Enhanced formation of aromatic amino acids increases fragrance without affecting flower longevity or pigmentation in Petunia × hybrida

Purple Petunia × hybrida V26 plants accumulate fragrant benzenoid‐phenylpropanoid molecules and anthocyanin pigments in their petals. These specialized metabolites are synthesized mainly from the aromatic amino acids phenylalanine. Here, we studied the profile of secondary metabolites of petunia plants, expressing a feedback‐insensitive bacterial form of 3‐deoxy‐di‐arabino‐heptulosonate 7‐phosphate synthase enzyme (AroG*) of the shikimate pathway, as a tool to stimulate the conversion of primary to secondary metabolism via the aromatic amino acids. We focused on specialized metabolites contributing to flower showy traits. The presence of AroG* protein led to increased aromatic amino acid levels in the leaves and high phenylalanine levels in the petals. In addition, the AroG* petals accumulated significantly higher levels of fragrant benzenoid‐phenylpropanoid volatiles, without affecting the flowers' lifetime. In contrast, AroG* abundance had no effect on flavonoids and anthocyanins levels. The metabolic profile of all five AroG* lines was comparable, even though two lines produced the transgene in the leaves, but not in the petals. This implies that phenylalanine produced in leaves can be transported through the stem to the flowers and serve as a precursor for formation of fragrant metabolites. Dipping cut petunia stems in labelled phenylalanine solution resulted in production of labelled fragrant volatiles in the flowers. This study emphasizes further the potential of this metabolic engineering approach to stimulate the production of specialized metabolites and enhance the quality of various plant organs. Furthermore, transformation of vegetative tissues with AroG* is sufficient for induced production of specialized metabolites in organs such as the flowers.     

Microscale Laser Surgery Demonstrates the Grasping Function of the Male Sex Combs in Drosophila melanogaster and Drosophila bipectinata

Male secondary sexual traits of animals are richly diversified in form and complexity, yet there are many species in which their precise function remains unknown. Within the genus Drosophila, species belonging to the melanogaster and obscura species groups have evolved a remarkable variety of sex combs, male‐limited secondary sexual traits located on the tarsi of both front legs. Information concerning sex comb function is minimal or absent, except for D. melanogaster, where previous studies indicate that the sex combs are used for grasping the female prior to copulation. These studies, however, do not unambiguously demonstrate comb function, because it has not been possible to ascribe observed behavioral outcomes of the various comb manipulations to changes in the combs per se. We used microscale laser surgery to manipulate comb size in D. melanogaster and D. bipectinata, and tested the hypothesis that the sex combs function as grasping devices in courtship, making them essential for copulation to ensue. Results of high‐resolution behavioral analysis in small observation arenas demonstrated that in both species in which sex combs were surgically eliminated, males were unable to grasp, mount or copulate. The combless foretarsi of these altered males slipped off the end (D. melanogaster) and sides (D. bipectinata) of the female abdomen when courting males attempted to grasp. In most cases, males whose sex combs were reduced but not completely removed exhibited similar copulation probabilities as surgical control males, a result we demonstrated in observation chambers as well as under more ecologically realistic conditions inside population cages where males and females interacted on the surface of fruit substrates. Thus, the sex combs in D. melanogaster and D. bipectinata are grasping devices, essential for mounting and copulation.     

Alzheimer's disease‐causing proline substitutions lead to presenilin 1 aggregation and malfunction

Do different neurodegenerative maladies emanate from the failure of a mutual protein folding mechanism? We have addressed this question by comparing mutational patterns that are linked to the manifestation of distinct neurodegenerative disorders and identified similar neurodegeneration‐linked proline substitutions in the prion protein and in presenilin 1 that underlie the development of a prion disorder and of familial Alzheimer's disease (fAD), respectively. These substitutions were found to prevent the endoplasmic reticulum (ER)‐resident chaperone, cyclophilin B, from assisting presenilin 1 to fold properly, leading to its aggregation, deposition in the ER, reduction of γ‐secretase activity, and impaired mitochondrial distribution and function. Similarly, reduced quantities of the processed, active presenilin 1 were observed in brains of cyclophilin B knockout mice. These discoveries imply that reduced cyclophilin activity contributes to the development of distinct neurodegenerative disorders, propose a novel mechanism for the development of certain fAD cases, and support the emerging theme that this disorder can stem from aberrant presenilin 1 function. This study also points at ER chaperones as targets for the development of counter‐neurodegeneration therapies.     

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ∼130 μs of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-μs scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.     

Assembly rules of ectoparasite communities across scales: combining patterns of abiotic factors,host composition,geographic space,phylogeny and traits

We investigated the role of environmental filtering as an underlying mechanism of assembly of compound communities of fleas parasitic on Palearctic small mammals at two spatial scales; a continental scale (encompassing regions across the entire Palearctic) and a regional scale (across sampling localities within Slovakia). We used the three‐table ordination (the RLQ analysis) and its extended version that links species occurrences with geographic space, environmental variables, and species traits and phylogeny (the ESLTP analysis). We asked whether environmental filtering acts as an assembly rule of compound communities of fleas and, if yes, a) whether the effect of environment on species composition of compound communities of fleas differs between spatial scales and b) what are the relative importance of the abiotic and host environments. We found that compound communities of fleas are, to a great extent, assembled via environmental filters that represent interplay between filtering via abiotic environment and filtering via host composition. The relative importance of these two components of environmental filtering differed between spatial scales. Host composition had a stronger effect on flea assembly than abiotic environment on the continental scale, while the opposite was true for the regional scale. The likely reason behind this scale‐dependence is that communities on the regional scale are mainly governed by ecological and epidemiological processes, while communities on the continental scale are mainly affected by evolutionary, biogeographic and historical forces.     

eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models

Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4–9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

This is a PLOS Computational Biology Software Article

     

The pharmacological activation of adenosine A1 and A3 receptors does not modulate the long- or short-term repopulating ability of hematopoietic stem and multipotent progenitor cells in mice

This study continues our earlier findings on the hematopoiesis-modulating effects of adenosine A₁ and A₃ receptor agonists that were performed on committed hematopoietic progenitor and precursor cell populations. In the earlier experiments, N ⁶-cyclopentyladenosine (CPA), an adenosine A₁ receptor agonist, was found to inhibit proliferation in the above-mentioned hematopoietic cell systems, whereas N ⁶-(3-iodobenzyl)adenosine-5′-N-methyluronamide (IB-MECA), an adenosine A₃ receptor agonist, was found to stimulate it. The topic of this study was to evaluate the possibility that the above-mentioned adenosine receptor agonists modulate the behavior of early hematopoietic progenitor cells and hematopoietic stem cells. Flow cytometric analysis of hematopoietic stem cells in mice was employed, as well as a functional test of hematopoietic stem and progenitor cells (HSPCs). These techniques enabled us to study the effect of the agonists on both short-term repopulating ability and long-term repopulating ability, representing multipotent progenitors and hematopoietic stem cells, respectively. In a series of studies, we did not find any significant effect of adenosine agonists on HSPCs in terms of their numbers, proliferation, or functional activity. Thus, it can be concluded that CPA and IB-MECA do not significantly influence the primitive hematopoietic stem and progenitor cell pool and that the hematopoiesis-modulating action of these adenosine receptor agonists is restricted to more mature compartments of hematopoietic progenitor and precursor cells.     

The Reactions of H-Phosphonates with Bifunctional Reagents. V. Functionalization of Support-Bound Oligonucleotides and Synthesis of Nonradioactive Hybridization Probes a

Abstract

Three methods for the functionalization of oligonucleotides with aminoalkyl moieties have been developed and their efficiencies were evaluated in the preparation of non-radioactive hybridization probes.

     

Stereochemistry of Internucleotide Bond Formation by the H-Phosphonate Method. 5. The Role of Brønsted and H-Bonding Base Catalysis in Ribonucleoside H-Phosphonate Condensation—Chemical and Stereochemical Consequences

Efficiency and stereoselectivity of condensations of ribonucleoside 3′-H-phosphonates with ethanol promoted by pivaloyl chloride were investigated as a function of tertiary amines used. Side reactions leading to an increased demand for the condensing agent were identified as derived from an attack of the pivalate anion at carbonyl centers of reactive pivaloyl derivatives. The conditions that secured quantitative yields of H-phosphonate diester condensations were assessed. Several tertiary amines promoted condensations with stereoselectivity higher than that observed for pyridine derivatives. A correlation between diastereoselectivity of the product formation and Brønsted and H-bonding basicities of the amine used was found.