bodies

The promyelocytic leukemia protein (PML) is a tumor suppressor protein that regulates a variety of important cellular processes, including gene expression, DNA repair and cell fate decisions. Integral to its function is the ability of PML to form nuclear bodies (NBs) that serve as hubs for the interaction and modification of over 90 cellular proteins. There are seven canonical isoforms of PML, which encode diverse C-termini generated by alternative pre-mRNA splicing. Recruitment of specific cellular proteins to PML NBs is mediated by protein–protein interactions with individual PML isoforms. Using a yeast two-hybrid screen employing peptide sequences unique to PML isoform I (PML-I), we identified an interaction with the eukaryotic initiation factor 3 subunit K (eIF3K), and in the process identified a novel eIF3K isoform, which we term eIF3K-2. We further demonstrate that eIF3K and PML interact both in vitro via pull-down assays, as well as in vivo within human cells by co-immunoprecipitation and co-immunofluorescence. In addition, eIF3K isoform 2 (eIF3K-2) colocalizes to PML bodies, particularly those enriched in PML-I, while eIF3K isoform 1 associates poorly with PML NBs. Thus, we report eIF3K as the first known subunit of the eIF3 translation pre-initiation complex to interact directly with the PML protein, and provide data implicating alternative splicing of both PML and eIF3K as a possible regulatory mechanism for eIF3K localization at PML NBs.     

Integration of New Genes into Cellular Networks,and Their Structural Maturation

It has been recently discovered that new genes can originate de novo from noncoding DNA, and several biological traits including expression or sequence composition form a continuum from noncoding sequences to conserved genes. In this article, using yeast genes I test whether the integration of new genes into cellular networks and their structural maturation shows such a continuum by analyzing their changes with gene age. I show that 1) The number of regulatory, protein–protein, and genetic interactions increases continuously with gene age, although with very different rates. New regulatory interactions emerge rapidly within a few million years, while the number of protein–protein and genetic interactions increases slowly, with a rate of 2–2.25 × 10⁻⁸/year and 4.8 × 10⁻⁸/year, respectively. 2) Gene essentiality evolves relatively quickly: the youngest essential genes appear in proto-genes ∼14 MY old. 3) In contrast to interactions, the secondary structure of proteins and their robustness to mutations indicate that new genes face a bottleneck in their evolution: proto-genes are characterized by high β-strand content, high aggregation propensity, and low robustness against mutations, while conserved genes are characterized by lower strand content and higher stability, most likely due to the higher probability of gene loss among young genes and accumulation of neutral mutations.