Investigation of Aminoglycosides Binding to G-Quadruplex DNA Using the FID Assay

The enzyme telomerase is known to maintain the length of chromosomes necessary for cell survival by adding nucleotides to the chromosomal ends; and this enzyme is overexpressed in 80-95% of malignant tumors, conferring cell immortality. The chromosome ends where telomerase acts upon are guanine-rich, which can fold into a DNA secondary structure called G-quadruplex (G4). Interestingly, telomerase cannot bind to G4; therefore, inducing G4 formation at the ends of chromosome regulates telomerase activity. Many small molecules, known as G4 ligands have been developed for stabilizing telomeric G-quadruplex DNA. In the present work, we sought to investigate a class of antibiotics (aminoglycosides) binding to G-quadruplex DNA using an FID assay. Aminoglycosides are known to bind to ribosomal RNA and A-form DNA, but their binding to G-quadruplex DNA remains unclear. Our results suggest that amongst nine aminoglycosides, neomycin has the best binding affinity toward G-quadruplex DNA. The experimental conditions and data analysis will be presented

Investigation of Aminoglycosides Binding to G-Quadruplex DNA Using the FID Assay

The enzyme telomerase is known to maintain the length of chromosomes necessary for cell survival by adding nucleotides to the chromosomal ends; and this enzyme is overexpressed in 80-95% of malignant tumors, conferring cell immortality. The chromosome ends where telomerase acts upon are guanine-rich, which can fold into a DNA secondary structure called G-quadruplex (G4). Interestingly, telomerase cannot bind to G4; therefore, inducing G4 formation at the ends of chromosome regulates telomerase activity. Many small molecules, known as G4 ligands have been developed for stabilizing telomeric G-quadruplex DNA. In the present work, we sought to investigate a class of antibiotics (aminoglycosides) binding to G-quadruplex DNA using an FID assay. Aminoglycosides are known to bind to ribosomal RNA and A-form DNA, but their binding to G-quadruplex DNA remains unclear. Our results suggest that amongst nine aminoglycosides, neomycin has the best binding affinity toward G-quadruplex DNA. The experimental conditions and data analysis will be presented

No disruption of rhizobial symbiosis during early stages of cowpea domestication.

Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen-fixing symbiosis between cowpea and root-nodulating Bradyrhizobium. We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and symbiosis trait variation among wild and early-domesticated cowpea genotypes. Cowpeas experienced modest decreases in genome-wide diversity during early domestication. Nonetheless, domesticated cowpeas responded efficiently to variation in symbiotic effectiveness, by forming more root nodules with nitrogen-fixing rhizobia and sanctioning nonfixing strains. Domesticated populations invested a larger proportion of host tissues into root nodules than wild cowpeas. Unlike soybean and wheat, cowpea showed no compelling evidence for degradation of symbiosis during domestication. Domesticated cowpeas experienced a less severe bottleneck than these crops and the low nutrient conditions in Africa where cowpea landraces were developed likely favored plant genotypes that gain substantial benefits from symbiosis. Breeders have largely neglected symbiosis traits, but artificial selection for improved plant responses to microbiota could increase plant performance and sustainability

Experimental evolution can enhance benefits of rhizobia to novel legume hosts.

Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host-symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host-symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance.

The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution