[50]

Chen R, Wong HL, Burns BP. 2019. New approaches to detect biosynthetic gene clusters in the environment. Medicines (Basel) 6(1): 32. A key reference for this group. AntiSMASH and ClustScan depend on signature enzyme, but ClustFinder is perhaps better at looking for novel BGC’s. EvoMining is a phylogenetic approach that assumes BGC’s came from repurposed enzymes. Heterologous expression, because most BGC’s are transcriptionally silent or are produced in very low amounts; alternatively one can use chemical elicitors.

Ymele-Leki P et al. 2012. A high-throughput screen identifies a new natural product with broad-spectrum antibacterial activity. PLos One 2012;7(2):e31307 . The screen is based on a color change as a function of pH: when a candidate is active bacteria don’t ferment. The candidate is first extracted from the source. They screened 39k such extracts and found 49 with reproducible antibacterial activity. False negative because of low amount of metabolite produced, or failed to extract.

Hettiarachchi S. et al. 2017. A rapid and efficient screening method for antibacterial compound-producing bacteria. Journal of Microbiology and Biotechnology 27(8). Describes the colony picking method. The target is spread plated, and the isolates (streaked) were colony-picked and arranged on the target plate. Zones of clearing were sought after incubation for 16h at 30degC. [JMB worth looking into for bacteria work]

Owen JG et al…Brady SF. 2015. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. PNAS USA 112(14): 4221-6. Describes the Brady process: degenerate primers amplifying from metagenome libraries. Supplement saved in Dropbox PCHRD: degenerate primer sequence, protocols, mass spec and NMR, BGC cluster annotation.

Tyurin AP et al. 2018. Chemical Elicitors of Antibiotic Biosynthesis in Actinomycetes. Microorganisms 6(2): 52. Review on chemicals that can induce silent BGC’s in Actinomycetes. They reviewed Shiela’s paper on synthetic Cl-ARC (chlorinated ARC), similar to triclosan which direct metabolism away from fatty acid to secondary metabolite. The elicitors seem to work in general by redirecting metabolism towards secondary metabolites. Others like antibiotics but we don’t know how: polyether antibiotics (promomycin, salinomycin, monensin, and nigericin), lincomycin, chloramphenicol (1/10 MIC) that act against ribosome (thiosteptone, spectinomycin), ivermectin, etoposide, inhibitors of histone deacetylase like valproic acid.

Cruz-Morales P et al. 2016. Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes. Genome Biol Evol 8(6):1906-16. Combine a genome and enzyme database across many bacteria and try to find signs that enzymes in central metabolism were being recruited into specialized. How? Maybe by association with other enzymes not typically associated with them in their centralized roles? Experiments inlude LC/MS and gene knockout to confirm.