Although exploitation of this mechanistic variability has produced novel polyketides, the structural foundation of this versatility is unclear. Domain organization and active site architecture of a. Structural biochemistrypolyketide synthases wikibooks. Computational identification and analysis of orphan.
This in turn facilitated rapid cloning and sequencing of. Methods for the detection of novel polyketide synthase pathways in. Nearly a quartercentury ago, the advent of molecular genetic tools in the field of natural product biosynthesis led to the remarkable revelation that the genes responsible for the biosynthesis, regulation, and selfresistance of complex polyketide antibiotics were clustered in the genomes of the bacteria that produced these compounds. Engineering a polyketide synthase for in vitro production. With the current advances in nmr instrumentation, software, and pulse. Acyltransferases as tools for polyketide synthase engineering. The structural enzymology of iterative aromatic polyketide. Palmitic acid is an example of a polyketide since it is formed by the condensation of one acetylcoa primer and seven malonylcoa extender units. Exploiting the biosynthetic potential of type iii polyketide synthases. Chalcone synthase like proteins are comparatively small proteins with a single polypeptide chain and. The origins of specificity in polyketide synthase protein interactions. Descriptors are arranged in a hierarchical structure, which enables searching at various levels of specificity. Khosla describes the modular enzymes that synthesize these antibiotics, with each module adding to a growing polyketide. Methods for the detection of novel polyketide synthase pathways.
Recent progress in the understanding of polyketide synthase pks continues to fuel the growth of. The structures of type i polyketide synthases natural. Video shows the mechanism of action of a polyketide synthase module reported by a university of michigan research team. Structural insights into dehydratase substrate selection for the. Type 1 polyketide synthase extender units inventors michael thomas, jo handelsman, yolande chan, angela podevels since its founding in 1925 as the patenting and licensing organization for the university of wisconsinmadison, warf has been working with business and industry to transform university research into products that benefit society. When people speak of polyketides, they most often are talking about type i polyketides.
Polyketide synthases pkss are responsible for the synthesis of. Pkss to create a wide variety of polyketide natural products. Natural biocombinatorics in the polyketide synthase genes of. Llc, and flexible loop residues were built with the program coot. Insights into how bacterial polyketide synthases pkss acquire new metabolic capabilities can guide future laboratory. High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in penicillium marneffei patrick c. The polyketide chains produced by a minimal polyketide synthase are often further derivatized and modified into bioactive natural products palmitic acid is an example of a polyketide since it is formed by the condensation of one acetylcoa primer and seven malonylcoa extender units. A structurefunction approach in engineering novel antibiotics. Debs 6deoxyerythronolide b synthase is a type 1 polyketide synthase responsible for the production of the macrolide 6deoxyerythronolide b 6deb, a aglycone precursor of the antibiotic erythromycin. Polyketide biosynthesis beyond the type i, ii and iii polyketide synthase paradigms ben shen recent literature on polyketide biosynthesis suggests that polyketide synthases have much greater diversity in both mechanism and structure than the current type i, ii and iii. Nov 22, 2010 the apicomplexan cryptosporidium parvum genome possesses a 25kb intronless open reading frame orf that predicts a multifunctional type i fatty acid synthase cpfas1 with at least 21 enzymatic domains. Phylogenomic and functional domain analysis of polyketide.
Polyketide antibiotics include many of the most commonly used antibiotics in medicine today such as erythromycin, rapamycin and avermectin. High diversity of polyketide synthase genes and the melanin. Identification of potential genes involved in polyketide biosynthesis was achieved by text searching the annotations ketosynthase, pks, polyketide synthase, ketoreductases. Structures and mechanisms of polyketide synthases the. Dissecting the functional role of polyketide synthases in. Reconstitution of a type ii polyketide synthase that. Evolutionary and functional analysis of mulberry type iii. Polyketide synthases pkss are structurally and functionally related to fatty acid synthases fass, as both enzyme classes catalyzes the condensation of activated primary metabolites acetylcoa and malonylcoa to form bketoacetyl polymers linked to the enzyme by thioester bonds. The crystal structure and cryoelectron microscopy of the loadingcondensing region of a nonreducing polyketide synthase reveals the insertion of a starterunit acyltransferase into the condensing. The biosyntheses of polyketides share striking similarities with fatty acid biosynthesis. Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by large, multidomain enzyme complexes termed polyketide synthases pkss.
Structurefunction analysis of the extended conformation. Salinipyrone and pacificanone are biosynthetic byproducts of the rosamicin polyketide synthase takayoshi awakawa,a, b max crsemann, ajason munguia,c nadine ziemert, victor nizet,c, d william fenical,a and bradley s. This has hampered structural and mechanistic characterization of pks. Numerous polyketide natural products have been isolated from organisms whose genomes have yet to be sequenced. Figure 5 type iii polyketide synthases are responsible for the synthesis of chalcones and stilbenes in plants and polyhydroxy phenols in bacteria. For polyketide synthases pkss, a family of bacterial enzymes, such.
A series of 12 recombinants expressing sets of polyketide synthase pks genes from the whie streptomyces coelicolor, sch s. Type i modular polyketide synthases pkss are enzyme assembly. Type i polyketide synthases pkss are multifunctional enzymes that are organized into modules, each of which minimally contains a. She introduces the sources of natural products and presents the biosynthesis of the main classes nonribosomal peptides, plant terpenoids, polyketides in fungi, modular polyketide synthases, polyketide polyethers, alkaloids, cofactors, and antibiotics and their uses in pharmaceuticals, as anticancer agents, and in drug discovery. The need for new drugs for common diseases and new antibiotics in the face of resistance has grown, while the process used by these microorganisms to create these drugs has. This article is from beilstein journal of organic chemistry, volume 10. The software antismash examines microbial genome data to identify and analyze biosynthetic gene clusters for a wide range of natural products. Because albocycline is predicted to be produced by a pks comprised of six. The emergence of resistant strains of human pathogens to current antibiotics, along with the demonstrated ability of polyketides as antimicrobial agents, provides strong motivation for understanding how polyketide antibiotics have evolved and diversified in nature. One of the primary challenges when studying pkss is the high reactivity of their poly. Mycocerosic acid synthase mas is a mycobacterial polyketide synthase pks responsible for the biosynthesis of c 20 c 28 branchedchain. Exploiting the mosaic structure of trans acyltransferase.
The structural organization of substrate loading in iterative. Abstract herein, we describe the syntheses of a complex biosynthesisintermediate analogue of the potent antitumor polyketide borrelidin and of reference molecules to determine the stereoselectivity of the dehydratase of borrelidin polyketide synthase module 3. This enzyme catalyzes the condensation of malonyl coa and enzymebound acyl group to afford complex fatty. The metabolic origins of each of the currently known polyketide synthase extender units are covered. Identification of a polyketide synthase gene responsible. This structurally diverse class of compounds shares a common methodology of biosynthesis employing modular enzyme systems called polyketide synthases pkss. An oxetanebased polyketide surrogate to probe substrate. Polyketides are biosynthesized by polyketide synthases pkss, multienzyme complexes derived evolutionarily from fatty acid synthases fass. Further research also proved the polyketide origin of the rubromycins skeleton by feeding u c3malonic acid to the rubromycinproducing strain, streptomyces sp. Modular polyketide synthases pkss of bacteria provide an enormous reservoir of natural chemical diversity. The following cartoon depicts the hypothetical dynamic model of an aromatic polyketide synthase. Skiba ma, sikkema ap, fiers wd, gerwick wh, sherman dh, aldrich cc et al. Mar 03, 2008 gradients are used to create energy that can power biological cyles. Polyketide synthase products include lipids with antibiotic, antifungal, antitumor, and predatordefense properties.
Type iii polyketide synthases in natural product biosynthesis. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Polyketide synthases harvard catalyst profiles harvard. The ks domain in an iterative pks can recapture the growing polyketide chain after each round of condensation and terminate polyketide biosynthesis at a precise stage. Pdf structure of a modular polyketide synthase researchgate.
Reaction products of omt12 were resolved on reverse phase columns using a linear gradient of 5% ch 3 cn in h 2 o with 0. The polyketide derived secondary metabolite ascochitine is produced by species in the didymellaceae family, including but not restricted to ascochyta species pathogens of coolseason food legumes. The stereochemistry of complex polyketide biosynthesis. Mycocerosic acid synthase mas is a mycobacterial polyketide synthase pks responsible for the biosynthesis of c 20 c 28 branchedchain fatty acids, key components of the specialized. Advances in polyketide synthase structure and function.
Download typeiii polyketide synthase prediction for free. Moorea, d salinipyrones and pacificanones are structurally related poly. The structures are depicted in cartoon representation helices shown as cylinders. Crystal structure of the acyltransferase domain of the iterative polyketide synthase in enediyne biosynthesis. In a noniterative modular pks, each module is used only once, and the polyketide intermediate is transferred to a downstream module for chain elongation. The sequencestructurefunction relationship of polyketide biosynthesis, compared with. Ascochitine is structurally similar to the wellknown mycotoxin citrinin and exhibits broadspectrum phytotoxicity and antimicrobial activities. Type i polyketide synthases pksi are modular multidomain enzymes involved in the biosynthesis of many natural products of industrial interest.
An in vitro platform for engineering and harnessing modular. Type i modular polyketide synthasesare enzyme assembly lines for the. However, because most of the type ii pkss studied so far were cloned according to the type ii pks paradigm, caution has to be taken to generalize type ii pkss for aromatic polyketide biosynthesis in. Genome based analysis of typei polyketide synthase and. All the polyketide products were characterized using electrospray ionization mass spectrometry. Pksiiipred is the type iii polyketide synthase prediction server based on svm. While type ii polyketide synthases pkss are known for producing aromatic compounds, a phylogenetically new subfamily of type ii pkss have been recently. The polyketide chains produced by a minimal polyketide synthase are often further derivatized and modified into bioactive natural products. Structure and function of polyketide biosynthetic enzymes. Division of pharmaceutical sciences, college of pharmacy, university of kentucky, 725 rose street, lexington, ky 40536, usa. Overview of polyketides and polyketide biosynthesis youtube. Polyketide synthase, cyclases, and oxidoreductases genes were identified in the.
Pks activities and biosynthesis of cannabinoids and. The modules are composed of enzymatic domains that share sequence and functional similarity. Iterative type i polyketide synthases for enediyne core. Jun 18, 2014 polyketide synthases are multidomain enzymes that produce polyketides, which form the basis of many therapeutic agents. An analysis of these genes may provide new targets for genetic improvement to increase relevant secondary metabolites and enhance the plant tolerance to biotic and. Polyketide synthases, also known as pkss, are a family of enzymes or enzyme complexes that produce polyketides, a large class of secondary metabolites, in bacteria, fungi, plants, and animals. Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases pkss using acylcoa precursors. Users can submit their protein sequences in fasta format to predict whether the given protein sequence belongs to type iii polyketide synthase or not. The mycolactone side chain is synthesized by a third synthase, mlsb. A plant type iii polyketide synthase that produces. Biosynthesis of polyketide synthase extender units natural. Polyketides are a large class of bioactive natural products with a wide range of structures and functions.
The modules are composed of enzymatic domains that share sequence and. B cartoon ribbon representation and c domain illustration of the 3. Structure of a modular polyketide synthase ncbi nih. Assembly of complex structures from these simple building blocks is carried out by enzyme complexes known as polyketide synthases pkss. Computational identification and analysis of orphan assembly. Polyketide biosynthesis beyond the type i, ii and iii. Engineering strategies for rational polyketide synthase design. Pdf programmable polyketide biosynthesis platform for. It is commonly found in the actinomycete bacteria, saccharopolyspora erythraea. Crystal structure of the acyltransferase domain of the. Bioactive complex polyketides with diverse structure and function. Complex reduced polyketides represent the largest class of natural products that have applications in medicine, agriculture, and animal health.
Jul 09, 2019 large enzyme complexes composed of a number of component enzymes that are found in streptomyces which biosynthesize macrolides and other polyketides. A polyketide synthase peptide synthetase gene cluster from an uncultured bacterial symbiont of paederus. Here we present the synthesis of unnatural unique polyketide alkaloid hybrid molecules by exploiting the enzyme reaction using precursordirected and. Examples of multistep polyketide biosynthetic processes. Polyketide synthase an overview sciencedirect topics. Plantspecific pkss are essential for the biosynthesis of antimicrobial phytoalexins. Mycocerosic acid synthase exemplifies the architecture of. Phylogenomic and functional domain analysis of polyketide synthases in fusarium daren w. Structural control of polyketide formation in plant. Biochemistry of polyketide synthases biotechnology set. The methods described have been used to successfully characterize the enediynespecific iterative type i polyketide synthase pkse. Although the architecture of cpfas1 resembles those of bacterial polyketide synthases pkss, this megasynthase is predicted to function as a fatty acyl elongase as our earlier studies have.
The phylogenetic reconstruction was performed by means of the mrbayes software version 3. Following each condensation reaction, the new betaketo group may be reduced, dehydrated, and reduced again as. Hspks1 from huperzia serrata is a type iii polyketide synthase pks with remarkable substrate tolerance and catalytic potential. Polyketide synthases is a descriptor in the national library of medicines controlled vocabulary thesaurus, mesh medical subject headings. An introduction to polyketide assembly lines ibiology.
Proctora abacterial foodborne pathogens and mycology research, usdaarsncaur, 1815 n. Polyketide synthases pkss generate molecular diversity by utilizing different starter molecules and by controlling the final length of the polyketide. Atp synthase is powered by a hydrogen gradient, located in the mitochondria. Studying natural biocombinatorics may aid in the development of concepts for experimental design of genes for the biosynthesis of new bioactive compounds. It detects pks gene clusters producing known polyketides, which are included in the database, by measuring the homology between protein sequences of an annotated genome and all pks sequences, and predicts unknown gene clusters to produce putative polyketide candidates by identifying domains. The reductase domain in a type i fatty acid synthase from the. May 27, 2012 an overview of polyketides and their biosynthesis. Identification of a polyketide synthase required for. Asmpks searches microbial genome sequences for modular pkss. Clustercad is a webbased toolkit designed to leverage the collinear structure and deterministic logic of type i modular polyketide synthases pkss for synthetic biology applications.
Identification of a polyketide synthase required for alternariol aoh and alternariol9methyl ether ame formation in alternaria alternata debjani saha1, ramona fetzner1, britta burkhardt2, joachim podlech3, manfred metzler2, ha dang4, christopher lawrence4, reinhard fischer1 1department of microbiology, karlsruhe institute of technology kit south campus, institute for applied. Reconstitution of a type ii polyketide synthase that catalyzes polyene formation. Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents. Complex bacterial aromatic polyketides can be produced through nonreducing polyketide pathways, where twocarbon units ch2co, ketides are polymerized into linear polyketide chains of various lengths by multicomponent enzyme complexes known as polyketide synthase minimal pks, and then can be folded to form aromatic structures.
Polyketide synthase secrets revealed june 23, 2014 issue. Multimodular polyketide synthases pkss are enzymatic assembly lines responsible for the biosynthesis of many structurally and pharmacologically diverse antibiotics. Engineered polyketide synthases pkss are promising synthetic biology platforms. Here we address the question of how the modularity of biosynthetic enzymes and the prevalence of multiple gene clusters in. A robust platform to study modular polyketide synthases pkss in vitro is still unavailable.
Polyketide synthase pks enzymatic activities were analyzed in crude protein extracts from cannabis plant tissues. Apr 30, 2014 in the present work, we compared secondary metabolite biosynthesis gene clusters of typei polyketide synthase pksi and nonribosomal peptide synthetase nrps among genomes of representative nocardia speciesstrains based on domain organization and amino acid sequence homology. A novel plantspecific type iii polyketide synthase pks that catalyzes formation of a pentaketide chromone, 5,7dihydroxy2methylchromone, from five molecules of malonylcoa, was cloned and sequenced from aloe aloe arborescens. His lab uses assembly line polyketide synthases as a system to investigate the potential to program biosynthetic pathways to produce new and. Fungal polyketide synthase pks 286 is a large protein and consists of a single set of module containing a keto synthase ks, an acyltransferase at, a thioesteraseclaisen cyclase tecyc, and two acyl carrier protein acp domains. Mulberry plants have abundant polyphenols, but very little is known about the mulberry type iii polyketide synthase genes. Type i polyketide synthases may have evolved through. Synthetic biology of polyketide synthases springerlink. The j5 dna assembly design automation software 22 was utilized to. Animation of a minimal type i iterative pks in action powerpoint created by. Abstractusnea longissima has a long history of use as a traditional medicine. Polyketides are biosynthesized by plants, fungi, and bacteria from the stepwise condensation of short chain carboxylic acidderived units.
Polyketide synthase how is polyketide synthase abbreviated. The ks domain phylogeny of 23 pksi clusters was determined. Pksi modules are minimally organized in three domains. Software employed primary data reduction sastool sastool sastool. The unique sequence and domain architecture of the pkse has enabled a pcrbased screening method capable of rapidly identifying and classifying unknown pkses specific for either 9 or 10membered enediyne cores. Weissman kj, smith cj, hanefeld u, aggarwal r, bycroft m, staunton j, leadlay pf 1998b the thioesterase of the erythromycinproducing polyketide synthase. Type iii polyketide synthases are important for the biosynthesis of flavonoids and various plant polyphenols.
Polyketide synthases pkss are structurally and functionally related to fatty acid. The polyketide synthase genes responsible for mycolactone biosynthesis are encoded on a giant plasmid. Evolution of polyketide synthases in bacteria pnas. For the identification of ks and kr domains, these sequences were further analysed by pksnrps analysis software 58 and hmmer 59 using an inhouse developed hmm. Domain organization and active site architecture of a polyketide synthase cmethyltransferase.
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