Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes.
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.
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Kou-San
KS
Ju
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Jiangtao
J
Gao
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
James R
JR
Doroghazi
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Kwo-Kwang A
KK
Wang
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Christopher J
CJ
Thibodeaux
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Steven
S
Li
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Emily
E
Metzger
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
John
J
Fudala
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Joleen
J
Su
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Microbiology, University of Illinois, Urbana, IL 61801;
Jun Kai
JK
Zhang
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Jaeheon
J
Lee
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Microbiology, University of Illinois, Urbana, IL 61801;
Joel P
JP
Cioni
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Bradley S
BS
Evans
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan;
Ryuichi
R
Hirota
Bacterial Foodborne Pathogens and Mycology Research, US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604;
David P
DP
Labeda
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Chemistry and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61081 vddonk@illinois.edu metcalf@illinois.edu.
Wilfred A
WA
van der Donk
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Microbiology, University of Illinois, Urbana, IL 61801; vddonk@illinois.edu metcalf@illinois.edu.
William W
WW
Metcalf
D039903:Actinobacteria / Q000737:chemistry* / Q000235:genetics*; D001483:Base Sequence; D001688:Biological Products / Q000737:chemistry*; D055808:Drug Discovery / Q000379:methods / Q000639:trends*; D015723:Gene Library; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods* / Q000639:trends; D008969:Molecular Sequence Data; D010757:Phosphorous Acids / Q000032:analysis*; D017422:Sequence Analysis, DNA
D001688:Biological Products; D010757:Phosphorous Acids; C570063:phosphonic acid
antibiotic; genome mining; natural products; phosphonic acid