A new pathway for polyketide synthesis in microorganisms

Oxidative Cyclization in Natural Product Biosynthesis

Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.

Draft Genome Sequence of an Anicemycin Producer, Streptomyces sp. TP-A0648

We report the draft genome sequence of Streptomyces sp. TP-A0648 isolated from a leaf of Aucuba japonica. This strain produces a new tumor cell growth inhibitor designated anicemycin. The genome harbors at least 12 biosynthetic gene clusters for polyketides and nonribosomal peptides, suggesting the potential to produce diverse secondary metabolites.

Expansion of chemical space for natural products by uncommon P450 reactions

This review focuses on unusual P450 reactions related to new chemistry, skeleton construction, structure re-shaping, and protein–protein interactions in natural product biosynthesis, which play significant roles in chemical space expansion for natural products.

Exploiting the Biosynthetic Potential of Type III Polyketide Synthases

Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases (PKSs) using acyl-CoA precursors. Recent studies in the engineering and structural characterization of PKSs have facilitated the use of target enzymes as biocatalysts to produce novel functionally optimized polyketides. These compounds may serve as potential drug leads. This review summarizes the insights gained from research on type III PKSs, from the discovery of chalcone synthase in plants to novel PKSs in bacteria and fungi. To date, at least 15 families of type III PKSs have been characterized, highlighting the utility of PKSs in the development of natural product libraries for therapeutic development.

Directed multistep biocatalysis using tailored permeabilized cells

: Recent developments in the field of biocatalysis using permeabilized cells are reviewed here, with a special emphasis on the newly emerging area of multistep biocatalysis using permeabilized cells. New methods of metabolic engineering using in silico network design and new methods of genetic engineering provide the opportunity to design more complex biocatalysts for the synthesis of complex biomolecules. Methods for the permeabilization of cells are thoroughly reviewed. We provide an extended review of useful available databases and bioinformatics tools, particularly for setting up genome-scale reconstructed networks. Examples described include phosphorylated carbohydrates, sugar nucleotides, and polyketides.

Heterologous gene expression and functional analysis of a type III polyketide synthase from Aspergillus niger NRRL 328

Type III polyketide synthases (PKSs) catalyze the formation of pyrone- and resorcinol-types aromatic polyketides. The genomic analysis of the filamentous fungus Aspergillus niger NRRL 328 revealed that this strain has a putative gene (chr_8_2: 2978617-2979847) encoding a type III PKS, although its functions are unknown. In this study, for functional analysis of this putative type III PKS designated as An-CsyA, cloning and heterologous expression of the An-CsyA gene (An-csyA) in Escherichia coli were performed. Recombinant His-tagged An-CsyA was successfully expressed in E. coli BL21 (DE3), purified by Ni(2+)-affinity chromatography, and used for in vitro assay. Tests on the substrate specificity of the His-tagged An-CsyA with myriad acyl-CoAs as starter substrates and malonyl-CoA as extender substrate showed that His-tagged An-CsyA accepted fatty acyl-CoAs (C2-C14) and produced triketide pyrones (C2-C14), tetraketide pyrones (C2-C10), and pentaketide resorcinols (C10-C14). Furthermore, acetoacetyl-CoA, malonyl-CoA, isobutyryl-CoA, and benzoyl-CoA were also accepted as starter substrates, and both of triketide pyrones and tetraketide pyrones were produced. It is noteworthy that the His-tagged An-CsyA produced polyketides from malonyl-CoA as starter and extender substrates and produced tetraketide pyrones from short-chain fatty acyl-CoAs as starter substrates. Therefore, this is the first report showing the functional properties of An-CsyA different from those of other fungal type III PKSs.

Molecular genetics of naringenin biosynthesis, a typical plant secondary metabolite produced by Streptomyces clavuligerus

Background

Some types of flavonoid intermediates seemed to be restricted to plants. Naringenin is a typical plant metabolite, that has never been reported to be produced in prokariotes. Naringenin is formed by the action of a chalcone synthase using as starter 4-coumaroyl-CoA, which in dicotyledonous plants derives from phenylalanine by the action of a phenylalanine ammonia lyase.

Results

A compound produced by Streptomyces clavuligerus has been identified by LC–MS and NMR as naringenin and coelutes in HPLC with a naringenin standard. Genome mining of S. clavuligerus revealed the presence of a gene for a chalcone synthase (ncs), side by side to a gene encoding a P450 cytochrome (ncyP) and separated from a gene encoding a Pal/Tal ammonia lyase (tal). Deletion of any of these genes results in naringenin non producer mutants. Complementation with the deleted gene restores naringenin production in the transformants. Furthermore, naringenin production increases in cultures supplemented with phenylalanine or tyrosine.

Conclusion

This is the first time that naringenin is reported to be produced naturally in a prokariote. Interestingly three non-clustered genes are involved in naringenin production, which is unusual for secondary metabolites. A tentative pathway for naringenin biosynthesis has been proposed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0373-7) contains supplementary material, which is available to authorized users.

Expanding the chemical space of polyketides through structure-guided mutagenesis of Vitis vinifera stilbene synthase

Several natural polyketides (PKs) have been associated with important pharmaceutical properties. Type III polyketide synthases (PKS) that generate aromatic PK polyketides have been studied extensively for their substrate promiscuity and product diversity. Stilbene synthase-like (STS) enzymes are unique in the type III PKS class as they possess a hydrogen bonding network, furnishing them with thioesterase-like properties, resulting in aldol condensation of the polyketide intermediates formed. Chalcone synthases (CHS) in contrast, lack this hydrogen-bonding network, resulting primarily in the Claisen condensation of the polyketide intermediates formed. We have attempted to expand the chemical space of this interesting class of compounds generated by creating structure-guided mutants of Vitis vinifera STS. Further, we have utilized a previously established workflow to quickly compare the wild-type reaction products to those generated by the mutants and identify novel PKs formed by using XCMS analysis of LC-MS and LC-MS/MS data. Based on this approach, we were able to generate 15 previously unreported PK molecules by exploring the substrate promiscuity of the wild-type enzyme and all mutants using unnatural substrates. These structures were specific to STSs and cannot be formed by their closely related CHS-like counterparts.

Tandem expression in E. coli of type III PKS and P450 genes from marine Streptomyces olivaceus FXJ 7.023 gives production of phenol and indole

The draft genome sequence of marine Streptomyces olivaceus strain FXJ 7.023 contains a cryptic Type III polyketide synthase (type III PKS) gene cluster, which is similar to the Streptomyces coelicolor THN biosynthesis gene cluster. A putative type III PKS (SoRppA) gene and its adjacent gene for cytochrome P450 158A2 (SoCYP158A2) of this gene cluster were cloned by PCR screening through a fosmid genomic library of S. olivaceus FXJ 7.023. Tandem expression of SoRppA and SoCYP158A2 in Escherichia coli strain BL21 (DE3) plysS resulted in obvious biosynthesis of phenol and indole, while heterologous expression of SoRppA or SoCYP158A2 alone did not. The engineered strain sorppAcyp158a2BL21 showed tolerance to phenol concentration up to 0.75 g/L. Continuous biosynthesis of phenol and indole by the immobilized engineered strain on macroporousresin was achieved, and the productivities of phenol and indole in extractant-free culture in 102 h were 0.08 and 1.525 g/L/h, respectively, with the highest production reached 0.67 and 14.48 g/L, respectively. These results suggest that the engineered strain and immobilized continuous fermentation process may provide potential for "green" production of phenol and indole.

Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase

A novel C17 resorcylic acid was synthesized by a structure-guided Vitis vinifera stilbene synthase (STS) mutant, in which threonine 197 was replaced with glycine (T197G). Altering the architecture of the coumaroyl binding and cyclization pocket of the enzyme led to the attachment of an extra acetyl unit, derived from malonyl-CoA, to p-coumaroyl-CoA. The resulting novel pentaketide can be produced strictly by STS-like enzymes and not by Chalcone synthase-like type III polyketide synthases; due to the unique thioesterase like activity of STS-like enzymes. We utilized a liquid chromatography mass spectrometry-based data analysis approach to directly compare the reaction products of the mutant and wild type STS. The findings suggest an easy to employ platform for precursor-directed biosynthesis and identification of unnatural polyketides by structure-guided mutation of STS-like enzymes.

Effects of exogenous nutrients on polyketide biosynthesis in Escherichia coli

Heterologous hosts are important platforms for engineering natural product biosynthesis. Escherichia coli is such a host widely used for expression of various biosynthetic enzymes. While numerous studies have been focused on optimizing the expression conditions for desired functional proteins, this work describes how supplement of exogenous nutrients into the fermentation broth influences the formation of natural products in E. coli. A type III polyketide synthase gene stts from Streptomyces toxytricini NRRL 15443 was heterogeneously expressed in E. coli BL21(DE3). This enzyme uses five units of malonyl-CoA to generate a polyketide 1,3,6,8-tetrahydroxynaphthalene, which can be spontaneously oxidized into a red compound flaviolin. In this work, we manipulated the fermentation broth of E. coli BL21(DE3)/pET28a-stts by supplying different nutrients including glucose and sodium pyruvate at different concentrations, from which six flaviolin derivatives 1-6 were produced. While addition of glucose yielded the production of 1-4, supplement of sodium pyruvate into the induced broth of E. coli BL21(DE3)/pET28a-stts resulted in the synthesis of 5 and 6, suggesting that different nutrients may enable E. coli to generate different metabolites. These products were purified and structurally characterized based on the spectral data, among which 2-6 are novel compounds. These molecules were formed through addition of different moieties such as acetone and indole to the flaviolin scaffold. The concentrations of glucose and sodium pyruvate and incubation time affect the product profiles. This work demonstrates that supplement of nutrients can link certain intracellular metabolites to the engineered biosynthetic pathway to yield new products. It provides a new approach to biosynthesizing novel molecules in the commonly used heterologous host E. coli.

Production of specialized metabolites by Streptomyces coelicolor A3(2)

The actinomycetes are well-known bioactive natural product producers, comprising the Streptomycetes, the richest drug-prolific family in all kingdoms, producing therapeutic compounds for the areas of infection, cancer, circulation, and immunity. Completion and annotation of many actinomycete genomes has highlighted further how proficient these bacteria are in specialized metabolism, which have been largely underexploited in traditional screening programs. The genome sequence of the model strain Streptomyces coelicolor A3(2), and subsequent development of genomics-driven approaches to understand its large specialized metabolome, has been key in unlocking the high potential of specialized metabolites for natural product genomics-based drug discovery. This review discusses systematically the biochemistry and genetics of each of the specialized metabolites of S. coelicolor and describes metabolite transport processes for excretion and complex regulatory patterns controlling biosynthesis.

One-pot enzymatic synthesis of merochlorin A and B

The polycycles merochlorin A and B are complex halogenated meroterpenoid natural products with significant antibacterial activities and are produced by the marine bacterium Streptomyces sp. strain CNH-189. Heterologously produced enzymes and chemical synthesis are employed herein to fully reconstitute the merochlorin biosynthesis in vitro. The interplay of a dedicated type III polyketide synthase, a prenyl diphosphate synthase, and an aromatic prenyltransferase allow formation of a highly unusual aromatic polyketide-terpene hybrid intermediate which features an unprecedented branched sesquiterpene moiety from isosesquilavandulyl diphosphate. As supported by in vivo experiments, this precursor is furthermore chlorinated and cyclized to merochlorin A and isomeric merochlorin B by a single vanadium-dependent haloperoxidase, thus completing the remarkably efficient pathway.

Alkyldihydropyrones, new polyketides synthesized by a type III polyketide synthase from Streptomyces reveromyceticus

Genome sequencing allows a rapid and efficient identification of novel catalysts that produce novel secondary metabolites. Here we describe the catalytic properties of dihydropyrone synthase A (DpyA), a novel type III polyketide synthase encoded in a linear plasmid of Streptomyces reveromyceticus. Heterologous expression of dpyA led to the accumulation of alkyldihydropyrones A (1), B (2), C (3) and D (4), which are novel dihydropyran compounds that exhibit weak cytotoxicity against the leukemia cell line HL-60. DpyA catalyzes the condensation of β-hydroxyl acid thioester and methylmalonyl-CoA to yield a triketide intermediate that then undergoes lactonization of a secondary alcohol and a thioester to give alkyldihydropyrone.

Aspergillus oryzae CsyB catalyzes the condensation of two β-ketoacyl-CoAs to form 3-acetyl-4-hydroxy-6-alkyl-α-pyrone

The type III polyketide synthases from fungi produce a variety of secondary metabolites including pyrones, resorcinols, and resorcylic acids. We previously reported that CsyB from Aspergillus oryzae forms α-pyrone csypyrone B compounds when expressed in A. oryzae. Feeding experiments of labeled acetates indicated that a fatty acyl starter is involved in the reaction catalyzed by CsyB. Here we report the in vivo and in vitro reconstitution analysis of CsyB. When CsyB was expressed in Escherichia coli, we observed the production of 3-acetyl-4-hydroxy-α-pyrones with saturated or unsaturated straight aliphatic chains of C9-C17 in length at the 6 position. Subsequent in vitro analysis using recombinant CsyB revealed that CsyB could accept butyryl-CoA as a starter substrate and malonyl-CoA and acetoacetyl-CoA as extender substrates to form 3-acetyl-4-hydroxy-6-propyl-α-pyrone. CsyB also afforded dehydroacetic acid from two molecules of acetoacetyl-CoA. Furthermore, synthetic N-acetylcysteamine thioester of β-ketohexanoic acid was converted to 3-butanoyl-4-hydroxy-6-propyl-α-pyrone by CsyB. These results therefore confirmed that CsyB catalyzed the synthesis of β-ketoacyl-CoA from the reaction of the starter fatty acyl CoA thioesters with malonyl-CoA as the extender through decarboxylative condensation and further coupling with acetoacetyl-CoA to form 3-acetyl-4-hydroxy-6-alkyl-α-pyrone. CsyB is the first type III polyketide synthase that synthesizes 3-acetyl-4-hydroxy-6-alkyl-α-pyrone by catalyzed the coupling of two β-ketoacyl-CoAs.

Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences

To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.

Preparative thin-layer chromatographic separation followed by identification of antifungal compound in Cassia laevigata by RP-HPLC and GC-MS

BACKGROUND

Several species of the genus Cassia are known for their antioxidant, antimicrobial and antidiabetic activities, but some of the lesser-known Cassia species, e.g. C. renigera, C. biflora and C. laevigata have not been studied for their biological activities.

RESULTS

Methanol extract of C. laevigata was fractionated by preparative thin-layer chromatography. The resulting six different fractions were tested against Fusarium oxysporum and Aspergillus niger for their antifungal activity. Due to higher antifungal activity of fraction 1 of C. laevigata, this was further analyzed by reversed-phase high-performance liquid chromatography (RP-HPLC), resulting in distinct separation of one compound at a retention time of 7.2 min with an absorbance of 252 nm. Further, this compound was analyzed by gas chromatography-mass spectrometry (GC-MS) for its putative structural identification. Mass spectra of this compound resembled the spectra of anthraquinone 1-carboxylic acid by NIST library search. The genomic-level expression of chalcone synthase, a key enzyme involved in the biosynthesis of polyketides, was increased in C. laevigata when compared to other Cassia species.

CONCLUSIONS

This study provides an insight into the higher antifungal activity of C. laevigata, including the identification of anthraquinone 1-carboxylic acid, which may be responsible for the antifungal activity.

Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways

Streptomyces, and related genera of Actinobacteria, are renowned for their ability to produce antibiotics and other bioactive natural products with a wide range of applications in medicine and agriculture. Streptomyces coelicolor A3(2) is a model organism that has been used for more than five decades to study the genetic and biochemical basis for the production of bioactive metabolites. In 2002, the complete genome sequence of S. coelicolor was published. This greatly accelerated progress in understanding the biosynthesis of metabolites known or suspected to be produced by S. coelicolor and revealed that streptomycetes have far greater potential to produce bioactive natural products than suggested by classical bioassay-guided isolation studies. In this article, efforts to exploit the S. coelicolor genome sequence for the discovery of novel natural products and biosynthetic pathways are summarized.

Subcellular localization of dinoflagellate polyketide synthases and fatty acid synthase activity

Dinoflagellates are prolific producers of polyketide secondary metabolites. Dinoflagellate polyketide synthases (PKSs) have sequence similarity to Type I PKSs, megasynthases that encode all catalytic domains on a single polypeptide. However, in dinoflagellate PKSs identified to date, each catalytic domain resides on a separate transcript, suggesting multiprotein complexes similar to Type II PKSs. Here, we provide evidence through coimmunoprecipitation that single-domain ketosynthase and ketoreductase proteins interact, suggesting a predicted multiprotein complex. In Karenia brevis (C.C. Davis) Gert Hansen & Ø. Moestrup, previously observed chloroplast localization of PKSs suggested that brevetoxin biosynthesis may take place in the chloroplast. Here, we report that PKSs are present in both cytosol and chloroplast. Furthermore, brevetoxin is not present in isolated chloroplasts, raising the question of what chloroplast-localized PKS enzymes might be doing. Antibodies to K. brevis PKSs recognize cytosolic and chloroplast proteins in Ostreopsis cf. ovata Fukuyo, and Coolia monotis Meunier, which produce different suites of polyketide toxins, suggesting that these PKSs may share common pathways. Since PKSs are closely related to fatty acid synthases (FAS), we sought to determine if fatty acid biosynthesis colocalizes with either chloroplast or cytosolic PKSs. [(3) H]acetate labeling showed fatty acids are synthesized in the cytosol, with little incorporation in chloroplasts, consistent with a Type I FAS system. However, although 29 sequences in a K. brevis expressed sequence tag database have similarity (BLASTx e-value <10(-10) ) to PKSs, no transcripts for either Type I (cytosolic) or Type II (chloroplast) FAS are present. Further characterization of the FAS complexes may help to elucidate the functions of the PKS enzymes identified in dinoflagellates.

Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways

Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.

Engineering microbial cells for the biosynthesis of natural compounds of pharmaceutical significance

Microbes constitute important platforms for the biosynthesis of numerous molecules of pharmaceutical interest such as antitumor, anticancer, antiviral, antihypertensive, antiparasitic, antioxidant, immunological agents, and antibiotics as well as hormones, belonging to various chemical families, for instance, terpenoids, alkaloids, polyphenols, polyketides, amines, and proteins. Engineering microbial factories offers rich opportunities for the production of natural products that are too complex for cost-effective chemical synthesis and whose extraction from their originating plants needs the use of many solvents. Recent progresses that have been made since the millennium beginning with metabolic engineering of microorganisms for the biosynthesis of natural products of pharmaceutical significance will be reviewed.

Engineering microbes for plant polyketide biosynthesis

Polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. Polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type I, type II or type III polyketide synthases (PKSs). Plant type III PKS enzymes, which will be the main focus of this review, are relatively small homodimeric proteins that catalyze iterative decarboxylative condensations of malonyl units with a CoA-linked starter molecule. This review will describe the plant type III polyketide synthetic pathway, including the synthesis of chalcones, stilbenes and curcuminoids, as well as recent work on the synthesis of these polyketides in heterologous organisms. The limitations and bottlenecks of heterologous expression as well as attempts at creating diversity through the synthesis of novel “unnatural” polyketides using type III PKSs will also be discussed. Although synthetic production of plant polyketides is still in its infancy, their potential as useful bioactive compounds makes them an extremely interesting area of study.

The evolution of phenylpropanoid metabolism in the green lineage

Phenolic secondary metabolites are only produced by plants wherein they play important roles in both biotic and abiotic defense in seed plants as well as being potentially important bioactive compounds with both nutritional and medicinal benefits reported for animals and humans as a consequence of their potent antioxidant activity. During the long evolutionary period in which plants have adapted to the environmental niches in which they exist (and especially during the evolution of land plants from their aquatic algal ancestors), several strategies such as gene duplication and convergent evolution have contributed to the evolution of this pathway. In this respect, diversity and redundancy of several key genes of phenolic secondary metabolism such as polyketide synthases, cytochrome P450s, Fe(2+)/2-oxoglutarate-dependent dioxygenases and UDP-glycosyltransferases have played an essential role. Recent technical developments allowing affordable whole genome sequencing as well as a better inventory of species-by-species chemical diversity have resulted in a dramatic increase in the number of tools we have to assess how these pathways evolved. In parallel, reverse genetics combined with detailed molecular phenotyping is allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. In this review, phenolic metabolite-related gene sequences (for a total of 65 gene families including shikimate biosynthetic genes) are compared across 23 independent species, and the phenolic metabolic complement of various plant species are compared with one another, in attempt to better understand the evolution of diversity in this crucial pathway.

Draft genome sequence of high-melanin-yielding Aeromonas media strain WS

We sequenced the genome of the high-melanin-yielding Aeromonas media strain WS and then analyzed genes potentially involved in melanin formation. The 4.2-Mb draft genome carries multiple genes responsible for pyomelanin synthesis and other candidate genes identified in our separate study, which have no homolog in other strains of Aeromonas species.

Molecular mechanism of manipulating seed coat coloration in oilseed Brassica species

Yellow seed is a desirable characteristic for the breeding of oilseed Brassica crops, but the manifestation of seed coat color is very intricate due to the involvement of various pigments, the main components of which are flavonols, proanthocyanidin (condensed tannin), and maybe some other phenolic relatives, like lignin and melanin. The focus of this review is to examine the genetics mechanism regarding the biosynthesis and regulation of these pigments in the seed coat of oilseed Brassica. This knowledge came largely from recent researches on the molecular mechanism of TRANSPARENT TESTA (tt) and similar mutations in the ancestry model plant of Brassica, Arabidopsis. Some key enzymes in the flavonoid (flavonols and proanthocyanidin) biosynthetic pathway have been characterized in tt mutants. Some orthologs to these TRANSPARENT TESTA genes have also been cloned in Brassica species. However, it is suggested that some alterative metabolism pathways, including lignin and melanin, might also be involved in seed color manifestation. Polyphenol oxidases, such as laccase, tyrosinase, or even peroxidase, participate in the oxidation step in proanthocyanidin, lignin, and melanin biosynthesis. Moreover, some researches also suggested that melanic pigment in black-seeded Brassica was several fold higher than in yellow-seeded Brassica. Although more experiments are required to evaluate the importance of lignin and melanin in seed coat browning, the current results suggest that the flavonols and proanthocyanidin are not the only roles affecting seed color.

Merochlorins A-D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases

Meroterpenoids are mixed polyketide-terpenoid natural products with a broad range of biological activities. Herein, we present the structures of four new meroterpenoid antibiotics, merochlorins A-D, produced by the marine bacterium Streptomyces sp. strain CNH-189, which possess novel chemical skeletons unrelated to known bacterial agents. Draft genome sequencing, mutagenesis, and heterologous biosynthesis in the genome-minimized model actinomycete Streptomyces coelicolor provided the 57.6 kb merochlorin gene cluster that contains two genes encoding rare bacterial vanadium-dependent haloperoxidase (VHPO) genes. Pathway expression of two different fosmid clones that differ largely by the presence or absence of the VHPO gene mcl40 resulted in the differential biosynthesis of merochlorin C, suggesting that Mcl40 catalyzes an unprecedented 15-membered chloronium-induced macrocyclization reaction converting merochlorin D to merochlorin C.

The O-methyltransferase SrsB catalyzes the decarboxylative methylation of alkylresorcylic acid during phenolic lipid biosynthesis by Streptomyces griseus

Streptomyces griseus contains the srs operon, which is required for phenolic lipid biosynthesis. The operon consists of srsA, srsB, and srsC, which encode a type III polyketide synthase, an O-methyltransferase, and a flavoprotein hydroxylase, respectively. We previously reported that the recombinant SrsA protein synthesized 3-(13'-methyltetradecyl)-4-methylresorcinol, using iso-C(16) fatty acyl-coenzyme A (CoA) as a starter substrate and malonyl-CoA and methylmalonyl-CoA as extender substrates. An in vitro SrsA reaction using [(13)C(3)]malonyl-CoA confirmed that the order of extender substrate condensation was methylmalonyl-CoA, followed by two extensions with malonyl-CoA. Furthermore, SrsA was revealed to produce an alkylresorcylic acid as its direct product rather than an alkylresorcinol. The functional SrsB protein was produced in the membrane fraction in Streptomyces lividans and used for the in vitro SrsB reaction. When the SrsA reaction was coupled, SrsB produced alkylresorcinol methyl ether in the presence of S-adenosyl-l-methionine (SAM). SrsB was incapable of catalyzing the O-methylation of alkylresorcinol, indicating that alkylresorcylic acid was the substrate of SrsB and that SrsB catalyzed the conversion of alkylresorcylic acid to alkylresorcinol methyl ether, namely, by both the O-methylation of the hydroxyl group (C-6) and the decarboxylation of the neighboring carboxyl group (C-1). O-methylated alkylresorcylic acid was not detected in the in vitro SrsAB reaction, although it was presumably stable, indicating that O-methylation did not precede decarboxylation. We therefore postulated that O-methylation was coupled with decarboxylation and proposed that SrsB catalyzed the feasible SAM-dependent decarboxylative methylation of alkylresorcylic acid. To the best of our knowledge, this is the first report of a methyltransferase that catalyzes decarboxylative methylation.

Biochemical characterization of a type III polyketide biosynthetic gene cluster from Streptomyces toxytricini

A type III polyketide biosynthetic gene cluster has been discovered in the industrially important strain Streptomyces toxytricini NRRL 15443, including four genes stp450-1, stts, stp450-2, and stmo. The stts gene encodes a putative type III polyketide synthase that is homologous to RppA, a 1,3,6,8-tetrahydroxynaphthalene (THN) synthase from Streptomyces griseus. The deduced protein product of stmo resembles the cupin-containing monooxygenase MomA from Streptomyces antibioticus that oxidizes THN into flaviolin. Two cytochrome P450s (CYPs), StP450-1 and StP450-2, are present in the gene cluster. StTS was overexpressed in Escherichia coli BL21(DE3) and identified as a THN synthase. The synthesized THN can be easily oxidized into flaviolin by air. Both CYPs were reconstituted in E. coli BL21(DE3) and can oxidize flaviolin to form oligomers. The k(cat)/K(m) values for StP450-1 and StP450-2 were 0.28 and 0.71 min⁻¹ mM⁻¹, respectively. UV irradiation test showed that expression of StTS in E. coli BL21(DE3) significantly protects the cells from UV radiation, and coexpression of StTS and StP450-1 provides even stronger protection.

Biosynthesis of phloroglucinol compounds in microorganisms--review

Phloroglucinol derivatives are a major class of secondary metabolites of wide occurrence in biological systems. In the bacteria kingdom, these compounds can only be synthesized by some species of Pseudomonads. Pseudomonas spp. could produce 2,4-diacetylphloroglucinol (DAPG) that plays an important role in the biological control of many plant pathogens. In this review, we summarize knowledge about synthesis of phloroglucinol compounds based on the DAPG biosynthetic pathway. Recent advances that have been made in understanding phloroglucinol compound biosynthesis and regulation are highlighted. From these studies, researchers have identified the biosynthesis pathway of DAPG. Most of the genes involved in the biosynthesis pathway have been cloned and characterized. Additionally, heterologous systems of the model microorganism Escherichia coli are constructed to produce phloroglucinol. Although further work is still required, a full understanding of phloroglucinol compound biosynthesis is almost within reach. This review also suggests new directions and attempts to gain some insights for better understanding of the biosynthesis and regulation of DAPG. The combination of traditional biochemistry and molecular biology with new systems biology and synthetic biology tools will provide a better view of phloroglucinol compound biosynthesis and a greater potential of microbial production.

Cloning and characterization of a type III polyketide synthase from Aspergillus niger

Type III polyketide synthases (PKSs) are the condensing enzymes that catalyze the formation of a myriad of aromatic polyketides in plant, bacteria, and fungi. Here we report the cloning and characterization of a putative type III PKS from Aspergillusniger, AnPKS. This enzyme catalyzes the synthesis of alkyl pyrones from C2 to C18 starter CoA thioesters with malonyl-CoA as an extender CoA through decaboxylative condensation and cyclization. It displays broad substrate specificity toward fatty acyl-CoA starters to yield triketide and tetraketide pyrones, with benzoyl-CoA as the most preferred starter. The optimal temperature and pH of AnPKS are 50°C and 8, respectively. Under optimal conditions, the enzyme shows the highest catalytic efficiency (k(cat)/K(m)) of 7.4×10(5)s(-1)M(-1) toward benzoyl-CoA. Homology modeling and site-directed mutagenesis were used to probe the molecular basis of its substrate specificity. This study should open doors for further engineering of AnPKS as a biocatalyst for synthesis of value-added polyketides.

Fatty acyl-AMP ligases and polyketide synthases are unique enzymes of lipid biosynthetic machinery in Mycobacterium tuberculosis

The cell envelope of Mycobacterium tuberculosis (Mtb) possesses a repertoire of unusual lipids that are believed to play an important role in pathogenesis. In this review, we specifically focus on computational, biochemical and structural studies in lipid biosynthesis that have established functional role of polyketide synthases (PKSs) and fatty acyl-AMP ligases (FAALs). Mechanistic and structural studies with FAALs suggest that this group of proteins may have evolved from omnipresent fatty acyl-CoA ligases (FACLs). FAALs activate fatty acids as acyl-adenylates and transfer them on to the PKSs which then produce unusual acyl chains that are the components of mycobacterial lipids. FAALs are a newly discovered family of enzymes; whereas involvement of PKSs in lipid metabolism was not known prior to their discovery in Mtb. Since Mtb genome contains multiple homologs of FAALs and PKSs and owing to the conserved reaction mechanism and overlapping substrate specificity; there is tempting opportunity to develop 'systemic drugs' against these enzymes as anti-tuberculosis agents.

Engineered biosynthesis of plant polyketides: structure-based and precursor-directed approach

Pentaketide chromone synthase (PCS) and octaketide synthase (OKS) are novel plant-specific type III polyketide synthases (PKSs) obtained from Aloe arborescens. Recombinant PCS expressed in Escherichia coli catalyzes iterative condensations of five molecules of malonyl-CoA to produce a pentaketide 5,7-dihydroxy-2-methylchromone, while recombinant OKS carries out sequential condensations of eight molecules of malonyl-CoA to yield octaketides SEK4 and SEK4b, the longest polyketides produced by the structurally simple type III PKS. The amino acid sequences of PCS and OKS are 91% identical, sharing 50-60% identity with those of other chalcone synthase (CHS) superfamily type III PKSs of plant origin. One of the most characteristic features is that the conserved active-site Thr197 of CHS (numbering in Medicago sativa CHS) is uniquely replaced with Met207 in PCS and with Gly207 in OKS, respectively. Site-directed mutagenesis and X-ray crystallographic analyses demonstrated that the chemically inert single residue lining the active-site cavity controls the polyketide chain length and the product specificity depending on the steric bulk of the side chain. On the basis of the crystal structures, an F80A/Y82A/M207G triple mutant of the pentaketide-producing PCS was constructed and shown to catalyze condensations of nine molecules of malonyl-CoA to produce an unnatural novel nonaketide naphthopyrone, whereas an N222G mutant of the octaketides-producing OKS yielded a decaketide benzophenone SEK15 from ten molecules of malonyl-CoA. On the other hand, the type III PKSs exhibited broad substrate specificities and catalytic potential. OKS accepted p-coumaroyl-CoA as a starter substrate to produce an unnatural novel C19 hexaketide stilbene and a C21 heptaketide chalcone. Remarkably, the C21 chalcone-forming activity was dramatically increased in the structure-guided OKS N222G mutant. In addition, OKS N222G mutant also yielded unnatural novel polyketides from phenylacetyl-CoA and benzoyl-CoA as a starter substrate. These results suggested that the engineered biosynthesis of plant polyketides by combination of the structure-based and the precursor-directed approach would lead to further production of chemically and structurally divergent unnatural novel polyketides.

Convergent strategies in biosynthesis

This review article focuses on how nature sometimes solves the same problem in the biosynthesis of small molecules but using very different approaches. Four examples, involving isopentenyl diphosphate, menaquinone, lysine, and aromatic polyketides, are highlighted that represent different strategies in convergent metabolism.

Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products

Furaquinocin is a natural polyketide-isoprenoid hybrid (meroterpenoid) that exhibits antitumor activity and is produced by the Streptomyces sp. strain KO-3988. Bioinformatic analysis of furaquinocin biosynthesis has identified Fur7 as a possible prenyltransferase that attaches a geranyl group to an unidentified polyketide scaffold. Here, we report the identification of a physiological polyketide substrate for Fur7, as well as its reaction product and the biochemical characterization of Fur7. A Streptomyces albus transformant (S. albus/pWHM-Fur2_del7) harboring the furaquinocin biosynthetic gene cluster lacking the fur7 gene did not produce furaquinocin but synthesized the novel intermediate 2-methoxy-3-methyl-flaviolin. After expression and purification from Escherichia coli, the recombinant Fur7 enzyme catalyzed the transfer of a geranyl group to 2-methoxy-3-methyl-flaviolin to yield 6-prenyl-2-methoxy-3-methyl-flaviolin and 7-O-geranyl-2-methoxy-3-methyl-flaviolin in a 10:1 ratio. The reaction proceeded independently of divalent cations. When 6-prenyl-2-methoxy-3-methyl-flaviolin was added to the culture medium of S. albus/pWHM-Fur2_del7, furaquinocin production was restored. The promiscuous substrate specificity of Fur7 was demonstrated with respect to prenyl acceptor substrates and prenyl donor substrates. The steady-state kinetic constants of Fur7 with each prenyl acceptor substrate were also calculated.

Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway

Acetoacetyl-CoA is the precursor of 3-hydroxy-3-methylglutaryl (HMG)-CoA in the mevalonate pathway, which is essential for terpenoid backbone biosynthesis. Acetoacetyl-CoA is also the precursor of poly-beta-hydroxybutyrate, a polymer belonging to the polyester class produced by microorganisms. The de novo synthesis of acetoacetyl-CoA is usually catalyzed by acetoacetyl-CoA thiolase via a thioester-dependent Claisen condensation reaction between two molecules of acetyl-CoA. Here, we report that nphT7, found in the mevalonate pathway gene cluster from a soil-isolated Streptomyces sp. strain, encodes an unusual acetoacetyl-CoA synthesizing enzyme. The recombinant enzyme overexpressed in Escherichia coli catalyzes a single condensation of acetyl-CoA and malonyl-CoA to give acetoacetyl-CoA and CoA. Replacement of malonyl-CoA with malonyl-(acyl carrier protein) resulted in loss of the condensation activity. No acetoacetyl-CoA synthesizing activity was detected through the condensation of two molecules of acetyl-CoA. Based on these properties of NphT7, we propose to name this unusual enzyme of the thiolase superfamily acetoacetyl-CoA synthase. Coexpression of nphT7 with the HMG-CoA synthase gene and the HMG-CoA reductase gene in a heterologous host allowed 3.5-fold higher production of mevalonate than when only the HMG-CoA synthase and HMG-CoA reductase genes were expressed. This result suggests that nphT7 can be used to significantly increase the concentration of acetoacetyl-CoA in cells, eventually leading to the production of useful terpenoids and poly-beta-hydroxybutyrate.