DNA junctions, antijunctions, and mesojunctions.

Antijunctions and mesojunctions are new classes of multistranded DNA complexes. They represent a generalization of DNA branched junction complexes, such as the Holliday recombination intermediate. Each strand of a conventional branched junction participates in two different double helices, and this is also true for mesojunctions and antijunctions. The helix axes of conventional branched junction complexes may be drawn to converge at a point, but this convergence occurs for lines drawn perpendicular to the helix axes of antijunctions. Mesojunctions are complexes that mix these features of junctions and antijunctions. Antijunction complexes require an even number of strands. We have synthesized the mesojunction containing three strands, the two mesojunctions containing four strands, and the antijunction containing four strands; we compare them with branched junctions containing three and four strands, derived by permutations of the same sequences. Each double helix is designed to contain 1.5 turns of DNA. A tendency to oligomerize makes it difficult to capture antijunctions and mesojunctions in stable discrete complexes, in contrast to conventional branched junctions. For both three-strand and four-strand complexes, Tm is highest for conventional branched junctions. Ferguson analysis indicates similarities in the occluded surface area of junctions, antijunctions, and one four-strand mesojunction, but the other four-strand mesojunction has a much lower apparent surface area. Hydroxyl radical cleavage patterns suggest that the four-strand antijunction and the low-surface-area four-strand mesojunction form stacking domains, analogous to the behavior of conventional branched junctions. These new structures are related to replicational and recombinational intermediates and to single-stranded nucleic acid knots.     

Differentiation of isomeric oligosaccharide structures by ESI tandem MS and GC-MS

A mixture of arabinoxylan oligosaccharides from wheat seedling was permethylated and analyzed by electrospray ion trap MS and GC-MS. The presence of isomeric structures differing in degree of branching and position of the branched residue along the xylose backbone was demonstrated for oligosaccharides with four and five monosaccharide residues. No isomeric structures were found for oligosaccharides with three monosaccharide residues. Linkage analysis by GC-MS reveals that xylose residues were substituted with single arabinoxyl residues at C-3.     

Structural investigation of the covalent and electrostatic binding of yeast cytochrome c to the surface of various ultrathin lipid multilayers using x-ray diffraction.

X-Ray diffraction was used to characterize the profile structures of ultrathin lipid multilayers having a bound surface layer of cytochrome c. The lipid multilayers were formed on an alkylated glass surface, using the Langmuir-Blodgett method. The ultrathin lipid multilayers of this study were: five monolayers of arachidic acid, four monolayers of arachidic acid with a surface monolayer of dimyristoyl phosphatidylserine, and four monolayers of arachidic acid acid with a surface monolayer of thioethyl stearate. Both the phosphatidylserine and the thioethyl stearate surfaces were found previously to covalently bind yeast cytochrome c, while the arachidic acid surface electrostatically binds yeast cytochrome c. Meridional x-ray diffraction data were collected from these lipid multilayer films with and without a bound yeast cytochrome c surface layer. A box refinement technique, previously shown to be effective in deriving the profile structures of ultrathin multilayer lipid films with and without electrostatically bound cytochrome c, was used to determine the multilayer electron density profiles. The surface monolayer of bound cytochrome c was readily apparent upon comparison of the multilayer electron density profiles for the various pairs of ultrathin multilayer films plus/minus cytochrome c for all cases. In addition, cytochrome c binding to the multilayer surface significantly perturbs the underlying lipid monolayers.     

Characterization of the Lipids of Six Strains of Bacteroides ruminicola

The lipids of six strains of Bacteroides ruminicola were characterized. The nonpolar lipid accounted for 6 to 24% of the total lipid and was composed of diglycerides, triglycerides, and free fatty acids. The phospholipid fraction contained phosphatidylethanolamine, phosphosphingolipids, and trace quantities of phosphatidic acid. In three strains the phosphosphingolipid fraction made up more than half of the total lipid. The fatty acids in the nonpolar, acyl- and phosphosphingolipid consisted of a homologous series of branched and normal chains from 12 to 19 carbons. The long-chain base isolated from the phosphosphingolipids consisted of a homologous series of branched and normal chains from 14 to 24 carbons.     

General and specific lipid–protein interactions in Na,K-ATPase

The molecular activity of Na,K-ATPase and other P2 ATPases like Ca^2 +-ATPase is influenced by the lipid environment via both general (physical) and specific (chemical) interactions. Whereas the general effects of bilayer structure on membrane protein function are fairly well described and understood, the importance of the specific interactions has only been realized within the last decade due particularly to the growing field of membrane protein crystallization, which has shed new light on the molecular details of specific lipid–protein interactions. It is a remarkable observation that specific lipid–protein interactions seem to be evolutionarily conserved, and conformations of specifically bound lipids at the lipid–protein surface within the membrane are similar in crystal structures determined with different techniques and sources of the protein, despite the rather weak lipid–protein interaction energy. Studies of purified detergent-soluble recombinant αβ or αβFXYD Na,K-ATPase complexes reveal three separate functional effects of phospholipids and cholesterol with characteristic structural selectivity. The observations suggest that these three effects are exerted at separate binding sites for phophatidylserine/cholesterol (stabilizing), polyunsaturated phosphatidylethanolamine (stimulatory), and saturated PC or sphingomyelin/cholesterol (inhibitory), which may be located within three lipid-binding pockets identified in recent crystal structures of Na,K-ATPase. The findings point to a central role of direct and specific interactions of different phospholipids and cholesterol in determining both stability and molecular activity of Na,K-ATPase and possible implications for physiological regulation by membrane lipid composition. This article is part of a special issue titled “Lipid–Protein Interactions.”     

Upregulation of the plant protein remorin correlates with dehiscence and cell maturation: A link with the maturation of plasmodesmata?

Remorins are plant-specific proteins found associated with plasma membrane microdomains, called lipid rafts. Recently, we have shown that this lipid raft marker also accumulated at plasmodesmata, likely within the plasma membrane lining these structures. Here, we have investigated the gene expression and protein accumulation patterns of remorin at the organ and cell type levels. We show that remorin level is significantly increased in dehiscent, mature and ageing tissues, as well as in source parts of the leaves, where mature branched plasmodesmata are in majority. these results suggest that remorin predominantly associates with mature branched plasmodesmata.Key words: plasma membrane, lipid rafts, plant protein remorin, plasmodesmata     

GRAZING OF FRESHWATER RHODOPHYTA1

Grazing of freshwater Rhodophyta was examined from three perspective: observation of algal fragments in gut contents of herbivores collecte from streams with populations of red algae, measurement of ignestion rates of three inveratebrates in single diet and choice experiments and analysis of potential food value of the rhodophytes by determining protein, carobohydrate, lipid and estimated caloric contents. The algal thallus forms studied were Audouinella violacea (Kütz.) Hamel, which consists of simple filaments growing in dense tufts, Batrachospermum virgatum (Kütz.) Sirod., which is a densely branched mucilaginous filament, and Tuomeya americanna (Harv.) Papenfuss, which is a branched cartilaginous psedoparenchyma. The thirteen invertebrate taxa containing pieces of one or more of these algae in theri guts included two amphipods, two mayfly larvae, three caddisfly larvae, one beetle larva, four chironomids and one snail. The frequencies with which the Rhodophyta were found in the gut contents were as follows: Audouinella 31%, Tuomeya 38%, Batrachospermum 46% and “chantransia stages” 54%. In all of the individual and choice experiments, Audouinella was ingested at the greates rate, followed by Batrachospermum and then Tuomeya, regardless, of the grazer. Audouinella had the highest protein and lipid contents while Tuomeya displayed the opposite trent. All three rhodophytes had very large calofic values (5.0–6.8 kcal μg^?1 dry weight) due to their high lipid and low ash contents. Therefore, preferential grazing of Audouinella appears to be bases on its simple thallus and high protein contents rather than its calorific value.     

Immunochemical similarity of synthetic alpha-(1----3)-branched D-glucans to dextran B1375

Anti-dextran B1375 antibodies were raised in rabbits by injecting formalin-killed Leuconostoc mesenteroides strain NRRL B1375, and the anti-dextran serum was used to examine native dextran B1375, and synthetic linear and four alpha-(1----3)-branched alpha-(1----6)-D-glucopyranans for similarities. The antiserum reacted with the homologous dextran B1375 and also with all the synthetic linear and branched glucans. Precipitation and precipitation-inhibition studies indicated that the antiserum contained at least three groups of antibodies with different specificities, the first specific for linear alpha-(1----6)-D-glucopyranan structure, the second specific for alpha-D-glycopyranosyl-(1----3)-branching and the last specific for another, unknown structure present in the dextran B1375 molecule. Two samples of the synthetic branched glucans were shown to be immunochemically the most similar to natural dextran B1375 by inhibition experiments.     

Crumpled structure of the custom hydrophobic lytic peptide cecropin B3.

The solution structure of a custom lytic peptide, cecropin B3 (CB3), having two identical hydrophobic segments on both the N- and C-termini, was investigated by two-dimensional NMR spectroscopy. The need to determine the structure of this peptide is rooted in its specific ability to lyse lipid layers that have a high content of anionic lipid. The lytic activities of CB3 on cell membranes including cancer cells and bacteria is found to be less than cecropin B1. The results show that CB3 has four discrete segments forming alpha helical structures. The crumpled structure of CB3 provides evidence for the lysis of the lipid layer being via a pathway that differs from pore formation. The results in this study provide strong clues towards a rational design for a potent antimicrobial and antitumor peptide.     

Identification of a potential bottleneck in branched chain fatty acid incorporation into triacylglycerol for lipid biosynthesis in agronomic plants

In plant, unusual fatty acids are produced by a limited number of species. The industrial benefits of these unusual structures have led several groups to study their production in transgenic plants. Their research results led to very modest accumulation in seeds which was largely due to a limited knowledge of the lipid metabolism and fatty acid transfer in plants. More specifically we need to better understand the substrate specificity and selectivity of acyltransferases which are required for the incorporation of these unusual fatty acids into storage triacylglycerols. In our studies we have compared the incorporation of [¹⁴C] Oleoyl-CoA and Branched Chain Acyls-CoA into [³H] LPA-C18:1 by the Lysophosphatidic acid Acyltransferase (LPAAT) from developing seeds of agronomic plants (flax (Linum usitatissimum) and rape (Brassica napus)) and from a plant capable of producing high amounts of hydroxy fatty acids (castor bean (Ricinus communis)). Our assays demonstrate that LPAATs of the three studied species (1) incorporated preferentially oleyl-CoA, (2) could incorporate cyclopropane acyl-CoA when added alone as a substrate, however very weakly for rapeseed and castor bean seeds, (3) presented a low capacity to incorporate methyl branched acyl-CoA when added alone as a substrate (4) weakly incorporated cyclopropane acyl-CoA and was unable to incorporate methyl branched acyl-CoA when presented with an equimolar mix of oleyl-CoA and branched chain acyl-CoA. In all cases, the LPAAT had a low affinity for branched chain acyl-CoAs. The results show that LPAAT activity from agronomic plants constitutes a bottleneck for the incorporation of branched Chain acyl-CoA into PA.     

Antioxidant activity of the halophyte Limonium tetragonum and its major active components

In this study, the antioxidant potentials of crude extracts and solvent-partitioned fractions of Limonium tetragonum were assessed by measuring their ability to scavenge intracellular reactive oxygen species (ROS) generated in HT-1080 cells. Following activity-oriented separation, four flavonol glycosides were isolated as active principles and their chemical structures were determined by 2 D NMR and by comparison with reported spectral data. The isolated compounds (1?C4) were evaluated for their antioxidant capacity using three different activity tests; degree of occurrence of intracellular ROS, lipid peroxidation in HT-1080 cells and the extent of oxidative damage of genomic DNA purified from HT-1080 cells. All compounds exhibited significantly inhibited the generation of intracellular ROS and lipid peroxidation in HT-1080 cells, and significantly inhibited DNA oxidation. In addition, direct free radical scavenging effects of these compounds were investigated using the electron spin resonance (ESR) spin-trap technique.     

General structure-activity relationship for poly(glycoamidoamine)s: the effect of amine density on cytotoxicity and DNA delivery efficiency

Herein, two new series of poly(glycoamidoamine)s (branched and linear) have been synthesized by polycondensation. The polymer repeat units have been designed to contain D-glucaramide, meso-galactaramide, D-mannaramide, or L-tartaramide structures and five or six ethyleneamine units to investigate the amine density effects on the bioactivity as compared to a similar series of poly(glycoamidoamine)s previously described that contain four ethyleneamines. These delivery vehicles were created to examine the effects that the number of secondary amines in the polymer repeat unit and the polymer structure (branched and linear) have on plasmid DNA (pDNA) binding affinity, polyplex formation, cell viability, and gene expression in the absence and presence of serum in the culture medium. The results reveal that the new polymers with higher amine density in the repeat unit do not significantly enhance the transfection efficiency compared to that of previous models containing four ethyleneamines, but an increase in cytotoxicity is noticed. Linear polymers reveal higher pDNA neutralization efficacy, gene expression, and toxicity than the branched versions containing a similar chemical structure, which may be caused by a higher protonation of the amine groups. With these new vectors, some interesting trends emerged. The galactaramide and tartaramide analogues revealed higher delivery efficiency than the glucaramide and mannaramide structures. In addition, the branched and linear structures containing five ethyleneamines in the repeat unit formed polyplexes at higher N/P ratios, which had lower zeta potential and lower delivery efficacy than the analogues with six ethyleneamines, and also the linear structures generally revealed higher delivery efficiency and toxicity when compared to those of their branched analogues.     

Aptamers that recognize the lipid moiety of the antibiotic moenomycin A

Moenomycin A is an amphiphilic phosphoglycolipid antibiotic that interferes with the transglycosylation step in peptidoglycan biosynthesis. The antibiotic consists of a branched pentasaccharide moiety, connected to the moenocinol lipid via a glycerophosphate linker. We have previously described the selection of aptamers that require the lipid group and the disaccharide epitopes of the oligosaccharide moiety for moenomycin binding. Here we report that the enriched moenomycin-binding library contains sequences that evolved for specific recognition of the unpolar lipid group of the antibiotic. These results suggest that the evolution of hydrophobic binding pockets in RNA molecules may be much more common than previously assumed.     

Efficient cell delivery mediated by lipid‐specific endosomal escape of supercharged branched peptides

Various densely charged polycationic species, whether of biological or synthetic origin, can penetrate human cells, albeit with variable efficiencies. The molecular underpinnings involved in such transport remain unclear. Herein, we assemble 1, 2 or 3 copies of the HIV peptide TAT on a synthetic scaffold to generate branched cell‐permeable prototypes with increasing charge density. We establish that increasing TAT copies dramatically increases the cell penetration efficiency of the peptides while simultaneously enabling the efficient cytosolic delivery of macromolecular cargos. Cellular entry involves the leaky fusion of late endosomal membranes enriched with the anionic lipid BMP. Derivatives with multiple TAT branches induce the leakage of BMP‐containing lipid bilayers, liposomal flocculation, fusion and an increase in lamellarity. In contrast, while the monomeric counterpart 1TAT binds to the same extent and causes liposomal flocculation, 1TAT does not cause leakage, induce fusion or a significant increase in lamellarity. Overall, these results indicate that an increase in charge density of these branched structures leads to the emergence of lipid specific membrane‐disrupting and cell‐penetrating activities.      

Structural insights into the lipid transfer mechanism of a non‐specific lipid transfer protein

The non‐specific lipid transfer proteins (nsLTPs) are multifunctional seed proteins engaged in several different physiological processes. The nsLTPs are stabilized by four disulfide bonds and exhibit a characteristic hydrophobic cavity, which is the primary lipid binding site. While these proteins are known to transfer lipids between membranes, the mechanism of lipid transfer has remained elusive. Four crystal structures of nsLTP from Solanum melongena, one in the apo‐state and three myristic acid bound states were determined. Among the three lipid bound states, two lipid molecules were bound on the nsLTP surface at different positions and one was inside the cavity. The lipid‐dependent conformational changes leading to opening of the cavity were revealed based on structural and spectroscopic data. The surface‐bound lipid represented a transient intermediate state and the lipid ultimately moved inside the cavity through the cavity gate as revealed by molecular dynamics simulations. Two critical residues in the loop regions played possible ‘gating’ role in the opening and closing of the cavity. Antifungal activity and membrane permeabilization effect of nsLTP against Fusarium oxysporum suggested that it could possibly involve in bleaching out the lipids. Collectively, these studies support a model of lipid transfer mechanism by nsLTP via intermediate states.     

The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the HDV antigenome and deaminates the amber/W adenosine. A previous report suggested that a branched secondary structure is necessary for editing in HDV genotype III. This branched structure, which is distinct from the characteristic unbranched rod structure required for HDV replication, was only partially characterized, and knowledge concerning its formation and stability was limited. Here, we examine the secondary structures, conformational dynamics, and amber/W site editing of HDV genotype III RNA using a miniaturized HDV genotype III RNA in vitro. Computational analysis of this RNA using the MPGAfold algorithm indicated that the RNA has a tendency to form both metastable and stable unbranched secondary structures. Moreover, native polyacrylamide gel electrophoresis demonstrated that this RNA forms both branched and unbranched rod structures when transcribed in vitro. As predicted, the branched structure is a metastable structure that converts readily to the unbranched rod structure. Only branched RNA was edited at the amber/W site by ADAR1 in vitro. The structural heterogeneity of HDV genotype III RNA is significant because not only are both conformations of the RNA functionally important for viral replication, but the ratio of the two forms could modulate editing by determining the amount of substrate RNA available for modification.     

蕨类植物精细胞运动器和细胞骨架的研究

介绍了近年来蕨类植物游动精子运动器和细胞骨架的研究进展.游动精子由配子体精子器中的非运动细胞发育形成,其分化过程包括了运动器官和细胞骨架的合成和组装.精子发生过程中形成的运动器的各部分结构包括鞭毛、基体、多层结构及附属结构;基体是细胞中新形成的结构,在不同类群的蕨类植物中分别由双中心粒、分支生毛体和生毛体产生.鞭毛、基体和多层结构中的微管带形成了游动精子三个独特的微管列阵,由于微管蛋白的后修饰作用这些微管列阵十分稳定;centrin是运动器中的重要成分,但功能尚不清楚,可能和细胞骨架及运动器的构建有关.     

The site-specific cleavage of synthetic Holliday junction analogs and related branched DNA structures by bacteriophage T7 endonuclease I

Various branched DNA structures were created from synthetic, partly complementary oligonucleotides combined under annealing conditions. Appropriate mixtures of oligonucleotides generated three specific branched duplex DNA molecules: (i) a Holliday junction analog having a fixed (immobile) crossover bounded by four duplex DNA branches, (ii) a similar Holliday junction analog which is capable of limited branch migration and, (iii) a Y-junction, with three duplex branches and fixed branch point. Each of these novel structures was specifically cleaved by bacteriophage T7 gene 3 product, endonuclease I. The cleavage reaction "resolved" the two Holliday structure analogs into pairs of duplex DNA products half the size of the original molecules. The point of cleavage in the fixed-junction molecules was predominantly one nucleotide removed to the 5' side of the expected crossover position. Multiple cleavage positions were mapped on the Holliday junction with the mobile, or variable, branch point, to sites consistent with the unrestricted movement of the phosphodiester crossover within the region of limited dyad symmetry which characterizes this molecule. Based on the cleavage pattern observed with this latter substrate, the enzyme displayed a modest degree of sequence specificity, preferring a pyrimidine on the 3' side of the cleavage site. Branched molecules that were partial duplexes (lower order complexes which possessed single-stranded as well as duplex DNA branches) were also substrates for the enzyme. In these molecules, the cleaved phosphodiester bonds were in duplex regions only and predominantly one nucleotide to the 5' side of the branch point. The phosphodiester positions 5' of the branch point in single-stranded arms were not cleaved. Under identical reaction conditions, individually treated oligonucleotides were completely refractory. Thus, cleavage by T7 endonuclease I displays great structural specificity with an efficiency that can vary slightly according to the DNA sequence.     

Further evidence that a cell wall precursor [C(55)-MurNAc-(peptide)-GlcNAc] serves as an acceptor in a sorting reaction

Previous studies suggested that a Gly-containing branch of cell wall precursor [C(55)-MurNAc-(peptide)-GlcNAc], which is often referred to as lipid II, might serve as a nucleophilic acceptor in sortase-catalyzed anchoring of surface proteins in Staphylococcus aureus. To test this hypothesis, we first simplified the procedure for in vitro biosynthesis of Gly-containing lipid II by using branched UDP-MurNAc-hexapeptide isolated from the cytoplasm of Streptomyces spp. Second, we designed a thin-layer chromatography-based assay in which the mobility of branched but not linear lipid II is shifted in the presence of both sortase and LPSTG-containing peptide. These results and those of additional experiments presented in this study further suggest that lipid II indeed serves as a natural substrate in a sorting reaction.     

Conduction of nonconjugative plasmids by F'' lac is not necessarily associated with transposition of the gamma delta sequence

The expression of fumarate reductase in Escherichia coli has been amplified over 30-fold by utilizing a recombinant plasmid, pFR63 , carrying the fumarate reductase operon. More than 50% of the inner-membrane protein could be accounted for by the enzyme, whereas the total amount of protein associated with the membrane fraction doubled. The membrane accommodated this excess fumarate reductase without reducing the levels of other membrane-associated enzymes. At the same time, the amount of membrane lipid increased such that the lipid/protein ratio remained constant, indicating that the total amount of membrane had doubled. Small alterations in fatty acid composition as well as a large increase in cardiolipin were detected in the fumarate reductase-enriched membranes. The excess membrane was localized in novel tubular structures which were observed in thin-section and negatively stained electron-microscopic preparations. The tubules only appeared after the cytoplasmic membrane became highly enriched in fumarate reductase. They branched from the cytoplasmic membrane and were fumarate reductase. They branched from the cytoplasmic membrane and were composed of an aggregate of fumarate reductase and lipid.