Structures of Complexes between Echinomycin and Duplex DNA

The structure of the bis intercalation complex of the depsipeptide antibiotic echinomycin with CGTACG 2 has been redetermined at a higher resolution 1.4 and new high resolution structures 1.1 1.5 are reported for the complexes of echinomycin with GCGTACGC 2 at both low and high ionic strengths and ACGTACGT 2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis intercalating antibiotics and the duplex DNA than were previously availabl

Serendipitous Sad Phasing of an Echinomycin Acgtacgt 2 Bisintercalation Complex

A new crystal form was obtained for the complex between ACGTACGT 2 and echinomycin and X ray data were collected to 1.6 . The structure was phased by the SAD method based on a single unexpected anomalous scatterer that could be identified as a mixture of nickel and zinc by measurements of the anomalous scattering at different wavelengths. This cation is coordinated by two guanines from two different duplexes and four water molecules. The structure resembles previously reported crystal structures of DNA echinomycin complexes, except that three of the eight base pairs flanking the echinomycin bisintercalator sites have the Watson Crick rather than the Hoogsteen configuration. Hoogsteen binding was found for the corresponding base pairs of the crystallographically independent duplex, indicating that the two configurations are very close in energ

Genes that mediate starch metabolism in developing and germinated barley grain

Published: 01 March 2021Starch is synthesized in the endosperm of developing barley grain, where it functions as the primary source of stored carbohydrate. In germinated grain these starch reserves are hydrolyzed to small oligosaccharides and glucose, which are transported to the embryo to support the growth of the developing seedling. Some of the mobilized glucose is transiently stored as starch in the scutellum of germinated grain. These processes are crucial for early seedling vigor, which is a key determinant of crop productivity and global food security. Several starch synthases (SS), starch-branching enzymes (SBEs), and starch debranching enzymes (isoamylases, ISA), together with a limit dextrinase (LD), have been implicated in starch synthesis from nucleotide-sugar precursors. Starch synthesis occurs both in the developing endosperm and in the scutellum of germinated grain. For the complete depolymerization of starch to glucose, α-amylase (Amy), β-amylase (Bmy), isoamylase (ISA), limit dextrinase (LD), and α-glucosidase (AGL) are required. Most of these enzymes are encoded by gene families of up to 10 or more members. Here RNA-seq transcription data from isolated tissues of intact developing and germinated barley grain have allowed us to identify the most important, specific gene family members for each of these processes in vivo and, at the same time, we have defined in detail the spatio-temporal coordination of gene expression in different tissues of the grain. A transcript dataset for 81,280 genes is publicly available as a resource for investigations into other cellular and biochemical processes that occur in the developing grain from 6 days after pollination.Helen M. Collins, Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Ilka Braumann, Jose A. Cuesta-Seijo, Birgitte Skadhauge, James Whelan, Vincent Bulone and Geoffrey B. Finche

Identification and spatio-temporal expression analysis of barley genes that encode putative modular xylanolytic enzymes

Arabinoxylans are cell wall polysaccharides whose re-modelling and degradation during plant development are mediated by several classes of xylanolytic enzymes. Here, we present the identification and new annotation of twelve putative (1,4)-β-xylanase and six β-xylosidase genes, and their spatio-temporal expression patterns during vegetative and reproductive growth of barley (Hordeum vulgare cv. Navigator). The encoded xylanase proteins are all predicted to contain a conserved carbohydrate-binding module (CBM) and a catalytic glycoside hydrolase (GH) 10 domain. Additional domains in some xylanases define three discrete phylogenetic clades: one clade contains proteins with an additional N-terminal signal sequence, while another clade contains proteins with multiple CBMs. Homology modelling revealed that all fifteen xylanases likely contain a third domain, a β-sandwich folded from two non-contiguous sequence segments that bracket the catalytic GH domain, which may explain why the full length protein is required for correct folding of the active enzyme. Similarly, predicted xylosidase proteins share a highly conserved domain structure, each with an N-terminal signal peptide, a split GH 3 domain, and a C-terminal fibronectin-like domain. Several genes appear to be ubiquitously expressed during barley growth and development, while four newly annotated xylanase and xylosidase genes are expressed at extremely high levels, which may be of broader interest for industrial applications where cell wall degradation is necessary.Natalie S. Betts, Helen M. Collins, Neil J. Shirley, Jose A. Cuesta-Seijo, Julian G. Schwerdt, Renee J. Phillipsa ... et al