Genome mining of novel rubiginones from Streptomyces sp. CB02414 and characterization of the post-PKS modification steps in rubiginone biosynthesis

Abstract

Background Rubiginones belong to the angucycline family of aromatic polyketides, and they have been shown to potentiate the vincristine (VCR)-induced cytotoxicity against VCR-resistant cancer cell lines. However, the biosynthetic gene clusters (BGCs) and biosynthetic pathways for rubiginones have not been reported yet. Results In this study, based on bioinformatics analysis of the genome of Streptomyces sp. CB02414, we predicted the functions of the two type II polyketide synthases (PKSs) BGCs. The rub gene cluster was predicted to encode metabolites of the angucycline family. Scale-up fermentation of the CB02414 wild-type strain led to the discovery of eight rubiginones, including five new ones (rubiginones J, K, L, M, and N). Rubiginone J was proposed to be the final product of the rub gene cluster, which features extensive oxidation on the A-ring of the angucycline skeleton. Based on the production profiles of the CB02414 wild-type and the mutant strains, we proposed a biosynthetic pathway for the rubiginones in CB02414. Conclusions A genome mining strategy enabled the efficient discovery of new rubiginones from Streptomyces sp. CB02414. Based on the isolated biosynthetic intermediates, a plausible biosynthetic pathway for the rubiginones was proposed. Our research lays the foundation for further studies on the mechanism of the cytochrome P450-catalyzed oxidation of angucyclines and for the generation of novel angucyclines using combinatorial biosynthesis strategies.

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum

“…At the same time, several angucyclinones including known compounds and many of their isomers were detected. In particular, panglimycin E ( Fotso et al, 2008 ), cangumycin ( Wang et al, 2019 ), ochromycinone ( Zhang et al, 2021 ), and emycin A ( Larsen et al, 1996 ), could be putatively identified ( Figure 4 ). Ochromycinone is known to inhibit the growth of B. subtilis and Pseudomonas aeruginosa , which might explain the bioactivity of LN549 extracts against Gram-positive bacteria, while activity against Gram-negative E. coli and P. putida used in our antimicrobial tests was not observed.…”

“…CB02414 responsible for the biosynthesis of several rubiginones and ochromycinone. The latter is a precursor of rubiginone and is modified by an O-methyltransferase to gain rubiginone B 2 ( Zhang et al, 2021 ). Utahmycin A, a 2-azaanthraquinone compound, putatively identified by LC-MS, might have its origin in BGC 2.16 as well.…”

Table_1.XLSX

“…At the same time, several angucyclinones including known compounds and many of their isomers were detected. In particular, panglimycin E (Fotso et al, 2008), cangumycin (Wang et al, 2019), ochromycinone (Zhang et al, 2021), and emycin A (Larsen et al, 1996), could be putatively identified (Figure 4). Ochromycinone is known to inhibit the growth of B. subtilis and Pseudomonas aeruginosa, which might explain the bioactivity of LN549 extracts against Gram-positive bacteria, while activity against Gramnegative E. coli and P. putida used in our antimicrobial tests was not observed.…”

“…CB02414 responsible for the biosynthesis of several rubiginones and ochromycinone. The latter is a precursor of rubiginone and is modified by an O-methyltransferase to gain rubiginone B 2 (Zhang et al, 2021). Utahmycin A, a 2-azaanthraquinone compound, putatively identified by LC-MS, might have its origin in BGC 2.16 as well.…”

Data_Sheet_1.PDF

“…At the same time, several angucyclinones including known compounds and many of their isomers were detected. In particular, panglimycin E (Fotso et al, 2008), cangumycin (Wang et al, 2019), ochromycinone (Zhang et al, 2021), and emycin A (Larsen et al, 1996), could be putatively identified (Figure 4). Ochromycinone is known to inhibit the growth of B. subtilis and Pseudomonas aeruginosa, which might explain the bioactivity of LN549 extracts against Gram-positive bacteria, while activity against Gramnegative E. coli and P. putida used in our antimicrobial tests was not observed.…”