Characterization of two novel non-reducing polyketide synthase genes from the lichen-forming fungus Hypogymnia physodes

Lichens are known to produce a variety of secondary metabolites including polyketides, which have valuable biological activities. Some polyketides are produced solely by lichens. The biosynthesis of these compounds is primarily governed by iterative type I polyketide synthases. Hypogymnia physodes synthesize polyketides such as physodic, physodalic and hydroxyphysodic acid and atranorin, which are non-reducing polyketides. Two novel non-reducing polyketide synthase (PKS) genes were isolated from a fosmid genomic library of a mycobiont of H. physodes using a 409bp fragment corresponding to part of the reductase (R) domain as a probe. H. physodes PKS1 (Hyopks1) and PKS2 (Hypopks2) contain keto synthase (KS), acyl transferase (AT), acyl carrier protein (ACP), methyl transferase (ME) and R domains. Classification based on phylogeny analysis using the translated KS and AT domains demonstrated that Hypopks1 and Hypopks2 are members of the fungal non-reducing PKSs clade III. This is the first report of non-reducing PKSs containing the R domain-mediated release mechanisms in lichens, which are also rare fungal type I PKS in non-lichenized filamentous fungi.     

Identification of anti-inflammatory polyketides from the coral-derived fungus Penicillium sclerotiorin: In vitro approaches and molecular-modeling

Four new polyketides, including an unusual naphthoquinone derivative (1), two azaphilone analogous (2, 7) and an α-pyrone (12), were isolated from the gorgonian-derived fungus Penicillium sclerotiorum CHNSCLM-0013 together with nine known compounds. Their structures were identified based on the 1D, 2D NMR, HRESIMS, single crystal X-ray diffraction and the absolute configurations were determined by comparing the ¹H NMR chemical shift and optical rotations with those reported in literature. In the bioassay, compounds 2, 6, 7, 10 and 12 exhibited significant inhibitory activities against the nitric oxide (NO) production in the LPS-induced macrophage RAW 264.7 with the IC₅₀ values in the range of 2.5–18.0 μM. Compounds 2, 6 and 7 exhibited the possible mechanism of downregulating the expression of iNOS and COX-2 in mRNA level. The primary structure-activity relationship was also discussed based on the molecular-modeling. This study will make a contribution to the chemical diversities of polyketides especially the azaphilone derivatives and the discovery of potential anti-inflammatory agent from marine fungi.     

Cytotoxic polyketides from endophytic fungus Phoma bellidis harbored in Ttricyrtis maculate

Four new polyketides, namely bellidisins A-D (1-4), were isolated from rice fermentation extract of endophytic fungus Phoma bellidis, along with three known compounds pinolidoxin (5), 5,6-epoxypinolidoxin (6), and 2-epi-herbarumin II (7). Their structures and absolute configurations were determined by 1D and 2D NMR, HRESIMS and ECD calculation. Their cytotoxicity was evaluated against human cancer cell lines HL-60, A549, SMMC-7721, MCF-7, and SW480. Compound 4 showed significant cytotoxicity on these five cell lines with IC₅₀ value ranged from 3.40 to 15.25 μM, which is stronger than cisplatin (4.86–27.70 μM).     

Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase

Tetracyclines are aromatic polyketides biosynthesized by bacterial type II polyketide synthases (PKSs). Understanding the biochemistry of tetracycline PKSs is an important step toward the rational and combinatorial manipulation of tetracycline biosynthesis. To this end, we have sequenced the gene cluster of oxytetracycline (oxy and otc genes) PKS genes from Streptomyces rimosus. Sequence analysis revealed a total of 21 genes between the otrA and otrB resistance genes. We hypothesized that an amidotransferase, OxyD, synthesizes the malonamate starter unit that is a universal building block for tetracycline compounds. In vivo reconstitution using strain CH999 revealed that the minimal PKS and OxyD are necessary and sufficient for the biosynthesis of amidated polyketides. A novel alkaloid (WJ35, or compound 2) was synthesized as the major product when the oxy-encoded minimal PKS, the C-9 ketoreductase (OxyJ), and OxyD were coexpressed in CH999. WJ35 is an isoquinolone compound derived from an amidated decaketide backbone and cyclized with novel regioselectivity. The expression of OxyD with a heterologous minimal PKS did not afford similarly amidated polyketides, suggesting that the oxy-encoded minimal PKS possesses novel starter unit specificity.     

Process and Metabolic Strategies for Improved Production of Escherichia coli-Derived 6-Deoxyerythronolide B

Recently, the feasibility of using Escherichia coli for the heterologous biosynthesis of complex polyketides has been demonstrated. In this report, the development of a robust high-cell-density fed-batch procedure for the efficient production of complex polyketides is described. The effects of various physiological conditions on the productivity and titers of 6-deoxyerythronolide B (6dEB; the macrocyclic core of the antibiotic erythromycin) in recombinant cultures of E. coli were studied in shake flask cultures. The resulting data were used as a foundation to develop a high-cell-density fermentation procedure by building upon procedures reported earlier for recombinant protein production in E. coli. The fermentation strategy employed consistently produced ~100 mg of 6dEB per liter, whereas shake flask conditions generated between 1 and 10 mg per liter. The utility of an accessory thioesterase (TEII from Saccharopolyspora erythraea) for enhancing the productivity of 6dEB in E. coli was also demonstrated (increasing the final titer of 6dEB to 180 mg per liter). In addition to reinforcing the potential for using E. coli as a heterologous host for wild-type- and engineered-polyketide biosynthesis, the procedures described in this study may be useful for the production of secondary metabolites that are difficult to access by other routes.     

New bioactive halenaquinone derivatives from South Pacific marine sponges of the genus Xestospongia

Bioassay-directed fractionation of South Pacific marine sponges of the genus Xestospongia has led to the isolation of a number of halenaquinone-type polyketides, including two new derivatives named xestosaprol C methylacetal 7 and orhalquinone 8. Chemical characterization of these two new compounds was achieved by extensive 1D and 2D NMR spectroscopic studies. Evaluation of anti-phospholipase A₂, anti-farnesyltransferase and antiplasmodial activities of this series is presented and structure/activity relationships are discussed. Orhalquinone 8 displayed a significant inhibition of both human and yeast farnesyltransferase enzymes, with IC₅₀ value of 0.40 μM and was a moderate growth inhibitor of Plasmodium falciparum.     

ABCG26-Mediated Polyketide Trafficking and Hydroxycinnamoyl Spermidines Contribute to Pollen Wall Exine Formation in Arabidopsis

Pollen grains are encased by a multilayered, multifunctional wall. The sporopollenin and pollen coat constituents of the outer pollen wall (exine) are contributed by surrounding sporophytic tapetal cells. Because the biosynthesis and development of the exine occurs in the innermost cell layers of the anther, direct observations of this process are difficult. The objective of this study was to investigate the transport and assembly of exine components from tapetal cells to microspores in the intact anthers of Arabidopsis thaliana. Intrinsically fluorescent components of developing tapetum and microspores were imaged in intact, live anthers using two-photon microscopy. Mutants of ABCG26, which encodes an ATP binding cassette transporter required for exine formation, accumulated large fluorescent vacuoles in tapetal cells, with corresponding loss of fluorescence on microspores. These vacuolar inclusions were not observed in tapetal cells of double mutants of abcg26 and genes encoding the proposed sporopollenin polyketide biosynthetic metabolon (ACYL COENZYME A SYNTHETASE5, POLYKETIDE SYNTHASE A [PKSA], PKSB, and TETRAKETIDE α-PYRONE REDUCTASE1), providing a genetic link between transport by ABCG26 and polyketide biosynthesis. Genetic analysis also showed that hydroxycinnamoyl spermidines, known components of the pollen coat, were exported from tapeta prior to programmed cell death in the absence of polyketides, raising the possibility that they are incorporated into the exine prior to pollen coat deposition. We propose a model where ABCG26-exported polyketides traffic from tapetal cells to form the sporopollenin backbone, in coordination with the trafficking of additional constituents, prior to tapetum programmed cell death.     

Chaetochromones A – C,Three New Polyketides from Mangrove Plant Derived Endophytic Fungus Phomopsis sp. SCSIO 41006

Three new polyketides, chaetochromones A – C ( 1  –  3 ), together with a chromone ( 4 ), were isolated from the ethyl acetate extract of mangrove‐derived fungus Phomopsis sp. SCSIO 41006. Their structures were elucidated by means of spectroscopic techniques (UV, IR, MS, 1D‐ and 2D‐NMR). The absolute configurations of the new compounds were established by CD data.     

Koninginin W,a New Polyketide from the Endophytic Fungus Trichoderma koningiopsis YIM PH30002

A new compound named koninginin W ( 1 ) and four known polyketides ( 2 – 5 ) were isolated from endophytic fungus Trichoderma koningiopsis YIM PH30002 of Panax notoginseng. The structures of 1 - 5 , including absolute configuration of 1 , were elucidated on the detailed analysis of the HR-ESI-MS, 1D and 2D NMR, and X-ray crystallographic data. Koninginin W ( 1 ) presented weak antibacterial activity against Escherichia coli, Bacillus subtilis and Salmonella typhimurium.     

Genome mining reveals the evolutionary origin and biosynthetic potential of basidiomycete polyketide synthases

Numerous polyketides are known from bacteria, plants, and fungi. However, only a few have been isolated from basidiomycetes. Large scale genome sequencing projects now help anticipate the capacity of basidiomycetes to synthesize polyketides. In this study, we identified and annotated 111 type I and three type III polyketide synthase (PKS) genes from 35 sequenced basidiomycete genomes. Phylogenetic analysis of PKS genes suggests that all main types of fungal iterative PKS had already evolved before the Ascomycota and Basidiomycota diverged. A comparison of genomic and metabolomic data shows that the number of polyketide genes exceeds the number of known polyketide structures by far. Exploiting these results to design degenerate PCR primers, we amplified and cloned the complete sequence of armB, a PKS gene from the melleolide producer Armillaria mellea. We expect this study will serve as a guide for future genomic mining projects to discover structurally diverse mushroom-derived polyketides.     

Activity of NADPH-generating pathways in relation to polyketide synthesis in the fungusAlternaria alternata

The synthesis of the secondary metabolites, polyketides, by fungi has been proposed to be regulated by theNADPH/NADP> ratio, which determines whether acetyl units are incorporated into fatty acids or polyketides. In the moldAlternaria alternata synthesis of the polyketide alternariol is inhibited by light while lipid synthesis is enhanced compared with mycelia grown in darkness. The activity andK_m values of enzymes in NADPH-generating pathways were measured in dark-grown (polyketide-producing) and light-grown (nonproducing) mycelia ofA. alternata. Glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, mannitol-1-phosphate dehydrogenase, mannitol-1-phosphatase, and NADP-isocitrate dehydrogenase each had a similar specific activity andK_m in light- compared with dark-grown cultures at the time of onset of polyketide synthesis. NADP-mannitol dehydrogenase activity was two times higher in dark-grown than in light-grown mycelia. TheK_m (mannitol) for the enzyme and the mycelial mannitol content were the same. When incorporation of [¹⁴C[mannitol into lipids was measuredin vivo the rate of mannitol oxidation was similar in light and darkness. These results suggest that the NADPH-generating capacity is not reduced in dark-grown as compared with light-grownA. alternata.     

Light effects on polyketide metabolism inAlternaria alternata

The time at which polyketide synthesis inAlternaria alternata is inhibited by white light was examined. Light exposure during the growth phase (no polyketide production) inhibited accumulation of polyketides at stationary growth phase. A light pulse during the production phase also inhibited further accumulation of polyketides. Two minutes of light applied during early production phase was enough to reduce polyketide levels significantly at the end of incubation relative to dark control.     

A PKS gene, pks-1, is involved in chaetoglobosin biosynthesis, pigmentation and sporulation in Chaetomium globosum

Chaetomium globosum is one of the most common fungi in nature. It is best known for producing chaetoglobosins; however, the molecular basis of chaetoglobosin biosynthesis is poorly understood in this fungus. In this study, we utilized RNA interference (RNAi) to characterize a polyketide synthase gene, pks-1, in C. globosum that is involved in the production of chaetoglobosin A. When pks-1 was knocked down by RNAi, the production of chaetoglobosin A dramatically decreased. Knock-down mutants also displayed a pigment-deficient phenotype. These results suggest that the two polyketides, melanin and chaetoglobosin, are likely to share common biosynthetic steps. Most importantly, we found that pks-1 also plays a critical role in sporulation. The silenced mutants of pks-1 lost the ability to produce spores. We propose that polyketides may modulate cellular development via an unidentified action. We also suggest that C. globosum pks-1 is unique because of its triple role in melanin formation, chaetoglobosin biosynthesis and sporulation. This work may shed light on chaetoglobosin biosynthesis and indicates a relationship between secondary metabolism and fungal morphogenesis.     

Diversity and evolution of polyketide biosynthesis gene clusters in the Ceratocystidaceae

Polyketides are secondary metabolites with diverse biological activities. Polyketide synthases (PKS) are often encoded from genes clustered in the same genomic region. Functional analyses and genomic studies show that most fungi are capable of producing a repertoire of polyketides. We considered the potential of Ceratocystidaceae for producing polyketides using a comparative genomics approach. Our aims were to identify the putative polyketide biosynthesis gene clusters, to characterize them and predict the types of polyketide compounds they might produce. We used sequences from nineteen species in the genera, Ceratocystis, Endoconidiophora, Davidsoniella, Huntiella, Thielaviopsis and Bretziella, to identify and characterize PKS gene clusters, by employing a range of bioinformatics and phylogenetic tools. We showed that the genomes contained putative clusters containing a non-reducing type I PKS and a type III PKS. Phylogenetic analyses suggested that these genes were already present in the ancestor of the Ceratocystidaceae. By contrast, the various reducing type I PKS-containing clusters identified in these genomes appeared to have distinct evolutionary origins. Although one of the identified clusters potentially allows for the production of melanin, their functional characterization will undoubtedly reveal many novel and important compounds implicated in the biology of the Ceratocystidaceae.     

New Rimocidin/CE-108 Derivatives Obtained by a Crotonyl-CoA Carboxylase/Reductase Gene Disruption in Streptomyces diastaticus var. 108: Substrates for the Polyene Carboxamide Synthase PcsA

The rimJ gene, which codes for a crotonyl-CoA carboxylase/reductase, lies within the biosynthetic gene cluster for two polyketides belonging to the polyene macrolide group (CE-108 and rimocidin) produced by Streptomyces diastaticus var. 108. Disruption of rimJ by insertional inactivation gave rise to a recombinant strain overproducing new polyene derivatives besides the parental CE-108 (2a) and rimocidin (4a). The structure elucidation of one of them, CE-108D (3a), confirmed the incorporation of an alternative extender unit for elongation step 13. Other compounds were also overproduced in the fermentation broth of rimJ disruptant. The new compounds are in vivo substrates for the previously described polyene carboxamide synthase PcsA. The rimJ disruptant strain, constitutively expressing the pcsA gene, allowed the overproduction of CE-108E (3b), the corresponding carboxamide derivative of CE-108D (3a), with improved pharmacological properties.     

Antimicrobial aromatic polyketides: a review of their antimicrobial properties and potential use in plant disease control

Aromatic polyketides are secondary metabolites widely found in bacteria, fungi, and plants, which are well-known for their diverse chemical structures and biological functions. The structural diversity of aromatic polyketides arises from a series of enzymatic modifications of the linear poly-β-ketone intermediates during biosynthesis. Their versatile bioactivities are exemplified by reports of their use as antibacterials, antifungals, antivirals, and antiparasitics. Despite many reports on the antimicrobial nature of aromatic polyketides, their potential use as plant disease control agents has still not been systematically explored and discussed. This review highlights examples of the use of aromatic polyketides as plant disease control agents and discusses their function and merits as agrochemicals.     

Passifloricins, polyketides alpha-pyrones from Passiflora foetida resin

Three polyketides alpha-pyrones, named passifloricins, were isolated from Passiflora foetida resin; their structures and relative configurations were assigned through 2D NMR spectroscopic analyses. These types of compounds were not detected in other passion flowers.     

Acylresorcinols from seed kernels of Myristica dactyloides

A new polyketide 1-(2,6-dihydroxyphenyl)9-(4-hydroxy-3-methoxyphenyl)nonan-1-one and five other polyketides 1-(2,6-dihydroxyphenyl)tetradecan-1-one and malabaricones A-D have been isolated from Myristica dactyloides seeds. ¹³C NMR of the first and the second mentioned compounds are also reported for the first time.     

Metabolically engineered Escherichia coli for efficient production of glycosylated natural products

Significant achievements in polyketide gene expression have made Escherichia coli one of the most promising hosts for the heterologous production of pharmacologically important polyketides. However, attempts to produce glycosylated polyketides, by the expression of heterologous sugar pathways, have been hampered until now by the low levels of glycosylated compounds produced by the recombinant hosts. By carrying out metabolic engineering of three endogenous pathways that lead to the synthesis of TDP sugars in E. coli, we have greatly improved the intracellular levels of the common deoxysugar intermediate TDP‐4‐keto‐6‐deoxyglucose resulting in increased production of the heterologous sugars TDP‐L‐mycarose and TDP‐d ‐desosamine, both components of medically important polyketides. Bioconversion experiments carried out by feeding 6‐deoxyerythronolide B (6‐dEB) or 3‐α‐mycarosylerythronolide B (MEB) demonstrated that the genetically modified E. coli B strain was able to produce 60‐ and 25‐fold more erythromycin D (EryD) than the original strain K207‐3, respectively. Moreover, the additional knockout of the multidrug efflux pump AcrAB further improved the ability of the engineered strain to produce these glycosylated compounds. These results open the possibility of using E. coli as a generic host for the industrial scale production of glycosylated polyketides, and to combine the polyketide and deoxysugar combinatorial approaches with suitable glycosyltransferases to yield massive libraries of novel compounds with variations in both the aglycone and the tailoring sugars.