antiSMASH 6.0: improving cluster detection and comparison capabilities

Microbial Biotechnolog

Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.

Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective targeting of the BAZ2B bromodomain by small molecule inhibitors has been recently reported, but no structural information is yet available on the interaction with its natural binding partner, acetylated histone H3K14ac. We have assigned the BAZ2B bromodomain and studied its interaction with H3K14ac acetylated peptides by NMR spectroscopy using both chemical shift perturbation (CSP) data and clean chemical exchange (CLEANEX-PM) NMR experiments. The latter was used to characterize water molecules known to play an important role in mediating interactions. Besides the anticipated Kac binding site, we consistently found the bromodomain BC loop as hotspots for the interaction. This information was used to create a data-driven model for the complex using HADDOCK. Our findings provide both structure and dynamics characterization that will be useful in the quest for potent and selective inhibitors to probe the function of the BAZ2B bromodomain.This is the final published version of the article. It has been published by the American Chemical Society in Biochemistry. The article can be accessed on their website here: http://pubs.acs.org/doi/abs/10.1021/bi500909d. It is freely available under a CC BY licence

Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale

Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.Christophe Lemetrea, Jeffrey Manikoa, Zachary Charlop-Powersa, Ben Sparrow, Andrew J. Lowec and Sean F. Brad

Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves

Caves are regarded as extreme habitats with appropriate conditions for the development of Actinobacteria. In comparison with other habitats, caves have not yet been the target of intensive screening for bioactive secondary metabolites produced by actinomycetes. As a primary screening strategy, we conducted a metagenomic analysis of the diversity and richness of a key gene required for non-ribosomal peptide (NRP) biosynthesis, focusing on cave-derived sediments from two Canadian caves (a lava tube and a limestone cave) to help us predict whether different types of caves may harbor drug-producing actinobacteria. Using degenerate PCR primers targeting adenylation domains (AD), a conserved domain in the core gene in NRP biosynthesis, a number of amplicons were obtained that mapped back to biomedically relevant NRP gene cluster families. This result guided our culture-dependent sampling strategy of actinomycete isolation from the volcanic caves of Canada (British Columbia) and Portugal (Azores) and subsequent characterization of their antibacterial and enzymatic activities. Multiple enzymatic and antimicrobial activities were identified from bacterial of the Arthrobacter and Streptomyces genera demonstrating that actinomycetes from volcanic caves are promising sources of antibacterial, antibiofilm compounds and industrially relevant enzymes. 15 páginas.-- 4 figuras.-- 3 tablas.-- referencias.-- The online version of this article (doi:10.1007/s00253-016-7932-7) contains supplementary material, which is available to authorized users.C. Riquelme was funded by the Regional Fund for Science and Technology and Pro-Emprego program of the Regional Government of the Azores, Portugal [M3.1.7/F/013/2011, M3.1.7/F/030/2011]. Her work was partly supported by National funds from the Foundation for Science and Technology of the Portuguese Government [Understanding Underground Biodiversity: Studies in Azorean Lava Tubes (reference TDC/AMB/70801/2006)]. A.Z. Miller acknowledges the support from the Marie Curie Intra-European Fellowship of the European Commission’s 7th Framework Programme (PIEF-GA-2012-328689). The authors would like to thank the TRU Innovation in Research Grant, TRU Undergraduate Research Enhancement (UREAP) Fund, Western Economic Diversification Canada Fund, Kent Watson (assisted with the Helmcken Falls Cave sample collection), Dr. Mario Jacques (U of Montreal for his assistance in biofilm culture), icholaus Vieira, Christian Stenner, and the Raspberry Rising Expedition team.We acknowledged the Canadian Ministry of Forests, Lands, and Natural Resource Operations for Park Use Permit#102172. The work done in the Brady lab was funded by NIH grant GM077516. Z. Charlop-Powers was also supported by NIH grant AI110029. The authors also wish to thank Fernando Pereira, Ana Rita Varela, Pedro Correia, Berta Borges, and Guida Pires for help during field and lab work in the Azores. The authors would like to thank Dr. Steven VanWagoner (TRU) and Drs. Julian Davies and Vivian Miao (UBC) for their invaluable comments in manuscript preparation. 15 páginas.-- figuras.-- Electronic supplementary material The online version of this article (doi:10.1007/s00253-016-7932-7) contains supplementary material, which is available to authorized users.Peer Reviewe