StreptomeDB 2.0 - An extended resource of natural products produced by streptomycetes

Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bac-terial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, Strep-tomeDB was the first database focusing on com-pounds produced by streptomycetes. The new ver-sion presented herein represents a major step for-ward: its content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background in-formation and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diver-sity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA se-quences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of com-pounds and scaffolds in an evolutionary context. Ad-ditionally, we have included predicted MS- and NMR-spectra of thousands of compounds for assignment of experimental data. The database is freely acces-sible vi

The secondary metabolite bioinformatics portal:Computational tools to facilitate synthetic biology of secondary metabolite production

AbstractNatural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field

Molecular analysis of co-infection of Scots pine seedlings with actinobacteria Streptomyces and Heterobasidion annosum

Heterobasidion annosum is a pathogenic fungus that causes extensive damage to many trees in temperate forests including Scots pine (Pinus Sylvestris). Various microbes have been studied for potential use as bio-control agents to inhibit or reduce the H. annosum infection of trees. This study examined the potential use of bacterial isolates, belonging to streptomyces genus, as a bio-control agent for Scots pine seedlings against H. annosum. Streptomyces species were isolated from surface of mycorrhizal fungi in the forest and they are known to have a mutualistic relationship with mycorrhizal fungi. The goal of this study was to understand the relationship between H. annosum and Streptomyces sp. A11. This was tested in in two settings, in presence of pine seedlings, growing in soil and in dual cultures. In the first setting, seedlings from different treatments were inoculated with Streptomyces sp. A11, H. annosum, co-inoculated with both species or grown in sterile conditions as control. After incubation period, growth and root development of seedlings were analysed. H. annosum grown in dual culture against Streptomyces sp. A11 was utilised for gene expression using quantitative real time PCR method. The results indicated that pine seedlings inoculated with both Streptomyces sp. A11 and H. annosum, had more severe infection compared to the seedlings infected with H. annosum alone. This implies that Streptomyces sp. A11 can interfere with pine’s defence response during interaction with H. annosum. Moreover, Streptomyces sp. A11 suppressed the growth of H. annosum in dual culture. The Suppression of H. annosum was potentially because of antifungal secondary metabolites that were produced by Streptomyces sp. A11. These secondary metabolites caused disruption in glucose metabolism and cell wall integrity of H. annosum. Future experiments should include mycorrhizal fungal species along with species tested in this study. Streptomyces sp. are known to respond differently in presence of specific species. The results for this study should be considered for studies of mycorrhizal associated streptomyces species and can be built upon for broader future investigation

Discovery of the amipurimycin and miharamycins biosynthetic gene clusters and insight into the biosynthesis of nogalamycin

Advancements in our ability to obtain high quality bacterial whole genome sequences have increased the rate natural product biosynthetic gene clusters are identified, but these projects require computational methods for gene annotation which are limited by their reliance on comparison to previously annotated genes. Thus, even in a well-defined cluster with a known product it may be difficult to predict how structural characteristics arise if they have no known precedent. Without further work, such limitations will continue to impede the utility of sequenced bacterial genomes. Biosyntheses of the peptidyl nucleoside antibiotics and atypical anthracyclines like nogalamycin are topics which exemplify these challenges. The peptidyl nucleoside antibiotics (PNAs) are a structurally complex group of natural products with diverse biological activities which could be useful for the development of novel antimicrobials. Amipurimycin and the miharamycins are remarkably similar PNAs elaborated by the bacteria Streptomyces miharaensis ATCC 19440 and Streptomyces novoguineensis CBS 199.78, respectively. Their dissimilarity to other well-characterized groups of antibiotics has presented a challenge to the study of their unique structural features. Herein, we describe the identification of the amipurimycin and miharamycins biosynthetic gene clusters though a comparative genomics approach. Besides providing insight into the biosynthesis of the rare amino acids adorning these PNA, our analysis revealed a plausible biosynthetic route to the unique 2-aminopurine nucleobase and suggests the core saccharides are generated by a polyketide synthase. The anthracyclines are a mainstay of chemotherapy, but their use is limited by fatal cardiotoxicity and tumor resistance. The structures of the anthracyclines are sensitive to modification, as even small changes can ablate their biological activity. Nevertheless, the diversification of anthracyclines through semi- or total syntheses is an ongoing effort. Nogalamycin is rare amongst the anthracyclines because of its extended ring system and unusual glycosylation pattern. It is hoped an understanding of the biosynthesis of nogalamycin could allow the incorporation of its uncommon structural features into other anthracyclines to develop novel compounds with improved actitivty. Towards this end, we investigated the biosynthesis of the amino sugar found in nogalamycin, nogalamine, to clarify ambiguous steps in the reported biosynthetic pathway for this sugar.Pharmaceutical Science

Finding new potential antimicrobials in natural environments : do bacterial isolates from ancient and modern woodland, and farmland show the ability to produce inhibitory compounds?

Research and development into the production of novel antimicrobials is greatly needed due to the current global threat that antimicrobial resistance is presenting. In the present study, modern and ancient forestlands, Friston Forest, (Sussex, UK), and New Forest, (Hampshire, UK), and Dawes Farm, (Warnham, West Sussex, UK) were sampled in the hope of isolating organisms with inhibitory activity and/or similar morphology to that of the Streptomyces spp. for further assessment of antagonistic activity against selected test bacteria. Perpendicular screening, and the newly developed starvation method, were used to characterise the inhibitory ability of organisms isolated against sensitive test strains of Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Proteus mirabilis. Organisms displaying inhibitory activity towards sensitive organisms were further tested using clinically isolated test organisms from the same genus. Perpendicular screening confirmed 11 (15.9%), 5 (14.7%), and 13 (30.2%) of the total organisms isolated from Friston Forest, New Forest and Dawes Farm respectively, with inhibitory activity towards one or more of the test organisms used, with eight of these displaying further inhibition of at least one of the clinical test organisms used in this method. The starvation method, used for further antibacterial screening, involving the incubation of the potential antimicrobial producing organisms in minimal media for long incubation periods, confirmed 21 (30.4%) 12 (35.3%), and 9 (20.9%) isolates from Friston Forest, New Forest, and Dawes Farm vets with inhibitory ability. All organisms isolated were tested using Gram staining, with those displaying resemblance to the Streptomyces spp. selected for further determinative identification using the polymerase chain reaction, with primers specific to the 16S rRNA gene of the Streptomyces genus. Nineteen isolates were determined as belonging to this genus, with 42.1% of the confirmed Streptomyces spp. displaying inhibitory activities. The same soil samples were used for the cultivation of potentially pathogenic bacteria, with biochemical testing used to determine the identity of each of the 222 organisms isolated, to a genus level. Across the three locations three isolates were identified as belonging to Salmonella spp., 21 as Staphylococcus aureus, nine Pseudomonas spp., two Staphylococcus epidermidis, four Klebsiella spp. and four Escherichia coli. The screening carried out in this study confirmed the ability for the isolation of pathogenic organisms as well as soil organisms with antibiotic producing capability, from the previously untested farm and forestland sampled