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ACS Synthetic Biology Nov 2023Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS)... (Review)
Review
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
Topics: Polyketide Synthases; Polyketides
PubMed: 37871264
DOI: 10.1021/acssynbio.3c00282 -
Natural Product Reports Oct 2018Covering: mid 1990s to 2018 Over the last two decades, diverse approaches have been explored to generate new polyketides by engineering polyketide synthases (PKSs).... (Review)
Review
Covering: mid 1990s to 2018 Over the last two decades, diverse approaches have been explored to generate new polyketides by engineering polyketide synthases (PKSs). Although it has been proven possible to produce new compounds by designed PKSs, engineering strategies failed to make polyketides available via widely applicable rules and protocols. Still, organic synthetic routes have to be employed whenever new polyketides are needed for applications in medicine, agriculture, and industry. In light of the rising demand for commodity products from feedstock and for fast and cheap access to pharmaceutical compounds, the need for harnessing PKSs to produce such molecules is more urgent than ever before. In this review, we focus on a multitude of approaches to engineer modular PKSs by swapping and replacing PKS modules and domains, which we analyze in the light of recent structural and biochemical data. We conclude with an outlook on possible strategies on how to increase success rates of PKS engineering in future.
Topics: Polyketide Synthases; Protein Domains; Protein Engineering; Recombinant Proteins
PubMed: 29938731
DOI: 10.1039/c8np00030a -
Angewandte Chemie (International Ed. in... Apr 2017Modular redefinition: A long-standing paradigm in modular polyketide synthase enzymology, namely the definition of a module, has been challenged by Abe and co-workers in...
Modular redefinition: A long-standing paradigm in modular polyketide synthase enzymology, namely the definition of a module, has been challenged by Abe and co-workers in their recent study. With this new understanding has emerged renewed hope for engineering these assembly lines to produce new materials and medicines.
Topics: Acyl Carrier Protein; Acyltransferases; Animals; Bacteria; Biocatalysis; Computational Biology; Evolution, Molecular; Fatty Acid Synthases; Humans; Polyketide Synthases; Polyketides; Protein Domains; Protein Engineering; Substrate Specificity
PubMed: 28322495
DOI: 10.1002/anie.201701281 -
Chembiochem : a European Journal of... Apr 2021Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a... (Review)
Review
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
Topics: Bacteria; Bacterial Proteins; Kinetics; Mutagenesis, Site-Directed; NADP; Polyketide Synthases; Polyketides; Protein Domains; Substrate Specificity
PubMed: 33185924
DOI: 10.1002/cbic.202000613 -
Science (New York, N.Y.) Nov 2021Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide...
Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution cryo–electron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and condensation steps, respectively. These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase, Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time.
Topics: Acyl Carrier Protein; Acylation; Acyltransferases; Catalytic Domain; Cryoelectron Microscopy; Crystallography, X-Ray; Hydro-Lyases; Lasalocid; Models, Molecular; Polyketide Synthases; Protein Conformation; Protein Domains; Protein Multimerization; Streptomyces
PubMed: 34735234
DOI: 10.1126/science.abi8532 -
Natural Product Reports Nov 2018Covering: up to early 2018 Polyketides and nonribosomal peptides are two major families of natural product with a broad range of biological activities. Polyketide... (Review)
Review
Covering: up to early 2018 Polyketides and nonribosomal peptides are two major families of natural product with a broad range of biological activities. Polyketide synthases (PKSs) assemble small acetic acid-type acyl building blocks into polyketides through C-C bonds, and nonribosomal peptide synthetases (NRPSs) assemble amino acids into peptides through amide bonds. PKS-NRPS hybrid assembly lines build structurally complex polyketide-amino acid/peptide hybrid molecules that incorporate both acyl and aminoacyl building blocks into their products. Their combined functionalities expand the biological activities of these molecules by mixing their chemical properties. Protein-protein interactions are necessary within PKS-NRPS hybrid assembly lines to achieve accurate linkage between the PKS and NRPS systems. This review summarizes the current understanding of the roles and importance of the protein-protein interactions in various PKS-NRPS hybrid assembly lines.
Topics: Aminoglycosides; Bacterial Proteins; Biosynthetic Pathways; Fungal Proteins; Lactams; Macrolides; Peptide Synthases; Peptides; Phenols; Polyketide Synthases; Polyketides; Protein Interaction Maps; Pyrroles
PubMed: 30074030
DOI: 10.1039/c8np00022k -
Current Opinion in Structural Biology Apr 2015Modular polyketide synthases (PKS) produce a vast array of bioactive molecules that are the basis of many highly valued pharmaceuticals. The biosynthesis of these... (Review)
Review
Modular polyketide synthases (PKS) produce a vast array of bioactive molecules that are the basis of many highly valued pharmaceuticals. The biosynthesis of these compounds is based on ordered assembly lines of multi-domain modules, each extending and modifying a specific chain-elongation intermediate before transfer to the next module for further processing. The first 3D structures of a full polyketide synthase module in different functional states were obtained recently by electron cryo-microscopy. The unexpected module architecture revealed a striking evolutionary divergence of the polyketide synthase compared to its metazoan fatty acid synthase homolog, as well as remarkable conformational rearrangements dependent on its biochemical state during the full catalytic cycle. The design and dynamics of the module are highly optimized for both catalysis and fidelity in the construction of complex, biologically active natural products.
Topics: Acyl Carrier Protein; Animals; Cryoelectron Microscopy; Evolution, Molecular; Humans; Polyketide Synthases; Protein Structure, Tertiary
PubMed: 25791608
DOI: 10.1016/j.sbi.2015.02.014 -
Bioscience, Biotechnology, and... Oct 2022In the social amoeba Dictyostelium discoideum, the polyketide MPBD (4-methyl-5-pentylbenzene-1,3-diol) regulates the gene expressions of cAMP signaling to make cells...
In the social amoeba Dictyostelium discoideum, the polyketide MPBD (4-methyl-5-pentylbenzene-1,3-diol) regulates the gene expressions of cAMP signaling to make cells aggregation-competent and also induces spore maturation. The polyketide synthase StlA is responsible for MPBD biosynthesis in D. discoideum and appears to be conserved throughout the major groups of the social amoeba (Dictyostelia). In this study, we analyzed the function of StlA in Polysphondylium violaceum by identifying the gene sequence and creating the knockout mutants. We found that Pv-stlA- mutants had defects only in cell aggregation but not in spore maturation, indicating that the function of StlA in inducing spore maturation is species-specific. We also found that MPBD could rescue the aggregation defect in Pv-stlA- mutants whereas the mutants normally exhibited chemotaxis to their chemoattractant, glorin. Our data suggest that StlA is involved in inducing aggregation in P. violaceum by acting on signaling pathways other than chemotaxis in P. violaceum.
Topics: Dictyostelium; Polyketide Synthases; Spores, Protozoan; Chemotactic Factors; Polyketides
PubMed: 35998316
DOI: 10.1093/bbb/zbac144 -
Journal of Industrial Microbiology &... Dec 2018Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures... (Review)
Review
Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures have prohibited detailed studies of their biosynthetic pathways. Creative, albeit non-definitive, methods have been developed to assign function to biosynthetic gene clusters in lieu of techniques such as gene knockout and heterologous expressions that are commonly applied to easily cultivatable organisms. We review a total of 81 completely sequenced polyketide synthase (PKS) genes from lichenizing fungi, comprising to our best efforts all complete and reported PKS genes in lichenizing fungi to date. This review provides an overview of the approaches used to locate and sequence PKS genes in lichen genomes, current approaches to assign function to lichen PKS gene clusters, and what polyketides are proposed to be biosynthesized by these PKS. We conclude with remarks on prospects for genomics-based natural products discovery in lichens. We hope that this review will serve as a guide to ongoing research efforts on polyketide biosynthesis in lichenizing fungi.
Topics: Biosynthetic Pathways; Fungal Proteins; Genome, Fungal; Genomics; Lichens; Multigene Family; Polyketide Synthases; Polyketides
PubMed: 30206732
DOI: 10.1007/s10295-018-2080-y -
Angewandte Chemie (International Ed. in... Aug 2023Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural...
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.
Topics: Polyketide Synthases; Antineoplastic Agents; Bacteria; Secondary Metabolism; Polyketides
PubMed: 37218580
DOI: 10.1002/anie.202304476