Genome mining of Streptomyces sp. CB00271 as a natural high-producer of β-rubromycin and the resulting discovery of β-rubromycin acid

Late-Stage Tailoring Steps in the Biosynthesis of β-Rubromycin Involve Successive Terminal Oxidations, a Selective Hydroxyl Reduction, and Distinctive O-Methylations

β-Rubromycin (1) has a unique O-methylated naphthoquinone moiety and is an efficient inhibitor of human telomerase. Through in vivo and in vitro investigations, we elucidated the biosynthetic tailoring steps of compound 1, which involve the carboxyl terminal via successive oxidizations by RubU and RubO1/RubO2, O-methylation of the carboxyl terminal by RubX, and reduction of C-3' hydroxyl by RubK. The final tautomerization of the naphthoquinone moiety is mediated by RubO, which anchors the transitional intermediate through O-methylation to form the naphthoquinone tautomer. The structure-activity relationship further revealed the significant influences of the terminal modification status on anticancer activities of rubromycins.

The exploration of high production of tiancimycins in Streptomyces sp. CB03234-S revealed potential influences of universal stress proteins on secondary metabolisms of streptomycetes

BACKGROUND

Universal stress proteins (USPs) are prevalent in various bacteria to cope with different adverse stresses, while their possible effects on secondary metabolisms of hosts are unclear. Tiancimycins (TNMs) are ten-membered endiynes possessing excellent potential for development of anticancer antibody-drug conjugates. During our efforts to improve TNMs titer, a high-producing strain Streptomyces sp. CB03234-S had been obtained and its possible high yield mechanism is being continuously explored to further enhance TNMs production.

RESULTS

In this work, the whole-genome resequencing and analysis results revealed a notable 583 kb terminal deletion containing 8 highly expressed usp genes in the genome of CB03234-S. The individual complementation of lost USPs in CB03234-S all showed differential effects on secondary metabolism, especially TNMs production. Among them, the overexpression of USP3 increased TNMs titer from 12.8 ± 0.2 to 31.1 ± 2.3 mg/L, while the overexpression of USP8 significantly reduced TNMs titer to only 1.0 ± 0.1 mg/L, but activated the production of porphyrin-type compounds. Subsequent genetic manipulations on USP3/USP8 orthologs in Streptomyces. coelicolor A3(2) and Streptomyces sp. CB00271 also presented clear effects on the secondary metabolisms of hosts. Further sequence similarity network analysis and Streptomyces-based pan‑genomic analysis suggested that the USP3/USP8 orthologs are widely distributed across Streptomyces.

CONCLUSION

Our studies shed light on the potential effects of USPs on secondary metabolisms of streptomycetes for the first time, and USPs could become novel targets for exploring and exploiting natural products in streptomycetes.

Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase

Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.

Streptomyces iakyrus TA 36 as First-Reported Source of Quinone Antibiotic γ-Rubromycin

A wide range of bioactive compounds with potential medical applications are produced by members of the genus Streptomyces. A new actinomycete producer of the antibiotic γ-rubromycin, designated TA 36, was isolated from an alpine soil sample collected in Peru (Machu Picchu). Morphological, physiological and biochemical characteristics of the strain, together with data obtained via phylogenetic analysis and MALDI-TOF MS, were used for the correct identification of the isolate. The isolate TA 36 showed morphological characteristics that were consistent with its classification within the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences showed that the TA 36 strain was most similar to S. iakyrus and S. violaceochromogenes with 99% similarity. Phylogenetic analysis together with the profile of whole cell proteins indicated that the strain tested could be identified as S. iakyrus TA 36. The crude extract Ext.5333.TA 36 showed various effects against the tested organisms with strong antimicrobial activity in the growth of Staphylococcus aureus (Newman) (MIC value of 0.00195 µg/µL). HPLC fractionation and LC/MS analysis of the crude extract led to the identification of the quinone antibiotic γ-rubromycin, a promising antitumour and antibacterial antibiotic. To the best of our knowledge, there is currently no report on the production of γ-rubromycin by S. iakyrus. Therefore, this study suggests S. iakyrus TA 36 as the first-reported source of this unique bioactive secondary metabolite.

Discovery and Biosynthetic Studies of a Highly Reduced Cinnamoyl Lipid, Tripmycin A, from an Endophytic Streptomyces sp

A Tripterygium wilfordii endophyte, Streptomyces sp. CB04723, was shown to produce an unusually highly reduced cytotoxic cinnamoyl lipid, tripmycin A (1). Structure-activity relationship studies revealed that both the cinnamyl moiety and the saturated fatty acid side chain are indispensable to the over 400-fold cytotoxicity improvement of 1 against the triple-negative breast cancer cell line MDA-MB-231 compared to 5-(2-methylphenyl)-4-pentenoic acid (2). Bioinformatical analysis, gene inactivation, and overexpression revealed that Hxs15 most likely acted as an enoyl reductase and was involved with the side chain reduction of 1, which provides a new insight into the biosynthesis of cinnamoyl lipids.

Isolation, biosynthesis, and biological activity of rubromycins derived from actinomycetes

Natural occurring aromatic polyketides from actinomycetes indicate a structurally and functionally diverse family of polycyclic polyphenols. Some of them are consequently suggested as lead structures for drug development. Among them, rubromycins are derived from a single C26 polyketide chain and exhibit an unusual bisbenzannulated [5,6]-spiroketal system that connects a highly oxygenated naphthazarin motif to an isocoumarin unit. This type of biosynthetically elusive polycyclic polyketides has shown promising pharmacological activities, including antimicrobial, anticancer, and enzyme inhibition activity. The unique structures, intriguing biosynthesis, and marked bioactivities of rubromycins have drawn considerable attention from several chemists and biologists. This review covers the isolation, characterization, biosynthesis, and biological studies of these structurally diverse and complex rubromycins.

Characterization of Chalkophomycin, a Copper(II) Metallophore with an Unprecedented Molecular Architecture

Metals play essential roles in life by coordination with small molecules, proteins, and nucleic acids. Although the coordination of copper ions in many proteins and methanobactins is known, the coordination chemistry of Cu(II) in natural products and their biological functions remain underexplored. Herein, we report the discovery of a Cu(II)-binding natural product, chalkophomycin (CHM, 1), from Streptomyces sp. CB00271, featuring an asymmetric square-coordination system of a bidentate diazeniumdiolate and a conjugated 1H-pyrrole 1-oxide-oxazoline. The structure of 1 may inspire the synthesis of Cu(II) chelators against neurodegenerative diseases or Cu(II)-based antitumor therapeutics.