MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

The Ubiquitous Soil Terpene Geosmin Acts as a Warning Chemical.

Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis, we found that geosmin altered the behavior of the bacteriophagous nematode Caenorhabditis elegans on agar plates in the absence of bacteria. Normal movement was restored in mutant worms lacking differentiated ASE (amphid neurons, single ciliated endings) neurons, suggesting that geosmin is a taste detected by the nematodal gustatory system. In a predation assay, geosmin and the related terpene 2-methylisoborneol reduced grazing on the bacterium Streptomyces coelicolor. Predation was restored by the removal of both terpene biosynthetic pathways or the introduction of C. elegans that lacked differentiated ASE taste neurons, leading to the apparent death of both bacteria and worms. While geosmin and 2-methylisoborneol appeared to be nontoxic, grazing triggered bacterial sporulation and the production of actinorhodin, a pigment coproduced with a number of toxic metabolites. In this system, geosmin thus appears to act as a warning signal indicating the unpalatability of its producers and reducing predation in a manner that benefits predator and prey. This suggests that molecular signaling may affect microbial predator-prey interactions in a manner similar to that of the well-studied visual markers of poisonous animal prey. IMPORTANCE One of the key chemicals that give soil its earthy aroma, geosmin is a frequent water contaminant produced by a range of unrelated microbes. Many animals, including humans, are able to detect geosmin at minute concentrations, but the benefit that this compound provides to its producing organisms is poorly understood. We found that geosmin repelled the bacterial predator Caenorhabditis elegans in the absence of bacteria and reduced contact between the worms and the geosmin-producing bacterium Streptomyces coelicolor in a predation assay. While geosmin itself appears to be nontoxic to C. elegans, these bacteria make a wide range of toxic metabolites, and grazing on them harmed the worms. In this system, geosmin thus appears to indicate unpalatable bacteria, reducing predation and benefiting both predator and prey. Aposematic signals are well known in animals, and this work suggests that metabolites may play a similar role in the microbial world.

Tuning residual chirality in carbon dots with anti-microbial properties.

Chirality remains a critical consideration in drug development and design, as well as in applications of enantioselective recognition and sensing. However, the preparation of chiral nanomaterials requires extensive post synthetic modifications with a chiral agent, coupled with extensive purification. This limits the use and application of chiral nanomaterials. Herein, we report a facile, one-step microwave-assisted synthesis of chiral carbon dots through the reaction of l- and d-cysteine amino acid precursors and citric acid. We modulated the synthetic parameters to preserve and tune the residual chiral properties of the dots and demonstrate that the reaction conditions play a critical role in dictating the chiral behaviour of the dots. Finally, in a proof of concept application we demonstrated that the synthesized carbon dots, particularly d-carbon dots inhibit bacterial growth at a lower concentration than l-carbon dots. By varying bacterial strains and chirality of the carbon dots, concentrations ranging from 0.25-4 mg mL-1 of the nanoparticles were required to inhibit microbial growth. The ability to preserve and tune chirality during synthesis can open up novel avenues and research directions for the development of enantioselective materials, as well as antibacterial films and surfaces.

Electrospun Upconverting Nanofibrous Hybrids with Smart NIR-Light-Controlled Drug Release for Wound Dressing.

Chronic wounds present a high risk of infection due to delayed and incomplete healing, leading to increased health risks and financial burden to health-care systems. Numerous approaches to promote wound healing have been extensively explored, especially the development of effective wound dressing materials embedded with therapeutic drug molecules. Despite advances made in this area, a remaining challenge to be addressed is the controlled, on-demand release of therapeutic molecules using noncytotoxic stimulus, for example, near-infrared (NIR) excitation. Here, we report a platform that allows for the development of electrospun poly(vinyl alcohol) (PVA) fibrous hybrids embedded with upconverting nanoparticles (UCNPs) and UV-cleavable levofloxacin conjugates for wound dressings. Upon irradiation with NIR light, the excited UCNPs emit UV light around 365 nm, which can cleave the o-nitrobenzyl (ONB) linkage of the levofloxacin conjugates in the PVA fiber, leading to controlled drug release. The release was observed to be triggered only under NIR and UV irradiation, with no effect in the dark. Furthermore, the antibacterial effect against Escherichia coli and Staphylococcus aureus was successfully demonstrated, highlighting the versatility of the electrospun upconverting fiber platform. The development of antibacterial fibrous meshes with on-demand release of encapsulated drugs is imperative for precise treatment of wound infections.