Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase

Abstract

Pseudouridimycin (PUM) is a novel pseudouridine-containing peptidyl-nucleoside antibiotic that inhibits bacterial RNA polymerase (RNAP) through a binding site and mechanism different from those of clinically approved RNAP inhibitors of the rifamycin and lipiarmycin (fidaxomicin) classes. PUM was discovered by screening microbial fermentation extracts for RNAP inhibitors. In this review, we describe the discovery and characterization of PUM. We also describe the RNAP-inhibitory and antibacterial properties of PUM. Finally, we review available information on the gene cluster and pathway for PUM biosynthesis and on the potential for discovering additional novel pseudouridine-containing nucleoside antibiotics by searching bacterial genome and metagenome sequences for sequences similar to pumJ, the pseudouridine-synthase gene of the PUM biosynthesis gene cluster.

Total synthesis and chemical stability of pseudouridimycin

“…The hGln residue side chain in PUM had previously been observed to undergo unusually facile amide hydrolysis under acidic conditions. 2,16 Prolonged exposure of synthetic 1 to final deprotection conditions (or acidic HPLC solvent mixtures) also resulted in significant side chain amide hydrolysis as judged by LCMS. To further explore the stability of 1, we measured its rate of decomposition in several aqueous buffers (Fig.…”

Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain

“…Production of PUM has been previously demonstrated only for Streptomyces spp. ID38640 and ID38673, from the NAICONS collection 14 , and for Streptomyces albus DSM 40763 34 , 35 . To investigate whether the strains harboring a PUM BGC did produce PUM and other metabolites shared with Streptomyces sp.…”

Metabolomic investigation of the pseudouridimycin producer, a prolific streptomycete

“…In addition to a few strains from the NAICONS collection, 14 PUM has been observed only in Streptomyces albus DSM 40763. 33, 34 We thus chose a few Streptomyces strains that harbor a PUM BGC: S. rimosus ATCC 10970, the oxytetracycline producer; S. mobaraensis DSM 40847, the producer of the NADH reductase inhibitor piericidin; S. eurocidicus ATCC 27428, the producer of the antifungal polyene eurocidin; and S. flocculus DSM 40313, the producer of the aminoquinone antibiotic streptonigrin. [ S. flocculus has been recently reclassified as later heterotypic synonyms of S. albus 35 and will be referred as S. albus DSM 40313 hereafter.]…”

“…In addition to a few strains from the NAICONS collection, 14 PUM has been observed only in Streptomyces albus DSM 40763. 33,34 We thus chose a few Streptomyces strains that harbor a PUM BGC: S. To delineate the relationship of the different PUM producers, we resorted to autoMLST 36 for a high-resolution species tree using multi-locus comparison. The resulting tree revealed ten major clades and three branches formed by a single strain each ( Supplementary Fig.…”