Allosteric interactions within subsites of a monomeric enzyme: kinetics of fluorogenic substrates of PI-specific phospholipase C

Two novel water-soluble fluorescein myo-inositol phosphate (FLIP) substrates, butyl-FLIP and methyl-FLIP, were used to examine the kinetics and subsite interactions of Bacillus cereus phosphatidylinositol-specific phospholipase C. Butyl-FLIP exhibited sigmoidal kinetics when initial rates are plotted versus substrate concentration. The data fit a Hill coefficient of 1.2-1.5, suggesting an allosteric interaction between two sites. Two substrate molecules bind to this enzyme, one at the active site and one at a subsite, causing an increase in activity. The kinetic behavior is mathematically similar to that of well-known cooperative multimeric enzymes even though this phosphatidylinositol-specific phospholipase C is a small, monomeric enzyme. The less hydrophobic substrate, methyl-FLIP, binds only to the active site and not the activator site, and thus exhibits standard hyperbolic kinetics. An analytical expression is presented that accounts for the kinetics of both substrates in the absence and presence of a nonsubstrate short-chain phospholipid, dihexanoylphosphatidylcholine. The fluorogenic substrates detect activation at much lower concentrations of dihexanoylphosphatidylcholine than previously reported.     

Conformation of alpha zeins in solid state by Fourier transform IR

The major maize storage proteins (alpha zeins) are deposited as an insoluble mass in the protein bodies of the endosperm. Because they are insoluble in water, most structural studies are performed in alcohol solutions. To solve the question raised by several authors about denaturation of the alpha zein structure by alcohol, we analyze the secondary structure of alpha zeins prepared with and without solubilization in alcohol (corn gluten meal and protein bodies with high concentrations of alpha zeins and traces of beta zeins). The secondary structures of alpha zeins are analyzed in the solid state by Fourier transform IR spectroscopy (FTIR) in KBr pellets and solid-state 13C-NMR spectroscopy. The proportion of secondary structures obtained by FTIR of alpha zeins prepared with and without solubilization in alcohol yield almost identical proportions of alpha helices and beta sheets. The proportion of alpha helices (43%) agrees with that measured by circular dichroism in an alcohol solution. However, the proportion of beta sheets (28%) is higher than the one measured by the same technique. Gluten and protein body samples with high beta zein content showed higher beta sheet and lower alpha helix proportions than that obtained for alpha zein preparations. The solid-state 13C-NMR spectra show the carbonyl peak for the alpha zeins at delta 176 and for the sample rich in beta zeins at delta 172, which demonstrates the presence of a high content of alpha helices and beta sheets, respectively. These results indicate that alcohol solubilization does not affect the conformation of alpha zeins, validating the secondary structure measurements in solution.     

Recombinant (2-->3)-alpha-sialyltransferase immobilized on nickel-agarose for preparative synthesis of sialyl Lewis(x) and Lewis(a) precursor oligosaccharides

The specificity of recombinant (2-->3)-alpha-sialyltransferase (ST3Gal-III), expressed in baculovirus-infected insect cells, has been determined with various oligosaccharide acceptors and sugar-nucleotide donors using a fluorescence based assay. Recombinant ST3Gal-III tagged with a polyhistidine tail was immobilized on Ni(2+)-NTA-Agarose as an active enzyme for use in the synthesis of three sialylated oligosaccharides: (i) the divalent molecule [alpha-Neu5Ac-(2-->3)-D-Galp-(1-->4)-beta-D-GlcpNAc-O-CH(2)](2)-C-(CH(2)OBn)(2) (12); (ii) the dansylated derivative, alpha-Neu5Ac-(2-->3)-D-Galp-(1-->3)-beta-D-GlcpNAc-O-(CH(2))(6)-NH-dansyl and; (iii) the tetrasacharide alpha-Neu5Ac-(2-->3)-beta-D-Galp-(1-->4)-beta-D-GlcpNAc-(1-->2)-alpha-D-Manp-O-CH(3). Compound 12 was itself prepared from the divalent N-acetyllactosamine molecule built on pentaerythritol by a chemo-enzymatic route.     

Vicariance and dispersal across Baja California in disjunct marine fish populations

Abstract.— Population disjunctions, as a first step toward complete allopatry, present an interesting situation to study incipient speciation. The geological formation of the Baja California Peninsula currently divides 19 species of fish into disjunct populations that are found on its Pacific Coast and in the northern part of the Gulf of California (also called the Sea of Cortez), but are absent from the Cape (Cabo San Lucas) region. We studied the genetic makeup of disjunct populations for 12 of these 19 fish species. Phylogeographic patterns for the 12 species can be separated into two major classes: a first group (eight species) showed reciprocal monophyly and high genetic divergence between disjunct populations. A second group (four species) displayed what appeared to be panmictic populations. Population structure between Pacific Coast populations, across the Punta Eugenia biogeographic boundary, was also evaluated. While dispersal potential (inferred by pelagic larval duration) was a poor predictor of population structure between Gulf of California and Pacific populations, we found that population genetic subdivision along the Pacific Coast at Punta Eugenia was always positively correlated with differentiation between Pacific and Gulf of California populations. Vicariant events, ongoing gene flow, and ecological characteristics played essential roles in shaping the population structures observed in this study.     

Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change

This study investigated the influence of reproductive strategy (benthic or pelagic eggs) and habitat preferences (lagoon or outer slope) on both diversity and genetic differentiation using a set of populations of seven coral reef fish species over different geographic scales within French Polynesia. We hypothesized that a Holocene sea-level decrease contributed to severe reduction of population size for species inhabiting lagoons and a subsequent decrease of genetic diversity. Conversely, we proposed that species inhabiting stable environments, such as the outer slope, should demonstrate higher genetic diversity but also more structured populations because they have potentially reached a migration-genetic drift equilibrium. Sequences of the 5' end of the mitochondrial DNA (mtDNA) control region were compared among populations sampled in five isolated islands within two archipelagos of French Polynesia. For all the species, no significant divergences among populations were found. Significant differences in mtDNA diversity between lagoonal and outer-slope species were demonstrated both for haplotype diversity and sequence divergence but none were found between species with different egg types. Pairwise mismatch distributions suggested rapid population growth for all the seven species involved in this study, but they revealed different distributions, depending on the habitat preference of the species. Although several scenarios can explain the observed patterns, the hypothesis of population size reduction events relative to Holocene sea-level regression and its consequence on French Polynesia coral reefs is the most parsimonious. Outer-slope species have undergone a probable weak and/or old bottleneck (outer reefs persisted during low sea level, leading to reef area reductions), whereas lagoonal species suffered a strong and/or recent bottleneck since Holocene sea-level regression resulted in the drying out of all the atolls that are maximum 70 meters deep. Since present sea level was reached between 5000 and 6000 years ago, different demographic events (bottlenecks or founder events) have lead to the actual populations of lagoons in French Polynesia.     

Segmental allopolyploidy and paleopolyploidy in species of Leucaena benth: evidence from meiotic behaviour analysis

In this paper we report meiotic behaviour in 28 accessions of the tetraploid (2n = 4x = 104 or 112) Leucaena confertiflora, L. diversifolia, L. involucrata, L. leucocephala, L. x spontanea and the diploid (2n = 2x = 52 or 56) L. shannonii and L. macrophylla. We compare and discuss our data with that on literature about polyploidy in the genus. Despite the general predominance of bivalent formation, quadrivalents and other associations were found in all the taxa analysed. In the diploid species. multiple associations were found in up to 62% of the cells in L. shannonii and 97.6% in L. macrophylla. In the tetraploid taxa irregularities such as univalents, trivalents and other multivalents were observed in varying proportions, up to 55% in L. involucrata. Mean meiotic indexes per accession in the diploids and tetraploids were over or near 90%, but pollen fertility varied from 54.2% to 87.3%. The rather frequent presence of quadrivalents in the diploid species supports a paleopolyploid origin. For the tetraploid taxa, the presence of quadrivalents reflect chromosomal homology due to polyploid origin. Even if an autotetraploid origin cannot be ruled out by cytological data alone, considering other existing evidence, it is probable that L. confertiflora, L. pallida, L. leucocephala and L. involucrata are segmental allopolyploids. However, an autopolyploid origin for L. diversifolia cannot be ruled out nor cytologically nor by other existing data.     

Database resources of the National Center for Biotechnology

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.     

Uptake of sialic acid by human erythrocyte. Characterization of a transport system

Upon incubation of human red blood cells (RBC) with [4-9-14C] N-acetylneuraminic acid, the cells incorporated this sugar, as demonstrated by the identification of labelled N-acetylmannosamine in the cytosol, as a result of the action of the sialic acid pyruvate-lyase we discovered previously (Biochimie 84 (2002) 655). The mechanism is saturable and indicates the presence of a limited number of transporter molecules in the RBC membrane. This transport process may have relevance to the desialylation of membrane glycoconjugates which occurs during ageing of erythrocytes.     

Stroma-mediated granulocyte-macrophage colony-stimulating factor (GM-CSF) control of myelopoiesis: spatial organisation of intercellular interactions

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is one of the major cytokines involved in control of haemopoiesis both in bone marrow and in extramedullar sites. Its biological activity depends upon the composition and physicochemical properties of the microenvironment provided by the supporting stroma. GM-CSF activity is modulated and controlled by the stromal heparan-sulphate proteoglycans, but their optimal interaction occurs only at low pH. We questioned whether the microenvironment organisation of the interface between stroma and haemopoietic cells provides such conditions. We studied myeloid progenitor proliferation in contact with bone marrow-derived and extramedullar stromas using electron microscopy and selective labelling of pericellular components. We present evidence that, upon interaction, the two cell types reorganise their interface both in shape and molecular composition. Haemopoietic cells extend projections that considerably increase the area of intercellular contact, and stromal cells form lamellipodia and carry out a redistribution of membrane-associated sialylated glycoconjugates and proteoglycans. Such rearrangements lead to extensive capping of negatively charged molecules at the interface between the supporting stroma and the haemopoietic cells, leading potentially to a local decrease in pH. Our results indicate that the distribution of negative charges at the cellular interface may be responsible for the selectivity of cell response to GM-CSF.Publication of the Millennium Institute for Tissue Bioengineering. The study was supported by PRONEX, CNPq and FINEP grants from the Brazilian Ministry of Science and Technology and a FAPERJ grant from the Rio de Janeiro State Government.