Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria

Panter, Fabian; Krug, Daniel; Baumann, Sascha; Müller, Rolf

doi:10.1039/c8sc01325j

Cited by 89 publications

(106 citation statements)

References 49 publications

Supporting

Mentioning

100

Contrasting

Unclassified

Order By: Relevance

“…Genes encoding immunity determinants commonly co-occur with the biosynthetic loci required for the production of natural product antibiotics, 14 a phenomenon that has inspired recent genome-mining efforts to identify novel scaffolds with known targets. [15][16][17] Comparative genomic analysis of the oba BGC characterized in P. fluorescens ATCC 39502 with other putative 1 BGCs present in the genomes of two P. fluorescens soil isolates, several Burkholderia species and Chitiniphilus shinanonensis DSM Table 1) allowed the identification of a minimal set of genes conserved across all clusters (Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

Self-immunity guided identification of threonyl-tRNA synthetase as the molecular target of obafluorin, a β-lactone antibiotic

Scott

Batey

Wiencek

et al. 2019

Preprint

View full text Add to dashboard Cite

To meet the ever-growing demand of antibiotic discovery, new chemical matter and antibiotic targets are urgently needed. Many potent natural product antibiotics which were previously discarded can also provide lead molecules and drug targets. One such example is the structurally unique β-lactone obafluorin, produced by Pseudomonas fluorescens ATCC 39502. Obafluorin is active against both Grampositive and -negative pathogens, however the biological target was unknown. We now report that obafluorin targets threonyl-tRNA-synthetase and we identify a homologue, ObaO, which confers self-immunity to the obafluorin producer. Disruption of obaO in P. fluorescens ATCC 39502 results in obafluorin sensitivity, whereas expression in sensitive E. coli strains confers resistance. Enzyme assays demonstrate that E. coli threonyl-tRNA synthetase is fully inhibited by obafluorin, whereas ObaO is only partly susceptible, exhibiting a very unusual partial inhibition mechanism.Altogether, our data highlight the utility of a self-immunity guided approach for the identification of an antibiotic target de novo and will ultimately enable the generation of improved obafluorin variants.

show abstract

Section: Resultsmentioning

confidence: 99%

Self-immunity guided identification of threonyl-tRNA synthetase as the molecular target of obafluorin, a β-lactone antibiotic

Scott

Batey

Wiencek

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…A gene cluster was identified adjacent to a predicted PRP (co-clustering), however, no corresponding compounds were reported before their study. Activation in the native host and heterologous expression of this gene cluster resulted in the isolation of pyxidicyclines, a group of new in inhibitors of E. coli DNA topoisomerase IV and human DNA topoisomerase I (85). Similarly, the fungal sesquiterpenoid aspterric acid, a potent herbicide, was obtained by the approach of co-clustering self-resistance gene and biosynthetic gene cluster as well (86).…”

Section: Perspectivesmentioning

confidence: 99%

Discovery of novel bioactive natural products driven by genome mining

Zhu

Shen

2018

DD&T

View full text Add to dashboard Cite

Microbial natural product is an important source for drug discovery. As more and more microbial genomes are sequenced, bioinformatics analysis shows that there are huge resources of novel natural products. Genome mining is a new strategy of natural product discovery based on gene cluster sequences and biosynthetic pathways. At the same time, it can directly associate the structures of natural products with synthetic pathways, and facilitate the study of biosynthesis and combinatorial biosynthesis. In this paper, the strategies of genome mining, including bioinformatics predictions, metabolomic comparisons and genetic manipulations, are reviewed, which shows a great advantage of this strategy in exploiting the potential of microbial natural products. With the development of genome mining methodology and techniques, it will be possible to realize rational exploitation of microbial natural product resources.

show abstract

“…Intrigued by these compounds, which exhibit potent 55 antibacterial activity, and as part of studies to decipher their biosynthetic pathway, we 56 employed targeted metabolomics to identify further congeners that may have been missed 57 during manual analysis of culture extracts. This led us to identify the formicapyridines (1)(2)(3)(4)(5)(6)(7)(8)(9), 58 pyridine containing polyketide alkaloids which represent additional products of the 59 are minor shunt metabolites that likely arise due to derailment of the formicamycin 70 biosynthetic pathway. Intrigued by these observations we investigated the possibility of 71 reprogramming, or evolving, the BGC such that the formicapyridines might become the 72 major products of the formicamycin BGC.…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, the methyl group atom C24 shows 218 enrichment and coupling to C1. The C2 atom of [1,[2][3][4][5][6][7][8][9][10][11][12][13] C2] sodium acetate is highlighted as a 219 blue circle, the C1 atom as a black circle, and the coupled unit by a bold line. The gene product ForD shows significant sequence similarity to aromatase/cyclases 238 (ARO/CYC) such as the N-terminal domain (pfam 03364) of the archetypical tetracenomycin 239 polyketide cyclase TcmN which belongs to the Bet v1-like superfamily (cl10022) 15 .…”

mentioning

confidence: 99%

See 1 more Smart Citation

Aromatic polyketide biosynthesis: fidelity, evolution and engineering

Qin

Devine²,

Hutchings³

et al. 2019

Preprint

View full text Add to dashboard Cite

14We report the formicapyridines which are structurally and biosynthetically related to the 15 pentacyclic fasamycin and formicamycin aromatic polyketides but comprise a rare pyridine 16 moiety. These new compounds are trace level metabolites formed by derailment of the major 17 biosynthetic pathway. Inspired by evolutionary logic we show that rational mutation of a 18 single gene in the biosynthetic gene cluster leads to a significant increase both in total 19 formicapyridine production and their enrichment relative to the fasamycins/formicamycins. 20Our observations broaden the polyketide biosynthetic landscape and identify a non-catalytic 21 role for ABM superfamily proteins in type II polyketide synthase assemblages for maintaining 22 biosynthetic pathway fidelity. 23 24 formicamycin (for) biosynthetic gene cluster (BGC). Products of type II PKS systems which 60 contain a pyridine moiety are extremely rare 7 . 61 62 Figure 1 | Chemical structures of metabolites isolated from Streptomyces formicae. 63Compounds 1-9 and 13 were discovered during this study whereas 10-12 and 14-26 were 64 reported in an earlier study 5 . 65Challis and co-workers recently showed that the majority of actinomycete derived polyketide 66 alkaloids, including those containing a pyridine moiety, arise from reactive intermediates 67 formed after transamination of aldehydes generated from reductive off-loading of the 68

show abstract

Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria

Abstract: Mining the genome to harvest from the metabolome: a well-directed search for bioactive natural products unearths the pyxidicyclines from Pyxidicoccus.

Cited by 89 publications

References 49 publications

Self-immunity guided identification of threonyl-tRNA synthetase as the molecular target of obafluorin, a β-lactone antibiotic

Self-immunity guided identification of threonyl-tRNA synthetase as the molecular target of obafluorin, a β-lactone antibiotic

Discovery of novel bioactive natural products driven by genome mining

Aromatic polyketide biosynthesis: fidelity, evolution and engineering

Contact Info

Product

Resources

About