Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

Abstract

Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N 5 -hydroxyarginine; valinophos, an N-acetyl L-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.natural products | genome mining | phosphonic acid | antibiotic

Biosynthetic Genes for the Tetrodecamycin Antibiotics

“…There are many secondary metabolites that possess chemical modifications, functional groups, or structures that, coupled with the genome sequence, enable accurate prediction of the cognate biosynthetic gene cluster. These include glycosylated compounds (32), nonribosomal peptides (33), enediynes (34), phosphonates (35), and halogenated compounds (36). Identifying related clusters in multiple organisms is also becoming a widely accepted means of informatically characterizing a new gene cluster (for example, the cluster associated with tambromycin [37]).…”

Identification and kinetics characterization of a wax ester hydrolase from a feather-degrading actinomycete

“…http://dx.doi.org/10.1101/178673 doi: bioRxiv preprint first posted online Aug. 21, 2017; (Ju et al 2015) and the previously reported lips221 sequence (Zhang et al 2008) was downloaded from GenBank (ID: EF429087.1) (Benson et al 2013). Genomic DNA served as template for a polymerase chain reaction (PCR) to amplify out the genes.…”

Isolation, Identification, and Characterization of the Novel Antibacterial Agent Methoxyphenyl-Oxime from Streptomyces pratensis QUBC97 Isolate

“…Identification of Streptomyces species and the bioactive compound(s) they produce are complex and problematic [1][2][3][4]. Major obstacles in identifying Streptomyces species include horizontal gene transfer, erroneous reporting of species [5], recombination, chromosome rearrangement that may take place in Streptomyces [6,7], and replacing the scientific species name with a number Volume 1 | Issue 1…”

“…Streptomyces grouped based on 16S similarity must then be distinguished based on morphological, molecular features, signature protein(s), DNA "tags", and/or distinguishable character of a species may provide such a simple system of species identification [this work, [3][4][5][8][9][10]. Taddei et al [3] applied morphological and biochemical tests to differentiate between 71 isolates obtained from Venezuelan soils.…”

“…These clusters may represent important tags for such strains allowing their separation from other actinomycetes. They also identified eleven undescribed compounds one of which is phosphonocystoximate [4]. Gao and Gupta discussed "The Molecular Signatures" for Actinobacteria.…”