Nanostructured dna-protein aggregates consisting of covalent oligonucleotide-streptavidin conjugates

Covalent conjugates consisting of streptavidin and a 24-mer single-stranded DNA oligonucleotide have been oligomerized by cross-linking with a 5',5'-bis-biotinylated 169-base-pair double-stranded DNA (dsDNA) fragment. The oligomeric conjugates formed have been analyzed by nondenaturing gel electrophoresis and scanning-force microscopy (SFM). The comparison of analogous oligomers, prepared from native STV and the bis-biotinylated dsDNA fragment, revealed that the covalent STV-oligonucleotide hybrid conjugates self-assemble to generate oligomeric aggregates of significant smaller size, containing on average only about 2.5 times less dsDNA fragments per aggregate. Likely, this is a consequence of electrostatic or steric repulsion between the dsDNA and the single-stranded oligomer covalently attached to the hybrid, as indicated from control experiments. Nevertheless, the single-stranded oligonucleotide moiety within the oligomeric conjugates can be used as a selective molecular handle for further functionalization and manipulation. For instance, it was used for specific DNA-directed immobilization at a surface, previously functionalized with complementary capture oligonucleotides. Moreover, we demonstrate that macromolecules, such as STV and antibody molecules, which are tagged with the complementary oligonucleotide, specifically bind to the supramolecular DNA-STV oligomeric conjugates. This leads to a novel class of functional DNA-protein conjugates, suitable, for instance, as reagents in immuno-PCR or as building blocks in molecular nanotechnology.     

Regulation of the GTPase cycle in post-translational signal recognition particle-based protein targeting involves cpSRP43

The chloroplast signal recognition particle consists of a conserved 54-kDa GTPase and a novel 43-kDa chromodomain protein (cpSRP43) that together bind light-harvesting chlorophyll a/b-binding protein (LHCP) to form a soluble targeting complex that is subsequently directed to the thylakoid membrane. Homology-based modeling of cpSRP43 indicates the presence of two previously identified chromodomains along with a third N-terminal chromodomain. Chromodomain deletion constructs were used to examine the role of each chromodomain in mediating distinct steps in the LHCP localization mechanism. The C-terminal chromodomain is completely dispensable for LHCP targeting/integration in vitro. The central chromodomain is essential for both targeting complex formation and integration because of its role in binding the M domain of cpSRP54. The N-terminal chromodomain (CD1) is unnecessary for targeting complex formation but is required for integration. This correlates with the ability of CD1 along with the ankyrin repeat region of cpSRP43 to regulate the GTPase cycle of the cpSRP-receptor complex.     

Identification of residues that contribute to receptor activation through the analysis of compensatory mutations in the G protein-coupled alpha-factor receptor

The alpha-factor receptor (Ste2p) stimulates mating of the yeast Saccharomyces cerevisiae. Ste2p belongs to the large family of G protein-coupled receptors that are characterized by seven transmembrane alpha-helices. Receptor activation is thought to involve changes in the packing of the transmembrane helix bundle. To identify residues that contribute to Ste2p activation, second-site suppressor mutations were isolated that restored function to defective receptors carrying either an F204S or Y266C substitution which affect residues at the extracellular ends of transmembrane domains 5 and 6, respectively. Thirty-five different suppressor mutations were identified. On their own, these mutations caused a range of phenotypes, including hypersensitivity, constitutive activity, altered ligand binding, and loss of function. The majority of the mutations affected residues in the transmembrane segments that are predicted to face the helix bundle. Many of the suppressor mutations caused constitutive receptor activity, suggesting they improved receptor function by partially restoring the balance between the active and inactive states. Analysis of mutations in transmembrane domain 7 implicated residues Ala281 and Thr282 in receptor activation. The A281T and T282A mutants were supersensitive to S. cerevisiae alpha-factor, but were defective in responding to a variant of alpha-factor produced by another species, Saccharomyces kluyveri. The A281T mutant also displayed 8.7-fold enhanced basal signaling. Interestingly, Ala281 and Thr282 are situated in approximately the same position as Lys296 in rhodopsin, which is covalently linked to retinal. These results suggest that transmembrane domain 7 plays a role in receptor activation in a wide range of G protein-coupled receptors from yeast to humans.     

Modeling of Galpha(s) and Galpha(i) regulation of human type V and VI adenylyl cyclase

We examined the kinetics of Galpha(s) and Galpha(i) regulation of human type V and type VI adenylyl cyclase (AC V and AC VI) in order to better model interactions between AC and its regulators. Activation of AC VI by Galpha(s) displayed classical Michaelis-Menten kinetics, whereas AC V activation by Galpha(s) was cooperative with a Hill coefficient of 1.4. The basal activity of human AC V, but not that of AC VI, was inhibited by Galpha(i). Both enzymes showed greater inhibition by Galpha(i) at low Galpha(s) concentrations; however, human AC V was activated by Galpha(i) at high Galpha(s) concentrations. Neither regulator had an effect on the K(m) for Mg-ATP. Mutations made within the Galpha(s) binding pocket of AC V (N1090D) and VI (F1078S) displayed 6- and 14-fold greater EC(50) values for Galpha(s) activation but had no effect on Galpha(i) inhibition of basal activity or K(m) for Mg-ATP. Galpha(s)-stimulated AC VI-F1078S was not significantly inhibited by Galpha(i), despite normal inhibition by Galpha(i) upon forskolin stimulation. Mechanistic models for Galpha(s) and Galpha(i) regulation of AC V and VI were derived to describe these results. Our models are consistent with previous studies, predicting a decrease in affinity of Galpha(i) in the presence of Galpha(s). For AC VI, Galpha(s) is required for inhibition but not binding by Galpha(i). For AC V, binding of two molecules of Galpha(s) and Galpha(i) to an AC dimer are required to fully describe the data. These models highlight the differences between AC V and VI and the complex interactions with two important regulators.     

Genetic structure and clonal diversity of an introduced pest in Chile, the cereal aphid Sitobion avenae

In Chile, the aphid Sitobion avenae is of recent introduction, lives on cultivated and wild Poaceae, and is thought to reproduce by permanent parthenogenesis. In order to study the genetic variability and population structure of this species, five microsatellite loci were typed from individual aphids collected from different cultivated and wild host plants, from different geographical zones, and years. Chilean populations showed a high degree of heterozygosity and a low genetic variability across regions and years, with four predominant genotypes representing nearly 90% of the sample. This pattern of low clonal diversity and high heterozygosity was interpreted as the result of recent founder events from a few asexually reproducing genotypes. Most geographical and temporal variation observed in the genetic composition resulted from fluctuations of a few predominant clones. In addition, comparisons of the genotypes found in Chile with those described in earlier surveys of S. avenae populations in Western Europe led us to identify 'superclones' with large geographical distribution and high ecological success, and to make a preliminary exploration of the putative origin(s) of S. avenae individuals introduced to Chile.     

Host selection by the generalist aphid Myzus persicae (Hemiptera: Aphididae) and its subspecies specialized on tobacco, after being reared on the same host

Decision-making during host selection by phytophagous insects has proved to be related to host range, with specialists taking faster decisions than generalists; however, this pattern fails to materialize in some host selection studies performed with aphids. Differences found in testing designs point to rearing effects on aphid host selection. To test whether specialization patterns derive from the nature of the aphid or as a consequence of rearing environment, host selection behaviours were compared between the generalist Myzus persicae (Sulzer) s.s. and its subspecies specialized on tobacco when reared on a common host and offered the choice of an alternative host and a non-host plant. Pre-alighting (host finding and attraction towards host volatiles) and post-alighting (leaf surface exploration and probing) behaviours did not differ between the generalist and the tobacco-specialist, except in the allocation of time to probing behaviour; furthermore, all specialists chose the host on which they performed best. Thus, although the specialist was not faster than the generalist, it showed a higher level of commitment to its preferred host plant.     

Supramolecular DNA-streptavidin nanocircles with a covalently attached oligonucleotide moiety

Covalent hybrid conjugates consisting of streptavidin (STV) and a 24-mer single-stranded DNA oligonucleotide have been used as a starting material for the synthesis of supramolecular nanocircles. For this, the covalent hybrid conjugates were oligomerized by cross-linking with 5 ,5 -bis-biotinylated double-stranded DNA (dsDNA) fragments of various length. Heat denaturation of the resulting oligomeric conjugates and subsequent rapid cooling led to the formation of the nanocircles, in which the oligonucleotide-containing STV molecule is coupled with both ends of the circular bis-biotinylated dsDNA fragment. The circular structure of the bioconjugates was established by electrophoretic studies including Ferguson plot analysis as well as by scanning force microscopy (SFM) inspection. The formation process and the stability against degradation by ligand exchange with free D-biotin was compared for the nanocircles obtained from covalent oligonucleotide-STV hybrids and native STV. The former nanocircles revealed a decreased stability with respect to ring opening than the circles obtained from native STV. This suggested that the affinity of the covalent oligonucleotide-STV hybrid for binding biotinylated DNA is significantly decreased. Nevertheless, the single-stranded oligonucleotide moiety of the hybrid nanocircles can be used as a molecular handle for further functionalization. For instance, it was used for the selective DNA-directed immobilization at a surface, previously functionalized with complementary capture oligonucleotides. Moreover, we demonstrate that a pair of nanocircles, containing complementary oligonucleotide moieties, can be hybridized to form specific dimers, thereby generating a novel type of supramolecular DNA-protein nanostructures.     

Pollen Types Used by the Native Stingless Bee, <Emphasis Type="Italic">Tetragonisca angustula</Emphasis> (Latreille), in an Amazon-Chiquitano Transitional Forest of Bolivia

Samples of corbicular and stored pollen gathered by Tetragonisca angustula (Latreille, 1811) in an Amazon-Chiquitano transitional forest during the dry season were analyzed. The pollen spectrum was established as well as the dynamics of the relationship between the stingless bee and the surrounding flora. Pollen samples obtained from three rational hives were subjected to acetolysis and 55 pollen types were identified, the most frequent being from Anadenanthera (Fabaceae), Chenopodiaceae, and Dydimopanax (Araliaceae). Significant differences in pollen families used between hives along the months of collection were found in stored pollen and non-significant differences in corbicular pollen. Mean values of alpha diversity (H′) showed T. angustula as a generalist while beta diversity qualitatively showed that pollen composition was similar between two hives both of which differed from the third hive. Pollen types in corbicular and stored pollen were in general related with richness of flowering plants in the foraging area; the pollen offer was less diverse than the pollen collected, and a trend to prefer the collection of pollen from the most abundant flowering species could be discerned. T. angustula showed polylectic feeding habits and a capacity to adapt to food availability.     

Bioprocess development for endospore production by Bacillus coagulans using an optimized chemically defined medium

Bacillus coagulans is a promising probiotic, because it combines probiotic properties of Lactobacillus and the ability of Bacillus to form endospores. Due to this hybrid relationship, cultivation of this organism is challenging. As the probiotics market continues to grow, there is a new focus on the production of these microorganisms. In this work, a strain-specific bioprocess for B. coagulans was developed to support growth on one hand and ensure sporulation on the other hand. This circumstance is not trivial, since these two metabolic states are contrary. The developed bioprocess uses a modified chemically defined medium which was further investigated in a one-factor-at-a-time assay after adaptation. A transfer from the shake flask to the bioreactor was successfully demonstrated in the scope of this work. The investigated process parameters included temperature, agitation and pH-control. Especially the pH-control improved the sporulation in the bioreactor when compared to shake flasks. The bioprocess resulted in a sporulation efficiency of 80%–90%. This corresponds to a sevenfold increase in sporulation efficiency due to a transfer to the bioreactor with pH-control. Additionally, a design of experiment (DoE) was conducted to test the robustness of the bioprocess. This experiment validated the beforementioned sporulation efficiency for the developed bioprocess. Afterwards the bioprocess was then scaled up from a 1 L scale to a 10 L bioreactor scale. A comparable sporulation efficiency of 80% as in the small scale was achieved. The developed bioprocess facilitates the upscaling and application to an industrial scale, and can thus help meet the increasing market for probiotics.     

Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA--streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates.

Modified biomolecules were used for the non-covalent assembly of novel bioconjugates. Hybrid molecules were synthesized from short single-stranded DNA and streptavidin by chemical methods using a heterobispecific crosslinker. The covalent attachment of an oligonucleotide moiety to streptavidin provides a specific recognition domain for a complementary nucleic acid sequence, in addition to the four native biotin-binding sites. These bispecific binding capabilities allow the hybrid molecules to serve as versatile connectors in a variety of applications. Bifunctional constructs have been prepared from two complementary hybrid molecules, each previously conjugated to biotinylated immunoglobulin G or alkaline phosphatase. The use of nucleic acid sequences as a template for the formation of an array of proteins is further demonstrated on two size scales. A macroscopic DNA array on a microtiter plate has been transformed into a comparable protein chip. A nano-scale array was made by hybridizing DNA-tagged proteins to specific positions along a RNA or DNA sequence. The generation of supramolecular bioconjugates was shown by quantitative measurements and gel-retardation assays.