Global and pathway-specific transcriptional regulations of pactamycin biosynthesis in Streptomyces pactum

Biological activities and metabolomic profiles of extracts from the marine sediment bacterium Nocardiopsis alba DP1B cultivated in different media

The soil bacterium DP1B was isolated from a marine sediment collected off the coast of Randayan Island, Kalimantan Barat, Indonesia and identified based on 16S rDNA as Nocardiopsis alba. The bacterium was cultivated in seven different media (A1, ISP1, ISP2, ISP4, PDB, PC-1, and SCB) with three different solvents [distilled water, 5 % NaCl solution, artificial seawater (ASW)] combinations, shaken at 200 rpm, 30 °C, for 7 days. The culture broths were extracted with ethyl acetate and each extract was tested for its antimicrobial activity and brine shrimp lethality, and the chemical diversity was assessed using thin-layer chromatography (TLC), gas chromatography (GC), and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The result showed that almost all extracts showed antibacterial but not antifungal activity, whereas their brine shrimp toxicity levels vary from high to low. The best medium/solvent combinations for antibacterial activity and toxicity were PC-1 (in either distilled water, 5% NaCl solution, or ASW) and SCB in ASW. Different chemical diversity profiles were observed on TLC, GC-MS, and LC-MS/MS. Extracts from the PC-1 cultures seem to contain a significant number of cyclic dipeptides, whereas those from the SCB cultures contain sesquiterpenes, indicating that media and solvent compositions can affect the secondary metabolite profiles of DP1B. In addition, untargeted metabolomic analyses using LC-MS/MS showed many molecular ions that did not match with those in the Global Natural Products Social Molecular Networking (GNPS) database, suggesting that DP1B has great potential as a source of new natural products.

Functional Studies and Revision of the NFAT-133/TM-123 Biosynthetic Pathway in Streptomyces pactum

The biosynthetic gene cluster of NFAT-133, an inhibitor of the nuclear factor of activated T cells, was recently identified in Streptomyces pactum ATCC 27456. This cluster is conspicuous by its highly disordered noncollinear type I modular polyketide synthase (PKS) genes that encode PKSs with one module more than those expected for the heptaketide NFAT-133 biosynthesis. Thus, the major metabolite NFAT-133 was proposed to derive from an octaketide analogue, TM-123. Here, we report that further bioinformatic analysis and gene inactivation studies suggest that NFAT-133 is not derived from TM-123 but rather a product of programmed KS7 extension skipping of a nascent heptaketide from the PKS assembly line that produces TM-123. Furthermore, identification of NFAT-133/TM-123 analogues from mutants of the ATCC 27456 strain suggests that NftN (a putative dehydrogenase), NftE (a cytochrome P450), and NftG (a putative hydrolase/decarboxylase) function "in trans" during the polyketide chain assembly processes.

A TetR family transcriptional regulator, SP_2854 can affect the butenyl-spinosyn biosynthesis by regulating glucose metabolism in Saccharopolyspora pogona

Background

Butenyl-spinosyn produced by Saccharopolyspora pogona exhibits strong insecticidal activity and a broad pesticidal spectrum. Currently, important functional genes involve in butenyl-spinosyn biosynthesis remain unknown, which leads to difficulty in efficiently understanding its regulatory mechanism, and improving its production by metabolic engineering.

Results

Here, we identified a TetR family transcriptional regulator, SP_2854, that can positively regulate butenyl-spinosyn biosynthesis and affect strain growth, glucose consumption, and mycelial morphology in S. pogona. Using targeted metabolomic analyses, we found that SP_2854 overexpression enhanced glucose metabolism, while SP_2854 deletion had the opposite effect. To decipher the overproduction mechanism in detail, comparative proteomic analysis was carried out in the SP-2854 overexpressing mutant and the original strain, and we found that SP_2854 overexpression promoted the expression of proteins involved in glucose metabolism.

Conclusion

Our findings suggest that SP_2854 can affect strain growth and development and butenyl-spinosyn biosynthesis in S. pogona by controlling glucose metabolism. The strategy reported here will be valuable in paving the way for genetic engineering of regulatory elements in actinomycetes to improve important natural products production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01808-2.

Positive regulation of MarR-type regulator slnO and improving salinomycin production of Streptomyces albus by multiple transcriptional regulations

The purpose of this study is to explore the function of MarR-family regulator slnO. In addition, the high-yield strain of salinomycin was constructed by using combined regulation strategies. Firstly the slnO gene over-expression strain (GO) was constructed in Streptomyces albus. Compared to wild type (WT) strain，salinomycin production in GO strain was increased about 28%. Electrophoretic mobility gel shift assays (EMSAs) confirmed that SlnO protein can bind specifically to the intergenic region of slnN-slnO, slnQ-slnA1 and slnF-slnT. qRT-PCR experiments also showed that slnA1, slnF, and slnT1 were significantly up-regulated, while the expression level of the slnN gene was down-regulated in GO strain. Secondly, slnN gene deletion strain (slnNDM) was used as the starting strain, and the pathway specific gene slnR in salinomycin gene cluster was over expressed in slnNDM. The new strain was named ZJUS01. The yield of salinomycin in ZJUS01 strain was 25% and 56% higher than that in slnNDM strain and WT strain. Above results indicate that the slnO gene has a positive regulation effect on the biosynthesis of salinomycin. Meanwhile, the yield of salinomycin could be greatly increased by manipulating multiple transcriptional regulations.

Modulation of Specialized Metabolite Production in Genetically Engineered Streptomyces pactum

Filamentous soil bacteria are known to produce diverse specialized metabolites. Despite having enormous potential as a source of pharmaceuticals, they often produce bioactive metabolites at low titers. Here, we show that inactivation of the pactamycin, NFAT-133, and conglobatin biosynthetic pathways in Streptomyces pactum ATCC 27456 significantly increases the production of the mitochondrial electron transport inhibitors piericidins. Similarly, inactivation of the pactamycin, NFAT-133, and piericidin pathways significantly increases the production of the heat-shock protein (Hsp) 90 inhibitor conglobatin. In addition, four new conglobatin analogues (B2, B3, F1, and F2) with altered polyketide backbones, together with the known analogue conglobatin B1, were identified in this mutant, indicating that the conglobatin biosynthetic machinery is promiscuous toward different substrates. Among the new conglobatin analogues, conglobatin F2 showed enhanced antitumor activity against HeLa and NCI-H460 cancer cell lines compared to conglobatin. Conglobatin F2 also inhibits colony formation of HeLa cells in a dose-dependent manner. Molecular modeling studies suggest that the new conglobatins bind to human Hsp90 and disrupt Hsp90/Cdc37 chaperone/co-chaperone interactions in the same manner as conglobatin. The study also showed that genes that are involved in piericidin biosynthesis are clustered in two different loci located distantly in the S. pactum genome.

Identification and Biological Activity of NFAT-133 Congeners from Streptomyces pactum

The soil bacterium Streptomyces pactum ATCC 27456 produces a number of polyketide natural products. Among them is NFAT-133, an inhibitor of the nuclear factor of activated T cells (NFAT) that suppresses interleukin-2 (IL-2) expression and T cell proliferation. Biosynthetic gene inactivation in the ATCC 27456 strain revealed the ability of this strain to produce other polyketide compounds including analogues of NFAT-133. Consequently, seven new derivatives of NFAT-133, TM-129-TM-135, together with a known compound, panowamycin A, were isolated from the culture broth of S. pactum ATCC 27456 ΔptmTDQ. Their chemical structures were elucidated on the basis of their HRESIMS, 1D and 2D NMR spectroscopy, and ECD calculation and spectral data. NFAT-133, TM-132, TM-135, and panowamycin A showed no antibacterial activity or cytotoxicity, but weakly reduced the production of LPS-induced nitric oxide in RAW264.7 cells in a dose-dependent manner. A revised chemical structure of panowamycin A and proposed modes of formation of the new NFAT-133 analogues are also presented.

Biological insights into the piericidin family of microbial metabolites

Extensively produced by members of the genus Streptomyces, piericidins are a large family of microbial metabolites, which consist of main skeleton of 4-pyridinol with methylated polyketide side chain. Nonetheless, these metabolites show differences in their bioactive potentials against micro-organisms, insects and tumour cells. Due to its close structural similarity with coenzyme Q, piericidins also possess an inhibitory activity against NADH dehydrogenase as well as Photosystem II. This review studied the latest research progress of piericidins, covering the chemical structure and physical properties of newly identified members, bioactivities, biosynthetic pathway with gene clusters and future prospect. With the increasing incidence of drug-resistant human pathogen strains and cancers, this review aimed to provide clues for the development of either new potential antibiotics or anti-tumour agents.

Natural Occurrence of Hybrid Polyketides from Two Distinct Biosynthetic Pathways in Streptomyces pactum

Nature has always been seemingly limitless in its ability to create new chemical entities. It provides vastly diverse natural compounds through a biomanufacturing process that involves myriads of biosynthetic machineries. Here we report a case of unusual formations of hybrid natural products that are derived from two distinct polyketide biosynthetic pathways, the NFAT-133 and conglobatin pathways, in Streptomyces pactum ATCC 27456. Their chemical structures were determined by NMR spectroscopy, mass spectrometry, and chemical synthesis. Genome sequence analysis and gene inactivation experiments uncovered the biosynthetic gene cluster of conglobatin in S. pactum. Biochemical studies of the recombinant thioesterase (TE) domain of the conglobatin polyketide synthase (PKS) as well as its S74A mutant revealed that the formation of these hybrid compounds requires an active TE domain. We propose that NFAT-133 can interfere with conglobatin biosynthesis by reacting with the TE-domain-bound intermediates in the conglobatin PKS assembly line to form hybrid NFAT-133/conglobatin products.

Biosynthesis of the Nuclear Factor of Activated T Cells Inhibitor NFAT-133 in Streptomyces pactum

NFAT-133 is a Streptomyces-derived aromatic polyketide compound with immunosuppressive, antidiabetic, and antitrypanosomal activities. It inhibits transcription mediated by nuclear factor of activated T cells (NFAT), leading to the suppression of interleukin-2 expression and T cell proliferation. It also activates the AMPK pathway in L6 myotubes and increases glucose uptake. In addition to NFAT-133, a number of its congeners, e.g., panowamycins and benwamycins, have been identified. However, little is known about their modes of formation in the producing organisms. Through genome sequencing of Streptomyces pactum ATCC 27456, gene inactivation, and genetic complementation experiments, the biosynthetic gene cluster of NFAT-133 and its congeners has been identified. The cluster contains a highly disordered genetic organization of type I modular polyketide synthase genes with several genes that are necessary for the formation of the aromatic core unit and tailoring processes. In addition, a number of new analogs of NFAT-133 were isolated and their chemical structures elucidated. It is suggested that the heptaketide NFAT-133 is derived from an octaketide intermediate, TM-123. The current study shows yet another unusual biosynthetic pathway involving a noncanonical polyketide synthase assembly line to produce a group of small molecules with valuable bioactivities.

Antibacterial Potential of Secondary Metabolites from Indonesian Marine Bacterial Symbionts

Indonesian marine environments are known to house diverse organisms. However, the potential for bacteria from these environments as a source of antibacterial agents has not been widely studied. This study aims to explore the antibacterial potential of secondary metabolites produced by bacterial symbionts from sponges and corals collected in the Indonesian waters. Extracts of 12 bacterial isolates from sponges or corals were prepared by cultivating the bacteria under a number of different media conditions and using agar well diffusion assays to test for antibacterial activity. In addition, the morphology, physiology, and biochemical characteristics and 16S rRNA sequence of each isolate were used to determine their taxonomic classification. All tested bacterial isolates were able to produce secondary metabolites with various levels of antibacterial activity depending on medium composition and culture conditions. Two of the bacteria (RS3 and RC4) showed strong antibacterial activities against both Gram-negative and Gram-positive bacteria. A number of isolates (RS1, RS3, and RC2) were co-cultured with mycolic acid-containing bacteria, Mycobacterium smegmatis or Rhodococcus sp. However, no improvements in their antibacterial activity were observed. All of the 12 bacteria tested were identified as Streptomyces spp. LC-MS analysis of EtOAc extracts from the most active strains RS3 and RC4 revealed the presence of a number of dactinomycin analogues and potentially new secondary metabolites. Symbiotic Streptomyces spp. from sponges and corals of the Indonesian marine environments have great potential as a source of broad-spectrum antibacterial agents.

Glycosylation of acyl carrier protein-bound polyketides during pactamycin biosynthesis

Glycosylation is a common modification reaction in natural products biosynthesis and has been known to be a post assembly line tailoring process in glycosylated polyketide biosynthesis. Here, we show that in pactamycin biosynthesis glycosylation can take place on an acyl carrier protein (ACP)-bound polyketide intermediate. Using in vivo gene inactivation, chemical complementation, and in vitro pathway reconstitution we demonstrate that the 3-aminoacetophenone moiety of pactamycin is derived from 3-aminobenzoic acid by a set of discrete polyketide synthase proteins via a 3-[3-aminophenyl]3-oxopropionyl-ACP intermediate. This ACP-bound intermediate is then glycosylated by an N-glycosyltransferase, PtmJ, providing a sugar precursor for the formation of the aminocyclopentitol core structure of pactamycin. This is the first example of glycosylation of a small molecule while tethered to a carrier protein. Additionally, we demonstrate that PtmO is a hydrolase that is responsible for the release of the ACP-bound product to a free β-ketoacid that subsequently undergoes decarboxylation.

The secondary metabolite pactamycin with potential for pharmaceutical applications: biosynthesis and regulation

The antitumor antibiotic pactamycin is a highly substituted aminocyclopentitol-derived secondary metabolite produced by the soil bacterium Streptomyces pactum. It has exhibited potent antibacterial, antitumor, antiviral, and antiprotozoal activities. Despite its outstanding biological activities, the complex chemical structure and broad-spectrum toxicity have hampered its development as a therapeutic, limiting its contribution to biomedical science to a role as a molecular probe for ribosomal function. However, a detailed understanding of its biosynthesis and how the biosynthesis is regulated has made it possible to tactically design and produce new pactamycin analogues, some of which have shown improved pharmacological properties. This mini-review describes the biosynthesis, regulation, engineered production, and biological activities of pactamycin and its congeners. It also highlights the suitability of biosynthetic methods as a feasible approach to generate new analogues of complex natural products and underscores the importance of utilizing biosynthetic enzymes as tools for chemoenzymatic production of structurally diverse bioactive compounds.