Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications.

Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.

Cavomycins A-C, Linear Oligomer Depsipeptides from an Annelid-Associated Streptomyces cavourensis.

Three unique linear oligomeric depsipeptides, designated as cavomycins A-C (1-3), were identified from Streptomyces cavourensis, a gut bacterium associated with the annelid Paraleonnates uschakovi. The structures of these depsipeptides were determined through a combination of spectroscopic methods and chemical derivatization techniques, including methanolysis, the modified Mosher's method, advanced Marfey's methods, and phenylglycine methyl ester derivatization. The unique dipeptidyl residue arrangements in compounds 1-3 indicate that they are not degradation products of valinomycin. Compound 2 and its methylation derivative 2a exhibited antiproliferative activity against PANC-1 pancreatic cancer cells with IC50 values of 1.2 and 1.7 µM, respectively.

Acidonemycins A-C, Glycosylated Angucyclines with Antivirulence Activity Produced by the Acidic Culture of Streptomyces indonesiensis.

The genome of Streptomyces indonesiensis is highly enriched with cryptic biosynthetic gene clusters (BGCs). The majority of these cryptic BGCs are transcriptionally silent in normal laboratory culture conditions as determined by transcriptome analysis. When cultured in acidic pH (pH 5.4), this strain has been shown to produce a set of new metabolites that were not observed in cultures of neutral pH (pH 7.4). The organic extract of the acidic culture displayed an antivirulence activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we report the structures of new glycosylated aromatic polyketides, named acidonemycins A-C (1-3), belonging to the family of angucyclines. Type II polyketide synthase BGC responsible for the production of 1-3 was identified by a transcriptome comparison between acidic (pH 5.4) and neutral (pH 7.4) cultures and further confirmed by heterologous expression in Streptomyces albus J1074. Of the three new compounds, acidonemycins A and B (1 and 2) displayed antivirulence activity against MRSA. The simultaneous identification of both antivirulent compounds and their BGC provides a starting point for the future effort of combinatorial biosynthesis.

Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus.

Secondary metabolites are produced at low titers by native producers due to tight regulations of their productions in response to environmental conditions. Synthetic biology provides a rational engineering principle for transcriptional optimization of secondary metabolite BGCs (biosynthetic gene clusters). Here, we demonstrate the use of synthetic biology principles for the development of a high-titer strain of the clinically important antibiotic daptomycin. Due to the presence of large NRPS (non-ribosomal peptide synthetase) genes with multiple direct repeats, we employed a top-down approach that allows transcriptional optimization of genes in daptomycin BGC with the minimum inputs of synthetic DNAs. The repeat-free daptomycin BGC was created through partial codon-reprogramming of a NRPS gene and cloned into a shuttle BAC vector, allowing BGC refactoring in a host with a powerful recombination system. Then, transcriptions of functionally divided operons were sequentially optimized through three rounds of DBTL (design-build-test-learn) cycles that resulted in up to ~2300% improvement in total lipopeptide titers compared to the wild-type strain. Upon decanoic acid feeding, daptomycin accounted for ∼ 40% of total lipopeptide production. To the best of our knowledge, this is the highest improvement of daptomycin titer ever achieved through genetic engineering of S. roseosporus. The top-down engineering approach we describe here could be used as a general strategy for the development of high-titer industrial strains of secondary metabolites produced by BGCs containing genes of large multi-modular NRPS and PKS enzymes.

A Medicinal Halophyte Ipomoea pes-caprae (Linn.) R. Br.: A Review of Its Botany, Traditional Uses, Phytochemistry, and Bioactivity.

Ipomoea pes-caprae (Linn.) R. Br. (Convolvulaceae) is a halophytic plant that favorably grows in tropical and subtropical countries in Asia, America, Africa, and Australia. Even though this plant is considered a pan-tropical plant, I. pes-caprae has been found to occur in inland habitats and coasts of wider areas, such as Spain, Anguilla, South Africa, and Marshall Island, either through a purposeful introduction, accidentally by dispersal, or by spreading due to climate change. The plant parts are used in traditional medicine for treating a wide range of diseases, such as inflammation, gastrointestinal disorders, pain, and hypertension. Previous phytochemical analyses of the plant have revealed pharmacologically active components, such as alkaloids, glycosides, steroids, terpenoids, and flavonoids. These phytoconstituents are responsible for the wide range of biological activities possessed by I. pes-caprae plant parts and extracts. This review arranges the previous reports on the botany, distribution, traditional uses, chemical constituents, and biological activities of I. pes-caprae to facilitate further studies that would lead to the discovery of novel bioactive natural products from this halophyte.

Antibacterial Bicyclic Fatty Acids from a Korean Colonial Tunicate Didemnum sp.

Five new bicyclic carboxylic acids were obtained by antibacterial activity-guided isolation from a Korean colonial tunicate Didemnum sp. Their structures were elucidated by the interpretation of NMR, MS and CD spectroscopic data. They all belong to the class of aplidic acids. Three of them were amide derivatives (1-3), and the other two were dicarboxylic derivatives (4 and 5). The absolute configurations were determined by a bisignate pattern of CD spectroscopy, which revealed that the absolute configurations of amides were opposite to those of dicarboxylates at every stereogenic centers. Compound 2 exhibited the most potent antibacterial activity (MIC, 2 µg/mL).

Saccharobisindole, Neoasterric Methyl Ester, and 7-Chloro-4(1H)-quinolone: Three New Compounds Isolated from the Marine Bacterium Saccharomonospora sp.

Analysis of the chemical components from the culture broth of the marine bacterium Saccharomonospora sp. CNQ-490 has yielded three novel compounds: saccharobisindole (1), neoasterric methyl ester (2), and 7-chloro-4(1H)-quinolone (3), in addition to acremonidine E (4), pinselin (5), penicitrinon A (6), and penicitrinon E (7). The chemical structures of the three novel compounds were elucidated by the interpretation of 1D, 2D nuclear magnetic resonance (NMR), and high-resolution mass spectrometry (HRMS) data. Compound 2 generated weak inhibition activity against Bacillus subtilis KCTC2441 and Staphylococcus aureus KCTC1927 at concentrations of 32 µg/mL and 64 µg/mL, respectively, whereas compounds 1 and 3 did not have any observable effects. In addition, compound 2 displayed weak anti-quorum sensing (QS) effects against S. aureus KCTC1927 and Micrococcus luteus SCO560.

Cadiolides J-M, antibacterial polyphenyl butenolides from the Korean tunicate Pseudodistoma antinboja.

Activity-guided fractionations of the tunicate Pseudodistoma antinboja yielded four new compounds of the cadiolide class (cadiolides J-M, 1, 3-5) along with a known one (cadiolide H, 2). The structures were defined by spectroscopic methods including X-ray crystallographic analysis. These compounds were evaluated for their antibacterial activity and exhibited potent antibacterial activity against all of the drug resistant strains tested with MICs comparable to those of marketed drugs such as vancomycin and linezolid.

Acredinone C and the Effect of Acredinones on Osteoclastogenic and Osteoblastogenic Activity.

A new inhibitor, acredinone C (1), of receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast differentiation was isolated from the culture broth of the fungus Acremonium sp. (F9A015) along with acredinones A (2) and B (3). The structure of acredinone C (1), which incorporates benzophenone and xanthone moieties, was established by the analyses of combined spectroscopic data including 1D and 2D NMR and MS. All of the acredinones studied efficiently inhibited the RANKL-induced formation of TRAP(+)-MNCs in a dose-dependent manner without any cytotoxicity up to 10 µM. Acredinone A showed dual activity in both osteoclast and osteoblast differentiation in vitro and good efficacy in an animal disease model of bone formation.

The Halicylindramides, Farnesoid X Receptor Antagonizing Depsipeptides from a Petrosia sp. Marine Sponge Collected in Korea.

Three new structurally related depsipeptides, halicylindramides F-H (1-3), and two known halicylindramides were isolated from a Petrosia sp. marine sponge collected off the shore of Youngdeok-Gun, East Sea, Republic of Korea. Their planar structures were elucidated by extensive spectroscopic data analyses including 1D and 2D NMR data as well as MS data. The absolute configurations of halicylindramides F-H (1-3) were determined by Marfey's method in combination with Edman degradation. The absolute configurations at C-4 of the dioxyindolyl alanine (Dioia) residues of halicylindramides G (2) and H (3) were determined as 4S and 4R, respectively, based on ECD spectroscopy. The C-2 configurations of Dioia in 2 and 3 were speculated to both be 2R based on the shared biogenesis of the halicylindramides. Halicylindramides F (1), A (4), and C (5) showed human farnesoid X receptor (hFXR) antagonistic activities, but did not bind directly to hFXR.

Monanchosterols A and B, bioactive bicyclo[4.3.1]steroids from a Korean sponge Monanchora sp.

Chemical investigation of a Korean marine sponge, Monanchora sp., led to the isolation of three new steroids (1-3). Compounds 1 and 2, designated as monanchosterols A and B, respectively, represent the first examples of steroids possessing the bicyclo[4.3.1] A/B ring system from a natural source. Compounds 1-3 were investigated for their anti-inflammatory activity by evaluating their inhibitory effects on the mRNA expression of IL-6, TNF-α, and COX-2 in the LPS-stimulated murine RAW264.7 macrophage cells. Compounds 2 and 3 exhibited significant inhibitory effects on the mRNA expression of IL-6 without notable cytotoxicity to the cells in a dose-dependent manner.

Acredinones A and B, voltage-dependent potassium channel inhibitors from the sponge-derived fungus Acremonium sp. F9A015.

Two new benzophenones, acredinones A (1) and B (2), were isolated from a marine-sponge-associated Acremonium sp. fungus. Their chemical structures were elucidated on the interpretation of spectroscopic data. The structure of 1 was confirmed by palladium-catalyzed hydrogenation, followed by spectroscopic data analysis. Acredinones A (1) and B (2) inhibited the outward K(+) currents of the insulin secreting cell line INS-1 with IC50 values of 0.59 and 1.0 µM, respectively.

Phorbaketals L-N, cytotoxic sesterterpenoids isolated from the marine sponge of the genus Phorbas.

Three new sesterterpenoids, phorbaketals L-N (1-3), were isolated from a marine sponge of the genus Phorbas and their complete structures were elucidated via analysis of HRFABMS and NMR spectroscopic data. Phorbaketal N (3) showed potent cytotoxicity against human pancreas cancer cells (IC50=11.4 µM).

Anmindenols A and B, inducible nitric oxide synthase inhibitors from a marine-derived Streptomyces sp.

Anmindenols A (1) and B (2), inhibitors of inducible nitric oxide synthase (iNOS), were isolated from a marine-derived bacterium Streptomyces sp. Their chemical structures were elucidated by interpreting various spectroscopic data, including IR, MS, and NMR. Anmindenols A and B are sesquiterpenoids possessing an indene moiety with five- and six-membered rings derived from isoprenyl units. The absolute configuration of C-4 in anmindenol B was determined by electronic circular dichroism (ECD) of a dimolybdenum complex. Anmindenols A (1) and B (2) inhibited nitric oxide production in stimulated RAW 264.7 macrophage cells with IC50 values of 23 and 19 µM, respectively.

Anithiactins A-C, modified 2-phenylthiazoles from a mudflat-derived Streptomyces sp.

Intensive investigation of the chemical components of a Streptomyces sp. isolated from mudflat sediments collected on the southern coast of the Korean peninsula led to the isolation of three new compounds, anithiactins A-C (1-3). The chemical structures of anithiactins A and C were determined by interpretation of NMR data analyses, while the chemical structure of anithiactin B was established from a combination of NMR spectroscopic and crystallographic data analyses. The structure of anithiactin A was also confirmed by total synthesis. These three anithiactins displayed moderate acetylcholinesterase inhibitory activity with no significant cytotoxicity.

Placotylene A, an inhibitor of the receptor activator of nuclear factor-κB ligand-induced osteoclast differentiation, from a Korean sponge Placospongia sp.

A new inhibitor, placotylene A (1), of the receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast differentiation, and a regioisomer of placotylene A, placotylene B (2), were isolated from a Korean marine sponge Placospongia sp. The chemical structures of placotylenes A and B were elucidated on the basis of 1D and 2D NMR, along with MS spectral analysis and revealed as an iodinated polyacetylene class of natural products. Placotylene A (1) displayed inhibitory activity against RANKL-induced osteoclast differentiation at 10 µM while placotylene B (2) did not show any significant activity up to 100 µM, respectively.

Ameliorative Effects of Korean-Red-Ginseng-Derived Polysaccharide on Antibiotic-Associated Diarrhea.

This study evaluated the ameliorative effects of Korean-red-ginseng-derived polysaccharide (KRG-P) on antibiotic-associated diarrhea (AAD) induced by administering lincomycin in mice. Changes of intestinal barrier proteins, the intestinal microbiome and short-chain fatty acid (SCFA) contents were investigated. Lincomycin was orally administered for 9 days to induce diarrhea; subsequently, 100 mg/kg and 300 mg/kg of KRG-P were administered orally for 12 days. The diarrhea was observed in the AAD group; further KRG-P administration improved the diarrhea. Analysis of changes in the intestinal microbial flora of the mice revealed that the harmful bacterial flora (such as Proteobacteria) were increased in the AAD group, whereas beneficial bacterial flora (such as Firmicutes) were decreased. However, KRG-P administration resulted in decreased Proteobacteria and increased Firmicutes, supporting the improvement of the microbial flora imbalance caused by AAD. Moreover, an analysis of the SCFAs (acetic acid, propionic acid, and butylic acid) in the caecum revealed that SCFAs' contents in the AAD group were substantially reduced but tended to increase upon KRG-P administration. Based on these results, KRG-P, which is primarily composed of carbohydrates can improve lincomycin-induced diarrhea, likely owing to the recovery of SCFA content by improving the intestinal microbial imbalance and intestinal barrier proteins.

Cytotoxic scalarane sesterterpenes from a Korean marine sponge Psammocinia sp.

Three novel scalarane sesterterpenes were isolated from a Korean marine sponge, Psammocinia sp., along with four known derivatives. Their structures were elucidated on the basis of NMR, MS and IR spectroscopic data. The three new compounds are 12-deacetoxy-23-hydroxyscalaradial (1), 12-dehydroxy-23-hydroxyhyrtiolide (2) and 12-O-acetyl-16-deacetoxy-23-acetoxyscalarafuran (3), respectively, and the four known compounds are 12-deacetoxy-23-hydroxyheteronemin (4), 12-deacetoxy-23-acetoxy-19-O-acetylscalarin (5), 12-deacetoxy-23-O-acetoxyheteronemin (6) and 12-deacetoxyscalaradial (7). They exhibited cytotoxicity against intractable human cancer cell lines A498, ACHN, MIA-paca and PANC-1, with an IC50 range of 0.4-48 µM.

Bioactive sesterterpenoids from a Korean sponge Monanchora sp.

Chemical investigation of a Korean marine sponge, Monanchora sp., yielded nine new sesterterpenoids (1-9) along with phorbaketals A-C (10-12). The planar structures were established on the basis of NMR and MS analysis, and the absolute configurations of 1-9 were defined using the modified Mosher's method and CD spectroscopic data analysis. Compounds 1-8, designated as phorbaketals D-K, possess a spiroketal-modified benzopyran moiety such as phorbaketal A, and their structural variations are due to oxidation and/or reduction of the tricyclic core or the side chain. Compound 9, designated as phorbin A, has a monocyclic structure and is proposed to be a possible biogenetic precursor of the phorbaketals. Compounds 1-9 were evaluated for cytotoxicity against four human cancer cell lines (A498, ACHN, MIA-paca, and PANC-1), and a few of them were found to exhibit cytotoxic activity.

Antibacterial butenolides from the Korean tunicate Pseudodistoma antinboja.

Six new (1, 2, and 5-8) and three known (3, 4, and 9) butenolide metabolites were isolated from the tunicate Pseudodistoma antinboja by activity-guided fractionations. The structures were elucidated by combined NMR and MS spectroscopic methods. These compounds were evaluated for their antibacterial activity, and most of them exhibited moderate to significant activity that selectively targeted Gram-positive strains and did not exhibit cytotoxicity in the MTT assay at 100 µM. Cadiolides 5-9 in particular exhibited significant antibacterial activity that was comparable to or even better than those of marketed drugs such as vancomycin and linezolid against all of the drug-resistant strains tested.