Jixun Zhan

A polyketide macrolactone synthase from the filamentous fungus Gibberella zeae

Resorcylic acid lactones represent a unique class of fungal polyketides and display a wide range of biological activities, such as nanomolar inhibitors of Hsp90 and MAP kinase. The biosynthesis of these compounds is proposed to involve two fungal polyketide synthases (PKS) that function collaboratively to yield a 14-membered macrolactone with a resorcylate core. We report here the reconstitution of Gibberella zeae PKS13, which is the nonreducing PKS associated with zearalenone biosynthesis. Using a small molecule mimic of the natural hexaketide starter unit, we reconstituted the entire repertoire of PKS13 activities in vitro, including starter-unit selection, iterative condensation, regioselective C2–C7 cyclization, and macrolactone formation. PKS13 synthesized both natural 14-membered and previously uncharacterized 16-membered resorcylic acid lactones, indicating relaxed control in both iterative elongation and macrocyclization. PKS13 exhibited broad starter-unit specificities toward fatty acyl-CoAs ranging in sizes between C6 and C16 and displayed the highest activity toward decanoyl-CoA. PKS13 was shown to be active in Escherichia coli and synthesized numerous alkyl pyrones and alkyl resorcylic esters without exogenously supplied precursors. We demonstrated that PKS13 can interact with E. coli fatty acid biosynthetic machinery and can be primed with fatty-acyl ACPp at low-micromolar concentrations. PKS13 synthesized new polyketides in E. coli when the culture was supplemented with synthetic precursors, showcasing its utility in precursor-directed biosynthesis. PKS13 is therefore a highly versatile polyketide macrolactone synthase that is useful in the engineered biosynthesis of polyketides, including resorcylic acid lactones that are not found in nature.

Type III polyketide synthases in natural product biosynthesis

Polyketides represent an important class of biologically active and structurally diverse compounds in nature. They are synthesized from acyl‐coenzyme A substrates by polyketide synthases (PKSs). PKSs are classified into three groups: types I, II, and III. This article introduces recent studies on type III PKSs identified from plants, bacteria, and fungi, and describes the catalytic functions of these enzymes in detail. Plant type III PKSs have been widely studied, as exemplified by chalcone synthase, which plays an important role in the synthesis of plant metabolites. Bacterial type III PKSs fall into five groups, many of which were identified from Streptomyces, a genus that has been well known for its production of bioactive molecules and genetic alterability. Although it was believed that type III PKSs exist exclusively in plants and bacteria, recent fungal genome sequencing projects and biochemical studies revealed the presence of type III PKSs in filamentous fungi, which provides a new chance to study fungal secondary metabolism and synthesize “unnatural” natural products. Type III PKSs have been used for the biosynthesis of novel molecules through precursor‐directed and structure‐based mutagenesis approaches.

Production of indole-3-acetic acid via the indole-3-acetamide pathway in the plant-beneficial bacterium, Pseudomonas chlororaphis O6, is inhibited by ZnO nanoparticles but enhanced by CuO nanoparticles

ABSTRACT The beneficial bacterium Pseudomonas chlororaphis O6 produces indole-3-acetic acid (IAA), a plant growth regulator. However, the pathway involved in IAA production in this bacterium has not been reported. In this paper we describe the involvement of the indole-3-acetamide (IAM) pathway in IAA production in P. chlororaphis O6 and the effects of CuO and ZnO nanoparticles (NPs). Sublethal levels of CuO and ZnO NPs differentially affected the levels of IAA secreted in medium containing tryptophan as the precursor. After 15 h of growth, CuO NP-exposed cells had metabolized more tryptophan than the control and ZnO NP-challenged cells. The CuO NP-treated cells produced higher IAA levels than control cultures lacking NPs. In contrast, ZnO NPs inhibited IAA production. Mixing of CuO and ZnO NPs resulted in an intermediate level of IAA production relative to the levels in the separate CuO and ZnO NP treatments. The effect of CuO NPs on IAA levels could be duplicated by ions at the concentrations released from the NPs. However, ion release did not account for the inhibition caused by the ZnO NPs. The mechanism underlying changes in IAA levels cannot be accounted for by effects on transcript accumulation from genes encoding a tryptophan permease or the IAM hydrolase in 15-h cultures. These findings raise the issue of whether sublethal doses of NPs would modify the beneficial effects of association between plants and bacteria.

A novel fungal flavin-dependent halogenase for natural product biosynthesis.

Halogenated molecules represent an important class of natural products, many of which are pharmaceutically relevant, such as chloramphenicol (antibacterial), vancomycin (antibacterial), and rebeccamycin (anticancer). Flavin-dependent halogenases have been identified as a major player in the introduction of halogen into activated organic molecules in natural product biosynthesis. However, the flavin-dependent halogenases identified so far are mainly prokaryotic tryptophan halogenases with strict substrate specificity. Most of these enzymes are involved in early biosynthetic steps of natural products to modify precursors such as tryptophan, which has limited their potential as biocatalysts to prepare various halogenated molecules. Considering the biological importance of halogens in natural products, a potent halogenase able to tailor diverse complex structures will be useful for enzymatic synthesis of novel halogenated compounds. Monocillin I (1) and radicicol (1 a) are potent heat shock protein 90 (Hsp90) inhibitors isolated from various fungi, of

Microbial transformations of artemisinin by Cunninghamella echinulata and Aspergillus niger

Microbial transformations of artemisinin 1 by Cunninghamella echinulata (AS 3.3400) and Aspergillus niger (AS 3.795) were carried out. Two products, 10β-hydroxyartemisinin 2 and 3α-hydroxydeoxyartemisinin 3, were obtained. Their structures were identified on the basis of chemical and spectroscopic data. 10β-Hydroxyartemisinin is a new compound.

Biotransformation of cinobufagin by cell suspension cultures of Catharanthus roseus and Platycodon grandiflorum

Abstract The biotransformations of cinobufagin ( 1 ), an animal-originated bufadienolide, by cell suspension cultures of Catharanthus roseus and Platycodon grandiflorum were investigated. Incubation for 6 days of 1 with C. roseus yielded four products, desacetylcinobufotalin ( 2 ), 3-epi-desacetylcinobufagin ( 3 ), 1β-hydroxyl desacetylcinobufagin ( 4 ) and 3-epi-desacetylcinobufotalin ( 5 ), among which 4 is a new compound. Time course investigation revealed that the biotransformation rates of two major products, 2 and 3 , reached their highest levels of 44.7 and 16.5%, respectively, on the third day after substrate administration. Compounds 2 – 5 showed more potent cytotoxic activities against HL-60 cell lines than the parent compound 1 . A plausible biotransformation pathway is proposed to account for the formation of the observed products. From the culture supernatant of P. grandiflorum , 2 was isolated in 37.8% yield after 8 days of incubation with 1 . Cinobufotalin ( 6 ) and desacetylcinobufagin ( 7 ) were also obtained as minor products. The two plant suspension cultures exhibited similar transformation patterns on compound 1 .

Rational reprogramming of fungal polyketide first-ring cyclization

Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the dihydroxyphenylacetic acid lactone dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal vs. bacterial folding mode difference is portable on creating hybrid enzymes, and we structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first-ring cyclizations will facilitate efforts to the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides.

Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases

Significance Benzenediol lactone (BDL) polyketides are privileged structures whose various members bind to distinct receptors or modulate the heat shock response and the immune system. BDLs are biosynthesized by collaborating polyketide synthase enzyme pairs in fungi. Coexpressing random heterocombinations of these enzymes from different BDL biosynthetic pathways in yeast cells is shown here to lead to the one-pot, one-step combinatorial biosynthesis of structurally diverse polyketides in practical amounts. Combinatorial biosynthesis promises to generate a novel unexplored source of bioactive molecules in an environmentally sustainable, economical, and inherently scalable manner. Broadening the medicinally relevant chemical space of polyketides by such methods will provide unnatural products as valuable entry points for drug discovery and development. Combinatorial biosynthesis aspires to exploit the promiscuity of microbial anabolic pathways to engineer the synthesis of new chemical entities. Fungal benzenediol lactone (BDL) polyketides are important pharmacophores with wide-ranging bioactivities, including heat shock response and immune system modulatory effects. Their biosynthesis on a pair of sequentially acting iterative polyketide synthases (iPKSs) offers a test case for the modularization of secondary metabolic pathways into “build–couple–pair” combinatorial synthetic schemes. Expression of random pairs of iPKS subunits from four BDL model systems in a yeast heterologous host created a diverse library of BDL congeners, including a polyketide with an unnatural skeleton and heat shock response-inducing activity. Pairwise heterocombinations of the iPKS subunits also helped to illuminate the innate, idiosyncratic programming of these enzymes. Even in combinatorial contexts, these biosynthetic programs remained largely unchanged, so that the iPKSs built their cognate biosynthons, coupled these building blocks into chimeric polyketide intermediates, and catalyzed intramolecular pairing to release macrocycles or α-pyrones. However, some heterocombinations also provoked stuttering, i.e., the relaxation of iPKSs chain length control to assemble larger homologous products. The success of such a plug and play approach to biosynthesize novel chemical diversity bodes well for bioprospecting unnatural polyketides for drug discovery.

Metabolic engineering of Escherichia coli for the biosynthesis of various phenylpropanoid derivatives.

Plants produce a variety of natural products with promising biological activities, such as the phenylpropanoids resveratrol and curcumin. While these molecules are naturally assembled through dedicated plant metabolic pathways, combinatorial biosynthesis has become an attractive tool to generate desired molecules. In this work, we demonstrated that biosynthetic enzymes from different sources can be recombined like legos to make various molecules. Seven biosynthetic genes from plants and bacteria were used to establish a variety of complete biosynthetic pathways in Escherichia coli to make valuable compounds. Different combinations of these biosynthetic bricks were made to design rationally various natural product pathways, yielding four phenylpropanoid acids (cinnamic acid, p-coumaric acid, caffeic acid, and ferulic acid), three bioactive natural stilbenoids (resveratrol, piceatannol and pinosylvin), and three natural curcuminoids (curcumin, bisdemethoxycurcumin and dicinnamoylmethane). A curcumin analog dicaffeoylmethane was synthesized by removing a methyltransferase from the curcumin biosynthetic pathway. Furthermore, introduction of a fungal flavin-dependent halogenase into the resveratrol biosynthetic pathway yielded a novel chlorinated molecule 2-chloro-resveratrol. This work thus provides a novel and efficient biosynthetic approach to creating various bioactive molecules. Further expansion of the library of the biosynthetic bricks will provide a resource for rational design of various phenylpropanoids via the combinatorial biosynthesis approach.

Insights into the Biosynthesis of 12-Membered Resorcylic Acid Lactones from Heterologous Production in Saccharomyces cerevisiae

The phytotoxic fungal polyketides lasiodiplodin and resorcylide inhibit human blood coagulation factor XIIIa, mineralocorticoid receptors, and prostaglandin biosynthesis. These secondary metabolites belong to the 12-membered resorcylic acid lactone (RAL12) subclass of the benzenediol lactone (BDL) family. Identification of genomic loci for the biosynthesis of lasiodiplodin from Lasiodiplodia theobromae and resorcylide from Acremonium zeae revealed collaborating iterative polyketide synthase (iPKS) pairs whose efficient heterologous expression in Saccharomyces cerevisiae provided a convenient access to the RAL12 scaffolds desmethyl-lasiodiplodin and trans-resorcylide, respectively. Lasiodiplodin production was reconstituted in the heterologous host by co-expressing an O-methyltransferase also encoded in the lasiodiplodin cluster, while a glutathione-S-transferase was found not to be necessary for heterologous production. Clarification of the biogenesis of known resorcylide congeners in the heterologous host helped to disentangle the roles that biosynthetic irregularities and chemical interconversions play in generating chemical diversity. Observation of 14-membered RAL homologues during in vivo heterologous biosynthesis of RAL12 metabolites revealed “stuttering” by fungal iPKSs. The close global and domain-level sequence similarities of the orthologous BDL synthases across different structural subclasses implicate repeated horizontal gene transfers and/or cluster losses in different fungal lineages. The absence of straightforward correlations between enzyme sequences and product structural features (the size of the macrocycle, the conformation of the exocyclic methyl group, or the extent of reduction by the hrPKS) suggest that BDL structural variety is the result of a select few mutations in key active site cavity positions.